Molecular characterization based on whole-genome sequencing and antimicrobial susceptibility of Streptococcus pneumoniae in Sichuan Province, China in 2023

Molecular characterization based on whole-genome sequencing and antimicrobial susceptibility of Streptococcus pneumoniae in Sichuan Province, China in 2023 | 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 Molecular characterization based on whole-genome sequencing and antimicrobial susceptibility of Streptococcus pneumoniae in Sichuan Province, China in 2023 Shu Huang, Laihong Shen, Rongmei Yuan, Hongyu Liao, Guo Chen, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5878875/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 Streptococcus pneumoniae is a major cause of pneumonia, meningitis and other invasive diseases resulting in high mortality and morbidity among children. In recent years, the issue of drug resistance in Streptococcus pneumoniae has become increasingly prominent, posing challenges to clinical treatment. Besides, the typing of Streptococcus pneumoniae is important information for evaluating the value of pneumococcal vaccines and developing immunization strategies. A total of 105 Streptococcus pneumoniae isolates were collected from ten cities in Sichuan Province in 2023. The leading serotypes were 19F (34.29%), 19A (10.48%), 3 (7.62%) and 6E (7.62%), with CC271 and GPSC1 being the predominant types. The overall coverage rates of 7-, 10-, 13-valent pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) and 23-valent pneumococcal polysaccharide vaccine (PPV23) were 45.71%, 45.71%, 64.78% and 69.52%, respectively. The antimicrobial susceptibility test of Streptococcus pneumoniae showed that most strains were resistant to erythromycin (ERY), clindamycin (CLI), tetracycline (TCY), and trimethoprim/sulfamethoxazole (SXT), with a multidrug resistance rate of 85.71%, and CLI/EY/TCY was the main resistance mode. The resistance rate of strains isolated from the children's group and the elderly group to SXT was higher than that of the adult group, and the difference was statistically significant (χ 2 = 12.143, p = 0.002). In summary, continuous monitoring of the antibiotic resistance of Streptococcus pneumoniae is crucial for controlling and preventing the development of antibiotic resistance in pneumococcal bacteria. Our research is beneficial for understanding the type distribution of Streptococcus pneumoniae in Sichuan province and guiding the rational use of drugs and adjustment of vaccination strategies in clinical practice. Streptococcus pneumoniae serotype molecular characterization antibiotics sensitivity whole-genome sequencing Figures Figure 1 Figure 2 Figure 3 Introduction Streptococcus pneumoniae ( S. pneumoniae ) is a Gram-positive diplococcus, with humans as its sole host. It often colonizes in the nasopharynx of the human body and is a common opportunistic pathogen[ 1 ]. When the body's immune system is weakened, S. pneumoniae can cause diseases such as pneumonia, bacteremia, otitis media, meningitis, etc. It has become the main pathogenic bacterium of community-acquired pneumonia (CAP)[ 2 ]. A global study on causes of death has also proved that more than half of the deaths caused by lower respiratory tract infections are attributed to infections with S. pneumoniae [ 3 ]. Currently, there are over one hundred serotypes of S. pneumoniae [ 4 ]. Although pneumococcal vaccines have a good protective effect against vaccine serotypes of invasive pneumococcal disease (IPD)[ 5 , 6 ], the current 'serotype replacement' has seriously undermined the protective effect of the vaccine[ 7 , 8 ]. Therefore, a long-term and continuous monitoring of pneumococcus is the basis for the prevention and control of pneumococcal disease, risk assessment, vaccine development and evaluation of vaccine effectiveness. With the abuse of antibiotics, the issue of antibiotic resistance in S. pneumoniae cannot be ignored. According to the statistics of Global Antimicrobial Surveillance System (GLASS) of the World Health Organization (WHO), Streptococcus pneumoniae is one of the four most commonly reported bacterial strains for antibiotic resistance[ 9 ]. According to the Bacterial Priority Pathogens List (BPPL) released by WHO in 2024, Streptococcus pneumoniae is classified as a moderate priority pathogen due to its resistance to macrolide[ 10 ]( https://www.who.int/publications/i/item/9789240093461 ). A study published by the Global Burden of Disease Working Group also shows that S. pneumoniae