Isolation & genomic characterisation of a Multidrug-Resistant Acinetobacter baumannii ST149 from India: An emerging threat beyond the known international clones

Isolation & genomic characterisation of a Multidrug-Resistant Acinetobacter baumannii ST149 from India: An emerging threat beyond the known international clones | 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 Isolation & genomic characterisation of a Multidrug-Resistant Acinetobacter baumannii ST149 from India: An emerging threat beyond the known international clones Sovon Acharya, Parmanand Kushwaha, Shailesh Desai, Langamba Angom Longjam, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6913949/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 Background Multidrug-resistant (MDR) Acinetobacter baumannii is a Gram-negative, non-motile, non-fermenting, and strictly aerobic bacillus. It causes high mortality and morbidity rates among hospitalized patients with a compromised immune system. Whole genome sequencing, Multilocus sequence typing (MLST) and clonal complex (CC) analysis enable us to get more information about the clonal diversity, molecular epidemiology of the bacteria, their AMR phenotype and virulence potential. This study was aimed to explore the genomic attributes of an A. baumannii strain isolated from the discarded culture plates infection to determine its virulence and antimicrobial resistance traits. Methods Here, we isolated a clinical isolate of carbapenem-resistant A. baumannii . Then we performed Transmission Electron Microscopy (TEM) and whole genome sequencing (WGS) through Illumina sequencing, followed by bioinformatics analyses. The genome was analysed for the phylogeny, antimicrobial resistance (AMR) genes, prophage regions and virulence-related genes, as well as the mobile genetic elements(MGEs) using various bioinformatics tools. Findings: Multilocus sequence typing (MLST) suggests the isolate as Acinetobacter baumannii ST149, a sequence type that is rarely reported in clinical settings. Phylogenetic analysis revealed that this strain does not cluster with the known International Clones (ICs), yet it harbors a broad repertoire of antimicrobial resistance (AMR) genes. Despite its low prevalence, this isolate (ST149) may pose a significant clinical threat due to its multidrug-resistant (MDR) phenotype and potentially hypervirulent nature. Whole-genome sequencing analysis further uncovered a complex resistome profile associated with various mobile genetic elements (MGEs), including integrons, gene cassettes, and prophage elements, all contributing to its adaptability and pathogenicity. Additionally, the genome encodes numerous hypothetical proteins, many of which remain functionally uncharacterized. Notably, structural prediction using AlphaFold2 identified one such hypothetical protein as a putative member of the Major Facilitator Superfamily (MFS) of transporters, suggesting a potential role in antimicrobial resistance. Horizontal Gene Transfer (HGT) Multi Drug-resistant (MDR) Antimicrobial Resistance (AMR) Multilocus Sequence Typing (MLST) Whole-genome Sequencing (WGS) Ventilator-associated Pneumonia (VAP) Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 1. Introduction Acinetobacter baumannii is a Gram-negative, opportunistic pathogen that has emerged as one of the most challenging causative agents of nosocomial infections globally. Its increasing association with hospital-acquired infections (HAIs), particularly in critically ill and immunocompromised patients, has led to significant concern in the healthcare community. Infections caused by A. baumannii are most commonly reported in intensive care units (ICUs), where they contribute to ventilator-associated pneumonia (VAP), bloodstream infections, catheter-associated urinary tract infections (CAUTIs), wound infections and surgical site infections. The resulting burden includes increased healthcare costs, prolonged hospitalisations, and elevated morbidity and mortality rates. Carbapenem-resistant A. baumannii (CRAB) is considered as one of the most critical pathogens according to the WHO priority pathogen list 2024 ( 1 , 2 , 4 , 5 , 6 , 29 ). Over the past few decades, this bacterium has undergone significant evolutionary changes attributing to its capacity to adapt rapidly within the genomic trajectory. They acquired antimicrobial resistance (AMR) and virulence genes possibly through horizontal gene transfer (HGT) systems involving mobile genetic elements (MGEs) such as transposons, integrons, and plasmids ( 30 , 31 ). Initial studies indicated that there are three major clonal groups across Europe, referred to as European clones I, II & III. Later these were reclassified as International Clones (ICs) 1, 2 & 3 respectively ( 37 ). Among the ICs, IC1 and IC2 have shown a remarkable global spread and were associated with the outbreaks of carbapenem-resistant and multidrug resistant (MDR) A. baumannii. Later on, subsequent investigation of genomic traits through WGS have expanded its classification to at least 8 international clones (ICs), with e of them showing a distinct antimicrobial resistant pattern along with different geographical distribution ( 32 , 33 ). These ICs carries carbapenemase genes such as bla OXA-23 , blaOXA-24/40 , and blaOXA-58 , typically embedded within the integrative conjugative elements and transposons. ( 34 , 36 , 37 ) On the other hand, genomic plasticity serves as the key factor in the success of these clonal lineages. The incorporation of Type 1 integron, pathogenic islands, enhance the organism's ability to withstand environmental pressure for their survival. Gene acquisition from diverse sources and genetic recombination plays a crucial role in the evolution of A. baumannii. While the international clones (ICs) dominate throughout the world, there are less prevalent non-IC sequence types like ST25, ST149 & ST78 that have also been found with the MDR genes. They can potentially become high-risk clones in the future ( 35 , 36 , 37 ). Carbapenem resistance in A. baumannii is primarily caused by class D β-lactamases that hydrolyse carbapenems, known as oxacillinases or OXAs ( 28 ). A recent study by Vijaykumar et al. (2022) found that most isolates in India were from the IC2 lineage, while clones IC 7 and 8 were less commonly found. Despite the clinical and epidemiological importance of CRAB in India, little is known about the genomic characteristics of A. baumannii strains. In particular, clonal complex 149. Here, we report the whole-genome sequencing and analysis of a CRAB isolate from India, which belongs to the sequence type 149 (ST-149). We performed phylogenetic analysis and also described its integrons, mobile genetic elements, genes associated with biofilm formation, virulence-associated genes, and antimicrobial resistance genes in order to determine its relationship with other isolates of A. baumannii from around the world. This study contributes to the growing body of genomic data on Indian CRAB isolates and clarifies their potential for pathogenicity and evolutionary adaptation of A. baumannii ST149. 2. Materials and Methods 2.1. Bacterial Isolation and Identification A. baumannii was isolated from a blood sample of the diagnostic lab in the Department of Microbiology, IQ City Medical College Hospital with ethics clearance and approval form institutional review board (IRB) taken a priori for the study (IQMC/IEC/Project/17/28). This study was approved by the Institutional Ethics Committee of IQ City Medical College & NH Hospital, Durgapur, India (Approval No. IQMC/IEC/Project/17/28). The Acinetobacter baumannii isolate in this study was recovered from discarded clinical culture plates without access to any patient-identifiable information. According to the International Ethical Guidelines for Health-related Research Involving Humans (CIOMS-WHO, 2016) and the Indian Council of Medical Research (ICMR) guidelines, such use of anonymized bacterial isolates without any associated personal data does not require individual patient consent, as it does not constitute human subject research The bacterial colony characteristics were assessed on MacConkey agar, and cellular morphology was observed via Gram staining under a light microscope. Confirmation of A. baumannii was done through PCR-based molecular detection targeting the species-specific region in the DNA gyrase subunit B gene. 2.2. Antimicrobial Susceptibility Test (AST) Antibiotic susceptibility testing was conducted with the Vitek2 compact system (bioMerieux, Inc.), utilising automated broth microdilutions. AST results were reconfirmed using the Kirby-Bauer disk diffusion method. The results were interpreted using the clinical and laboratory standard institute (CLSI) guidelines. ( 9 ) 2.3. Single-cell imaging by Transmission Electron Microscopy (TEM) The copper grid was soaked with the concentrated bacterial solution for 5 minutes and stained with 1% uranyl acetate before transmission electron microscopy imaging was performed. ( 10 ) 2.4. Bacterial DNA extraction (CTAB method), library preparation and WGS A 1.5 ml bacterial overnight culture was pelleted by centrifugation at 4000 rpm for 5 min and the supernatant was discarded. Phenol-chloroform extraction method was followed for genomic DNA isolation from the pelleted cells. Qualitative and quantitative analysis was done by fluorescent (Qubit fluorometer 4.0) and 0.8% agarose gel electrophoresis respectively. The libraries were prepared using the manufacturer instructions of QIAGEN® QIAseq FX DNA Library Kit. These libraries were sequenced in a 2 × 150bp paired-end run using the NovaSeq 6000 (Illumina) with v1.5 reagents (300 cycles). 2.5. Genome assembly, annotation, and bioinformatic analysis After assessing the quality of raw reads with FastQC ( https://www.bioinformatics.babraham.ac.uk/projects/ , last accessed on May 15, 2025), subsequent analyses were conducted on the Galaxy platform ( https://usegalaxy.eu/ , last accessed on May 15, 2025) utilizing various available tools on the platform. Adapter trimming and removal of low-quality reads were carried out by FastP, ( 11 ) followed by genome assembly with Unicycler v.0.8.4.0 ( https://github.com/rrwick/Unicycler , last accessed on May 15, 2025 ) with quality assessment of the assembly was performed with Quast. The assembled genome sequence was initially annotated through Prokka ( 12 ) and compared with further annotation performed by the RAST server ( https://rast.nmpdr.org/ , last accessed on May 15, 2025). Multilocus sequence typing (MLST) analysis was conducted using the A. baumannii database available on PubMLST ( https://pubmlst.org/ , last accessed on May 15, 2025). ABR genes were analysed using tools from the Center for Genomic Epidemiology ( http://www.genomicepidemiology.org/ , last accessed on May 15, 2025), including ResFinder ( https://cge.cbs.dtu.dk/services/ResFinder/ ) and the Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca/ , last accessed on May 15, 2025). Tools available on The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) ( https://www.bv-brc.org/ , last accessed on May 15, 2025) platform was also used to confirm and validate the results of our study by providing additional insights and cross-referencing the outcomes obtained from other analysis platforms. ( 13 ) ISEscan was used to find MGE from the whole genome sequence. The Proksee platform was used for visualization of the genome and creating a circular map of the genome. The Phigaro tool/platform was used to identify prophage elements. ( 14 ) Virulence factor-associated genes were identified by using Virulence Factor Database (VFDB: https://ngdc.cncb.ac.cn/databasecommons/database/id/516 , last accessed on May 15, 2025) ( 15 ) which was later reconfirmed using BacWGSTdb ( 16 ). In addition, integron finder 2.0 was used to identify the presence of integrons in the genome and ( 17 ) islandViewer 4 was used for the identification and visualisation of genomic islands. ( 18 ) The NCBI-BLAST was used for pairwise comparison of sequences and AlphaFold was being used for structure prediction ( 38 ). 2.6. Phylogenetic analysis Phylogenetic analysis was performed by using AutoMLST, a web-based tool that constructs high-resolution bacterial phylogenies based on concatenated alignments of conserved single-copy housekeeping genes. The genome sequences of this isolate were uploaded to the AutoMLST server (last accessed on May 15, 2025), which delineated bacterial spp before selecting ~ 100 conserved marker genes shared across the genomes ( 40 ). The selected genes were aligned using MAFFT, and the alignments were concatenated into a supermatrix. A maximum likelihood phylogenetic tree was inferred using IQ-TREE2 ( 39 ), with model selection and ultrafast bootstrapping performed internally by AutoMLST to assess branch support. 