Pan-Genome Analysis with Virulence Factors: Charting the Genomic Landscape of Uropathogenic Escherichia coli (UPEC)

Pan-Genome Analysis with Virulence Factors: Charting the Genomic Landscape of Uropathogenic Escherichia coli (UPEC) | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Pan-Genome Analysis with Virulence Factors: Charting the Genomic Landscape of Uropathogenic Escherichia coli (UPEC) Lavanya Shankar Salian, Anusree Sajeevan, Krishna Prasath S K, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3982260/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Urinary tract infections remain a worldwide health challenge, affecting over 150 million individuals annually, with significant morbidity and healthcare costs. Escherichia coli is the chief uropathogen (50–90%) in uncomplicated, community-acquired urinary tract infections. Numerous virulence factors are expressed by Uropathogenic Escherichia coli (UPEC), allowing the bacteria to cause urinary tract infections. Despite large-scale sequencing efforts to raise clinical awareness of UPEC, not much is known about the diversity and functions of virulence factors. To understand and elucidate the genetic diversity, evolutionary characteristics, and virulence profile, efforts were taken to construct the pan-genome of UPEC using 212 publicly available complete genome sets. The UPEC pan-genome was open in nature i.e. its size increases indefinitely when adding new genomes and showed extensive genome variability. These UPEC strains had diverse virulence gene content, and four potential core virulence genes ( dhak, fimH-1, H-2, uspABCDFG, yehD ) have been identified. The conserved mechanisms for their pathogenicity were related to adherence, motility, and immune modulation. The study underscores the crucial role of bacterial adhesins, particularly fimH , in mediating UPEC attachment to uroepithelial cells, enhancing persistence, and resisting mechanical elimination by urine flow. The investigation into fimH single-nucleotide polymorphisms aids in understanding UPEC epidemiological types. The datasets provide in-depth analysis of genomic diversity and virulence profiles of UPEC strains, paving the way for the development of effective preventive and therapeutic strategies. Therefore, the identified virulence factors with further research can serve as potential targets for vaccine and antibiotic development, facilitating genetic studies and clinical research for enhanced UTI management. UPEC Urinary tract infection Pangenome Virulence factors Figures Figure 1 Figure 2 Figure 3 Background Globally, urinary tract infections (UTIs) are one of the most prevalent health conditions found in clinical settings. Despite significant efforts, UTIs continue to impact over 150 million people across the globe, carrying an elevated risk of morbidity and expensive medical expenses. In the US, UTIs are the cause of over 11 million physician visits and 470,000 hospitalizations in 2006, at an estimated cost of $ 3.5 billion [ 1 , 2 ]. In 2019, more than 404.6 million [95% UI (uncertainty intervals) 359.4-446.5] individuals had UTIs globally and nearly 236,786 people (198,433–259,034) died of UTIs, contributing to 5.2 million. From 4,715.0 (4,174.2-5,220.6) per 100,000 population in 1990 to 5,229.3 (4,645.3-5,771.2) per 100,000 population in 2019, the age-standardized incidence rate rose [ 3 ]. In a report by Christy V R et al [ 3 ], A study on UTI in the Kanyakumari area of South India found that 40.53 percent of older men (those in the 61–90 age bracket) were affected by this condition [ 3 ]. In addition to the women in the reproductive age group, the UTI infection in women with menopausal age was found to be high. About 16.88% of the UTI culture-positive women (391 cases) were in the age group 51–60 [ 3 ]. The incidence of UTI in between reproductive age (21–30 years) and premenopausal, menopausal, and post-menopausal stage women also endured high incidence of UTI was mentioned in Christy V R et al ,. In the women in the age group 51–60 years, the incidence of UTI is relatively high. Also, the recurrence of infection is posing a significant challenge in the treatment of UTI [ 3 ]. Infections are more common in women, children, the elderly, diabetics, and people with uroliths and urinary catheters [ 4 ]. UTIs are categorized as either uncomplicated or complicated clinically. Healthy individuals who do not have any structural or neurological abnormalities in their urinary system are at risk for uncomplicated UTIs, such as cystitis and pyelonephritis. Factors such as urinary obstruction, urine retention, immunosuppression, renal failure, pregnancy, indwelling catheters or other drainage devices, and compromised host defence are linked to complicated UTIs [ 1 ]. The physiological resistance of men to UTIs is higher. Women's shorter urethras make it easier for the disease-causing microbes to get through the bladder and the urine opening [ 5 ]. The ORENUC system classifies the risk factors according to the phenotype: O , no known risk factors; R , recurrent UTIs ; E , extra urogenital risk factor; N , nephropathic diseases; U , urologic resolvable (transient) risk factors; C, permanent external urinary catheter and unresolved urologic risk factors [ 6 ]. As expected, rather than carrying a particular component, the virulence of UPECs appears to be related to the coordinated expression of multiple genes, which change depending on the urinary districts they colonize. Commensal E. coli and UPECs possess a strong genetic resemblance, hence it is challenging to identify these pathogens; in fact, the existence of E. coli strains in symptomatic patients' urine samples suffices for identifying a UPEC strain [ 7 , 8 ]. The well-characterized strain UPEC89 has mostly been used to investigate the virulence of UPEC during urinary tract infections [ 4 ]. Multilocus sequence type 95 (ST95) isolate UPEC89 is regarded as a prototypical UPEC isolate and has been widely utilized in investigations of virulence genes linked to UTI [ 10 , 12 ]. It is critical to comprehend which genes contribute to UPEC fitness during UTI to create novel strategies for disease prevention and treatment. The attachment of bacteria to uroepithelial cells is a crucial stage in the initiation and progression of UTIs. Bacterial ligands, which are typically tiny proteins positioned at the tips of bacterial fimbriae, promote E.coli attachment by binding to carbohydrate residues in the host cell wall and acting as receptors [ 9 , 15 ]. Thus, E.coli adherence to host receptors is a function that is often mediated by the bacteria's adhesions to host cell receptors. [ 9 , 16 ]. The bacterial attachment increases the persistence of E. coli and enables bacteria to withstand mechanical elimination by urine flow and frequent urination. Several forms of adhesins, such as type 1 fimbriae, are necessary for the identification and attachment to urinary tract receptors [ 9 , 17 ]. The adhesive subunit of type 1 fimbriae, fimH is a primary determinant of UPEC adhesions and has a high tropism for urinary tract receptors; as a result, fimH adhesion is critical for E. coli colonization of many habitats [ 5 , 6 ]. UPEC adhesions are primarily determined by fimH , the sticky subunit of type 1 fimbriae. fimH adhesion has a strong tropism for receptors in the urinary system, E.coli must colonize a variety of habitats [ 9 ]. Furthermore, a screening technique for UPEC epidemiological type involves the analysis of fimH single-nucleotide polymorphisms (SNPs) [ 10 , 11 ]. A study on pangenome analysis of Campylobacter reported by Chaofang Zhong et al. , revealed the open nature of Campylobacter and identified 6 potential core virulence genes. Their research advances our knowledge of Campylobacter virulence, improves the utilization of potential drugs in medication development, and lowers the risk of Campylobacter infections. Prabha K. Bista et al. , performed the genomic characterization to distinguish the F.necrophorum subspecies phenotypically by identifying both general and subspecies-specific virulence genes through a custom search-based analysis. Here, they recommended that next research should concentrate on identifying their virulence genes to assess their potential as vaccine targets to stop fusobacterial infections in cattle. This study was performed to determine the various virulence genes and their evolutionary relationships among isolates belonging to the same species in the UPEC89 clade. The progression of UTIs is significantly influenced by the virulence factors of UPEC strains like (type 1 fimbriae, p fimbriae, curli fimbriae, amphibole adhesion, and flagellum). Apart from these hemolysins, siderophores, and cytotoxic necrotizing factor 1 also play crucial roles in the virulence of UPEC [ 9 ]. The aforementioned virulence factors are critical for extra-intestinal survival, UPEC colonization, and the production of cytopathic effects. Furthermore, expression of UPEC unique virulence factors may exacerbate UTIs and increase uropathogenicity [ 5 , 7 , 8 ]. Methods Public genome resources, Accession numbers, Annotation, Comparison For the pan-genome analysis, the genomic sequences for UPEC , including the whole-genome sequences of 212 strains, were downloaded from the Reference Sequence (RefSeq) database and the details were obtained from NCBI Pathogen detection beta ( https://www.ncbi.nlm.nih.gov/pathogens/ , accessed on August 2023). The genome-scale study used the most complete strain sampling of each UPEC strain to date. We chose the genome with the highest assembly level and full-genome representation in the NCBI database. The sequences considered in the study were from an isolation source – Urine (only Clinical samples from Humans). Consequently, 213 genomes, which consisted of 212 complete genomes and 1 draft genome, were included in this study ( Table 1 ). Table 1 Isolates with their assembly number (NCBI Pathogen detection ) Strain name Assembly number Geography 1 UPEC-2 GCA_000779395.1 USA:WA 2 UPEC-3 GCA_000777375.1 USA:WA 3 UPEC-4 GCA_000777155.1 USA:WA 4 UPEC-7 GCA_000776175.1 USA:WA 5 UPEC-8 GCA_000776195.1 USA:WA 6 UPEC-9 GCA_000776795.1 USA:WA 7 UPEC-10 GCA_000785355.1 USA:WA 8 UPEC-14 GCA_000780675.1 USA:WA 9 UPEC-15 GCA_000780435.1 USA:WA 10 UPEC-23 GCA_000776045.1 USA:WA 11 UPEC-22 GCA_000778635.1 USA:WA 12 UPEC-24 GCA_000778285.1 USA:WA 13 UPEC-28 GCA_000777585.1 USA:WA 14 UPEC-29 GCA_000777395.1 USA:WA 15 UPEC-30 GCA_000777355.1 USA:WA 16 UPEC-31 GCA_000777325.1 USA:WA 17 UPEC-33 GCA_000777285.1 USA:WA 18 UPEC-34 GCA_000777265.1 USA:WA 19 UPEC-36 GCA_000777215.1 USA:WA 20 UPEC-37 GCA_000777235.1 USA:WA 21 UPEC-38 GCA_000777195.1 USA:WA 22 UPEC-39 GCA_000777165.1 USA:WA 23 UPEC-40 GCA_000777135.1 USA:WA 24 UPEC-41 GCA_000777095.1 USA:WA 25 UPEC-43 GCA_000777105.1 USA:WA 26 UPEC-45 GCA_000777065.1 USA:WA 27 UPEC-48 GCA_000777025.1 USA:WA 28 UPEC-50 GCA_000776995.1 USA:WA 29 UPEC-51 GCA_000776965.1 USA:WA 30 UPEC-53 GCA_000776935.1 USA:WA 31 UPEC-54 GCA_000776925.1 USA:WA 32 UPEC-55 GCA_000776915.1 USA:WA 33 UPEC-56 GCA_000776775.1 USA:WA 34 UPEC-57 GCA_000776275.1 USA:WA 35 UPEC-58 GCA_000776115.1 USA:WA 36 UPEC-59 GCA_000776675.1 USA:WA 37 UPEC-60 GCA_000776505.1 USA:WA 38 UPEC-61 GCA_000776565.1 USA:WA 39 UPEC-62 GCA_000776055.1 USA:WA 40 UPEC-64 GCA_000785235.1 USA:WA 41 UPEC-65 GCA_000776615.1 USA:WA 42 UPEC-66 GCA_000785255.1 USA:WA 43 UPEC-69 GCA_000776335.1 USA:WA 44 UPEC-70 GCA_000776815.1 USA:WA 45 UPEC-72 GCA_000776475.1 USA:WA 46 UPEC-73 GCA_000776375.1 USA:WA 47 UPEC-74 GCA_000776595.1 USA:WA 48 UPEC-75 GCA_000776655.1 USA:WA 49 UPEC-76 GCA_000776235.1 USA:WA 50 UPEC-77 GCA_000776155.1 USA:WA 51 UPEC-78 GCA_000776065.1 USA:WA 52 UPEC-79 GCA_000776415.1 USA:WA 53 UPEC-80 GCA_000776035.1 USA:WA 54 UPEC-81 GCA_000776135.1 USA:WA 55 UPEC-82 GCA_000776285.1 USA:WA 56 UPEC-83 GCA_000776355.1 USA:WA 57 UPEC-84 GCA_000776215.1 USA:WA 58 UPEC-85 GCA_000776455.1 USA:WA 59 UPEC-87 GCA_000776745.1 USA:WA 60 UPEC-88 GCA_000776535.1 USA:WA 61 UPEC-89 GCA_000776635.1 USA:WA 62 UPEC-90 GCA_000776835.1 USA:WA 63 UPEC-91 GCA_000776855.1 USA:WA 64 UPEC-93 GCA_000776695.1 USA:WA 65 UPEC-94 GCA_000776735.1 USA:WA 66 UPEC-95 GCA_000776435.1 USA:WA 67 UPEC-97 GCA_000776395.1 USA:WA 68 UPEC-98 GCA_000776315.1 USA:WA 69 UPEC-99 GCA_000776255.1 USA:WA 70 UPEC-100 GCA_000779215.1 USA:PACIFIC NORTHWEST 71 UPEC-101 GCA_000779055.1 USA:WA 72 UPEC-103 GCA_000781455.1 USA:WA 73 UPEC-104 GCA_000781435.1 USA:WA 74 UPEC-105 GCA_000781415.1 USA:WA 75 UPEC-106 GCA_000781385.1 USA:WA 76 UPEC-107 GCA_000781375.1 USA:WA 77 UPEC-108 GCA_000781335.1 USA:WA 78 UPEC-109 GCA_000781355.1 USA:WA 79 UPEC-110 GCA_000781315.1 USA:WA 80 UPEC-111 GCA_000781275.1 USA:WA 81 UPEC-112 GCA_000781295.1 USA:WA 82 UPEC-113 GCA_000781255.1 USA:WA 83 UPEC-114 GCA_000781235.1 USA:WA 84 UPEC-115 GCA_000781215.1 USA:WA 85 UPEC-116 GCA_000781195.1 USA:WA 86 UPEC-117 GCA_000781175.1 USA:WA 87 UPEC-118 GCA_000781115.1 USA:WA 88 UPEC-119 GCA_000781145.1 USA:WA 89 UPEC-120 GCA_000781095.1 USA:WA 90 UPEC-121 GCA_000781075.1 USA:WA 91 UPEC-123 GCA_000781045.1 USA:WA 92 UPEC-124 GCA_000781035.1 USA:WA 93 UPEC-125 GCA_000781005.1 USA:WA 94 UPEC-126 GCA_000780995.1 USA:WA 95 UPEC-127 GCA_000780965.1 USA:WA 96 UPEC-128 GCA_000780915.1 USA:WA 97 UPEC-129 GCA_000780925.1 USA:WA 98 UPEC-130 GCA_000780895.1 USA:WA 99 UPEC-131 GCA_000780875.1 USA:WA 100 UPEC-132 GCA_000780845.1 USA:WA 101 UPEC-133 GCA_000780835.1 USA:WA 102 UPEC-134 GCA_000780815.1 USA:WA 103 UPEC-135 GCA_000780795.1 USA:WA 104 UPEC-136 GCA_000780695.1 USA:WA 105 UPEC-137 GCA_000780655.1 USA:WA 106 UPEC-138 GCA_000780775.1 USA:WA 107 UPEC-139 GCA_000780755.1 USA:WA 108 UPEC-140 GCA_000780735.1 USA:WA 109 UPEC-141 GCA_000780715.1 USA:WA 110 UPEC-142 GCA_000780635.1 USA:WA 111 UPEC-143 GCA_000780615.1 USA:WA 112 UPEC-144 GCA_000780595.1 USA:WA 113 UPEC-145 GCA_000780575.1 USA:WA 114 UPEC-146 GCA_000780555.1 USA:WA 115 UPEC-147 GCA_000780535.1 USA:WA 116 UPEC-148 GCA_000780495.1 USA:WA 117 UPEC-149 GCA_000780475.1 USA:WA 118 UPEC-150 GCA_000780415.1 USA:WA 119 UPEC-151 GCA_000780355.1 USA:WA 120 UPEC-153 GCA_000780335.1 USA:WA 121 UPEC-154 GCA_000780315.1 USA:WA 122 UPEC-155 GCA_000780295.1 USA:WA 123 UPEC-156 GCA_000780235.1 USA:WA 124 UPEC-157 GCA_000780215.1 USA:WA 125 UPEC-158 GCA_000780195.1 USA:WA 126 UPEC-159 GCA_000780175.1 USA:WA 127 UPEC-161 GCA_000780155.1 USA:WA 128 UPEC-162 GCA_000780135.1 USA:WA 129 UPEC-166 GCA_000780115.1 USA:WA 130 UPEC-169 GCA_000780095.1 USA:WA 131 UPEC-170 