is one of the six major pathogens closely related to bacterial resistance[ 11 ]. Our study aims to explore the molecular typing and antibiotic resistance of S. pneumoniae through whole-genome sequencing and antibiotics susceptibility test, providing a relevant reference for the epidemic prevention and control of S. pneumoniae . Materials and methods Isolation and identification of Streptococcus pneumoniae strains Our study collected 105 clinical S. pneumoniae strains from ten cities of Sichuan Province, China in 2023, including Chengdu, Dazhou, Deyang, Guangyuan, Luzhou, Mianyang, Nanchong, Neijiang, Panzhihua and Ziyang. The cultured samples were blood (4 strains), cerebrospinal fluid (1 strain), and respiratory tract (100 strains), including sputum (96 strains) and bronchoalveolar lavage fluid (4 strains). The gender information of 1 patient was missing, and the remainder included 65 males and 39 females. Of these, 73 patients (69.52%) were ≤ 18-year-old children, 10 patients were 18 ~ 65 years old, and 22 patients (20.95%) were older than 65 years old. According to the "National Guide to Clinical Laboratory Procedures", the strains were inoculated onto Colombian blood plates and cultured at 37 ℃ in a 5% CO2-enriched atmosphere for 18–20 hours. After cultivation the identification was confirmed by an automatic matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (EXS3000, Zybio). At the same time, ANI (Average Nucleotide Identity, https://pubmlst.org/bigsdb?db=pubmlst_rmlst_seqdef_kiosk ) was used to identify the species based on the results of whole-genome sequencing, in order to exclude non-pneumococcal pathogens. The S. pneumoniae isolates are stored in skim milk culture storage tubes at -80°C for subsequent analysis. Antimicrobial Susceptibility Test (AST) Subcultured S. pneumoniae strains on the Colombian blood plates were used for antibiotic susceptibility test by the Customized AST plate CHNSTRF from Thermo Fisher Scientific, using the following agents: penicilin (PEN), cefepime (FEP), cefotaxime (CTX), amoxicillin (AMX), erythromycin (ERY), meropenem (MEM), vancomycin (VAN), clindamycin (CLI), chloramphenicol (CHL), tetracycline (TCY), moxifloxacin (MFX), levofloxacin (LVX), trimethoprim / sulfamethoxazole (SXT) and linezolid (LNZ). The broth medium containing split horse blood CAMHB-LHB also comes from Thermo Fisher Scientific. After culturing for 18–20 hours, the results were read using Thermo Scientific Sensititre Vizion. Minimum inhibitory concentrations (MICs) of the antimicrobial agents were interpreted according to the Clinical and Laboratory Standards Institute (CLSI) documents M100 34th edition. WHONET 2024 software recommended by WHO was used to input antimicrobial susceptibility testing data and conduct sensitivity analysis. The multiple-drug resistance (MDR) phenotype was defined as being resistant to three or more different classes of antimicrobial agents. Streptococcus pneumoniae ATCC49619 was used as a quality control strain. Genome Sequencing and Assembly The total DNA of S. pneumoniae strains was extracted by using FastPure Bacterial DNA Isolation Mini Kit (Vazyme, China). Proteinase k and RNAse used in the laboratory are both from Vazyme. DNA purity quotient was tested by using spectrophotometer NanoDropTM 2000 (Thermo Fisher Scientific, Waltham, MA, United States). Purified DNA was simultaneously fragmented and tagged with adapters by using the TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, China). We used Illumina platform to sequence, and a series of data processing was carried out on the raw data, mainly including removing reads with 5 bp of ambiguous bases, removing reads with 20 bp of low quality (≤ Q20) bases, adapter contamination, and duplication contamination. Denovo was used to assemble bacterial genome sequencing data from scratch to obtain the optimal contig. Data Analysis Based on Whole Genome Sequencing Qualified reads were used to predict the capsular serotypes of the strains using PneumoKIty ( https://github.com/CarmenSheppard/PneumoKITy )[ 12 ]. And capsular serotypes and Global Pneumococcal Sequencing Cluster (GPSC) of these genomes were also determined using the global genomic surveillance platform PathogenWatch ( https://pathogen.watch/ )[ 13 ]. The genome sequence of each S. pneumoniae isolate was submitted to PubMLST ( https://pubmlst.org )[ 14 ] Streptococcus pneumoniae database and aligned to multilocus sequence typing (MLST) housekeeping genes aroE, gdh, gki, recP, spi, xpt, and ddl