3. Results 3.1. Isolation, Identification, and Genomic Characterisation led to annotation yielding 4039 predicted proteins The antimicrobial sensitivity test (AST) indicated that this isolate is only sensitive to Tigecycline and exhibited intermediate-level sensitivity to colistin. The genome sequencing was performed using the WGS method. Using a standard quality control and adapter trimming tool, FastP on the Galaxy platform trimming was performed. Approximately 16.389052 million Illumina high-quality reads were trimmed to 16.099834 million. We obtained a genome size of the isolate approximately 4.2 Mb comprising a single circular chromosome (4,191,980 bp), which is circular. The whole genome contains 39% Guanine-Cytosine (GC) content. Annotation of the genome using the Prokka tool showed that the genome encodes 4039 predicted genes. Among them, 3970 CDS, 4 rRNAs, 64 tRNAs, and 1 tmRNA (Fig. 2 ). One CRISPR-related sequence was found. The sequence type of this isolate was ST1506 (31-33-67-40-1-95-7) under the Oxford MLST scheme. Under the Pasture MLST scheme, this genome belongs to ST149 ( 3 – 12 – 11 – 2 – 14 – 9 – 14 ). The strain is not part of the well-known highly pathogenic ICs, and yet it possesses all the AMR genes (Table 2 ) possibly exhibiting a hypervirulence phenotype. To evaluate genomic attributes, predicted genes were functionally categorised using subsystems (Fig. 2 ). The isolate's broad metabolic adaptability was highlighted by the fact that the majority of its genes (782 genes across 97 subsystems) were linked to metabolism. Genes related to energy production (230 genes, 30 subsystems), stress response, defence, and virulence (133 genes, 38 subsystems), and protein processing (220 genes across 40 subsystems) came next. The bacterium's ability to adapt to its environment and possible resistance mechanisms is highlighted by the significant representation of genes linked to stress and virulence. Table 2 Antimicrobial Resistance (AMR) Genes. Serial No. Resistance Gene Identity (%) Coverage (%) Phenotype Accession No. 1 armA 100.00 100.0 Amikacin, Gentamicin, Tobramycin, Isepamicin, Netilmicin AY220558 2 aph(3')-VI 99.23 100.0 Amikacin KC170992 3 aph( 6 )-Id 100.00 100.0 Streptomycin M28829 4 aph(3'')-Ib 100.00 99.88 Streptomycin AF024602 5 aph(3'')-Ib 99.88 100.0 Streptomycin AF321551 6 aph(3'')-Ib 99.88 100.0 Streptomycin AF313472 7 aph(3'')-Ib 99.88 100.0 Streptomycin AF321550 8 blaADC-25 96.70 99.91 Unknown Beta-lactam EF016355 9 blaOXA-203 99.88 100.0 Unknown Beta-lactam HQ998857 10 blaPER-7 100.00 100.0 Amoxicillin, Amoxicillin + Clavulanic acid, Ampicillin, Ampicillin + Clavulanic acid, Cefotaxime, Cefoxitin, Cefepime, Ceftazidime, Piperacillin, Piperacillin + Tazobactam, Ticarcillin, Ticarcillin + Clavulanic acid, Aztreonam HQ713678 11 blaOXA-23 100.00 100.0 Imipenem, Meropenem AY795964 12 msr(E) 100.00 100.0 Erythromycin, Azithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S FR751518 13 mph(E) 100.00 100.0 Erythromycin DQ839391 14 cmlA1 99.68 100.0 Chloramphenicol M64556 15 ARR-2 100.00 100.0 Rifampicin HQ141279 16 sul1 100.00 100.0 Sulfamethoxazole U12338 17 sul1 100.00 100.0 Sulfamethoxazole U12338 18 sul2 100.00 85.42 Sulfamethoxazole AJ830710 19 sul2 100.00 85.42 Sulfamethoxazole AY034138 20 tet(B) 100.00 100.0 Doxycycline, Tetracycline, Minocycline AP000342 3.2. AMR Gene Profiling Reveals Active Efflux of the Chemotherapeutic Agents. A thorough resistome is found in this isolate's genome, according to whole genome sequence (WGS) analysis using the ResFinder tool. There are several AMR genes that provide resistance to a variety of antimicrobial chemotherapeutic drugs. Interestingly, this isolate contains blaOXA-23, a class D β-lactamase that hydrolyses carbapenem and is closely linked to A. baumannii's carbapenem resistance. Additionally, it was identified that the PER-7 gene, which codes for an extended-spectrum β-lactamase (ESBL), provides resistance to broad-spectrum cephalosporins. In addition, this isolate contains genes linked to resistance to aminoglycosides, such as armA, aph(3′)-VI, and aph( 6 )-Id, which are known to inactivate various types of aminoglycosides by enzymatic modification. These results are consistent with the tobramycin, gentamicin, and amikacin resistance phenotype. Additionally, the presence of the gene qacEΔ1, associated with the reduced susceptibility to quaternary ammonium compounds and disinfectants such as chlorhexidine, was identified, suggesting potential tolerance to antiseptics and disinfectants used in clinical settings. Efflux-related resistance genes were also detected, including adeR, a regulatory gene for the RND family AdeABC pump, and AbaQ, a major facilitator superfamily (MFS) transporter gene, likely contributing to multidrug resistance via active efflux of the chemotherapeutic agents. 3.3. Virulence and Biofilm-Associated Genes Show Diverse Repertoire of Virulence-associated Genes A diverse repertoire of virulence-associated genes were identified from this isolate using the VFDB tool (Table 4 )Genes related to quorum sensing and regulation, such as abaI and abaR , were detected and are involved in N-acyl-homoserine lactone synthesis and transcriptional regulation of virulence. Multiple genes were identified encoding efflux pumps like adeF , adeG , adeH even as they contribute to both AMR and virulence phenotype. As they harbour genes encoding siderophore (Acinetobactin) synthesis proteins ( basA–J ), the sSiderophores receptor and transport system ( bauA–F ) were present to enable iron acquisition in iron-limited host environments. Table 4 Virulence Genes Present in this isolate. S. No. Gene Contig Identity (%) Position Description 1 basJ 1 97.78 56573..57742 acinetobactin biosynthesis protein BasJ 2 basI 1 96.83 57867..58622 phosphopantetheinyl transferase component of acinetobactin biosynthesis protein BasI 3 basH 1 98.23 58633..59367 non-ribosomal peptide biosynthesis thioesterase BasH 4 barB 1 97.49 59439..61034 siderophore efflux system of the ABC superfamily 5 barA 1 96.52 61031..62641 siderophore efflux system of the ABC superfamily 6 basG 1 98.87 62887..64038 acinetobactin biosynthesis protein BasF 7 basF 1 97.7 64155..65024 aryl carrier protein BasF 8 entE 1 96.56 65042..66670 non-ribosomal peptide synthetase adenylate-forming enzyme of acinetobactin synthesis 9 basD 1 96.67 66925..69774 acinetobactin biosynthesis protein BasD 10 bauA 1 99.3 71199..73481 TonB-dependent siderophore receptor BauA 11 bauB 1 98.45 73567..74535 ferric siderophore ABC transporter, periplasmic siderophore-binding protein 12 bauC 1 97.15 75309..76256 ferric siderophore ABC transporter, permease protein BauC 13 bauD 1 96.44 76270..77197 ferric siderophore ABC transporter, permease protein BauD 14 bfmS 10 98.18 106102..107751 signal transduction histidine kinase 15 bfmR 10 98.88 107784..108500 biofilm-controlling response regulator 16 abaI 11 99.46 61431..61982 N-acyl-L-homoserine lactone synthetase 17 abaR 11 98.19 59461..60177 DNA-binding HTH domain-containing protein 18 plc 11 97.83 137693..139861 phospholipase C 19 ompA 16 99.25 95503..96573 outer membrane protein OmpA 20 adeG 2 97.04 19093..22272 cation/multidrug efflux pump 21 csuE 2 97.16 132548..133567 Csu pilus tip adhesin CsuE 22 pgaD 2 99.57 205626..206090 poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD 23 plcD 25 98.89 24110..25735 phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase The isolate also carries genes for outer membrane protein A (ompA) and phospholipase C (plc), both of which are linked to host cell adhesion, invasion, and cytotoxicity. The presence of these virulence factors suggests that this strain is well-equipped for survival in host-associated and nosocomial environments, with enhanced capabilities for persistence, immune evasion, and pathogenesis (Table 4 ).Furthermore, analysis with the IslandViewer4 identified multiple pathogenicity islands are present within this isolate. One such island contains tetR, a class B tetracycline repressor regulating tetA, providing tetracycline resistance. Other islands carry per1, emrE_2, and cmlA5, encoding an ESBL, a multidrug efflux transporter, and a chloramphenicol MFS transporter, respectively. These are flanked by insertion elements (e.g., ISAba125, ISAba14, IS10A, ISEc29), facilitating HGT (Fig. 4 ). 3.5. MGE Indicates Genomic Architecture Associated with Multiple Resistant Determinants Analysis using MobileElementFinder and VRprofile2 revealed a complex mobile genetic region within the A. baumannii genome, spanning approximately 112,000 to 117,000 bp (Fig. 5 ). This region is characterized by the co-localisation of multiple ABR genes (red) interspersed with attC recombination sites (cyan), indicating the presence of gene cassettes, likely organized within integrons or integron-like structures. An integrase gene (blue) and a nearby transposase (yellow) suggest this resistance island is part of a composite MGE, capable of HGT. Additionally, genes involved in conjugation and mobility would further support the potential for inter-strain dissemination. The AMR genes are flanked by segments encoding hypothetical proteins, which may represent uncharacterised functions or additional cargo genes. This genomic architecture, involving multiple resistance determinants embedded within a recombination- and mobility-associated framework, highlights the organism’s ability to acquire and disseminate antimicrobial resistance traits. Contig 28 harbours multiple resistance genes—including armA , bla PER-7 , mph(E) , msr(E) , ARR-2 , qacE , and sul1 —alongside the insertion sequence ISec29 (IS4 family). This co-localisation suggests the presence of a mobile resistance island, where the insertion element may facilitate HGTed AMR genes (Table 3 ). The physical clustering of resistance determinants with a MGE reflects a high potential for dissemination and highlights the genomic plasticity of A. baumannii . Table 3 This table contains a list of AMR genes and MGE (ISEc29) are physically located in close proximity on the same contig. The position of the ISEc29 in contig is 4503–5827. This result was obtained from the Mobile Element Finder analysis. Sl no. Gene name Phenotype Accession Position in contig # ISEc29 Insertion sequence FJ187822 4503–5827 AMR Genes 1 armA isepamicin, netilmicin, amikacin, gentamicin, tobramycin AY220558 6437–7210 2 qacE cetylpyridinium chloride, ethidium bromide, chlorhexidine, benzylkonium chloride X68232 18742–19023 3 blaPER-7 cefoxitin, ampicillin, ticarcillin, amoxicillin, cefotaxime, ampicillin + clavulanic acid, aztreonam, amoxicillin + clavulanic acid, ceftazidime, cefepime, piperacillin + tazobactam, ticarcillin + clavulanic acid, piperacillin HQ713678 14646–15572 4 sul1 sulfamethoxazole U12338 11892–12731 5 mph€ erythromycin DQ839391 1723–2607 6 sul1 sulfamethoxazole U12338 17843–18682 7 msr€ azithromycin,erythromycin, virginiamycin s, pristinamycin ia, quinupristin FR751518 2663–4138 8 ARR-2 rifampicin HQ141279 20795–21247 9 cmlA1 chloramphenicol M64556 19215–20474 Finally, using AlphaFold2, several hypothetical proteins were structurally predicted and one of them showed homology to MFS transporters, suggesting a role in antibiotic efflux and resistance (Supplementary Fig. 1). 4. Discussion In India, infections caused by A. baumannii among hospitalized patients are increasingly lethal. The prevalence of hospital-acquired infections linked to this bacterial pathogen, particularly among immunocompromised patients is becoming a matter of significant concern. Initially, when this bacterium was first identified, it was not characterised as particularly pathogenic or virulent compared to how it is perceived today. Understanding the evolution and epidemiology of this organism is essential for grasping its current implications in public health. While this bacterium exhibits a high degree of heterogeneity, these variations can be traced back to the bacterium's dynamic and adaptable genomic structure, which allows it to evolve and respond to environmental pressures effectively.Moreover, the mechanisms behind its virulence are influenced by a multitude of factors rather than a single determinant. This complexity is a result of its hypervirulence activity, which enhances its capability to survive and thrive in various conditions, ultimately contributing to its pathogenicity and AMR phenotype. A comprehensive understanding of these aspects is vital for developing effective strategies to combat infections caused by this bacterium. The comprehensive analysis of the whole genome sequence of the multidrug-resistant bacterial isolate, identified as sequence type 1506 (ST 1506) through MLST, reveals significant insights into its genetic structure. Though not part of the well-characterised international clones (ICs), this strain harboured a wide array of AMR genes, mobile genetic elements (MGEs), and pathogenicity islands, all contributing to its enhanced resistance and virulence potential. The spatiotemporal regulation of these genes’ differential expression is vital for the transformation of a relatively non-pathogenic variant of A. baumannii into a highly resistant strain capable of evading treatment. As this MDR strain emerges, it presents multiple potential routes for transmission, raising concerns for public health. Furthermore, it is noteworthy that this strain exhibits similarities to isolates found in Afghanistan (MRSN14427) and Nepal (KSK2) & India (Our Isolate from the eastern part of India & B11911 from the Southern part of India), suggesting a potential link or common ancestry that could assist in tracking its spread and informing strategies for intervention against such antimicrobial resistance (Supplementary Fig. 2) ( 34 , 45 ). The continuous acquisition of AMR genes from a variety of sources has enabled bacteria to become increasingly MDR, further complicating treatment options in clinical settings. It may, however be possible that MGEs, bacteriophages, and HGTs have played pivotal roles