GCA_000780035.1 USA:WA 132 UPEC-171 GCA_000780015.1 USA:WA 133 UPEC-172 GCA_000779995.1 USA:WA 134 UPEC-173 GCA_000779955.1 USA:WA 135 UPEC-175 GCA_000779915.1 USA:WA 136 UPEC-176 GCA_000779895.1 USA:WA 137 UPEC-177 GCA_000779875.1 USA:WA 138 UPEC-179 GCA_000779835.1 USA:WA 139 UPEC-180 GCA_000779815.1 USA:WA 140 UPEC-181 GCA_000779795.1 USA:WA 141 UPEC-182 GCA_000779735.1 USA:WA 142 UPEC-184 GCA_000779715.1 USA:WA 143 UPEC-185 GCA_000779695.1 USA:WA 144 UPEC-186 GCA_000779585.1 USA:WA 145 UPEC-187 GCA_000779675.1 USA:WA 146 UPEC-188 GCA_000779635.1 USA:WA 147 UPEC-189 GCA_000779565.1 USA:WA 148 UPEC-193 GCA_000779545.1 USA:WA 149 UPEC-195 GCA_000779515.1 USA:WA 150 UPEC-196 GCA_000779475.1 USA:WA 151 UPEC-197 GCA_000779425.1 USA:WA 152 UPEC-200 GCA_000779335.1 USA:WA 153 UPEC-201 GCA_000779255.1 USA:WA 154 UPEC-202 GCA_000779295.1 USA:WA 155 UPEC-203 GCA_000785325.1 USA:WA 156 UPEC-205 GCA_000778545.1 USA:WA 157 UPEC-207 GCA_000778485.1 USA:WA 158 UPEC-208 GCA_000778565.1 USA:WA 159 UPEC-209 GCA_000778465.1 USA:WA 160 UPEC-211 GCA_000778585.1 USA:WA 161 UPEC-212 GCA_000778475.1 USA:WA 162 UPEC-213 GCA_000778785.1 USA:WA 163 UPEC-219 GCA_000778725.1 USA:WA 164 UPEC-220 GCA_000778705.1 USA:WA 165 UPEC-221 GCA_000778895.1 USA:WA 166 UPEC-225 GCA_000778955.1 USA:WA 167 UPEC-226 GCA_000778685.1 USA:WA 168 UPEC-227 GCA_000778935.1 USA:WA 169 UPEC-228 GCA_000778815.1 USA:WA 170 UPEC-229 GCA_000776715.1 USA:WA 171 UPEC-230 GCA_000778435.1 USA:WA 172 UPEC-232 GCA_000778415.1 USA:WA 173 UPEC-233 GCA_000778395.1 USA:WA 174 UPEC-235 GCA_000778375.1 USA:WA 175 UPEC-236 GCA_000778355.1 USA:WA 176 UPEC-237 GCA_000778335.1 USA:WA 177 UPEC-238 GCA_000778315.1 USA:WA 178 UPEC-239 GCA_000778275.1 USA:WA 179 UPEC-243 GCA_000778235.1 USA:WA 180 UPEC-244 GCA_000778215.1 USA:WA 181 UPEC-248 GCA_000778175.1 USA:WA 182 UPEC-249 GCA_000778135.1 USA:WA 183 UPEC-250 GCA_000778105.1 USA:WA 184 UPEC-251 GCA_000778095.1 USA:WA 185 UPEC-253 GCA_000778075.1 USA:WA 186 UPEC-254 GCA_000778055.1 USA:WA 187 UPEC-255 GCA_000778035.1 USA:WA 188 UPEC-256 GCA_000777995.1 USA:WA 189 UPEC-257 GCA_000778015.1 USA:WA 190 UPEC-258 GCA_000777975.1 USA:WA 191 UPEC-259 GCA_000777945.1 USA:WA 192 UPEC-260 GCA_000777895.1 USA:WA 193 UPEC-261 GCA_000777845.1 USA:WA 194 UPEC-265 GCA_000777835.1 USA:WA 195 UPEC-266 GCA_000777815.1 USA:WA 196 UPEC-269 GCA_000777735.1 USA:WA 197 UPEC-271 GCA_000777695.1 USA:WA 198 UPEC-273 GCA_000777675.1 USA:WA 199 UPEC-274 GCA_000777655.1 USA:WA 200 UPEC-276 GCA_000777625.1 USA:WA 201 UPEC-277 GCA_000777605.1 USA:WA 202 UPEC-281 GCA_000777555.1 USA:WA 203 UPEC-282 GCA_000777535.1 USA:WA 204 UPEC-284 GCA_000777515.1 USA:WA 205 UPEC-285 GCA_000777495.1 USA:WA 206 UPEC-286 GCA_000777475.1 USA:WA 207 UPEC-287 GCA_000777455.1 USA:WA 208 UPEC-288 GCA_000777435.1 USA:WA 209 UPEC-289 GCA_000777415.1 USA:WA 210 UPEC V2-6 GCA_009761195.1 BRAZIL:SAO PAULO 211 UPEC U34 GCA_009761205.1 BRAZIL:SAO PAULO 212 UPEC _252 GCA_007858995.1 BRAZIL:SAO PAULO 213 UPEC EC 193 GCA_002507495.1 CHINA:FUJIAN Pan-genome and core genome construction . The pan-genome analysis was carried out using Roary v3.13.0 [ 9 , 10 ], utilizing the genome annotation in GFF3 format generated by Prokka (Version 1.14.6) (Rapid Prokaryotic Genome Annotation) [ 11 , 12 ]. The analysis was conducted with the following parameters: 90% identity threshold for BLASTp [Basic Local Alignment Search Tool (Protein-Protein)][ 13 ]. Functional classification of orthologous cluster analysis For the annotation of pan-genome genes with COG (Cluster of Orthologous groups), a whole-genome BLASTp search was performed against the NCBI COG database with an E-value cutoff of 1 × 10 − 5 . Phylogenetic analysis. A parsimony tree was created of the 212 studied UPEC strains using PhyML (PHYlogenetic inferences using Maximum Likelihood) version 3.1 in Roary [ 9 , 10 ] with 100 bootstrap replicates[ 9 , 10 ]. Virulence factor analysis. To identify the potential virulence-associated genes in the chosen clade of UPEC89 genomes were aligned against the VFDB (Virulence factor database) 2.0 (2.0.3 version) with 90% threshold for identity, 60% minimum length, 90% coverage, and an E-value cut-off of 1 × 10 − 5 with a FASTA (.fna) input files[ 14 – 16 ]. Also, a bacterial synteny was evaluated and visualized by multiple whole-genome alignment using progressive Mauve[ 17 ] RESULTS Pan-genome analysis of 212 UPEC isolates To capture the entire genomic diversity of UPEC strains, 212 strains with complete genomes ( Table 1 ) were chosen for the pan-genome study. Each of these represented the genome with the highest assembly level when multiple strain sequences were available for UPEC strains. A total of 39,874 gene families [ 18 ] were identified of which 2,385 (6.36%) were shared by all the 212 analysed genomes, constituting the core genome (gene families present in all 212 analysed genomes). The accessory genome included 19,487 (48.8%) gene families shared by at least two species, and 18,011 (45.2 %) nique gene families were found in only one strain, constituting the unique genome (Fig. 1 a, Table 2 ). This high proportion of unique genome (45.2 %) urther supports the intragenus heterogeneity of Escherichia and confirms the previously observed highly diverse nature of this bacteria at the whole-genome level. The variable genes (accessory genes and unique genes) account for about 94% of the whole pan-genome, signifying the high level of genetic diversity in the members of Escherichia coli and that the genus is a very heterogeneous population. The sizes of the core genome and pan-genome for the 212 analysed UPEC strain genomes were estimated to be 2,385 and 39,874 genes, respectively. The number of genomes examined greatly influences the size of the core genome and pan-genome. The curves of the core genome and pan-genome size of these UPEC strains genomes, with the increase of the number of genomes demonstrated that the pan-genome size increased almost exponentially with the number of genomes, while the core genome size was being narrowed. When the number of added genomes reached 212, the size of the pan-genome still increased (Fig. 1 b). The complete pan-genome of the UPEC strains was likely to be larger than 212 genomes. This trend continued with the addition of multiple genomes. Similarly, In Fig. 1 c, upon observing the number of new genes, it became apparent that the count of unique genes steadily increased with the addition of each new analyzed genome (Fig. 1 c), indicating the open nature of the pangenome. Together this result signified a high level of intraspecific genetic diversity in UPEC and indicated that diversity within the species cannot be captured by a single reference genome. As a result, as more species are identified and analyzed, the global gene repertoire of the UPEC strains will change considerably in the future. Functional features of the UPEC pan-genome Orthologous proteins are those that share a common evolutionary origin and are typically found in different species. COGs are widely used in comparative genomics to study the evolutionary relationships between genes and genomes [ 19 – 21 ]. Researchers can compare the distribution and conservation of COGs across different species to gain insights into the evolution of specific functions and processes [ 21 ]. When a gene is assigned a COG ID, it means that the protein product of that gene belongs to a particular orthologous group, and other proteins in the same COG are considered orthologs. Orthologous proteins generally perform similar functions in different organisms, and the assignment of a COG ID provides information about the likely function of the protein based on the functional annotation associated with that COG [ 21 ] . To clarify the functional characteristics of the UPEC genome, we employed the clusters of orthologous groups (GOG) analysis to examine whether the core, accessory, and unique genomes in the pan-genome had exhibited distinct COG profiles. The functional categories of the genes were assigned to core, accessory, and unique classes, and the results showed that the gene families in the UPEC core genome were enriched for genes involved in “translation, ribosomal structure, and biogenesis”(J) (Fig. 2 )[ 20 , 22 ]. Therefore, the COG analysis results highlighted that more core genes perform fundamental housekeeping functions than accessory genes and unique genes. Considering the open state of the UPEC pan-genome, the results of the COG enrichment analysis of UPEC accessory genes and unique genes, especially “amino acid transport and metabolism” (E), “replication, recombination, and repair” (L), “cell wall/membrane/envelope biogenesis” (M), and “inorganic ion transport and metabolism” (P), were consistent with the perspective that larger genomes tend to accumulate functions to enable organisms to achieve a higher degree of ecological diversification[ 19 ]. In addition, the virulence-associated functional categories, such as “cell motility” (N), “inorganic ion transport and metabolism” (P), “signal transduction mechanisms” (T), and “defence mechanisms” (V), were prominently represented in the variable component of the pan-genome [ 19 ], which might contribute to UPEC pathogenicity (Fig. 2 )[ 20 , 22 ]. Phylogenetic analysis The parsimony tree reported in Fig. 3 depicts the selected clade consisting of UPEC89. This clade was chosen as its genome is well characterized and plays a significant role in pathogenesis. Now the isolates belonging to this clade were further chosen for virulence genes analysis[ 23 ]. Prediction of Common and Unique virulence genes within UPEC89 clade The virulence factors encoded by the pathogen genome enable the organism to manipulate host immune defenses, enhance a pathogen disease-inducing potential, and largely determine the outcome of infections. Thus, comprehensive knowledge of virulence factors is crucial to gain insights into the pathogenesis. We identified a total of 35 virulence genes (Table 3 ), including both common and unique ones, as reported in Table 2 and Table 3 , across the 6 UPEC strains. Among these, 5 were core genes, 4 were soft-core genes, 5 were shell genes, 3 were cloud genes, and 10 were unique genes (Table 1 ,Table 2 and Table 4 ). The virulence determinants of the pathogenicity of these UPEC strains include flagella, iron uptake, invasion, lipooligosaccharide (LOS), capsule, exotoxin, type IV secretion system (T4SS), and adherence[ 1 , 24 ]. Table 2 Summary statistics Sl. no. Genome type Range Number of genes Genes in UPEC89 clade 1 Core genes 99% <=strains < = 100% 1528 5 2 Soft core genes 95% <=strains < = 99% 857 4 3 Shell genes 15% <=strains < = 95% 3866 5 4 Cloud genes 2% <=strains < = 15% 15612 3 5 Unique Genes 1% <=strains < = 2% 18011 10 6 Total genes 39874 Table 3 Common virulence genes Common virulence genes 1 AslA Not determined 2 chuA Outer membrane hemin receptor 3 dhaK Dihydroxyacetone kinase (also designated ptnC) 4 fimH Type 1 fimbriae 5 fyuA Siderophore receptor 6 gad Glutamate decarboxylase 7 ibeA Invasin of brain endothelial cells 8 irp2 High molecular weight protein 2 non-ribosomal peptide synthetase 9 iss Increased serum survival 10 kpsE Not determined 11 nlpl Polysialic acid transport protein; Group 2 capsule 12 sitA Iron transport protein/for manganese acquisition system 13 terC Tellurium ion resistance protein 14 usp Uropathogenic specific protein 15 yehA Outer membrane lipoprotein, YHD fimbriael cluster 16 yehB Usher, YHD fimbriael cluster 17 yehC Chaperone, YHD fimbriael cluster 18 yehD Major pilin subunit, YHD fimbriael cluster 19 yfcV Fimbrial protein Table 4 Unique Virulence Genes Unique virulence genes UPEC-59 UPEC-70 UPEC-89 UPEC-101 UPEC-208 UPEC-266 0 faeD aalB 0 fdeC papC faeI aalG hlyF faeC iroN faeH Position of virulence genes of chosen clade The position of virulence genes belonging to all six isolates was constructed with the help of data obtained from VFDB[ 14 , 15 , 25 ] in which genes with only 100% identity and HSP (High scoring segment pair) length equal to Virulence gene length were chosen, and data from Roary output [ 9 , 10 ](Table 5 , S1). So, to validate these results, a synteny analysis using the Mauve program was performed. These identified virulence genes exhibited remarkable conservation in gene order and pattern, as evidenced by their consistent flanking by the same neighbouring genes. Table 5 Position of Virulence genes of six isolates of chosen clade Position of virulence gene Function Core genome 1 dhaK PEP-Dependent dihydroxyacetone kinase,dihydroxyacetone binding subunit DHAK 2 fimH-1 Type-1 fimbrin D-mannose specific adhesin 3 fimH-2 Type-1 fimbrin D-mannose specific adhesin 4 uspA Universal stress protein A 5 uspB Universal stress protein B 6 uspC Universal stress protein C 7 uspD Universal stress protein D 8 uspF Universal stress protein F 9 uspG Universal stress protein G 10 yehD Putative fimbrial-like protein yehD Accessory genome 1 dhak_2 PEP-Dependent dihydroxyacetone kinase,dihydroxyacetone binding subunit DHAK 2 fyuA Pesticin receptor 3 yehA Putative fimbrial-like protein yehA 4 yehB Outer membrane usher protein yehB 5 yehB_1 Outer membrane usher protein yehB 6 yehB_2 Outer membrane usher protein yehB 7 yehB_3 Outer membrane usher protein yehB 8 yehC Putative fimbrial chaperone yehC 9 yehC_1 Putative fimbrial chaperone yehC 10 yehD Putative fimbrial-like protein yehD 11 yehD_1 Putative fimbrial-like protein yehD Unique genome 1 papC Outer membrane usher protein papC Discussion Antimicrobial resistance (AMR) has been increasingly documented in bacteria responsible for urinary tract infections (UTIs) over the past few decades. The emergence of UTIs poses a significant public health concern, contributing to a diminished quality of life for affected individuals and imposing substantial clinical and economic challenges. Uropathogenic E. coli (UPEC), a widespread gram-negative pathogen and a member of the Enterobacteriaceae family, is globally recognized as the primary cause of UTIs [ 26 , 27 ]. With an increase in UPEC pathogenesis, finding virulence genes that can be used to treat associated illnesses is essential. The rapid rise of sequencing technologies and genomic analysis has provided an important platform for exploring causes of pathogenicity, as well as determining virulence genes and antimicrobial resistance patterns. However, the challenge arises from the absence of reference genomes for more virulent strains, as only a few sequenced genomes are publicly available, making phylogenetic