alleles to obtain the ST type of each strain, then the BioNumerics software was used to construct a phylogenetic tree of S. pneumoniae isolates based on MLST. Upload the whole genome sequencing data to the online analyzing platform BacWGSTdb ( http://bacdb.cn/BacWGSTdb/index.php )[ 15 – 17 ] to perform sequence alignment to obtain the carrying status of drug-resistance genes and virulence genes of our S. pneumoniae strains. Date Processing The data was processed with Microsoft Excel and Word. The figures were created by BioNumerics7.6 and Graphd Prism 8.0 software. Statistical analysis was conducted using SPSS 22.0 software. Count data is expressed as percentages (%), and inter group comparisons are conducted using the Chi-square test or Fisher's exact probability method, p < 0.05 was considered as statistically significant. Results Antibiotical susceptibility of Streptococcus pneumoniae isolates The susceptibilities of 105 S. pneumoniae isolates to 14 antibiotics are shown in Table 1 . As we can see, in our experiment, all strains of S. pneumoniae were sensitive to LNZ and VAN; The sensitivity to ERY, CLI, TCY and SXT is low, with resistance rates as high as 92.38%, 82.86%, 86.87%, and 60.95%; The resistance rate to PEN, FEP, CTX, AMX, MFX and LVX is low, while the sensitivity rate is high, at 84.73%, 74.28%, 86.87%, 70%, 96.19%, and 97.14%, respectively. It is worth noting that in our AST of 105 strains of S. pneumoniae , a total of 90 strains were resistant to antibiotics of class 3 or above, with a MDR rate of 85.71%. These strains exhibited various resistance patterns, with CLI/ERY/TCY being the predominant resistance pattern. Moreover, the specific MDR combinations varied among different serotypes of S. pneumoniae isolates. For instance, in serotypes 19F and 23F, the most common MDR combination was CHL/CLI/ERY/TCY, while in serotype 19A, the most common MDR combination was CHL/CLI/ERY/TCY/SXT (Table S1 ). Table 1 Resistance of 105 Streptococcus pneumoniae strains to 14 antibiotics, including penicilin (PEN), cefepime (FEP), cefotaxime (CTX), amoxicillin (AMX), erythromycin (ERY), meropenem (MEM), vancomycin (VAN), clindamycin (CLI), chloramphenicol (CHL), tetracycline (TCY), moxifloxacin (MFX), levofloxacin (LVX), trimethoprim / sulfamethoxazole (SXT) and linezolid (LNZ) Antimicrobial agent Susceptible Intermediate Resistant n(%) MIC(ug/mL) n(%) MIC(ug/mL) n(%) MIC(ug/mL) Penicilin Non-meningitis 88(83.81) ≤ 2 16(15.24) 4 0(0.00) ≥ 8 Penicilin Meningitis 1(0.95) ≤ 0.06 0(0.00) - 0(0.00) ≥ 0.12 Cefepime Non-meningitis 77(73.33) ≤ 1 27(25.71) 2 0(0.00) ≥ 4 Cefepime Meningitis 1(0.95) ≤ 0.5 0(0.00) 1 0(0.00) ≥ 2 Cefotaxime Non-meningitis 94(89.52) ≤ 1 4(3.81) 2 6(5.72) ≥ 4 Cefotaxime Meningitis 1(0.95) ≤ 0.5 0(0.00) 1 0(0.00) ≥ 2 Amoxicillin 73(70) ≤ 2 32(30) 4 0(0.00) ≥ 8 Erythromycin 6(5.72) ≤ 0.25 2(1.90) 0.5 97(92.38) ≥ 1 Meropenem 52(49.52) ≤ 0.25 34(32.38) 0.5 19(18.10) ≥ 1 Vancomycin 105(100.00) ≤ 1 0(0.00) - 0 - Clindamycin 17(16.19) ≤ 0.25 1(0.95) 0.5 87(82.86) ≥ 1 Chloramphenicol 56(53.33) ≤ 4 0(0.00) 49(46.67) ≥ 8 Tetracycline 13(12.38) ≤ 1 1(0.95) 2 91(86.67) ≥ 4 Moxifloxacin 101(96.19) ≤ 1 4(3.81) 2 0(0.00) ≥ 4 Levofloxacin 102(97.14) ≤ 2 3(2.86) 4 0(0.00) ≥ 8 Trimethoprim / Sulfamethoxazole 25(23.81) ≤ 0.5/9.5 16(15.24) 1/19 − 2/38 64(60.95) ≥ 4/76 Linezolid 105(100.00) ≤ 2 0(0.00) - 0(0.00) - The results of AST (including resistant and intermediate) of S. pneumoniae strains isolated from patients of different ages are shown in Table 2 . The insensitivity rate of strains isolated from the children's group and the elderly group to trimethoprim/sulfamethoxazole was higher than that of the adult group, and the difference was statistically significant (χ 2 = 12.143, p = 0.002). There was no statistically significant difference in insensitivity to other antibiotics among the three age groups (p > 0.05). Table 2 Insensitivity of 105 strains of Streptococcus pneumoniae isolated from patients of different ages Antimicrobial agent Children/% Adult/% Elderly/% X2 p Penicilin 0(0/73) 0(0/10) 0(0/22) NA NA Cefepime 0(0/73) 0(0/10) 0(0/22) NA NA Cefotaxime 5.48(4/73) 0(0/10) 9.09(2/22) 1.079 0.583 Amoxicillin 0(0/73) 0(0/10) 0(0/22) NA NA Erythromycin 94.52(69/73) 80.00(8/10) 90.91(20/22) 2.720 0.257 Meropenem 20.55(15/73) 0(0/10) 18.18(4/22) 2.506 0.286 Vancomycin 0(0/73) 0(0/10) 0(0/22) NA NA Clindamycin 80.82(59/73) 90.00(9/10) 86.36(19/22) 0.763 0.683 Chloramphenicol 42.47(31/73) 40.00(4/10) 63.64(14/22) 3.242 0.198 Tetracycline 87.67(64/73) 