in facilitating the bacteria's success as a pathogen exhibiting hypervirulence phenotype. Numerous studies are currently underway globally to develop antimicrobial chemotherapeutic agents and vaccine candidates aimed at combating this organism; nevertheless, only a limited number of effective treatment options are available for successfully managing the infection. Genetically engineered bacteriophage therapy, antimicrobial peptides, and monoclonal antibody-based immunotherapy represent potential strategies to address A. baumannii infections ( 43 ). The various mechanisms utilised by bacteria to endure may include microevolution, whereby a non-pathogenic bacterium acquires the genetic elements necessary to become pathogenic, posing a significant threat to human health ( 23 , 24 , 25 , 26 , 27 ). This isolate demonstrated susceptibility exclusively to Tigecycline, a tetracycline antibiotic, while exhibiting intermediate resistance to colistin (Table 1 ). Additionally, this isolate presents resistance to various antibiotics, including third-generation aminoglycosides, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and fluoroquinolones. The findings of this study are in close alignment with the research conducted by Gaffer et al. 2022 ( 44 ), which identified that cases of neonatal sepsis caused by A. baumannii are predominantly sensitive to tigecycline and colistin. In the context of neonates, carbapenems are frequently regarded as the first-line treatment for lower respiratory tract infections; however, the increasing rates of resistance are a matter of considerable concern. In our study, we have observed an intermediate level of resistance against colistin alongside the presence of macrolide resistance genes within the genome of this isolate from India. The bacteria are progressively acquiring all resistance genes, evolving into a superbug. This isolate carries multiple IS elements and associated resistance genes. The ISAba125 promoter allows bacteria to over-express specific AMR genes, facilitating positive selection ( 41 ). This isolate carrying ISAba125 might be crucial for its AMR phenotype. Table 1 AST result by Kirby-Bauer disk diffusion test & MICs of antibiotics. S. No. Antibiotic Zone of Inhibition (mm) CLSI Breakpoint (Susceptible ≥ mm) Interpretation 1 Ceftazidime (CAZ 30) 0 ≥ 14 Resistant 2 Co-trimoxazole (COT 25) 0 ≥ 10 Resistant 3 Imipenem (IMP 10) 0 ≥ 18 Resistant 4 Colistin (CL 10) 12 ≥ 13 Intermediate 5 Ciprofloxacin (CIP 5) 0 ≥ 15 Resistant 6 Gentamicin (GEN 10) 0 ≥ 12 Resistant 7 Cefepime (FEP 30) 8 ≥ 14 Resistant 8 Meropenem (MEM 10) 0 ≥ 14 Resistant Class I integrons serve as pivotal contributors to the evolution of ABR, given their capacity to integrate and express a diverse array of resistance genes. Consequently, they represent a significant variable in the dissemination of ABR in A. baumannii ( 42 ). Class I integrons augment the mobility of antimicrobial resistance gene cassettes, culminating in a more pronounced AMR phenotype and subsequent positive selection. The isolate harbours a Class I integron, in conjunction with several antimicrobial resistance genes, which presents a significant threat. The production of bacterial biofilms allows these pathogens to evade the host's immune response and reduces their susceptibility to chemotherapeutic agents. This isolate demonstrates the capability to produce biofilm in an in vitro biofilm formation assay. Taken together, we provide new insights into the evolution of the AMR patterns of the A. baumannii isolates prevalent in India, which may influence the global burden of bacterial infections. While our study demonstrates less prevalent A. baumannii could be classified as CRAB, it may possess all the requisite tools to evolve into a hypervirulent strain in various regions across the globe. This was supported by the genomic surveillance using WGS approach facilitating the identification and investigation of the genomic characteristics of these strains on a global scale. However, our work has certain limitations, a large isolate from several sup-population stratification could have yielded better characterisation. Nonetheless, we hope genomic data we produced could assist in designing immunoinformatics-based subunit vaccines targeting the prevalent A. baumannii strains in India, besides understanding the polymorphisms present in various genes. 5. Conclusion This study presents the comprehensive genomic analysis of a multidrug-resistant Acinetobacter baumannii ST149 isolate from the eastern part of India, a sequence type that lies outside the major ICs and yet it exhibits significant resistance and virulence potential. The WGSrevealed the presence of multiple AMRgenes, MGEs, integrons, and virulence factors, including those involved in iron acquisition, biofilm formation, and stress adaptation. Notably, the co-localisation of AMR genes with insertion sequences highlights the potential for HGT dissemination. Structural prediction of hypothetical proteins by Alphafold2 revealed the role of uncharacterized hypothetical proteins contributing to resistance phenotype. Our findings emphasise that underrepresented sequence types like ST149 may represent a growing clinical threat, warranting early recognition and targeted response strategies. Declarations Data availability: The raw reads of Whole Genome Sequencing (WGS) data have been submitted to SRA and NCBI and can be accessed through the BioProject accession number PRJNA1201564. Conflict of interest statement: The authors have stated explicitly that there are no conflicts of interest in connection with this article. Ethics statement: This study was approved by the Institutional Ethics Committee of IQ City Medical College & NH Hospital, Durgapur, India (Approval No. IQMC/IEC/Project/17/28). The Acinetobacter baumannii isolate in this study was recovered from discarded clinical culture plates without access to any patient-identifiable information. According to the International Ethical Guidelines for Health-related Research Involving Humans (CIOMS-WHO, 2016) and the Indian Council of Medical Research (ICMR) guidelines, such use of anonymized bacterial isolates without any associated personal data does not require individual patient consent, as it does not constitute human subject research Authors’ contribution: SA, PK, PS & GC contributed to the study design. LAL, BC, PK, and SA collected bacterial samples. Genomic data was analysed and interpreted by SA, PK, AG, AV, SD1, SD2, PS, and GC. TEM was done by SA, PK & SG. SA and PK designed the figures. The manuscript was written by SA and PK. GC, RSPR, and PS co-edited the manuscript with SD1, MR, LK, SD1, SD2, AV. PS & GC supervised the study. All authors had full access to all the data in the study and accepted the responsibility for the decision to submit for publication. Authors’ Contributions (CRediT taxonomy) Conceptualization : SA, PK, PS, GC Sample collection : LAL, BC, PK, SA Data analysis : SA, PK, AG, AV, SD1, SD2, PS, GC Investigation & TEM : SA, PK, SG Visualization : SA, PK Writing – original draft : SA, PK Writing – review & editing : SD1, MR, LK, SD2, AV, GC, RSPR, PS Supervision : PS, GC All authors reviewed and approved the final manuscript. Ethical statement: This study was approved by the Institutional Ethics Committee of IQ City Medical College & NH Hospital, Durgapur, India (Approval No. IQMC/IEC/Project/17/28). The Acinetobacter baumannii isolate used in this work was obtained from discarded clinical culture plates, with no access to patient-identifiable information. In accordance with the International Ethical Guidelines for Health-related Research Involving Humans (CIOMS-WHO, 2016) and the Indian Council of Medical Research (ICMR) guidelines, the use of anonymized bacterial isolates without linked personal data does not constitute human subject research and therefore does not require individual informed consent. We have carefully followed the CIOMS-WHO (2016) International Ethical Guidelines for Health-related Research Involving Humans https://cioms.ch/publications/ ➤ Guideline 3: Use of de-identified, minimal-risk samples may not require consent. ICMR National Ethical Guidelines (2017) https://ethics.ncdirindia.org/ ➤ Section: “Biological Materials and Data” permits use of unlinked, anonymized clinical samples without consent under specified conditions. U.S. DHHS – Common Rule (45 CFR 46) (For international reviewers) https://www.ecfr.gov/current/ ➤ Research on non-identifiable biospecimens is not considered human subject research. Funding: This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. References Nemec A, Dijkshoorn L, Van Der Reijden TJK. Long-term predominance of two pan-European clones among multi-resistant Acinetobacter baumannii strains in the Czech Republic. J Med Microbiol. 2004;53(2):147–53. Abraham EP. The Antibiotics. Compr Biochem. 1963;11(4):181–224. Gadea FX, Šavrda J, Paidarová I. The structure of Ar3+. Chem Phys Lett. 1994;223(4):369–76. Voulgari E, Zarkotou O, Ranellou K, Karageorgopoulos DE, Vrioni G, Mamali V, et al. Outbreak of OXA-48 carbapenemase-producing Klebsiella pneumoniae in Greece involving an ST11 clone. J Antimicrob Chemother. 2013;68(1):84–8. Liu BT, Su WQ. Whole genome sequencing of NDM-1-producing serotype k1 st23 hypervirulent klebsiella pneumoniae in china. J Med Microbiol. 2019;68(6):866–73. Jiang L, Yu Y, Zeng W, Guo J, Lv F, Wang X et al. 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International clones of high risk of acinetobacter baumannii—Definitions, history, properties and perspectives. Microorganisms. 2023;11(8):2115. Shelenkov A, Petrova L, Zamyatin M, Mikhaylova Y, Akimkin V. Diversity of international high-risk clones of Acinetobacter baumannii revealed in a Russian multidisciplinary medical center during 2017–2019. Antibiotics. 2021;10(8):1009. Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596(7873):583–9. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Von Haeseler A, Lanfear R. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37(5):1530–4. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res. 2019;47(W1):W276–82. Hamidian M, Hancock DP, Hall RM. Horizontal transfer of an ISAba125-activated ampC gene between Acinetobacter baumannii strains leading to cephalosporin resistance. J Antimicrob Chemother. 2013;68(1):244–5. Firoozeh F, Ghorbani M, Zibaei M, Badmasti F, Farid M, Omidinia N, Bakhshi F. Characterization of class 1 integrons in metallo-β-lactamase-producing Acinetobacter baumannii isolates from hospital environment. BMC Res Notes. 2023;16(1):365. Kashyap R, Tiwari S, Bhattacharya S. Innovative strategies in the fight against bacterial infections: Phage therapy, nanotechnology, and new antimicrobial agents for multidrug-resistant pathogens. Results Chem. 2025 Apr;30:102304. Cavallo I, Oliva A, Pages R, Sivori F, Truglio M, Fabrizio G, Pasqua M, Pimpinelli F, Di Domenico EG. Acinetobacter baumannii in the critically ill: complex infections get complicated. Front Microbiol. 2023;14:1196774. Balaji V, Rajenderan S, Anandan S, Biswas I. Genome sequences of two multidrug-resistant Acinetobacter baumannii clinical strains isolated from southern India. Genome Announcements. 2015;3(5):10–128. Supplementary Material Supplementary Figures 1 and 2 are not available with this version. Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-6913949","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":489199060,"identity":"56bd5d7b-a024-46ae-8b2c-5c534add20e2","order_by":0,"name":"Sovon Acharya","email":"","orcid":"","institution":"Amity University","correspondingAuthor":false,"prefix":"","firstName":"Sovon","middleName":"","lastName":"Acharya","suffix":""},{"id":489199061,"identity":"9e88d551-0e79-447e-9cb7-f94a9605fc50","order_by":1,"name":"Parmanand Kushwaha","email":"","orcid":"","institution":"Amity 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University","correspondingAuthor":false,"prefix":"","firstName":"Gyaneshwer","middleName":"","lastName":"Chaubey","suffix":""}],"badges":[],"createdAt":"2025-06-17 11:38:27","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6913949/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6913949/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":87575322,"identity":"8ff103eb-466d-42d6-a31b-1e8613699e3b","added_by":"auto","created_at":"2025-07-25 11:37:22","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":512294,"visible":true,"origin":"","legend":"\u003cp\u003e(a) Gram staining, (b) TEM and (c) PCR to characterise the\u003cem\u003e Acinetobacter baumanii\u003c/em\u003e, targeting the GyrB gene. The transmission electron microscopy of the clinical isolate shows that it is a typical coccobacilli shape and Gram-negative bacteria.\u003c/p\u003e","description":"","filename":"Fig1.png","url":"https://assets-eu.researchsquare.com/files/rs-6913949/v1/ccc5f7c8905ced81efd80a51.png"},{"id":87575323,"identity":"24c56229-57d0-4a72-8a27-07500d5c6b7f","added_by":"auto","created_at":"2025-07-25 11:37:22","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1621778,"visible":true,"origin":"","legend":"\u003cp\u003eA circular graphical display of the distribution of the genome annotations is prepared. The outermost ring represents the complete circular genome of \u003cem\u003eA. baumannii\u003c/em\u003e. From outer to inner rings, the contigs, CDS on the forward strand, CDS on the reverse strand, RNA genes, CDS with homology to known antimicrobial resistance genes, CDS with homology to known virulence factors, GC content and GC skew. The colors of the CDS on the forward and reverse strand are according to the subsystem. Image created using BV-BRC Server.