analysis and the identification of potential virulence factors difficult. To overcome this challenge at hand, this study focused on performing a custom-based virulence gene search using all 212 UPEC strains, which enabled to broaden the search probability. Based on this search, a total of 30 virulence genes were identified which are distributed among the isolates belonging to the UPEC89 clade consisting of 6 UPEC strains. Some of these virulence genes were explicitly found in only one strain whereas 20 factors were common among them. For example, virulence genes encoding E coli cells polymeric protein structures called K88 fimbriae on their surface i.e. faeC in UPEC89, papC gene in UPEC266 is required for the formation of digalactoside-binding Pap pili was found only in this strain [ 28 ]. On the other hand, Universal stress proteins like uspA were commonly found. In UPEC strains, for instance, adhesion is vitally important to overcome host defences in the urinary tract and resist the flushing effect of the urine. Hence, previous reports from Barbara Nesta have documented the role and conserveness of fdeC in UPEC strains [ 29 ]. fdeC (factor adherence E.coli ) is known for its ability to mediate E. coli adhesion to mammalian cells and extracellular matrix [ 29 ]. Although fdeC may share functional homology with other adhesins localized on the E. coli surface, its host cell-dependent expression suggests a specific role during colonization. Also, the expression of fdeC on the bacterial surface is triggered by the interaction of E.coli with host cells [ 29 ]. In this study, the pathogenesis of UPEC is studied to identify virulence markers of various strains that cause UTIs. Virulence factors, as potential diagnostic indicators, help clinicians manage patients and anticipate the evolution of infection in the host body [ 30 ]. Hence, A particular emphasis was placed on the analysis of strain-specific distribution of virulence factors. The population structure of UPEC strains has not received much attention in research so far. The study included 212 UPEC strains for which the whole genome has been sequenced (latest [2014] RefSeq strains of UPEC) for our analyses. In this comparative genomics study, the genome of UPEC strains was assembled to create the pan-genome to understand its nature, its genomic variability and strain relatedness, and its pathogenic diversity [ 31 ]. Additionally, Chen et al ., used bioinformatics methods to determine that the core genome size of E. coli was 2,865 genes[ 32 ]. This number was derived from a data set consisting of the genomic contents of seven isolates, two of which were Shigella flexneri isolates[ 32 ]. Similarly, conserved genes or core genes are used to understand UPEC strains’ phylogeny. In the analysis, it is revealed that a wide range of genomic variability, with only 1,530 (3.9%) core genes shared in species shown in the Pan genome of UPEC pie chart. The accessory genes contributed to 19,478 genes (48.8%) of the pan-genome, thus indicating substantial heterogeneity among UPEC strains. All bacteria have developed ways to transfer or acquire genes through various mechanisms with high recombination rates [ 33 ]. The variability we observed within these species indicates that these bacterial species had been through a series of evolutionary events, suggesting that these core genes may be essential for the survival of the bacteria [ 33 ]. Also, the open pan-genome nature of species indicates that the species is still evolving by gene acquisition and diversification and hence there is a need to identify genes and target them that are stable [ 34 ]. Table 4 gives us information about the diverse virulence gene content and 4 potential core virulence genes like Dhak, usp(ABCDHG),fimH-1, fimH-2, and yehD and a unique gene papC in UPEC266. As reported by Christoph Bachler that DhaK is an enzyme component that functions as a transcriptional coregulator [ 35 ]. The family of sequence-related enzymes known as dha kinases uses either ATP or a phosphoprotein from the sugar phosphotransferase system (PTS) as phosphate donors. PTS-dependent kinases comprise a third component (DhaM), which is homologous to PTS proteins, and two subunits (DhaK, DhaL), which are homologous to DAK. Beutler et al ., (2001) found that DhaK and DhaL were elevated in the proteome of E. coli lacking enzyme I (EI), the master enzyme of the PTS, and that EI is essential for Dha kinase activity[ 36 ]. Lin and colleagues [ 37 , 38 ] also showed that E.coli grown on Dha exhibited increased Dha kinase activity [ 35 ]. Therefore, the common core virulence gene dhak can be a promising target. As well as Universal stress protein genes like uspA, uspB, uspC, uspD, uspF, uspG , and yehD, fimH-1 ,2 were found to be core virulence genes. Therefore, total of 4 core virulence genes were found. Escherichia coli uspA is generated in response to numerous environmental assaults [ 16 ]. The precise functions of the Usp proteins and Usp domains are still unknown, despite advances in our understanding of the regulation of the E.coli uspA gene; in certain instances, they seem to be connected to resistance to agents that damage DNA and to respiratory uncouplers [ 16 ]. Since conserved Usp domains or UspA proteins are found in eukaryotes [ 16 ], they seem to play a crucial role in these organisms in addition to bacteria and archaea. It's interesting to note that organisms that include usp genes typically have many copies of these genes[ 16 ]. As previously noted, the bacterial usp genes typically encode a single Usp domain in a small (about 14–15 kD) protein or a bigger (approximately 30 kD) protein that combines two Usp domains in tandem[ 16 ]. Depending on the organism, these variants vary in relative abundance and distribution. E.coli , for instance, has one tandem type and five tiny Usps [ 16 ], the exact roles of the Usp proteins and Usp domains remain enigmatic; they appear, in some cases, to be linked to resistance to DNA-damaging agents and respiratory uncouplers. Also, yehD gene encodes the putative fimbrial-like adhesin protein; Part of the yehABCD fimbrial operon, which contributes to adhesion to various surfaces in specific environmental niches[ 39 ]. Also, the results of synteny showed a pattern of conservation of gene order in these core virulence genes. Hence, the presence of these genes in conserved regions suggests a fundamental role highlights their evolutionary significance, and underscores their essential role in the bacteria's ability to establish infections[ 40 ] Conclusions In this study, we conducted a comparative pan-genome analysis of 212 UPEC clinical isolates, revealing their pan-genome characteristics, genomic diversity, virulence, and antimicrobial profiles. This study provides a snapshot of the genomic diversity of different UPEC pathological strains that support the metabolic and pathogenic diversity of 212 UPEC strains. The pan-genome of 212 UPEC members was found to be open and exhibited a high level of genomic variability, of which about 94% was variable. The COG analysis highlighted the adaptive functions of variable genes. These species have abundant virulence genes with functions that mirror pathogenicity differences, such as flagella and endotoxin. Furthermore, all studied UPEC strains contained the dhak (PEP-Dependent dihydroxyacetone kinase, dihydroxyacetone binding subunit DHAK), uspA (Universal stress protein-A), uspB (Universal stress protein-B), uspC (Universal stress protein-C), uspD (Universal stress protein-D), fimH-1 and − 2 ( Type-1 fimbrin D-mannose specific adhesin ) and yehD (putative fimbrial like protein yehD ). The virulence genes identified in this work will permit genetic and clinical research on UPEC strains by enabling the efficient utilization of candidates for vaccine and antibiotic development. Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not Applicable Availability of data and materials The datasets generated during the current study are available here, Summary Statistics: Galaxy Version 3.13.0+galaxy2 , Roary(version 3.13.0) https://usegalaxy.eu/api/datasets/4838ba20a6d86765f2287d53338183f6/display?to_ext=tabular Pan-genome vs. core-genome plot: Galaxy Version 3.13.0+galaxy2 , Roary(version 3.13.0) https://usegalaxy.eu/api/datasets/4838ba20a6d86765f3f1a320cf610f14/display?to_ext=txt. Plot representing number of unique and new genes : Galaxy Version 3.13.0+galaxy2 , Roary(version 3.13.0) https://usegalaxy.eu/api/datasets/4838ba20a6d86765e2a6db40eb3e631b/display?to_ext=txt. https://usegalaxy.eu/api/datasets/4838ba20a6d867656426394d12b42413/display?to_ext=txt. Functional Features : COG NCBI https://www.ncbi.nlm.nih.gov/research/cog Phylogenetic Analysis: Galaxy Version 3.13.0+galaxy2 , Roary(version 3.13.0) https://usegalaxy.eu/api/datasets/4838ba20a6d86765ed02b935b98ffb04/display?to_ext=nhx https://usegalaxy.eu/visualization/phyloviz?id=70f250ef8e555079 Virulence Finder: https://cge.food.dtu.dk/services/VirulenceFinder/ Competing interests The authors declare that they have no competing interests. Funding Not Applicable Author’s Contribution APS and SMS collaborated in the conceptualization and study design. LSS conducted an extensive literature survey, analyzed the data, and drafted the manuscript. AS generated the framework of the manuscript, synchronized the flow of information, and provided crucial insights in developing the manuscript. LSS, KPSK, and AS implemented revisions based on valuable feedback from APS and SMS. All authors have collectively reviewed and approved prior submission. Acknowledgments LSS and AS thank the members of the Quorum Sensing Lab for their support. The authors acknowledge SASTRA Deemed to be University, Thanjavur, India for extending infrastructure support to carry out this work. References Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol. 2015;13:269–84. Bruxvoort KJ, Bider-Canfield Z, Casey JA, Qian L, Pressman A, Liang AS, et al. Outpatient Urinary Tract Infections in an Era of Virtual Healthcare: Trends From 2008 to 2017. Clinical Infectious Diseases. 2020;71:100–8. VR C, G A, R M, P D, RAJA S. Epidemiology of urinary tract infection in south India. Biomed Res Clin Pract. 2019;4. Dias RCS, Moreira BM, Riley LW. Use of fimH Single-Nucleotide Polymorphisms for Strain Typing of Clinical Isolates of Escherichia coli for Epidemiologic Investigation. J Clin Microbiol. 2010;48:483–8. Hojati Z, Molaie R, Gholipour A. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-3982260","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":275721267,"identity":"4ce10d20-49f3-409b-aea0-492d401d5ca8","order_by":0,"name":"Lavanya Shankar Salian","email":"","orcid":"","institution":"SASTRA Deemed to be University","correspondingAuthor":false,"prefix":"","firstName":"Lavanya","middleName":"Shankar","lastName":"Salian","suffix":""},{"id":275721268,"identity":"a7624324-fe68-46d6-a8cf-7a69c2e88f41","order_by":1,"name":"Anusree Sajeevan","email":"","orcid":"","institution":"SASTRA Deemed to be University","correspondingAuthor":false,"prefix":"","firstName":"Anusree","middleName":"","lastName":"Sajeevan","suffix":""},{"id":275721272,"identity":"01691a80-d7b9-4bc7-a024-e8f020977eea","order_by":2,"name":"Krishna Prasath S K","email":"","orcid":"","institution":"SASTRA Deemed to be University","correspondingAuthor":false,"prefix":"","firstName":"Krishna","middleName":"Prasath S","lastName":"K","suffix":""},{"id":275721274,"identity":"a48b186e-4034-4aac-a0f9-ebdd4347e0e1","order_by":3,"name":"Suma Mohan S","email":"","orcid":"","institution":"SASTRA Deemed to be University","correspondingAuthor":false,"prefix":"","firstName":"Suma","middleName":"Mohan","lastName":"S","suffix":""},{"id":275721276,"identity":"b684c890-d78c-4d75-affe-439fd1825b2f","order_by":4,"name":"Adline Princy Solomon","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABCUlEQVRIiWNgGAWjYFCC5IYDIIoNRHxAEufBrSURoYVxBpJSvFrgTGYe/EohgL89sfFwQcWdfD7p9mfSNn/s7O2lDz9g+FHDIGOOQ4vEmYcNh2eceWbZJnMgTTq3LTmxhy/NgLHnGAOPZQMOPTcSGw7zth02YJNIOCad28CcwMPDYMDA28DAY3AAuw55sJZ/IC2JbdIWf+rteXjYPzD+xaPFAKylAaQlmU2age0wYw8PjwEzPlsMQX7hOfYMqCWN2bK37XhizxmegsMyxyRwapE7nnz4M0/NHQP5GekPb/z4U23P3sO+8eGbGht7XFqgACzLIoHElcClFEUL8wcCqkbBKBgFo2CEAgBgw1i7WaEpkgAAAABJRU5ErkJggg==","orcid":"","institution":"SASTRA Deemed to be University","correspondingAuthor":true,"prefix":"","firstName":"Adline","middleName":"Princy","lastName":"Solomon","suffix":""}],"badges":[],"createdAt":"2024-02-23 15:09:22","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3982260/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3982260/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":51973824,"identity":"6e151b51-6b0c-4405-9f22-ffa4cda51fc8","added_by":"auto","created_at":"2024-03-04 19:03:35","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":514665,"visible":true,"origin":"","legend":"\u003cp\u003ea The UPEC pie chart of pan-genome\u0026nbsp;\u003c/p\u003e\n\u003cp\u003ePan-genome can be subdivided into three categories: (i) the core genome (the set of genes shared by all genomes), (ii) the accessory genome (the set of genes present in some but not all genomes), and (iii) the unique genome (genes that are unique to a single genome).Created using https://www.meta-chart.com/pie.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eb \u003c/strong\u003eThe pan-genome vs. core-genome plot of UPEC genomes.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ec\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003e \u003c/strong\u003e\u003c/em\u003ePlot representing the numbers of new and unique genes found as each isolate of UPEC strains is added\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-3982260/v1/97d5f21b54a53e17c8b8eea5.png"},{"id":51973822,"identity":"bfe65090-5512-4097-89c5-c79df415398b","added_by":"auto","created_at":"2024-03-04 19:03:35","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":65137,"visible":true,"origin":"","legend":"\u003cp\u003eDistribution of COG categories in UPEC core, accessory, and unique genomes.