70.00(7/10) 90.91(20/22) 2.810 0.245 Moxifloxacin 0(0/73) 0(0/10) 0(0/22) NA NA Levofloxacin 0(0/73) 0(0/10) 0(0/22) NA NA Trimethoprim / Sulfamethoxazole 67.12(49/73) 10.00(1/10) 63.64(14/22) 12.143 0.002 Linezolid 0(0/73) 0(0/10) 0(0/22) NA NA Serotype distribution of Streptococcus pneumoniae A total of 24 serotypes were involved in 105 strains of S. pneumoniae in this study, the main serotypes were 19F (34.29%), 19A (10.48%), 3 (7.62%) and 6E (7.62%). The serotype coverage rates for 7- and 10-pneumococcal conjugate vaccines (PCV7, PCV10) were both 45.71%. And there were 8 serotypes and 68 isolates (64.78%) were covered by 13-pneumococcal conjugate vaccine (PCV13), as well as 10 serotypes and 73 isolates (69.52%) were covered by 23-valent pneumococcal polysaccharide vaccine (PPV23). There were 6 cases of mucoid S. pneumoniae strains in our experiment, all of which belonged to serotype 3(Fig. 1 ). Genotyping characteristics of Streptococcus pneumoniae strains The 105 S. pneumoniae isolates were further molecular typed. As we can see from Fig. 2 , 45 different STs were classified, among which ST271 was the dominant type with 32 strains (30.48%), followed by ST320 type with 11 strains (10.48%), and the remaining 62 strains belongs to 43 different ST types. The black solid lines in this figure indicate that each MLST type has at least four or more identical alleles. And the MLST types with six or more identical alleles were classified as the same clonal complexes (CC) in our experiment (with black thick solid line). It can be seen that there are different genotypes in different cities, but they are also interrelated with each other. Eighteen STs were divided into 7 clone complexes, named CC230, CC271, CC338, CC505, CC902, CC7752 and CC11972, representing for 63.81% of all isolates (Table S2 ), the rest 38 STs were ungrouped. CC271 (including ST271, ST320, ST1937, ST7962 and ST19441) is the most prevalent clonal complexe which accounted for 44.76% (n = 47) of the strains, and its serotype belongs to 19F (n = 36) and 19A (n = 11) (Table 3 ). Table 3 Distribution of serotypes and STs in different CCs CC ST Serotype n (%) 230 9396,230,709 23A,23F,24 3 (2.86) 271 271,320,1937,7962,19441 19A,19F,35C 47 (44.76) 338 338,5242 23A 2 (1.90) 505 505,15272 3 5 (4.76) 902 902,19393 6B 3 (2.86) 7752 7752,2754 11B,35C 4 (3.81) 11972 11972,14097 15A 3 (2.86) Among our S. pneumoniae 105 strains belong to 28 GPSCs (6 strains were not assigned), the most prevalent GPSC was GPSC1 (Fig. 3 ). GPSC1 contains 46 strains (35 strains of serotype 19F and 11 strains of serotype 19A), with MLST types including ST271 (n = 31), ST320 (n = 11), ST7962 (n = 2), ST1937 (n = 1), and ST19441 (n = 1). GPSC23 contains 7 strains, all of serotype 6E, with MLST types including ST90 (n = 6) and ST13962 (n = 1) (Table S2 ). Drug resistance genes and virulence genes of Streptococcus pneumoniae A total of 9 drug resistance genes were detected in 105 S. pneumoniae strains, including macrolides (remB, mefA, msrD), tetracyclines (lsa (C), tetA (60), tetM), aminoalcohols (cat (pC194)) and aminoglycoside resistance genes (aph (3') -III, ant (6) -Ia) (Table 4 ). Among them, one isolate does not carry any resistance gene, which is consistent with its AST phenotype experiment. It is sensitive to all antibiotics in the experiment. 104 strains (99.05%) carry the ermB gene, 47 strains carry both mefA and msr(D), and 101 strains (96.19%) carry the tetM gene. Based on our drug susceptibility phenotype experiments, it was found that among the 96 strains exhibiting erythromycin resistance, 45.83% carried both ermB and mefA + msr (D) genes, while the rest carried ermB alone. Among the 88 strains exhibiting tetracycline resistance, all carry the resistance gene tetM. Table 4 The drug resistance genes in the streptococcus pneumoniae strains [n (%)] Drug resistance genes Streptococcus pneumoniae (n = 105) Macrolides ermB 104(99.05) mefA 47(44.76) msrD 47(44.76) Tetracyclines lsa(C) 1(0.95) tetA(60) 1(0.95) tetM 101(96.19) Amphenicols cat(pC194) 6(5.71) Aminoglycosides aph(3')-III 1(0.95) ant(6)-Ia 1(0.95) Besides, our 105 S. pneumoniae strains identified five classes of virulence factors, including adhesion genes (pspC, cbpG, pce, pavA, pfbA, piantB, sipA, rrgA, rrgB, rrgC, srtG1, srtG2, srtC1, srtC2, srtC3), exotoxin gene(ply), ectoenzyme genes (cbpD, lytA, lytB, hysA, nanA, nanB), immunomodulatory factors (cps4A) and nutritional metabolic factors (cps4B, cps4D, zmpC, psaA)(Table 5 ).Among these virulence genes, the