\u003c/p\u003e","description":"","filename":"Fig2.png","url":"https://assets-eu.researchsquare.com/files/rs-6913949/v1/6100841e2d4c8af97464ea8b.png"},{"id":87575327,"identity":"cc6c5aef-18fa-4cdb-b4d4-4bc81005ecd1","added_by":"auto","created_at":"2025-07-25 11:37:22","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":87516,"visible":true,"origin":"","legend":"\u003cp\u003eSubsystem distribution of annotated genes in \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e. Metabolism-related genes were the most abundant, followed by genes involved in protein processing, energy generation, and virulence/stress response.\u003c/p\u003e","description":"","filename":"Fig3.png","url":"https://assets-eu.researchsquare.com/files/rs-6913949/v1/ef40331076ecff3a6b6b552e.png"},{"id":87576690,"identity":"bdb0617c-f70b-4e5d-ba9a-5b42f83fe4fc","added_by":"auto","created_at":"2025-07-25 11:45:22","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":575241,"visible":true,"origin":"","legend":"\u003cp\u003eGenomic islands (GIs) in the genome of the \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e clinical isolate were predicted using IslandViewer 4. Circular (a) \u0026amp; horizontal visualisation (b) of predicted genomic islands are shown, with blocks colored according to the prediction method; IslandPick (green), IslandPath-DIMOB (blue), SIGI-HMM (orange), Islander (turquoise) as well as the integrated results (dark red). Virulence genes (purple for curated, light purple for homologs), AMRantimicrobial resistance genes (pink for curated, light pink for homologs) and pathogen-associated genes (yellow) are also visible as circular glyphs. The circular representation (Fig. 4) illustrates the locations of predicted genomic islands along the chromosome, with several islands clustered around the 1.5 Mb, 3.0 Mb, and 4.2–4.3 Mb regions. Accordingly these islands are highlighted with colored blocks (blue, orange, and red), indicating predictions by different algorithms. Gene content analysis within the islands revealed the presence of multiple hypothetical proteins, as well as genes associated with ABR and virulence. The region around 4.275–4.305 Mb (highlighted at the bottom zoomed-in view) contains a dense cluster of GIs, harbouring several resistance genes \u0026amp; mobile genetic elements (MGEs), indicating a possible hotspot for gene acquisition \u0026amp; genomic plasticity of this strain. These findings underscore the contribution of genomic islands to the adaptive evolution of \u003cem\u003eA. baumannii\u003c/em\u003e, especially regarding antimicrobial resistance. The right panel (C) lists genes located within the predicted islands, including several resistance and mobility-associated genes.\u003c/p\u003e","description":"","filename":"Fig4.png","url":"https://assets-eu.researchsquare.com/files/rs-6913949/v1/8f8e354aa5c4995e1f4c9c1c.png"},{"id":87577333,"identity":"e345451e-83c2-4712-b779-d0243ffa21a3","added_by":"auto","created_at":"2025-07-25 11:53:22","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":28738,"visible":true,"origin":"","legend":"\u003cp\u003eGenomic region from \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e visualized by VRprofile2. Red blocks represent ABR genes; cyan blocks denote attC sites; blue represents integrase; and yellow shows a transposase, indicating the presence of a mobile resistance island.\u003c/p\u003e","description":"","filename":"Fig5.png","url":"https://assets-eu.researchsquare.com/files/rs-6913949/v1/02c7b15e57d0b69cf2f15917.png"},{"id":87575337,"identity":"a9164435-1b80-43d1-b038-bef576fe33c1","added_by":"auto","created_at":"2025-07-25 11:37:22","extension":"jpg","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":719829,"visible":true,"origin":"","legend":"\u003cp\u003eWhole-genome phylogenetic tree of \u003cem\u003eAcinetobacter\u003c/em\u003especies.\u003c/p\u003e\n\u003cp\u003eThis phylogenetic tree, built using AutoMLST, shows the evolutionary relationships between bacterial strains based on conserved genes. Each tip represents a strain or species, and the branches show how closely related they are.The clinical isolate analysed in this study is shown in red. The tree was constructed using AutoMLST based on core genome alignments. Our isolate (highlighted in red) clustered firmly within the \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e clade, confirming its species identity and genetic affiliation with clinically significant MDR strains. Clustering within the \u003cem\u003eA. baumannii\u003c/em\u003e clade confirms its taxonomic identity and reveals close evolutionary proximity to other multidrug-resistant strains. The tree topology also clearly separated \u003cem\u003eA. baumannii\u003c/em\u003e from related species such as \u003cem\u003eA. nosocomialis\u003c/em\u003e, \u003cem\u003eA. pittii\u003c/em\u003e, and environmental \u003cem\u003eAcinetobacter\u003c/em\u003e species, providing strong taxonomic resolution. These findings indicate that the isolate belongs to a well-supported lineage of pathogenic \u003cem\u003eA. baumannii\u003c/em\u003e, potentially linked to hospital-acquired infections and antimicrobial resistance dissemination.\u003c/p\u003e","description":"","filename":"Fig6.jpg","url":"https://assets-eu.researchsquare.com/files/rs-6913949/v1/202a39c9b07be7b6251eb64f.jpg"},{"id":91679385,"identity":"a4e6183c-eb2e-495f-968e-3905252f8425","added_by":"auto","created_at":"2025-09-19 06:17:05","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":4522893,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6913949/v1/1c163562-c320-485b-8be3-8e844c10ec81.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Isolation \u0026 genomic characterisation of a Multidrug-Resistant Acinetobacter baumannii ST149 from India: An emerging threat beyond the known international clones","fulltext":[{"header":"1. Introduction","content":"\u003cp\u003e\u003cem\u003eAcinetobacter baumannii\u003c/em\u003e is a Gram-negative, opportunistic pathogen that has emerged as one of the most challenging causative agents of nosocomial infections globally. Its increasing association with hospital-acquired infections (HAIs), particularly in critically ill and immunocompromised patients, has led to significant concern in the healthcare community. Infections caused by \u003cem\u003eA. baumannii\u003c/em\u003e are most commonly reported in intensive care units (ICUs), where they contribute to ventilator-associated pneumonia (VAP), bloodstream infections, catheter-associated urinary tract infections (CAUTIs), wound infections and surgical site infections. The resulting burden includes increased healthcare costs, prolonged hospitalisations, and elevated morbidity and mortality rates. Carbapenem-resistant \u003cem\u003eA. baumannii\u003c/em\u003e (CRAB) is considered as one of the most critical pathogens according to the WHO priority pathogen list 2024 (\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eOver the past few decades, this bacterium has undergone significant evolutionary changes attributing to its capacity to adapt rapidly within the genomic trajectory. They acquired antimicrobial resistance (AMR) and virulence genes possibly through horizontal gene transfer (HGT) systems involving mobile genetic elements (MGEs) such as transposons, integrons, and plasmids (\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e, \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eInitial studies indicated that there are three major clonal groups across Europe, referred to as European clones I, II \u0026amp; III. Later these were reclassified as International Clones (ICs) 1, 2 \u0026amp; 3 respectively (\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e). Among the ICs, IC1 and IC2 have shown a remarkable global spread and were associated with the outbreaks of carbapenem-resistant and multidrug resistant (MDR) A. baumannii. Later on, subsequent investigation of genomic traits through WGS have expanded its classification to at least 8 international clones (ICs), with e of them showing a distinct antimicrobial resistant pattern along with different geographical distribution (\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e, \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e). These ICs carries carbapenemase genes such as \u003cem\u003ebla\u0026thinsp;\u0026lt;\u0026thinsp;sub\u0026thinsp;\u0026gt;\u0026thinsp;OXA-23\u0026lt;/sub\u0026gt;\u003c/em\u003e, \u003cem\u003eblaOXA-24/40\u0026lt;/sub\u0026gt;\u003c/em\u003e, and \u003cem\u003eblaOXA-58\u0026lt;/sub\u0026gt;\u003c/em\u003e, typically embedded within the integrative conjugative elements and transposons. (\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e, \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e, \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e)\u003c/p\u003e\u003cp\u003eOn the other hand, genomic plasticity serves as the key factor in the success of these clonal lineages. The incorporation of Type 1 integron, pathogenic islands, enhance the organism's ability to withstand environmental pressure for their survival. Gene acquisition from diverse sources and genetic recombination plays a crucial role in the evolution of A. baumannii. While the international clones (ICs) dominate throughout the world, there are less prevalent non-IC sequence types like ST25, ST149 \u0026amp; ST78 that have also been found with the MDR genes. They can potentially become high-risk clones in the future (\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e, \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e, \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e). Carbapenem resistance in \u003cem\u003eA. baumannii\u003c/em\u003e is primarily caused by class D β-lactamases that hydrolyse carbapenems, known as oxacillinases or OXAs (\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e). A recent study by Vijaykumar et al. (2022) found that most isolates in India were from the IC2 lineage, while clones IC 7 and 8 were less commonly found. Despite the clinical and epidemiological importance of CRAB in India, little is known about the genomic characteristics of A. baumannii strains. In particular, clonal complex 149. Here, we report the whole-genome sequencing and analysis of a CRAB isolate from India, which belongs to the sequence type 149 (ST-149). We performed phylogenetic analysis and also described its integrons, mobile genetic elements, genes associated with biofilm formation, virulence-associated genes, and antimicrobial resistance genes in order to determine its relationship with other isolates of A. baumannii from around the world. This study contributes to the growing body of genomic data on Indian CRAB isolates and clarifies their potential for pathogenicity and evolutionary adaptation of A. baumannii ST149.\u003c/p\u003e"},{"header":"2. Materials and Methods","content":"\u003cp\u003e\u003cb\u003e2.1. Bacterial Isolation and Identification\u003c/b\u003e\u003c/p\u003e\u003cp\u003e\u003cem\u003eA. baumannii\u003c/em\u003e was isolated from a blood sample of the diagnostic lab in the Department of Microbiology, IQ City Medical College Hospital with ethics clearance and approval form institutional review board (IRB) taken a priori for the study (IQMC/IEC/Project/17/28). This study was approved by the Institutional Ethics Committee of IQ City Medical College \u0026amp; NH Hospital, Durgapur, India (Approval No. IQMC/IEC/Project/17/28). The \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e isolate in this study was recovered from discarded clinical culture plates without access to any patient-identifiable information. According to the International Ethical Guidelines for Health-related Research Involving Humans (CIOMS-WHO, 2016) and the Indian Council of Medical Research (ICMR) guidelines, such use of anonymized bacterial isolates without any associated personal data does not require individual patient consent, as it does not constitute human subject research\u003c/p\u003e\u003cp\u003eThe bacterial colony characteristics were assessed on MacConkey agar, and cellular morphology was observed via Gram staining under a light microscope. Confirmation of \u003cem\u003eA. baumannii\u003c/em\u003e was done through PCR-based molecular detection targeting the species-specific region in the DNA gyrase subunit B gene.