\u003c/p\u003e\n\u003cp\u003eCOG Categories: C-Energy production and conversion; D-Cell cycle control; cell division chromosome partitioning; E-Amino acid transport \u0026amp; metabolism; F-Nucleotide transport \u0026amp; metabolism; G-Carbohydrate transport \u0026amp; metabolism; H-Coenzyme transport \u0026amp; metabolism; I- Lipid transport and metabolism; J- Translation, ribosomal structure, and biogenesis; K-Transcription; L-Replication, Recombination, and Repair; ; M -Cell wall/membrane/envelope biogenesis; N-Cell motility; O-Post translational modification, protein turnover, chaperones; P- Inorganic ion transport and metabolism; Q- Secondary metabolites biosynthesis, transport and catabolism ; R- General function prediction only; S- Function Unknown; T -Signal transduction mechanisms; U-Intracellular trafficking, secretion \u0026amp; vesicular transport; V-Defense mechanisms; W-Extracellular structures; Z-Cytoskeleton.\u003c/p\u003e","description":"","filename":"FIGURE2.png","url":"https://assets-eu.researchsquare.com/files/rs-3982260/v1/991d58fb9b8cb901cb924134.png"},{"id":51973823,"identity":"0f0a7636-6890-4258-b382-df350650676b","added_by":"auto","created_at":"2024-03-04 19:03:35","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":59715,"visible":true,"origin":"","legend":"\u003cp\u003eParsimony tree of UPEC89 clade obtained from Roary results\u003c/p\u003e","description":"","filename":"FIGURE3.png","url":"https://assets-eu.researchsquare.com/files/rs-3982260/v1/c4f76d49deaed463041b0083.png"},{"id":53535651,"identity":"fbfe77bb-99a7-42d9-ae75-96ecd308cfaa","added_by":"auto","created_at":"2024-03-27 07:36:46","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":735280,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3982260/v1/ba9d9514-9df4-4a48-9857-abab6389d090.pdf"},{"id":51973825,"identity":"b44232af-512c-437d-a529-7c2a653120d5","added_by":"auto","created_at":"2024-03-04 19:03:36","extension":"csv","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":11379568,"visible":true,"origin":"","legend":"","description":"","filename":"Supplementarymaterial1.csv","url":"https://assets-eu.researchsquare.com/files/rs-3982260/v1/c33257a704b0f75ce45b5962.csv"}],"financialInterests":"No competing interests reported.","formattedTitle":"Pan-Genome Analysis with Virulence Factors: Charting the Genomic Landscape of Uropathogenic Escherichia coli (UPEC)","fulltext":[{"header":"Background","content":"\u003cp\u003eGlobally, urinary tract infections (UTIs) are one of the most prevalent health conditions found in clinical settings. Despite significant efforts, UTIs continue to impact over 150\u0026nbsp;million people across the globe, carrying an elevated risk of morbidity and expensive medical expenses. In the US, UTIs are the cause of over 11\u0026nbsp;million physician visits and 470,000 hospitalizations in 2006, at an estimated cost of \u003cspan\u003e$\u003c/span\u003e3.5\u0026nbsp;billion [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. In 2019, more than 404.6\u0026nbsp;million [95% UI (uncertainty intervals) 359.4-446.5] individuals had UTIs globally and nearly 236,786 people (198,433\u0026ndash;259,034) died of UTIs, contributing to 5.2\u0026nbsp;million. From 4,715.0 (4,174.2-5,220.6) per 100,000 population in 1990 to 5,229.3 (4,645.3-5,771.2) per 100,000 population in 2019, the age-standardized incidence rate rose [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. In a report by Christy V R \u003cem\u003eet al\u003c/em\u003e [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e], A study on UTI in the Kanyakumari area of South India found that 40.53 percent of older men (those in the 61\u0026ndash;90 age bracket) were affected by this condition [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. In addition to the women in the reproductive age group, the UTI infection in women with menopausal age was found to be high. About 16.88% of the UTI culture-positive women (391 cases) were in the age group 51\u0026ndash;60 [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. The incidence of UTI in between reproductive age (21\u0026ndash;30 years) and premenopausal, menopausal, and post-menopausal stage women also endured high incidence of UTI was mentioned in Christy V R \u003cem\u003eet al\u003c/em\u003e,. In the women in the age group 51\u0026ndash;60 years, the incidence of UTI is relatively high. Also, the recurrence of infection is posing a significant challenge in the treatment of UTI [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. Infections are more common in women, children, the elderly, diabetics, and people with uroliths and urinary catheters [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eUTIs are categorized as either uncomplicated or complicated clinically. Healthy individuals who do not have any structural or neurological abnormalities in their urinary system are at risk for uncomplicated UTIs, such as cystitis and pyelonephritis. Factors such as urinary obstruction, urine retention, immunosuppression, renal failure, pregnancy, indwelling catheters or other drainage devices, and compromised host defence are linked to complicated UTIs [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. The physiological resistance of men to UTIs is higher. Women's shorter urethras make it easier for the disease-causing microbes to get through the bladder and the urine opening [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThe ORENUC system classifies the risk factors according to the phenotype: \u003cem\u003eO\u003c/em\u003e, no known risk factors; \u003cem\u003eR\u003c/em\u003e, recurrent UTIs ; \u003cem\u003eE\u003c/em\u003e, extra urogenital risk factor; \u003cem\u003eN\u003c/em\u003e, nephropathic diseases; \u003cem\u003eU\u003c/em\u003e, urologic resolvable (transient) risk factors; C, permanent external urinary catheter and unresolved urologic risk factors [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eAs expected, rather than carrying a particular component, the virulence of UPECs appears to be related to the coordinated expression of multiple genes, which change depending on the urinary districts they colonize. Commensal \u003cem\u003eE. coli\u003c/em\u003e and UPECs possess a strong genetic resemblance, hence it is challenging to identify these pathogens; in fact, the existence of \u003cem\u003eE. coli\u003c/em\u003e strains in symptomatic patients' urine samples suffices for identifying a UPEC strain [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThe well-characterized strain UPEC89 has mostly been used to investigate the virulence of UPEC during urinary tract infections [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Multilocus sequence type 95 (ST95) isolate UPEC89 is regarded as a prototypical UPEC isolate and has been widely utilized in investigations of virulence genes linked to UTI [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e, \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. It is critical to comprehend which genes contribute to UPEC fitness during UTI to create novel strategies for disease prevention and treatment. The attachment of bacteria to uroepithelial cells is a crucial stage in the initiation and progression of UTIs. Bacterial ligands, which are typically tiny proteins positioned at the tips of bacterial fimbriae, promote \u003cem\u003eE.coli\u003c/em\u003e attachment by binding to carbohydrate residues in the host cell wall and acting as receptors [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. Thus, \u003cem\u003eE.coli\u003c/em\u003e adherence to host receptors is a function that is often mediated by the bacteria's adhesions to host cell receptors. [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. The bacterial attachment increases the persistence of \u003cem\u003eE. coli\u003c/em\u003e and enables bacteria to withstand mechanical elimination by urine flow and frequent urination. Several forms of adhesins, such as type 1 fimbriae, are necessary for the identification and attachment to urinary tract receptors [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. The adhesive subunit of type 1 fimbriae, \u003cem\u003efimH\u003c/em\u003e is a primary determinant of UPEC adhesions and has a high tropism for urinary tract receptors; as a result, \u003cem\u003efimH\u003c/em\u003e adhesion is critical for \u003cem\u003eE. coli\u003c/em\u003e colonization of many habitats [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. UPEC adhesions are primarily determined by \u003cem\u003efimH\u003c/em\u003e, the sticky subunit of type 1 fimbriae. \u003cem\u003efimH\u003c/em\u003e adhesion has a strong tropism for receptors in the urinary system, \u003cem\u003eE.coli\u003c/em\u003e must colonize a variety of habitats [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. Furthermore, a screening technique for UPEC epidemiological type involves the analysis of \u003cem\u003efimH\u003c/em\u003e single-nucleotide polymorphisms (SNPs) [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e, \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eA study on pangenome analysis of \u003cem\u003eCampylobacter\u003c/em\u003e reported by Chaofang Zhong \u003cem\u003eet al.\u003c/em\u003e, revealed the open nature of \u003cem\u003eCampylobacter\u003c/em\u003e and identified 6 potential core virulence genes. Their research advances our knowledge of Campylobacter virulence, improves the utilization of potential drugs in medication development, and lowers the risk of Campylobacter infections. Prabha K. Bista \u003cem\u003eet al.\u003c/em\u003e, performed the genomic characterization to distinguish the \u003cem\u003eF.necrophorum\u003c/em\u003e subspecies phenotypically by identifying both general and subspecies-specific virulence genes through a custom search-based analysis. Here, they recommended that next research should concentrate on identifying their virulence genes to assess their potential as vaccine targets to stop fusobacterial infections in cattle. This study was performed to determine the various virulence genes and their evolutionary relationships among isolates belonging to the same species in the UPEC89 clade. The progression of UTIs is significantly influenced by the virulence factors of UPEC strains like (type 1 fimbriae, p fimbriae, curli fimbriae, amphibole adhesion, and flagellum). Apart from these hemolysins, siderophores, and cytotoxic necrotizing factor 1 also play crucial roles in the virulence of UPEC [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. The aforementioned virulence factors are critical for extra-intestinal survival, UPEC colonization, and the production of cytopathic effects. Furthermore, expression of UPEC unique virulence factors may exacerbate UTIs and increase uropathogenicity [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e].\u003c/p\u003e"},{"header":"Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003ePublic genome resources, Accession numbers, Annotation, Comparison\u003c/h2\u003e \u003cp\u003eFor the pan-genome analysis, the genomic sequences for \u003cem\u003eUPEC\u003c/em\u003e, including the whole-genome sequences of 212 strains, were downloaded from the Reference Sequence (RefSeq) database and the details were obtained from NCBI Pathogen detection beta (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.ncbi.nlm.nih.gov/pathogens/\u003c/span\u003e\u003cspan address=\"https://www.ncbi.nlm.nih.gov/pathogens/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, accessed on August 2023). The genome-scale study used the most complete strain sampling of each UPEC strain to date. We chose the genome with the highest assembly level and full-genome representation in the NCBI database. The sequences considered in the study were from an isolation source \u0026ndash; Urine (only Clinical samples from Humans). Consequently, 213 genomes, which consisted of 212 complete genomes and 1 draft genome, were included in this study ( Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eIsolates with their assembly number (NCBI Pathogen detection )\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"4\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eStrain name\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAssembly number\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeography\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779395.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777375.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777155.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776175.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776195.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776795.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e 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align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778285.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777585.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e 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colname=\"c3\"\u003e \u003cp\u003eGCA_000777325.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-33\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777285.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-34\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777265.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e 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colname=\"c2\"\u003e \u003cp\u003eUPEC-38\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777195.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-39\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777165.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777135.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-41\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777095.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777105.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e26\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-45\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777065.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e27\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-48\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777025.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776995.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e29\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-51\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776965.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-53\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776935.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e31\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-54\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776925.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-55\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776915.