carrier rates of pavA, ply, pytA, cps4a and psaA were all 99.05% (n = 104). Table 5 The virulence genes in the streptococcus pneumoniae strains [n (%)] Virulence genes Streptococcus pneumoniae (n = 105) Adhesion genes pspC 1(0.95) cbpG 34(32.38) pce 85(80.95) pavA 104(99.05) pfbA 61(58.1) pitA 45(42.86) pitB 45(42.86) sipA 45(42.86) rrgA 45(42.86) rrgB 42(40) rrgC 52(49.52) srtG1 45(42.86) srtG2 45(42.86) srtC1 52(49.52) srtC2 52(49.52) srtC3 42(40) Exotoxin gene ply 104(99.05) Ectoenzyme genes cbpD 97(92.38) lytA 104(99.05) lytB 28(26.67) lytC 100(95.24) hysA 101(96.19) nanA 82(78.1) nanB 94(89.52) Immunomodulatory factors cps4A 104(99.05) Nutritional metabolic factors cps4B 103(98.1) cps4D 49(46.67) zmpC 2(1.9) psaA 104(99.05) And the carrier rate of cps4B, hysA, lytC and cpbD was 98.1% (n = 103), 96.19% (n = 101), 95.24% (n = 100) and 92.38% (n = 97), respectively. Discussion Streptococcus pneumoniae , as an important human pathogen, is the main cause of community-acquired pneumonia, meningitis, sepsis, and other invasive pneumococcal diseases[ 2 ]. With the widespread use of antibiotics, the resistance of S. pneumoniae to multiple antibiotics has become increasingly severe, posing a significant challenge to global public health[ 18 – 20 ]. In this study, we utilized whole-genome sequencing data analysis and AST of S. pneumoniae strains to analyze and assess the drug resistance characteristics, serotype distribution, and the presence of virulence and resistance genes in clinical isolates of S. pneumoniae . This is aimed at providing guidance for clinical treatment and scientific basis for the optimization of pneumococcal vaccines. In recent years, the insensitivity rate of Streptococcus pneumoniae strains to antibiotics in China has remained at a high level. Fang Chao et al. found that the resistance rates of pneumococcal isolates from children in China to erythromycin, clindamycin, and tetracycline were as high as 97.9%, 95.9%, and 93.2%, respectively[ 21 ]. In our antimicrobial susceptibility testing of the 105 strains of pneumococcus this time, we found that the results were similar to the previously reported drug resistance of S. pneumoniae . The strains showed high resistance rates to erythromycin and tetracycline, but high sensitivity to levofloxacin and moxifloxacin. No S. pneumoniae strains resistant to vancomycin and linezolid were found[ 22 ]. In addition, we also observed the distribution patterns of the resistance genes in these strains. Although 104 strains contained the macrolide ermB gene, only 96 strains exhibited erythromycin resistance, among which 44 strains simultaneously contained the ermB + mef(A) + msr(D) genes. The ermB gene is widely present in streptococcus pneumoniae and other bacteria worldwide and is one of the main genes causing resistance to macrolide. In some regions, the carrier rate of ermB gene is very high. For example, in Hebei Province, the carrier rate of ermB in S. pneumoniae is as high as 96.00%. Bacteria carrying the ermB gene may be resistant to multiple antibiotics at the same time, which increases the difficulty of treatment and may lead to the emergence of multidrug-resistant bacteria[ 23 ]. Some S. pneumoniae strains may simultaneously carry the mef(A) and ermB genes, showing resistance to macrolide and lincosamide antibiotics (MLSB type), and the msr(D) gene can be cotranscribed with mef(A), leading to bacterial resistance to antibiotics[ 24 ]. Although 101 strains were detected tet(M) gene, only 88 strains exhibited tetracycline resistance. It can be seen from this that the presence of these resistance genes does not directly lead to the emergence of a resistant phenotype in the strains, but may be related to the development of antibiotics resistance in S. pneumoniae . At the same time, these data can remind us to use antibiotics more rationally in clinical treatment to reduce the further development of resistant strains. It also emphasizes the importance of continuously monitoring the changing trends of pneumococcus drug resistance, so as to provide timely guidance for clinical treatment. We identified a total of 29 virulence genes in 5 categories. Among them, the detection rates of Adhesion gene pavA, Exotoxin gene ply, Ectoenzyme genes lytA, hysA, lytC, Immunomodulatory genes cps4A, cps4B, and Nutritional metabolic gene psaA were relatively high. This is similar to the reports from Hebei Province and Shanghai, but contrary to the results reported in Ningbo[ 23 , 25 , 26 ]. This suggests that the