\u003c/p\u003e\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003e\u003cb\u003e2.2. Antimicrobial Susceptibility Test (AST)\u003c/b\u003e\u003c/h2\u003e\u003cp\u003eAntibiotic susceptibility testing was conducted with the Vitek2 compact system (bioMerieux, Inc.), utilising automated broth microdilutions. AST results were reconfirmed using the Kirby-Bauer disk diffusion method. The results were interpreted using the clinical and laboratory standard institute (CLSI) guidelines. (\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e)\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec4\" class=\"Section2\"\u003e\u003ch2\u003e2.3. Single-cell imaging by Transmission Electron Microscopy (TEM)\u003c/h2\u003e\u003cp\u003eThe copper grid was soaked with the concentrated bacterial solution for 5 minutes and stained with 1% uranyl acetate before transmission electron microscopy imaging was performed. (\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e)\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec5\" class=\"Section2\"\u003e\u003ch2\u003e2.4. Bacterial DNA extraction (CTAB method), library preparation and WGS\u003c/h2\u003e\u003cp\u003eA 1.5 ml bacterial overnight culture was pelleted by centrifugation at 4000 rpm for 5 min and the supernatant was discarded. Phenol-chloroform extraction method was followed for genomic DNA isolation from the pelleted cells. Qualitative and quantitative analysis was done by fluorescent (Qubit fluorometer 4.0) and 0.8% agarose gel electrophoresis respectively. The libraries were prepared using the manufacturer instructions of QIAGEN\u0026reg; QIAseq FX DNA Library Kit. These libraries were sequenced in a 2\u003cb\u003e\u0026times;\u003c/b\u003e150bp paired-end run using the NovaSeq 6000 (Illumina) with v1.5 reagents (300 cycles).\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec6\" class=\"Section2\"\u003e\u003ch2\u003e2.5. Genome assembly, annotation, and bioinformatic analysis\u003c/h2\u003e\u003cp\u003eAfter assessing the quality of raw reads with FastQC (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.bioinformatics.babraham.ac.uk/projects/\u003c/span\u003e\u003cspan address=\"https://www.bioinformatics.babraham.ac.uk/projects/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025), subsequent analyses were conducted on the Galaxy platform (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://usegalaxy.eu/\u003c/span\u003e\u003cspan address=\"https://usegalaxy.eu/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025) utilizing various available tools on the platform. Adapter trimming and removal of low-quality reads were carried out by FastP, (\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e) followed by genome assembly with Unicycler v.0.8.4.0 \u003cb\u003e(\u003c/b\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/rrwick/Unicycler\u003c/span\u003e\u003cspan address=\"https://github.com/rrwick/Unicycler\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025\u003cb\u003e)\u003c/b\u003e with quality assessment of the assembly was performed with Quast. The assembled genome sequence was initially annotated through Prokka (\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e) and compared with further annotation performed by the RAST server (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://rast.nmpdr.org/\u003c/span\u003e\u003cspan address=\"https://rast.nmpdr.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025). Multilocus sequence typing (MLST) analysis was conducted using the \u003cem\u003eA. baumannii\u003c/em\u003e database available on PubMLST (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://pubmlst.org/\u003c/span\u003e\u003cspan address=\"https://pubmlst.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025). ABR genes were analysed using tools from the Center for Genomic Epidemiology (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://www.genomicepidemiology.org/\u003c/span\u003e\u003cspan address=\"http://www.genomicepidemiology.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025), including ResFinder (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://cge.cbs.dtu.dk/services/ResFinder/\u003c/span\u003e\u003cspan address=\"https://cge.cbs.dtu.dk/services/ResFinder/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) and the Comprehensive Antibiotic Resistance Database (CARD; \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://card.mcmaster.ca/\u003c/span\u003e\u003cspan address=\"https://card.mcmaster.ca/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025). Tools available on The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.bv-brc.org/\u003c/span\u003e\u003cspan address=\"https://www.bv-brc.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025) platform was also used to confirm and validate the results of our study by providing additional insights and cross-referencing the outcomes obtained from other analysis platforms. (\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e) ISEscan was used to find MGE from the whole genome sequence. The Proksee platform was used for visualization of the genome and creating a circular map of the genome. The Phigaro tool/platform was used to identify prophage elements. (\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e) Virulence factor-associated genes were identified by using Virulence Factor Database (VFDB: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://ngdc.cncb.ac.cn/databasecommons/database/id/516\u003c/span\u003e\u003cspan address=\"https://ngdc.cncb.ac.cn/databasecommons/database/id/516\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, last accessed on May 15, 2025) (\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e) which was later reconfirmed using BacWGSTdb (\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e). In addition, integron finder 2.0 was used to identify the presence of integrons in the genome and (\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e) islandViewer 4 was used for the identification and visualisation of genomic islands. (\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e) The NCBI-BLAST was used for pairwise comparison of sequences and AlphaFold was being used for structure prediction (\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e).\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec7\" class=\"Section2\"\u003e\u003ch2\u003e2.6. Phylogenetic analysis\u003c/h2\u003e\u003cp\u003ePhylogenetic analysis was performed by using AutoMLST, a web-based tool that constructs high-resolution bacterial phylogenies based on concatenated alignments of conserved single-copy housekeeping genes. The genome sequences of this isolate were uploaded to the AutoMLST server (last accessed on May 15, 2025), which delineated bacterial spp before selecting\u0026thinsp;~\u0026thinsp;100 conserved marker genes shared across the genomes (\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e). The selected genes were aligned using MAFFT, and the alignments were concatenated into a supermatrix. A maximum likelihood phylogenetic tree was inferred using IQ-TREE2 (\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e), with model selection and ultrafast bootstrapping performed internally by AutoMLST to assess branch support.\u003c/p\u003e\u003c/div\u003e"},{"header":"3. Results","content":"\u003cdiv id=\"Sec9\" class=\"Section2\"\u003e\u003ch2\u003e3.1. Isolation, Identification, and Genomic Characterisation led to annotation yielding 4039 predicted proteins\u003c/h2\u003e\u003cp\u003eThe antimicrobial sensitivity test (AST) indicated that this isolate is only sensitive to Tigecycline and exhibited intermediate-level sensitivity to colistin. The genome sequencing was performed using the WGS method. Using a standard quality control and adapter trimming tool, FastP on the Galaxy platform trimming was performed. Approximately 16.389052\u0026nbsp;million Illumina high-quality reads were trimmed to 16.099834\u0026nbsp;million. We obtained a genome size of the isolate approximately 4.2 Mb comprising a single circular chromosome (4,191,980 bp), which is circular. The whole genome contains 39% Guanine-Cytosine (GC) content. Annotation of the genome using the Prokka tool showed that the genome encodes 4039 predicted genes. Among them, 3970 CDS, 4 rRNAs, 64 tRNAs, and 1 tmRNA (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). One CRISPR-related sequence was found. The sequence type of this isolate was ST1506 (31-33-67-40-1-95-7) under the Oxford MLST scheme. Under the Pasture MLST scheme, this genome belongs to ST149 (\u003cspan additionalcitationids=\"CR4 CR5 CR6 CR7 CR8 CR9 CR10 CR11\" citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u0026ndash;\u003cspan additionalcitationids=\"CR3 CR4 CR5 CR6 CR7 CR8 CR9 CR10 CR11 CR12 CR13\" citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u0026ndash;\u003cspan additionalcitationids=\"CR10 CR11 CR12 CR13\" citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e). The strain is not part of the well-known highly pathogenic ICs, and yet it possesses all the AMR genes (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e2\u003c/span\u003e) possibly exhibiting a hypervirulence phenotype. To evaluate genomic attributes, predicted genes were functionally categorised using subsystems (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). The isolate's broad metabolic adaptability was highlighted by the fact that the majority of its genes (782 genes across 97 subsystems) were linked to metabolism. Genes related to energy production (230 genes, 30 subsystems), stress response, defence, and virulence (133 genes, 38 subsystems), and protein processing (220 genes across 40 subsystems) came next. The bacterium's ability to adapt to its environment and possible resistance mechanisms is highlighted by the significant representation of genes linked to stress and virulence.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\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 2\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eAntimicrobial Resistance (AMR) Genes.\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"6\"\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=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eSerial No.\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eResistance Gene\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003eIdentity (%)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eCoverage (%)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePhenotype\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAccession No.\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\u003earmA\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eAmikacin, Gentamicin, Tobramycin, Isepamicin, Netilmicin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAY220558\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\u003eaph(3')-VI\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e99.23\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eAmikacin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eKC170992\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\u003eaph(\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e)-Id\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eStreptomycin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eM28829\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\u003eaph(3'')-Ib\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e99.88\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eStreptomycin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAF024602\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\u003eaph(3'')-Ib\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e99.88\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eStreptomycin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAF321551\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\u003eaph(3'')-Ib\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e99.88\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eStreptomycin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAF313472\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eaph(3'')-Ib\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e99.88\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eStreptomycin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAF321550\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eblaADC-25\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e96.70\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e99.91\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eUnknown Beta-lactam\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eEF016355\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eblaOXA-203\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e99.88\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eUnknown Beta-lactam\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eHQ998857\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eblaPER-7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eAmoxicillin, Amoxicillin\u0026thinsp;+\u0026thinsp;Clavulanic acid, Ampicillin, Ampicillin\u0026thinsp;+\u0026thinsp;Clavulanic acid, Cefotaxime, Cefoxitin, Cefepime, Ceftazidime, Piperacillin, Piperacillin\u0026thinsp;+\u0026thinsp;Tazobactam, Ticarcillin, Ticarcillin\u0026thinsp;+\u0026thinsp;Clavulanic acid, Aztreonam\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eHQ713678\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e11\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eblaOXA-23\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eImipenem, Meropenem\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAY795964\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\u003emsr(E)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eErythromycin, Azithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eFR751518\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\u003emph(E)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eErythromycin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eDQ839391\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e14\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ecmlA1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e99.68\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eChloramphenicol\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eM64556\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e15\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eARR-2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eRifampicin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eHQ141279\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e16\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003esul1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eSulfamethoxazole\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eU12338\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\u003esul1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eSulfamethoxazole\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eU12338\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\u003esul2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e85.42\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eSulfamethoxazole\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAJ830710\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e19\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003esul2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e85.42\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eSulfamethoxazole\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAY034138\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e20\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003etet(B)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e100.00\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e100.