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e33\u003c/p\u003e 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align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-69\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776335.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e44\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776815.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e 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colname=\"c3\"\u003e \u003cp\u003eGCA_000776595.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e48\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-75\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776655.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e49\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-76\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776235.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e 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colname=\"c2\"\u003e \u003cp\u003eUPEC-79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776415.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e53\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776035.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e54\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-81\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776135.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e55\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-82\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776285.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e56\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-83\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776355.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-84\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776215.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e58\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-85\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000776455.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e59\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-87\u003c/p\u003e \u003c/td\u003e 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colname=\"c2\"\u003e \u003cp\u003eUPEC-101\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779055.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-103\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781455.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-104\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781435.1\u003c/p\u003e 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align=\"left\" colname=\"c1\"\u003e \u003cp\u003e76\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-107\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781375.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e77\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-108\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781335.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e78\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-109\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781355.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-110\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781315.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-111\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781275.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e 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\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-114\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781235.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e84\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-115\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781215.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e85\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-116\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e 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\u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e88\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-119\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781145.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e89\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-120\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781095.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-121\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781075.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e91\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-123\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781045.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e92\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-124\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781035.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e93\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-125\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000781005.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e94\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-126\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780995.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e95\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-127\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780965.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e96\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-128\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780915.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e97\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-129\u003c/p\u003e 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colname=\"c2\"\u003e \u003cp\u003eUPEC-141\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780715.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e110\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-142\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780635.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e111\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-143\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780615.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e112\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-144\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780595.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e113\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-145\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780575.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e114\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-146\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780555.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e115\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-147\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780535.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e116\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-148\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780495.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e117\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-149\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780475.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e118\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-150\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780415.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e119\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-151\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780355.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e120\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-153\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780335.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e121\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-154\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780315.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e122\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-155\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780295.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e123\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-156\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780235.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e124\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-157\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780215.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e125\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-158\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780195.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e126\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-159\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780175.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e127\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-161\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780155.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e 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align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780095.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e131\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-170\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780035.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-171\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000780015.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e 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colname=\"c2\"\u003e \u003cp\u003eUPEC-184\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779715.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e143\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-185\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779695.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e144\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-186\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779585.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e145\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-187\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779675.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e146\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-188\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779635.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e147\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-189\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779565.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e148\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-193\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779545.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e149\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e 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\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e152\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-200\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779335.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e153\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-201\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779255.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e154\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-202\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000779295.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e155\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-203\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000785325.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e156\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-205\u003c/p\u003e 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colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e159\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-209\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778465.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e160\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-211\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778585.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e 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align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778725.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e164\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-220\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778705.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e165\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-221\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778895.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e 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colname=\"c2\"\u003e \u003cp\u003eUPEC-236\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778355.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e176\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-237\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778335.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e177\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-238\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778315.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e178\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-239\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778275.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e179\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-243\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778235.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e180\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-244\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778215.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e181\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-248\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778175.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e182\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e 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colname=\"c1\"\u003e \u003cp\u003e187\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-255\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778035.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e188\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-256\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777995.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e189\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-257\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000778015.