positive detection rate of virulence genes varies by region. In pneumococcal isolates from China, lytA, ply, hysA, and nanA are the most common virulence genes, with positive rates ranging from 95–100%. The pavA and psaA genes are significantly associated with the occurrence of pneumococcal bacteremia and meningitis[ 27 , 28 ]. Most isolates carried lytA, ply, psaA, nanA, pavA, and piaA, which is similar to other cities in China[ 28 ]. Based on the current research findings, we believe that these virulence factors, lytA, ply, psaA, nanA, pavA, and piaA, may become potential candidates for future vaccines. A total of 53 serotypes of S. pneumoniae have been reported in China, with the most common serotype being 19F[ 29 ]. In our current experiment, the most common serotypes were 19F (36 strains, 34.29%) and 19A (11 strains, 10.48%). For the 19F serotype strains, there were 4 ST types, among which ST271 was the predominant MLST type (32 strains, 88.89%). For the 19A serotype strains, there was only one ST320 type, which is similar to the report from Zhongjiang County, Sichuan Province previously[ 30 ]. The CC271 is one of the most important clonal complexes of S. pneumoniae in China at present, and the two dominant clones are 19F ST271-B and 19A ST320[ 31 ]. Similarly, in our experiment, CC271 was the most popular CC. GPSC1, which was the most frequent in our study, was associated with serotypes 19F and 19A, and the isolates were mostly multidrug-resistant. Studies have confirmed that pneumococcal vaccination can significantly reduce pneumonia caused by vaccine-covered serotypes (VT). Understanding the distribution of pneumococcal serotypes is a key factor in formulating vaccination strategies. In China, PCV13 was launched in June 2017 and quickly replaced PCV7 as the main pneumococcal conjugate vaccine for children due to its broader serotype coverage and better cost-effectiveness. However, according to the data reported by the Chinese Center for Disease Control and Prevention, although the vaccination rate of pneumococcal vaccine in Sichuan Province increased year by year from 2019 to 2021, by 2021, the full-course vaccination completion rate in Sichuan Province was still only 16.45%, far lower than that of the eastern regions during the same period[ 32 ]. In this study, the vaccine-covered serotypes of PCV7 and PCV10 accounted for 45.71%, the vaccine-covered serotypes of PCV13 accounted for 64.76%, and the vaccine-covered serotypes of PPV23 accounted for 69.52%. It can be seen that pneumococcal vaccination not only reduces the risk of individual illness and the severity of the disease, and reduces the use of antimicrobial drugs; but also reduces the carriage rate of pneumococcus, effectively reducing the spread of the disease among the population. In summary, the antibiotic resistance of streptococcus pneumoniae is a complex and serious issue. It requires in-depth understanding of its resistance mechanisms through molecular typing, detection of resistance genes, and research on serotype distribution, in order to guide the rational use of drugs in clinical practice and vaccination strategies. At the same time, continuous monitoring of antibiotic resistance is crucial for controlling and preventing the development of antibiotic resistance in pneumococcus. Conclusion The leading serotypes of Streptococcus pneumoniae were 19F, 19A, 3 and 6E in Sichuan, with CC271 and GPSC1 being the predominant complex types. The overall coverage rates of PCV7, PCV10, PCV13 and PPV23 were 45.71%, 45.71%, 64.78% and 69.52%, respectively. The most of the Streptococcus pneumoniae isolates were resistant to erythromycin, clindamycin, tetracycline and trimethoprim/sulfamethoxazole, with a multidrug resistance rate of 85.71%, and CLI/EY/TCY was the main resistance mode. Timely vaccination with pneumococcal vaccine and control of antibiotics abuse are crucial for controlling the infection of Streptococcus pneumoniae . Abbreviations S. Pneumonia: Streptococcus pneumoniae CAP: community-acquired pneumonia IPD: invasive pneumococcal disease GLASS: Global Antimicrobial Surveillance System WHO: World Health Organization BPPL: Bacterial Priority Pathogens List ANI: Average Nucleotide Identity PEN: penicilin FEP: cefepime CTX: cefotaxime AMX: amoxicillin ERY: erythromycin MEM: meropenem VAN: vancomycin CLI: clindamycin CHL: chloramphenicol TCY: tetracycline MFX: moxifloxacin LVX: levofloxacin SXT: trimethoprim / sulfamethoxazole LNZ: linezolid MIC: Minimum inhibitory concentration CLSI: Clinical and Laboratory Standards Institute MDR: multiple-drug resistance MLST: multilocus sequence typing CC: clonal complexe VT: vaccine-covered serotype PCV7/PCV10/PCV13: 7-, 10-, 13-valent pneumococcal conjugate vaccines PPV23: 23-valent pneumococcal polysaccharide vaccine Declarations Ethics approval and consent to participate: This study was conducted according to the principles of the Declaration of Helsinki. The research protocol was reviewed and approved by the Ethics Committee of the Sichuan Provincial Center for Disease Control and Prevention (No. SCCDCIRB2023-001). The study was conducted in accordance with the local legislation and institutional requirements. Consent for publication: Not applicable. Availability of data and materials: The data that supports the findings of this study are available in the supplementary material. Competing interests: The authors declare no competing interests in this study. Funding: This study was supported by Sichuan Science and Technology Program (No. 2022ZDZX0017). The funders played no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Authors' contributions: HS and SLH contributed equally to this work. HS, YRM, LHY, LWB, SLH, CG and LTR performed the strains culture and DNA extraction; HS, YRM, LHY and ZLZ performed data analysis and plotting of figures, and drafted the manuscript; HS and ZLZ participated in the design of the study; HS, YRM, LHY and ZLZ critically reviewed the manuscript. Acknowledgements: Not applicable. References Lewnard JA, Tahtinen PA, Laine MK, Lindholm L, Jalava J, Huovinen P, Lipsitch M, Ruohola A: Impact of Antimicrobial Treatment for Acute Otitis Media on Carriage Dynamics of Penicillin-Susceptible and Penicillin-Nonsusceptible Streptococcus pneumoniae . J Infect Dis 2018, 218 (9):1356-1366. Musher DM, Thorner AR: Community-acquired pneumonia . N Engl J Med 2014, 371 (17):1619-1628. Collaborators GBDCoD: Global, regional, and national age-sex specific mortality for 264 causes of death, 1980-2016: a systematic analysis for the Global Burden of Disease Study 2016 . Lancet 2017, 390 (10100):1151-1210. Rodrigo C, Lim WS: The relevance of pneumococcal serotypes . Curr Infect Dis Rep 2014, 16 (4):403. Chapman TJ, Olarte L, Dbaibo G, Houston AM, Tamms G, Lupinacci R, Feemster K, Buchwald UK, Banniettis N: PCV15, a pneumococcal conjugate vaccine, for the prevention of invasive pneumococcal disease in infants and children . Expert Rev Vaccines 2024, 23 (1):137-147. Briles DE, Paton JC, Mukerji R, Swiatlo E, Crain MJ: Pneumococcal Vaccines . Microbiol Spectr 2019, 7 (6). Weinberger DM, Warren JL, Dalby T, Shapiro ED, Valentiner-Branth P, Slotved HC, Harboe ZB: Differences in the Impact of Pneumococcal Serotype Replacement in Individuals With and Without Underlying Medical Conditions . Clin Infect Dis 2019, 69 (1):100-106. Nurhonen M, Auranen K: Optimal serotype compositions for Pneumococcal conjugate vaccination under serotype replacement . PLoS Comput Biol 2014, 10 (2):e1003477. Ajulo S, Awosile B: Global antimicrobial resistance and use surveillance system (GLASS 2022): Investigating the relationship between antimicrobial resistance and antimicrobial consumption data across the participating countries . PLoS One 2024, 19 (2):e0297921. World Health Organization . WHO bacterial priority pathogens list. (2024). https://www.who.int/publications/i/item/9789240093461 (2024) . . Collaborators GBDAR: Global burden of bacterial antimicrobial resistance 1990-2021: a systematic analysis with forecasts to 2050 . Lancet 2024, 404 (10459):1199-1226. Sheppard CL, Manna S, Groves N, Litt DJ, Amin-Chowdhury Z: PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data . MICROBIAL GENOMICS 2022, 8 (12):mgen000904. Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing C, Bentley SD, Page AJ, Keane JA: SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data . Microb Genom 2018, 4 (7). Jolley KA, Bray JE, Maiden MCJ: Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications . Wellcome Open Res 2018, 3 :124. Ruan Z, Feng Y: BacWGSTdb, a database for genotyping and source tracking bacterial pathogens . Nucleic Acids Res 2016, 44 (D1):D682-687. Feng Y, Zou S, Chen H, Yu Y, Ruan Z: BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking . Nucleic Acids Res 2021, 49 (D1):D644-D650. Ruan Z, Yu Y, Feng Y: The global dissemination of bacterial infections necessitates the study of reverse genomic epidemiology . Brief Bioinform 2020, 21 (2):741-750. Lourenco J, Daon Y, Gori A, Obolski U: Pneumococcal