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eDoxycycline, Tetracycline, Minocycline\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eAP000342\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\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e\u003ch2\u003e3.2. AMR Gene Profiling Reveals Active Efflux of the Chemotherapeutic Agents.\u003c/h2\u003e\u003cp\u003eA thorough resistome is found in this isolate's genome, according to whole genome sequence (WGS) analysis using the ResFinder tool. There are several AMR genes that provide resistance to a variety of antimicrobial chemotherapeutic drugs. Interestingly, this isolate contains blaOXA-23, a class D β-lactamase that hydrolyses carbapenem and is closely linked to A. baumannii's carbapenem resistance. Additionally, it was identified that the PER-7 gene, which codes for an extended-spectrum β-lactamase (ESBL), provides resistance to broad-spectrum cephalosporins. In addition, this isolate contains genes linked to resistance to aminoglycosides, such as armA, aph(3\u0026prime;)-VI, and aph(\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e)-Id, which are known to inactivate various types of aminoglycosides by enzymatic modification. These results are consistent with the tobramycin, gentamicin, and amikacin resistance phenotype. Additionally, the presence of the gene qacEΔ1, associated with the reduced susceptibility to quaternary ammonium compounds and disinfectants such as chlorhexidine, was identified, suggesting potential tolerance to antiseptics and disinfectants used in clinical settings. Efflux-related resistance genes were also detected, including adeR, a regulatory gene for the RND family AdeABC pump, and AbaQ, a major facilitator superfamily (MFS) transporter gene, likely contributing to multidrug resistance via active efflux of the chemotherapeutic agents.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\u003ch2\u003e3.3. Virulence and Biofilm-Associated Genes Show Diverse Repertoire of Virulence-associated Genes\u003c/h2\u003e\u003cp\u003eA diverse repertoire of virulence-associated genes were identified from this isolate using the VFDB tool (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e4\u003c/span\u003e)Genes related to quorum sensing and regulation, such as \u003cem\u003eabaI\u003c/em\u003e and \u003cem\u003eabaR\u003c/em\u003e, were detected and are involved in N-acyl-homoserine lactone synthesis and transcriptional regulation of virulence. Multiple genes were identified encoding efflux pumps like \u003cem\u003eadeF\u003c/em\u003e, \u003cem\u003eadeG\u003c/em\u003e, \u003cem\u003eadeH\u003c/em\u003e even as they contribute to both AMR and virulence phenotype. As they harbour genes encoding siderophore (Acinetobactin) synthesis proteins (\u003cem\u003ebasA\u0026ndash;J\u003c/em\u003e), the sSiderophores receptor and transport system (\u003cem\u003ebauA\u0026ndash;F\u003c/em\u003e) were present to enable iron acquisition in iron-limited host environments.\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eVirulence Genes Present in this isolate.\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"6\"\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=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eS. No.\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eGene\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003eContig\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eIdentity (%)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePosition\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c6\"\u003e\u003cp\u003eDescription\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\u003ebasJ\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e97.78\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e56573..57742\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eacinetobactin biosynthesis protein BasJ\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\u003ebasI\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e96.83\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e57867..58622\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003ephosphopantetheinyl transferase component of acinetobactin biosynthesis protein BasI\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\u003ebasH\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e98.23\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e58633..59367\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003enon-ribosomal peptide biosynthesis thioesterase BasH\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\u003ebarB\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e97.49\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e59439..61034\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003esiderophore efflux system of the ABC superfamily\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\u003ebarA\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e96.52\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e61031..62641\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003esiderophore efflux system of the ABC superfamily\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\u003ebasG\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e98.87\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e62887..64038\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eacinetobactin biosynthesis protein BasF\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ebasF\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e97.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e64155..65024\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003earyl carrier protein BasF\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eentE\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e96.56\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e65042..66670\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003enon-ribosomal peptide synthetase adenylate-forming enzyme of acinetobactin synthesis\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ebasD\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e96.67\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e66925..69774\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eacinetobactin biosynthesis protein BasD\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ebauA\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e99.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e71199..73481\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eTonB-dependent siderophore receptor BauA\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e11\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ebauB\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e98.45\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e73567..74535\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eferric siderophore ABC transporter, periplasmic siderophore-binding protein\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\u003ebauC\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e97.15\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e75309..76256\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eferric siderophore ABC transporter, permease protein BauC\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\u003ebauD\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e96.44\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e76270..77197\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eferric siderophore ABC transporter, permease protein BauD\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e14\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ebfmS\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e98.18\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e106102..107751\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003esignal transduction histidine kinase\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e15\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ebfmR\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e98.88\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e107784..108500\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003ebiofilm-controlling response regulator\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e16\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eabaI\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e11\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e99.46\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e61431..61982\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eN-acyl-L-homoserine lactone synthetase\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\u003eabaR\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e11\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e98.19\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e59461..60177\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eDNA-binding HTH domain-containing protein\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\u003eplc\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e11\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e97.83\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e137693..139861\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003ephospholipase C\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e19\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eompA\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e16\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e99.25\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e95503..96573\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eouter membrane protein OmpA\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e20\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eadeG\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e97.04\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e19093..22272\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003ecation/multidrug efflux pump\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e21\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ecsuE\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e97.16\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e132548..133567\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eCsu pilus tip adhesin CsuE\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\u003epgaD\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e99.57\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e205626..206090\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003epoly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD\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\u003eplcD\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e25\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e98.89\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e24110..25735\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003ephosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase\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\u003eThe isolate also carries genes for outer membrane protein A (ompA) and phospholipase C (plc), both of which are linked to host cell adhesion, invasion, and cytotoxicity. The presence of these virulence factors suggests that this strain is well-equipped for survival in host-associated and nosocomial environments, with enhanced capabilities for persistence, immune evasion, and pathogenesis (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e4\u003c/span\u003e).Furthermore, analysis with the IslandViewer4 identified multiple pathogenicity islands are present within this isolate. One such island contains tetR, a class B tetracycline repressor regulating tetA, providing tetracycline resistance. Other islands carry per1, emrE_2, and cmlA5, encoding an ESBL, a multidrug efflux transporter, and a chloramphenicol MFS transporter, respectively. These are flanked by insertion elements (e.g., ISAba125, ISAba14, IS10A, ISEc29), facilitating HGT (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e\u003ch2\u003e3.5. MGE Indicates Genomic Architecture Associated with Multiple Resistant Determinants\u003c/h2\u003e\u003cp\u003eAnalysis using MobileElementFinder and VRprofile2 revealed a complex mobile genetic region within the \u003cem\u003eA. baumannii\u003c/em\u003e genome, spanning approximately 112,000 to 117,000 bp (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e). This region is characterized by the co-localisation of multiple ABR genes (red) interspersed with attC recombination sites (cyan), indicating the presence of gene cassettes, likely organized within integrons or integron-like structures. An integrase gene (blue) and a nearby transposase (yellow) suggest this resistance island is part of a composite MGE, capable of HGT. Additionally, genes involved in conjugation and mobility would further support the potential for inter-strain dissemination. The AMR genes are flanked by segments encoding hypothetical proteins, which may represent uncharacterised functions or additional cargo genes. This genomic architecture, involving multiple resistance determinants embedded within a recombination- and mobility-associated framework, highlights the organism\u0026rsquo;s ability to acquire and disseminate antimicrobial resistance traits.