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e190\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-258\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777975.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e191\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-259\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777945.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e192\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-260\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777895.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e193\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-261\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777845.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e194\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-265\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777835.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e195\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-266\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777815.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e196\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-269\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777735.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e197\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-271\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777695.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e198\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-273\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777675.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e199\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-274\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777655.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e200\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-276\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777625.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e201\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-277\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777605.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e202\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-281\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777555.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e203\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-282\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777535.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e204\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-284\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777515.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e205\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-285\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777495.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e206\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-286\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777475.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e207\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-287\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777455.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e208\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-288\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777435.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e209\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC-289\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000777415.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUSA:WA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e210\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC V2-6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_009761195.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eBRAZIL:SAO PAULO\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e211\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC U34\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_009761205.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eBRAZIL:SAO PAULO\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e212\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC _252\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_007858995.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eBRAZIL:SAO PAULO\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e213\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eUPEC EC 193\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_002507495.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCHINA:FUJIAN\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003ePan-genome and core genome construction\u003c/b\u003e.\u003c/p\u003e \u003cp\u003eThe pan-genome analysis was carried out using Roary v3.13.0 [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e], utilizing the genome annotation in GFF3 format generated by Prokka (Version 1.14.6) (Rapid Prokaryotic Genome Annotation) [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e, \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. The analysis was conducted with the following parameters: 90% identity threshold for BLASTp [Basic Local Alignment Search Tool (Protein-Protein)][\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003eFunctional classification of orthologous cluster analysis\u003c/h2\u003e \u003cp\u003eFor the annotation of pan-genome genes with COG (Cluster of Orthologous groups), a whole-genome BLASTp search was performed against the NCBI COG database with an E-value cutoff of 1 \u0026times; 10\u003csup\u003e\u0026minus;\u0026thinsp;5\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003e \u003cb\u003ePhylogenetic analysis.\u003c/b\u003e \u003c/p\u003e \u003cp\u003eA parsimony tree was created of the 212 studied UPEC strains using PhyML (PHYlogenetic inferences using Maximum Likelihood) version 3.1 in Roary [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e] with 100 bootstrap replicates[\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003cb\u003eVirulence factor analysis.\u003c/b\u003e \u003c/p\u003e \u003cp\u003eTo identify the potential virulence-associated genes in the chosen clade of UPEC89 genomes were aligned against the VFDB (Virulence factor database) 2.0 (2.0.3 version) with 90% threshold for identity, 60% minimum length, 90% coverage, and an E-value cut-off of 1 \u0026times; 10\u0026thinsp;\u0026minus;\u0026thinsp;5 with a FASTA (.fna) input files[\u003cspan additionalcitationids=\"CR15\" citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Also, a bacterial synteny was evaluated and visualized by multiple whole-genome alignment using progressive Mauve[\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]\u003c/p\u003e \u003c/div\u003e"},{"header":"RESULTS","content":"\u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003ePan-genome analysis of 212 UPEC isolates\u003c/h2\u003e \u003cp\u003eTo capture the entire genomic diversity of UPEC strains, 212 strains with complete genomes ( Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e) were chosen for the pan-genome study. Each of these represented the genome with the highest assembly level when multiple strain sequences were available for \u003cem\u003eUPEC\u003c/em\u003e strains. A total of 39,874 gene families [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e] were identified of which 2,385 (6.36%) were shared by all the 212 analysed genomes, constituting the core genome (gene families present in all 212 analysed genomes). The accessory genome included 19,487 (48.8%) gene families shared by at least two species, and 18,011 (45.2 %) nique gene families were found in only one strain, constituting the unique genome (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e1\u003c/span\u003ea, Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e2\u003c/span\u003e). This high proportion of unique genome (45.2 %) urther supports the intragenus heterogeneity of \u003cem\u003eEscherichia\u003c/em\u003e and confirms the previously observed highly diverse nature of this bacteria at the whole-genome level. The variable genes (accessory genes and unique genes) account for about 94% of the whole pan-genome, signifying the high level of genetic diversity in the members of \u003cem\u003eEscherichia coli\u003c/em\u003e and that the genus is a very heterogeneous population.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThe sizes of the core genome and pan-genome for the 212 analysed UPEC strain genomes were estimated to be 2,385 and 39,874 genes, respectively. The number of genomes examined greatly influences the size of the core genome and pan-genome. The curves of the core genome and pan-genome size of these UPEC strains genomes, with the increase of the number of genomes demonstrated that the pan-genome size increased almost exponentially with the number of genomes, while the core genome size was being narrowed. When the number of added genomes reached 212, the size of the pan-genome still increased (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e1\u003c/span\u003eb). The complete pan-genome of the UPEC strains was likely to be larger than 212 genomes. This trend continued with the addition of multiple genomes. Similarly, In Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e1\u003c/span\u003ec, upon observing the number of new genes, it became apparent that the count of unique genes steadily increased with the addition of each new analyzed genome (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e1\u003c/span\u003ec), indicating the open nature of the pangenome. Together this result signified a high level of intraspecific genetic diversity in UPEC and indicated that diversity within the species cannot be captured by a single reference genome. As a result, as more species are identified and analyzed, the global gene repertoire of the UPEC strains will change considerably in the future.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003eFunctional features of the UPEC pan-genome\u003c/h2\u003e \u003cp\u003eOrthologous proteins are those that share a common evolutionary origin and are typically found in different species. COGs are widely used in comparative genomics to study the evolutionary relationships between genes and genomes [\u003cspan additionalcitationids=\"CR20\" citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. Researchers can compare the distribution and conservation of COGs across different species to gain insights into the evolution of specific functions and processes [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. When a gene is assigned a COG ID, it means that the protein product of that gene belongs to a particular orthologous group, and other proteins in the same COG are considered orthologs. Orthologous proteins generally perform similar functions in different organisms, and the assignment of a COG ID provides information about the likely function of the protein based on the functional annotation associated with that COG [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e] .\u003c/p\u003e \u003cp\u003eTo clarify the functional characteristics of the UPEC genome, we employed the clusters of orthologous groups (GOG) analysis to examine whether the core, accessory, and unique genomes in the pan-genome had exhibited distinct COG profiles. The functional categories of the genes were assigned to core, accessory, and unique classes, and the results showed that the gene families in the UPEC core genome were enriched for genes involved in \u0026ldquo;translation, ribosomal structure, and biogenesis\u0026rdquo;(J) (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e2\u003c/span\u003e)[\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e, \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eTherefore, the COG analysis results highlighted that more core genes perform fundamental housekeeping functions than accessory genes and unique genes. Considering the open state of the UPEC pan-genome, the results of the COG enrichment analysis of UPEC accessory genes and unique genes, especially \u0026ldquo;amino acid transport and metabolism\u0026rdquo; (E), \u0026ldquo;replication, recombination, and repair\u0026rdquo; (L), \u0026ldquo;cell wall/membrane/envelope biogenesis\u0026rdquo; (M), and \u0026ldquo;inorganic ion transport and metabolism\u0026rdquo; (P), were consistent with the perspective that larger genomes tend to accumulate functions to enable organisms to achieve a higher degree of ecological diversification[\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. In addition, the virulence-associated functional categories, such as \u0026ldquo;cell motility\u0026rdquo; (N), \u0026ldquo;inorganic ion transport and metabolism\u0026rdquo; (P), \u0026ldquo;signal transduction mechanisms\u0026rdquo; (T), and \u0026ldquo;defence mechanisms\u0026rdquo; (V), were prominently represented in the variable component of the pan-genome [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e], which might contribute to UPEC pathogenicity (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e2\u003c/span\u003e)[\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e, \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003ePhylogenetic analysis\u003c/h3\u003e\n\u003cp\u003eThe parsimony tree reported in Fig.\u0026nbsp;\u003cspan\u003e3\u003c/span\u003e depicts the selected clade consisting of UPEC89. This clade was chosen as its genome is well characterized and plays a significant role in pathogenesis. Now the isolates belonging to this clade were further chosen for virulence genes analysis[\u003cspan\u003e23\u003c/span\u003e].\u003c/p\u003e\n\u003cdiv id=\"Sec9\"\u003e\n \u003ch2\u003ePrediction of Common and Unique virulence genes within UPEC89 clade\u003c/h2\u003e\n \u003cp\u003eThe virulence factors encoded by the pathogen genome enable the organism to manipulate host immune defenses, enhance a pathogen disease-inducing potential, and largely determine the outcome of infections. Thus, comprehensive knowledge of virulence factors is crucial to gain insights into the pathogenesis. We identified a total of 35 virulence genes (Table\u0026nbsp;\u003cspan\u003e3\u003c/span\u003e), including both common and unique ones, as reported in Table\u0026nbsp;\u003cspan\u003e2\u003c/span\u003e and Table\u0026nbsp;\u003cspan\u003e3\u003c/span\u003e, across the 6 UPEC strains.\u003c/p\u003e\n \u003cdiv\u003e\n \u003cdiv\u003e\u0026nbsp;\u003c/div\u003e\n \u003c/div\u003e\n \u003cp\u003eAmong these, 5 were core genes, 4 were soft-core genes, 5 were shell genes, 3 were cloud genes, and 10 were unique genes (Table\u0026nbsp;\u003cspan\u003e1\u003c/span\u003e,Table\u0026nbsp;\u003cspan\u003e2\u003c/span\u003e and Table\u0026nbsp;\u003cspan\u003e4\u003c/span\u003e). The virulence determinants of the pathogenicity of these UPEC strains include flagella, iron uptake, invasion, lipooligosaccharide (LOS), capsule, exotoxin, type IV secretion system (T4SS), and adherence[\u003cspan\u003e1\u003c/span\u003e, \u003cspan\u003e24\u003c/span\u003e].\u003c/p\u003e\n \u003cdiv\u003e\n \u003ctable id=\"Tab3\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv\u003eTable 2\u003c/div\u003e\n \u003cdiv\u003e\n \u003cp\u003eSummary statistics\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"5\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSl. no.\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGenome type\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eRange\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eNumber of genes\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGenes in UPEC89 clade\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCore genes\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e99% \u0026lt;=strains\u0026thinsp;\u0026lt;\u0026thinsp;=\u0026thinsp;100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1528\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSoft core genes\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e95% \u0026lt;=strains\u0026thinsp;\u0026lt;\u0026thinsp;=\u0026thinsp;99%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e857\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eShell genes\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e15% \u0026lt;=strains\u0026thinsp;\u0026lt;\u0026thinsp;=\u0026thinsp;95%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3866\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCloud genes\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2% \u0026lt;=strains\u0026thinsp;\u0026lt;\u0026thinsp;=\u0026thinsp;15%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e15612\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUnique Genes\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1% \u0026lt;=strains\u0026thinsp;\u0026lt;\u0026thinsp;=\u0026thinsp;2%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e18011\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e10\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eTotal genes\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e39874\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n \u003ctable border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv\u003eTable 3\u003c/div\u003e\n \u003cdiv\u003e\n \u003cp\u003eCommon virulence genes\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\" colspan=\"3\"\u003e\n \u003cp\u003eCommon virulence genes\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAslA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNot determined\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003echuA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOuter membrane hemin receptor\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003edhaK\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDihydroxyacetone kinase (also designated ptnC)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efimH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eType 1 fimbriae\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efyuA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSiderophore receptor\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egad\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGlutamate decarboxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e7\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eibeA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eInvasin of brain endothelial cells\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eirp2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eHigh molecular weight protein 2 non-ribosomal peptide synthetase\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e9\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eiss\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eIncreased serum survival\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ekpsE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNot determined\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003enlpl\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePolysialic acid transport protein; Group 2 capsule\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e12\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003esitA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eIron transport protein/for manganese acquisition system\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eterC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eTellurium ion resistance protein\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eusp\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUropathogenic specific protein\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e15\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOuter membrane lipoprotein, YHD fimbriael cluster\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUsher, YHD fimbriael cluster\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e17\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eChaperone, YHD fimbriael cluster\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMajor pilin subunit, YHD fimbriael cluster\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e19\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyfcV\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eFimbrial protein\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cdiv\u003e\n \u003ctable id=\"Tab4\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv\u003eTable 4\u003c/div\u003e\n \u003cdiv\u003e\n \u003cp\u003eUnique Virulence Genes\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"6\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\" colspan=\"6\"\u003e\n \u003cp\u003eUnique virulence genes\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUPEC-59\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUPEC-70\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUPEC-89\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUPEC-101\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUPEC-208\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUPEC-266\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efaeD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eaalB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efdeC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epapC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efaeI\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eaalG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehlyF\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efaeC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eiroN\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efaeH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec10\"\u003e\n \u003ch2\u003ePosition of virulence genes of chosen clade\u003c/h2\u003e\n \u003cp\u003eThe position of virulence genes belonging to all six isolates was constructed with the help of data obtained from VFDB[\u003cspan\u003e14\u003c/span\u003e, \u003cspan\u003e15\u003c/span\u003e, \u003cspan\u003e25\u003c/span\u003e] in which genes with only 100% identity and HSP (High scoring segment pair) length equal to Virulence gene length were chosen, and data from Roary output [\u003cspan\u003e9\u003c/span\u003e, \u003cspan\u003e10\u003c/span\u003e](Table\u0026nbsp;\u003cspan\u003e5\u003c/span\u003e, S1). So, to validate these results, a synteny analysis using the Mauve program was performed. These identified virulence genes exhibited remarkable conservation in gene order and pattern, as evidenced by their consistent flanking by the same neighbouring genes.\u003c/p\u003e\n \u003cdiv\u003e\n \u003ctable id=\"Tab5\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv\u003eTable 5\u003c/div\u003e\n \u003cdiv\u003e\n \u003cp\u003ePosition of Virulence genes of six isolates of chosen clade\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"3\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\u0026nbsp;\u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003ePosition of virulence gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eFunction\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\u0026nbsp;\u003c/th\u003e\n \u003cth align=\"left\" colspan=\"2\"\u003e\n \u003cp\u003eCore genome\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003edhaK\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePEP-Dependent dihydroxyacetone kinase,dihydroxyacetone binding subunit DHAK\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efimH-1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eType-1 fimbrin D-mannose specific adhesin\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efimH-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eType-1 fimbrin D-mannose specific adhesin\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003euspA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUniversal stress protein A\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003euspB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUniversal stress protein B\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003euspC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUniversal stress protein C\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e7\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003euspD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUniversal stress protein D\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003euspF\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUniversal stress protein F\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e9\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003euspG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUniversal stress protein G\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePutative fimbrial-like protein yehD\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\" colspan=\"2\"\u003e\n \u003cp\u003e\u003cstrong\u003eAccessory genome\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003edhak_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePEP-Dependent dihydroxyacetone kinase,dihydroxyacetone binding subunit DHAK\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efyuA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePesticin receptor\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePutative fimbrial-like protein yehA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOuter membrane usher protein yehB\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehB_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOuter membrane usher protein yehB\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehB_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOuter membrane usher protein yehB\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e7\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehB_3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOuter membrane usher protein yehB\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePutative fimbrial chaperone yehC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e9\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehC_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePutative fimbrial chaperone yehC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePutative fimbrial-like protein yehD\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyehD_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePutative fimbrial-like protein yehD\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\" colspan=\"2\"\u003e\n \u003cp\u003e\u003cstrong\u003eUnique genome\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epapC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOuter membrane usher protein papC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eAntimicrobial resistance (AMR) has been increasingly documented in bacteria responsible for urinary tract infections (UTIs) over the past few decades. The emergence of UTIs poses a significant public health concern, contributing to a diminished quality of life for affected individuals and imposing substantial clinical and economic challenges. Uropathogenic \u003cem\u003eE. coli\u003c/em\u003e (UPEC), a widespread gram-negative pathogen and a member of the Enterobacteriaceae family, is globally recognized as the primary cause of UTIs [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e, \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. With an increase in UPEC pathogenesis, finding virulence genes that can be used to treat associated illnesses is essential. The rapid rise of sequencing technologies and genomic analysis has provided an important platform for exploring causes of pathogenicity, as well as determining virulence genes and antimicrobial resistance patterns. However, the challenge arises from the absence of reference genomes for more virulent strains, as only a few sequenced genomes are publicly available, making phylogenetic analysis and the identification of potential virulence factors difficult. To overcome this challenge at hand, this study focused on performing a custom-based virulence gene search using all 212 UPEC strains, which enabled to broaden the search probability. Based on this search, a total of 30 virulence genes were identified which are distributed among the isolates belonging to the UPEC89 clade consisting of 6 UPEC strains. Some of these virulence genes were explicitly found in only one strain whereas 20 factors were common among them. For example, virulence genes encoding \u003cem\u003eE coli\u003c/em\u003e cells polymeric protein structures called K88 fimbriae on their surface i.e. \u003cem\u003efaeC\u003c/em\u003e in UPEC89, \u003cem\u003epapC\u003c/em\u003e gene in UPEC266 is required for the formation of digalactoside-binding Pap pili was found only in this strain [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. On the other hand, Universal stress proteins like \u003cem\u003euspA\u003c/em\u003e were commonly found.