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003eContig 28 harbours multiple resistance genes\u0026mdash;including \u003cem\u003earmA\u003c/em\u003e, \u003cem\u003ebla\u0026thinsp;\u0026lt;\u0026thinsp;sub\u0026thinsp;\u0026gt;\u0026thinsp;PER-7\u0026lt;/sub\u0026gt;\u003c/em\u003e, \u003cem\u003emph(E)\u003c/em\u003e, \u003cem\u003emsr(E)\u003c/em\u003e, \u003cem\u003eARR-2\u003c/em\u003e, \u003cem\u003eqacE\u003c/em\u003e, and \u003cem\u003esul1\u003c/em\u003e\u0026mdash;alongside the insertion sequence ISec29 (IS4 family). This co-localisation suggests the presence of a mobile resistance island, where the insertion element may facilitate HGTed AMR genes (Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). The physical clustering of resistance determinants with a MGE reflects a high potential for dissemination and highlights the genomic plasticity of \u003cem\u003eA. baumannii\u003c/em\u003e.\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eThis table contains a list of AMR genes and MGE (ISEc29) are physically located in close proximity on the same contig. The position of the ISEc29 in contig is 4503\u0026ndash;5827. This result was obtained from the Mobile Element Finder analysis.\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"5\"\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\u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eSl no.\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eGene name\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003ePhenotype\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eAccession\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePosition in contig\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e#\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eISEc29\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eInsertion sequence\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eFJ187822\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e4503\u0026ndash;5827\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e\u003cb\u003eAMR Genes\u003c/b\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003earmA\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eisepamicin, netilmicin, amikacin, gentamicin, tobramycin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eAY220558\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e6437\u0026ndash;7210\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\u003eqacE\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003ecetylpyridinium chloride, ethidium bromide, chlorhexidine, benzylkonium chloride\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eX68232\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e18742\u0026ndash;19023\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\u003eblaPER-7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003ecefoxitin, ampicillin, ticarcillin, amoxicillin, cefotaxime, ampicillin\u0026thinsp;+\u0026thinsp;clavulanic acid, aztreonam, amoxicillin\u0026thinsp;+\u0026thinsp;clavulanic acid, ceftazidime, cefepime, piperacillin\u0026thinsp;+\u0026thinsp;tazobactam, ticarcillin\u0026thinsp;+\u0026thinsp;clavulanic acid, piperacillin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eHQ713678\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e14646\u0026ndash;15572\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\u003esul1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003esulfamethoxazole\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eU12338\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e11892\u0026ndash;12731\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\u003emph\u0026euro;\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eerythromycin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eDQ839391\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e1723\u0026ndash;2607\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\u003esul1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003esulfamethoxazole\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eU12338\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e17843\u0026ndash;18682\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003emsr\u0026euro;\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003eazithromycin,erythromycin, virginiamycin s, pristinamycin ia, quinupristin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eFR751518\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e2663\u0026ndash;4138\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eARR-2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003erifampicin\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eHQ141279\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e20795\u0026ndash;21247\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ecmlA1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003echloramphenicol\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eM64556\u003c/span\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e19215\u0026ndash;20474\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\u003eFinally, using AlphaFold2, several hypothetical proteins were structurally predicted and one of them showed homology to MFS transporters, suggesting a role in antibiotic efflux and resistance (Supplementary Fig.\u0026nbsp;1).\u003c/p\u003e\u003c/div\u003e"},{"header":"4. Discussion","content":"\u003cp\u003eIn India, infections caused by \u003cem\u003eA. baumannii\u003c/em\u003e among hospitalized patients are increasingly lethal. The prevalence of hospital-acquired infections linked to this bacterial pathogen, particularly among immunocompromised patients is becoming a matter of significant concern. Initially, when this bacterium was first identified, it was not characterised as particularly pathogenic or virulent compared to how it is perceived today. Understanding the evolution and epidemiology of this organism is essential for grasping its current implications in public health. While this bacterium exhibits a high degree of heterogeneity, these variations can be traced back to the bacterium's dynamic and adaptable genomic structure, which allows it to evolve and respond to environmental pressures effectively.Moreover, the mechanisms behind its virulence are influenced by a multitude of factors rather than a single determinant. This complexity is a result of its hypervirulence activity, which enhances its capability to survive and thrive in various conditions, ultimately contributing to its pathogenicity and AMR phenotype. A comprehensive understanding of these aspects is vital for developing effective strategies to combat infections caused by this bacterium.\u003c/p\u003e\u003cp\u003eThe comprehensive analysis of the whole genome sequence of the multidrug-resistant bacterial isolate, identified as sequence type 1506 (ST 1506) through MLST, reveals significant insights into its genetic structure. Though not part of the well-characterised international clones (ICs), this strain harboured a wide array of AMR genes, mobile genetic elements (MGEs), and pathogenicity islands, all contributing to its enhanced resistance and virulence potential.\u003c/p\u003e\u003cp\u003eThe spatiotemporal regulation of these genes\u0026rsquo; differential expression is vital for the transformation of a relatively non-pathogenic variant of \u003cem\u003eA. baumannii\u003c/em\u003e into a highly resistant strain capable of evading treatment.\u003c/p\u003e\u003cp\u003eAs this MDR strain emerges, it presents multiple potential routes for transmission, raising concerns for public health. Furthermore, it is noteworthy that this strain exhibits similarities to isolates found in Afghanistan (MRSN14427) and Nepal (KSK2) \u0026amp; India (Our Isolate from the eastern part of India \u0026amp; B11911 from the Southern part of India), suggesting a potential link or common ancestry that could assist in tracking its spread and informing strategies for intervention against such antimicrobial resistance (Supplementary Fig.\u0026nbsp;2) (\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e, \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eThe continuous acquisition of AMR genes from a variety of sources has enabled bacteria to become increasingly MDR, further complicating treatment options in clinical settings. It may, however be possible that MGEs, bacteriophages, and HGTs have played pivotal roles in facilitating the bacteria's success as a pathogen exhibiting hypervirulence phenotype. Numerous studies are currently underway globally to develop antimicrobial chemotherapeutic agents and vaccine candidates aimed at combating this organism; nevertheless, only a limited number of effective treatment options are available for successfully managing the infection. Genetically engineered bacteriophage therapy, antimicrobial peptides, and monoclonal antibody-based immunotherapy represent potential strategies to address \u003cem\u003eA. baumannii\u003c/em\u003e infections (\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e). The various mechanisms utilised by bacteria to endure may include microevolution, whereby a non-pathogenic bacterium acquires the genetic elements necessary to become pathogenic, posing a significant threat to human health (\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e, \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e, \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e, \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eThis isolate demonstrated susceptibility exclusively to Tigecycline, a tetracycline antibiotic, while exhibiting intermediate resistance to colistin (Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Additionally, this isolate presents resistance to various antibiotics, including third-generation aminoglycosides, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and fluoroquinolones. The findings of this study are in close alignment with the research conducted by Gaffer et al. 2022 (\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e), which identified that cases of neonatal sepsis caused by \u003cem\u003eA. baumannii\u003c/em\u003e are predominantly sensitive to tigecycline and colistin. In the context of neonates, carbapenems are frequently regarded as the first-line treatment for lower respiratory tract infections; however, the increasing rates of resistance are a matter of considerable concern. In our study, we have observed an intermediate level of resistance against colistin alongside the presence of macrolide resistance genes within the genome of this isolate from India. The bacteria are progressively acquiring all resistance genes, evolving into a superbug. This isolate carries multiple IS elements and associated resistance genes. The ISAba125 promoter allows bacteria to over-express specific AMR genes, facilitating positive selection (\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e). This isolate carrying ISAba125 might be crucial for its AMR phenotype.\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab4\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eAST result by Kirby-Bauer disk diffusion test \u0026amp; MICs of antibiotics.\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"5\"\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=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eS. No.\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eAntibiotic\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003eZone of Inhibition (mm)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eCLSI Breakpoint (Susceptible\u0026thinsp;\u0026ge;\u0026thinsp;mm)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e\u003cp\u003eInterpretation\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\u003eCeftazidime (CAZ 30)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u0026ge;\u0026thinsp;14\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eResistant\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\u003eCo-trimoxazole (COT 25)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u0026ge;\u0026thinsp;10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eResistant\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\u003eImipenem (IMP 10)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u0026ge;\u0026thinsp;18\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eResistant\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\u003eColistin (CL 10)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e12\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u0026ge;\u0026thinsp;13\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eIntermediate\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\u003eCiprofloxacin (CIP 5)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u0026ge;\u0026thinsp;15\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eResistant\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\u003eGentamicin (GEN 10)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u0026ge;\u0026thinsp;12\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eResistant\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eCefepime (FEP 30)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u0026ge;\u0026thinsp;14\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eResistant\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eMeropenem (MEM 10)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e\u0026ge;\u0026thinsp;14\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eResistant\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\u003eClass I integrons serve as pivotal contributors to the evolution of ABR, given their capacity to integrate and express a diverse array of resistance genes. Consequently, they represent a significant variable in the dissemination of ABR in \u003cem\u003eA. baumannii\u003c/em\u003e (\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e). Class I integrons augment the mobility of antimicrobial resistance gene cassettes, culminating in a more pronounced AMR phenotype and subsequent positive selection. The isolate harbours a Class I integron, in conjunction with several antimicrobial resistance genes, which presents a significant threat. The production of bacterial biofilms allows these pathogens to evade the host's immune response and reduces their susceptibility to chemotherapeutic agents. This isolate demonstrates the capability to produce biofilm in an \u003cem\u003ein vitro\u003c/em\u003e biofilm formation assay.\u003c/p\u003e\u003cp\u003eTaken together, we provide new insights into the evolution of the AMR patterns of the \u003cem\u003eA. baumannii\u003c/em\u003e isolates prevalent in India, which may influence the global burden of bacterial infections. While our study demonstrates less prevalent \u003cem\u003eA. baumannii\u003c/em\u003e could be classified as CRAB, it may possess all the requisite tools to evolve into a hypervirulent strain in various regions across the globe. This was supported by the genomic surveillance using WGS approach facilitating the identification and investigation of the genomic characteristics of these strains on a global scale. However, our work has certain limitations, a large isolate from several sup-population stratification could have yielded better characterisation. Nonetheless, we hope genomic data we produced could assist in designing immunoinformatics-based subunit vaccines targeting the prevalent \u003cem\u003eA. baumannii\u003c/em\u003e strains in India, besides understanding the polymorphisms present in various genes.\u003c/p\u003e"},{"header":"5. Conclusion","content":"\u003cp\u003eThis study presents the comprehensive genomic analysis of a multidrug-resistant \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e ST149 isolate from the eastern part of India, a sequence type that lies outside the major ICs and yet it exhibits significant resistance and virulence potential. The WGSrevealed the presence of multiple AMRgenes, MGEs, integrons, and virulence factors, including those involved in iron acquisition, biofilm formation, and stress adaptation. Notably, the co-localisation of AMR genes with insertion sequences highlights the potential for HGT dissemination. Structural prediction of hypothetical proteins by Alphafold2 revealed the role of uncharacterized hypothetical proteins contributing to resistance phenotype. Our findings emphasise that underrepresented sequence types like ST149 may represent a growing clinical threat, warranting early recognition and targeted response strategies.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eData availability:\u003c/strong\u003e The raw reads of Whole Genome Sequencing (WGS) data have been submitted to SRA and NCBI and can be accessed through the BioProject accession number PRJNA1201564.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of interest statement:\u003c/strong\u003e The authors have stated explicitly that there are no conflicts of interest in connection with this article.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics statement:\u0026nbsp;\u003c/strong\u003eThis study was approved by the Institutional Ethics Committee of IQ City Medical College \u0026amp; NH Hospital, Durgapur, India (Approval No. IQMC/IEC/Project/17/28). The \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e isolate in this study was recovered from discarded clinical culture plates without access to any patient-identifiable information. According to the International Ethical Guidelines for Health-related Research Involving Humans (CIOMS-WHO, 2016) and the Indian Council of Medical Research (ICMR) guidelines, such use of anonymized bacterial isolates without any associated personal data does not require individual patient consent, as it does not constitute human subject research\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026rsquo; contribution:\u003c/strong\u003e SA, PK, PS \u0026amp; GC contributed to the study design. LAL, BC, PK, and SA collected bacterial samples. Genomic data was analysed and interpreted by SA, PK, AG, AV, SD1, SD2, PS, and GC. TEM was done by SA, PK \u0026amp; SG. SA and PK designed the figures. The manuscript was written by SA and PK. \u0026nbsp;GC, RSPR, and PS co-edited the manuscript with SD1, MR, LK, SD1, SD2, AV. PS \u0026amp; GC supervised the study. All authors had full access to all the data in the study and accepted the responsibility for the decision to submit for publication.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026rsquo; Contributions (CRediT taxonomy)\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConceptualization\u003c/strong\u003e: SA, PK, PS, GC\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSample collection\u003c/strong\u003e: LAL, BC, PK, SA\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData analysis\u003c/strong\u003e: SA, PK, AG, AV, SD1, SD2, PS, GC\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eInvestigation \u0026amp; TEM\u003c/strong\u003e: SA, PK, SG\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eVisualization\u003c/strong\u003e: SA, PK\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eWriting \u0026ndash; original draft\u003c/strong\u003e: SA, PK\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eWriting \u0026ndash; review \u0026amp; editing\u003c/strong\u003e: SD1, MR, LK, SD2, AV, GC, RSPR, PS\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSupervision\u003c/strong\u003e: PS, GC\u003c/p\u003e\n\u003cp\u003eAll authors reviewed and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthical statement:\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThis study was approved by the Institutional Ethics Committee of IQ City Medical College \u0026amp; NH Hospital, Durgapur, India (Approval No. IQMC/IEC/Project/17/28). The \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e isolate used in this work was obtained from discarded clinical culture plates, with no access to patient-identifiable information. In accordance with the International Ethical Guidelines for Health-related Research Involving Humans (CIOMS-WHO, 2016) and the Indian Council of Medical Research (ICMR) guidelines, the use of anonymized bacterial isolates without linked personal data does not constitute human subject research and therefore does not require individual informed consent. We have carefully followed the\u0026nbsp;\u003c/p\u003e\n\u003col start=\"1\" type=\"1\"\u003e\n \u003cli\u003eCIOMS-WHO (2016)\u003cbr\u003e\u0026nbsp;International Ethical Guidelines for Health-related Research Involving Humans\u003cbr\u003e\u0026nbsp;https://cioms.ch/publications/\u003cbr\u003e\u0026nbsp;➤ Guideline 3: Use of de-identified, minimal-risk samples may not require consent.\u003c/li\u003e\n \u003cli\u003eICMR National Ethical Guidelines (2017)\u003cbr\u003e\u0026nbsp;https://ethics.ncdirindia.org/\u003cbr\u003e\u0026nbsp;➤ Section: \u0026ldquo;Biological Materials and Data\u0026rdquo; permits use of unlinked, anonymized clinical samples without consent under specified conditions.\u003c/li\u003e\n \u003cli\u003eU.S. DHHS \u0026ndash; Common Rule (45 CFR 46) (For international reviewers)\u003cbr\u003e\u0026nbsp;https://www.ecfr.gov/current/\u003cbr\u003e\u0026nbsp;➤ Research on non-identifiable biospecimens is not considered human subject research.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003e\u003cstrong\u003eFunding:\u003c/strong\u003e This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eNemec A, Dijkshoorn L, Van Der Reijden TJK. 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Genome Announcements. 2015;3(5):10\u0026ndash;128.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"},{"header":"Supplementary Material","content":"\u003cp\u003eSupplementary Figures 1 and 2 are not available with this version.\u003c/p\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":"Horizontal Gene Transfer (HGT), Multi Drug-resistant (MDR), Antimicrobial Resistance (AMR), Multilocus Sequence Typing (MLST), Whole-genome Sequencing (WGS), Ventilator-associated Pneumonia (VAP)","lastPublishedDoi":"10.21203/rs.3.rs-6913949/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6913949/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eMultidrug-resistant (MDR) \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e is a Gram-negative, non-motile, non-fermenting, and strictly aerobic bacillus. It causes high mortality and morbidity rates among hospitalized patients with a compromised immune system. Whole genome sequencing, Multilocus sequence typing (MLST) and clonal complex (CC) analysis enable us to get more information about the clonal diversity, molecular epidemiology of the bacteria, their AMR phenotype and virulence potential. This study was aimed to explore the genomic attributes of an \u003cem\u003eA. baumannii\u003c/em\u003e strain isolated from the discarded culture plates infection to determine its virulence and antimicrobial resistance traits.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e\u003cp\u003eHere, we isolated a clinical isolate of carbapenem-resistant \u003cem\u003eA. baumannii\u003c/em\u003e. Then we performed Transmission Electron Microscopy (TEM) and whole genome sequencing (WGS) through Illumina sequencing, followed by bioinformatics analyses. The genome was analysed for the phylogeny, antimicrobial resistance (AMR) genes, prophage regions and virulence-related genes, as well as the mobile genetic elements(MGEs) using various bioinformatics tools.\u003c/p\u003e\u003ch2\u003eFindings:\u003c/h2\u003e\u003cp\u003eMultilocus sequence typing (MLST) suggests the isolate as \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e ST149, a sequence type that is rarely reported in clinical settings. Phylogenetic analysis revealed that this strain does not cluster with the known International Clones (ICs), yet it harbors a broad repertoire of antimicrobial resistance (AMR) genes. Despite its low prevalence, this isolate (ST149) may pose a significant clinical threat due to its multidrug-resistant (MDR) phenotype and potentially hypervirulent nature. Whole-genome sequencing analysis further uncovered a complex resistome profile associated with various mobile genetic elements (MGEs), including integrons, gene cassettes, and prophage elements, all contributing to its adaptability and pathogenicity. Additionally, the genome encodes numerous hypothetical proteins, many of which remain functionally uncharacterized. Notably, structural prediction using AlphaFold2 identified one such hypothetical protein as a putative member of the Major Facilitator Superfamily (MFS) of transporters, suggesting a potential role in antimicrobial resistance.\u003c/p\u003e","manuscriptTitle":"Isolation \u0026amp; genomic characterisation of a Multidrug-Resistant Acinetobacter baumannii ST149 from India: An emerging threat beyond the known international clones","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-07-25 11:37:18","doi":"10.21203/rs.3.rs-6913949/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":"8a0721d3-be7b-4edd-9ba3-5bfd89ad170f","owner":[],"postedDate":"July 25th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-09-24T20:08:12+00:00","versionOfRecord":[],"versionCreatedAt":"2025-07-25 11:37:18","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6913949","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6913949","identity":"rs-6913949","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}