\u003c/p\u003e \u003cp\u003eIn UPEC strains, for instance, adhesion is vitally important to overcome host defences in the urinary tract and resist the flushing effect of the urine. Hence, previous reports from Barbara Nesta have documented the role and conserveness of \u003cem\u003efdeC\u003c/em\u003e in UPEC strains [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. \u003cem\u003efdeC\u003c/em\u003e (factor adherence \u003cem\u003eE.coli\u003c/em\u003e) is known for its ability to mediate \u003cem\u003eE. coli\u003c/em\u003e adhesion to mammalian cells and extracellular matrix [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. Although \u003cem\u003efdeC\u003c/em\u003e may share functional homology with other adhesins localized on the E. coli surface, its host cell-dependent expression suggests a specific role during colonization. Also, the expression of \u003cem\u003efdeC\u003c/em\u003e on the bacterial surface is triggered by the interaction of \u003cem\u003eE.coli\u003c/em\u003e with host cells [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn this study, the pathogenesis of UPEC is studied to identify virulence markers of various strains that cause UTIs. Virulence factors, as potential diagnostic indicators, help clinicians manage patients and anticipate the evolution of infection in the host body [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. Hence, A particular emphasis was placed on the analysis of strain-specific distribution of virulence factors. The population structure of UPEC strains has not received much attention in research so far. The study included 212 UPEC strains for which the whole genome has been sequenced (latest [2014] RefSeq strains of UPEC) for our analyses.\u003c/p\u003e \u003cp\u003eIn this comparative genomics study, the genome of UPEC strains was assembled to create the pan-genome to understand its nature, its genomic variability and strain relatedness, and its pathogenic diversity [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. Additionally, Chen \u003cem\u003eet al\u003c/em\u003e., used bioinformatics methods to determine that the core genome size of \u003cem\u003eE. coli\u003c/em\u003e was 2,865 genes[\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. This number was derived from a data set consisting of the genomic contents of seven isolates, two of which were \u003cem\u003eShigella flexneri\u003c/em\u003e isolates[\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. Similarly, conserved genes or core genes are used to understand UPEC strains\u0026rsquo; phylogeny. In the analysis, it is revealed that a wide range of genomic variability, with only 1,530 (3.9%) core genes shared in species shown in the Pan genome of UPEC pie chart. The accessory genes contributed to 19,478 genes (48.8%) of the pan-genome, thus indicating substantial heterogeneity among UPEC strains. All bacteria have developed ways to transfer or acquire genes through various mechanisms with high recombination rates [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. The variability we observed within these species indicates that these bacterial species had been through a series of evolutionary events, suggesting that these core genes may be essential for the survival of the bacteria [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. Also, the open pan-genome nature of species indicates that the species is still evolving by gene acquisition and diversification and hence there is a need to identify genes and target them that are stable [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e gives us information about the diverse virulence gene content and 4 potential core virulence genes like Dhak, usp(ABCDHG),fimH-1, fimH-2, and yehD and a unique gene papC in UPEC266. As reported by Christoph Bachler that DhaK is an enzyme component that functions as a transcriptional coregulator [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]. The family of sequence-related enzymes known as dha kinases uses either ATP or a phosphoprotein from the sugar phosphotransferase system (PTS) as phosphate donors. PTS-dependent kinases comprise a third component (DhaM), which is homologous to PTS proteins, and two subunits (DhaK, DhaL), which are homologous to DAK. Beutler \u003cem\u003eet al\u003c/em\u003e., (2001) found that DhaK and DhaL were elevated in the proteome of E. coli lacking enzyme I (EI), the master enzyme of the PTS, and that EI is essential for Dha kinase activity[\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e]. Lin and colleagues [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e, \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e] also showed that \u003cem\u003eE.coli\u003c/em\u003e grown on Dha exhibited increased Dha kinase activity [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]. Therefore, the common core virulence gene \u003cem\u003edhak\u003c/em\u003e can be a promising target. As well as Universal stress protein genes like \u003cem\u003euspA, uspB, uspC, uspD, uspF, uspG\u003c/em\u003e, and \u003cem\u003eyehD, fimH-1\u003c/em\u003e,2 were found to be core virulence genes. Therefore, total of 4 core virulence genes were found. \u003cem\u003eEscherichia coli uspA\u003c/em\u003e is generated in response to numerous environmental assaults [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. The precise functions of the Usp proteins and Usp domains are still unknown, despite advances in our understanding of the regulation of the \u003cem\u003eE.coli uspA\u003c/em\u003e gene; in certain instances, they seem to be connected to resistance to agents that damage DNA and to respiratory uncouplers [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Since conserved Usp domains or UspA proteins are found in eukaryotes [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e], they seem to play a crucial role in these organisms in addition to bacteria and archaea. It's interesting to note that organisms that include \u003cem\u003eusp\u003c/em\u003e genes typically have many copies of these genes[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. As previously noted, the bacterial usp genes typically encode a single Usp domain in a small (about 14\u0026ndash;15 kD) protein or a bigger (approximately 30 kD) protein that combines two Usp domains in tandem[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Depending on the organism, these variants vary in relative abundance and distribution. \u003cem\u003eE.coli\u003c/em\u003e, for instance, has one tandem type and five tiny Usps [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e], the exact roles of the Usp proteins and Usp domains remain enigmatic; they appear, in some cases, to be linked to resistance to DNA-damaging agents and respiratory uncouplers. Also, \u003cem\u003eyehD\u003c/em\u003e gene encodes the putative fimbrial-like adhesin protein; Part of the \u003cem\u003eyehABCD\u003c/em\u003e fimbrial operon, which contributes to adhesion to various surfaces in specific environmental niches[\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e]. Also, the results of synteny showed a pattern of conservation of gene order in these core virulence genes. Hence, the presence of these genes in conserved regions suggests a fundamental role highlights their evolutionary significance, and underscores their essential role in the bacteria's ability to establish infections[\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eIn this study, we conducted a comparative pan-genome analysis of 212 UPEC clinical isolates, revealing their pan-genome characteristics, genomic diversity, virulence, and antimicrobial profiles. This study provides a snapshot of the genomic diversity of different UPEC pathological strains that support the metabolic and pathogenic diversity of 212 UPEC strains. The pan-genome of 212 UPEC members was found to be open and exhibited a high level of genomic variability, of which about 94% was variable. The COG analysis highlighted the adaptive functions of variable genes. These species have abundant virulence genes with functions that mirror pathogenicity differences, such as flagella and endotoxin. Furthermore, all studied UPEC strains contained the \u003cem\u003edhak\u003c/em\u003e (PEP-Dependent dihydroxyacetone kinase, dihydroxyacetone binding subunit DHAK), \u003cem\u003euspA\u003c/em\u003e (Universal stress protein-A), \u003cem\u003euspB\u003c/em\u003e (Universal stress protein-B), \u003cem\u003euspC\u003c/em\u003e (Universal stress protein-C), \u003cem\u003euspD\u003c/em\u003e (Universal stress protein-D), \u003cem\u003efimH-1\u003c/em\u003e and \u003cem\u003e\u0026minus;\u0026thinsp;2\u003c/em\u003e ( Type-1 fimbrin D-mannose specific adhesin ) and \u003cem\u003eyehD\u003c/em\u003e(putative fimbrial like protein \u003cem\u003eyehD\u003c/em\u003e). The virulence genes identified in this work will permit genetic and clinical research on UPEC strains by enabling the efficient utilization of candidates for vaccine and antibiotic development.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot Applicable\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe datasets generated during the current study are available here,\u003c/p\u003e\n\u003cp\u003eSummary Statistics:\u003c/p\u003e\n\u003cp\u003eGalaxy Version 3.13.0+galaxy2 , Roary(version 3.13.0) https://usegalaxy.eu/api/datasets/4838ba20a6d86765f2287d53338183f6/display?to_ext=tabular \u003c/p\u003e\n\u003cp\u003ePan-genome vs. core-genome plot:\u003c/p\u003e\n\u003cp\u003eGalaxy Version 3.13.0+galaxy2 , Roary(version 3.13.0) https://usegalaxy.eu/api/datasets/4838ba20a6d86765f3f1a320cf610f14/display?to_ext=txt. Plot representing number of unique and new genes :\u003c/p\u003e\n\u003cp\u003eGalaxy Version 3.13.0+galaxy2 , Roary(version 3.13.0) https://usegalaxy.eu/api/datasets/4838ba20a6d86765e2a6db40eb3e631b/display?to_ext=txt. \u003c/p\u003e\n\u003cp\u003ehttps://usegalaxy.eu/api/datasets/4838ba20a6d867656426394d12b42413/display?to_ext=txt. Functional Features :\u003c/p\u003e\n\u003cp\u003eCOG NCBI\u003c/p\u003e\n\u003cp\u003ehttps://www.ncbi.nlm.nih.gov/research/cog \u003c/p\u003e\n\u003cp\u003ePhylogenetic Analysis:\u003c/p\u003e\n\u003cp\u003eGalaxy Version 3.13.0+galaxy2 , Roary(version 3.13.0) https://usegalaxy.eu/api/datasets/4838ba20a6d86765ed02b935b98ffb04/display?to_ext=nhx \u003c/p\u003e\n\u003cp\u003ehttps://usegalaxy.eu/visualization/phyloviz?id=70f250ef8e555079 \u003c/p\u003e\n\u003cp\u003eVirulence Finder:\u003c/p\u003e\n\u003cp\u003ehttps://cge.food.dtu.dk/services/VirulenceFinder/ \u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot Applicable\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor\u0026rsquo;s Contribution\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAPS and SMS collaborated in the conceptualization and study design. LSS conducted an extensive literature survey, analyzed the data, and drafted the manuscript. AS generated the framework of the manuscript, synchronized the flow of information, and provided crucial insights in developing the manuscript. LSS, KPSK, and AS implemented revisions based on valuable feedback from APS and SMS. All authors have collectively reviewed and approved prior submission.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eLSS and AS thank the members of the Quorum Sensing Lab for their support. The authors acknowledge SASTRA Deemed to be University, Thanjavur, India for extending infrastructure support to carry out this work. \u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eFlores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. 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Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics. Front Microbiol. 2022;13.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"UPEC, Urinary tract infection, Pangenome, Virulence factors","lastPublishedDoi":"10.21203/rs.3.rs-3982260/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3982260/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eUrinary tract infections remain a worldwide health challenge, affecting over 150\u0026nbsp;million individuals annually, with significant morbidity and healthcare costs. \u003cem\u003eEscherichia coli\u003c/em\u003e is the chief uropathogen (50\u0026ndash;90%) in uncomplicated, community-acquired urinary tract infections. Numerous virulence factors are expressed by Uropathogenic Escherichia coli (UPEC), allowing the bacteria to cause urinary tract infections. Despite large-scale sequencing efforts to raise clinical awareness of UPEC, not much is known about the diversity and functions of virulence factors. To understand and elucidate the genetic diversity, evolutionary characteristics, and virulence profile, efforts were taken to construct the pan-genome of UPEC using 212 publicly available complete genome sets. The UPEC pan-genome was open in nature i.e. its size increases indefinitely when adding new genomes and showed extensive genome variability. These UPEC strains had diverse virulence gene content, and four potential core virulence genes (\u003cem\u003edhak, fimH-1, H-2, uspABCDFG, yehD\u003c/em\u003e) have been identified. The conserved mechanisms for their pathogenicity were related to adherence, motility, and immune modulation. The study underscores the crucial role of bacterial adhesins, particularly \u003cem\u003efimH\u003c/em\u003e, in mediating UPEC attachment to uroepithelial cells, enhancing persistence, and resisting mechanical elimination by urine flow. The investigation into \u003cem\u003efimH\u003c/em\u003e single-nucleotide polymorphisms aids in understanding UPEC epidemiological types. The datasets provide in-depth analysis of genomic diversity and virulence profiles of UPEC strains, paving the way for the development of effective preventive and therapeutic strategies. Therefore, the identified virulence factors with further research can serve as potential targets for vaccine and antibiotic development, facilitating genetic studies and clinical research for enhanced UTI management.\u003c/p\u003e","manuscriptTitle":"Pan-Genome Analysis with Virulence Factors: Charting the Genomic Landscape of Uropathogenic Escherichia coli (UPEC)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-03-04 19:03:30","doi":"10.21203/rs.3.rs-3982260/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"29b68c87-3757-4913-90bf-fdd6961888fc","owner":[],"postedDate":"March 4th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2024-03-27T07:28:38+00:00","versionOfRecord":[],"versionCreatedAt":"2024-03-04 19:03:30","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3982260","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3982260","identity":"rs-3982260","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}