Competition Modulates Antibiotic Resistance in the Pre-Vaccination Era: A Modelling Study . Vaccines (Basel) 2021, 9 (3). Karcic E, Aljicevic M, Bektas S, Karcic B: Antimicrobial Susceptibility/Resistance of Streptococcus Pneumoniae . Mater Sociomed 2015, 27 (3):180-184. Watkins ER, Kalizang'Oma A, Gori A, Gupta S, Heyderman RS: Factors affecting antimicrobial resistance in Streptococcus pneumoniae following vaccination introduction . Trends Microbiol 2022, 30 (12):1135-1145. Fang C, Chen X, Zhou M: Clinical characteristics and antimicrobial resistance of pneumococcal infections from 9 children's hospitals in 2016 . Chinese Journal of Pediatrics 2018, 56 (8):582-586. (in Chinese) Huang X, Ying L, Zhang X, Zhang J, Long S, Yu H: 2017 surveillance of bacterial resistance in Sichuan province . Chinese Journal of Antibiotics 2018, 43 (9):1143-1150. (in Chinese) Wang Y, Cao Y, Jia Z, He B, Sun Y: Drug resistance gene and virulence gene carriage of the children infected invasive Streptococcus pneumoniae . China Tropical Medicine 2022, 6 . (in Chinese) He J: The current situation and characteristics of bacterial resistance in China . World Latest Medicine Information 2017, 17 (72). (in Chinese) Zhao W, Pan F, Wang B, Wang C, Sun Y, Zhang T, Shi Y, Zhang H: Epidemiology Characteristics of Streptococcus pneumoniae From Children With Pneumonia in Shanghai: A Retrospective Study . Frontiers in Cellular and Infection Microbiology 2019, 9 . (in Chinese) Zhang Q, Lv Y, Wang S, Wang L, Ma H, Deng Z: Investigation of resistant genes and virulence genes of Streptococcus pneumonia . Chinese Journal of Nosocomiology 2017, 23 . (in Chinese) Dong Y, Huang W, Luo T, Zhang C, Wu L: Prevalence of virulence genes in Streptococcus pneumoniae strains isolated from clinical patients . Chinese Journal of Microbiology and Immunology 2009, 29 (2):177-180. (in Chinese) Wang Y, Cai P, Jiang X, Wang C, Mi Z: Prevalence of virulence genes in Streptococcus pneumoniae strains isolated from clinical patients and its clinical research . Chinese Journal of Nosocomiology 2016, 8 :3. (in Chinese) Su N, Han X, Yang Y, Lin J: Distribution characteristics of serotypes of invasive pneumococcal disease in Chinese mainland children . National Medical Journal of China 2016, 18 (16). (in Chinese) Tang P, Du Q, Zeng H, Yuan L, Gao W, Liu D, Jia J, Yao K: Serotype and drug resistance of 192 isolates of Streptococcus pneumoniae, a study in Zhongjiang County People's Hospital, Sichuan . DISEASE SURVEILLANCE 2021, 36 (2):147-151. (in Chinese) Zeng Y, Song Y, Cui L, Wu Q, Wang C, Coelho AC, Zhang G, Wei D, Li C, Zhang J et al : Phylogenomic insights into evolutionary trajectories of multidrug resistant S. pneumoniae CC271 over a period of 14 years in China . Genome Med 2023, 15 (1):46. (in Chinese) Liu L, Zhang Z, Zhang X, Xu C, Song Y, Li L, Ye J: Coverage of 13-Valent Pneumococcal Conjugate Vaccine Among Children 0-15 Months of Age - 9 Provinces, China, 2019-2021 . CHINA CDC WEEKLY 2023, 5 (17):6.(in Chinese) Additional Declarations No competing interests reported. Supplementary Files TABLES1.xls Table S1 Sensitivity information of 105 Streptococcus pneumoniae strains to 14 antibiotics TABLES2.xls Table S2 Typing characteristics based on whole-genome sequencing of 105 Streptococcus pneumoniae strains 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. 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Prevention","correspondingAuthor":false,"prefix":"","firstName":"Laihong","middleName":"","lastName":"Shen","suffix":""},{"id":407720748,"identity":"78e5722d-017e-4feb-8a3b-df6c1616505b","order_by":2,"name":"Rongmei Yuan","email":"","orcid":"","institution":"Sichuan Center for Disease Control and Prevention","correspondingAuthor":false,"prefix":"","firstName":"Rongmei","middleName":"","lastName":"Yuan","suffix":""},{"id":407720749,"identity":"1deb4662-35af-4019-a2d3-6777e61806be","order_by":3,"name":"Hongyu Liao","email":"","orcid":"","institution":"Sichuan Center for Disease Control and Prevention","correspondingAuthor":false,"prefix":"","firstName":"Hongyu","middleName":"","lastName":"Liao","suffix":""},{"id":407720750,"identity":"c5dd6c63-ec38-4b0e-9779-78b7d7f8608a","order_by":4,"name":"Guo Chen","email":"","orcid":"","institution":"Mianyang Center for Disease Control and Prevention","correspondingAuthor":false,"prefix":"","firstName":"Guo","middleName":"","lastName":"Chen","suffix":""},{"id":407720751,"identity":"da9f8c63-4271-4f27-9be9-375399178c0d","order_by":5,"name":"Tianrong Li","email":"","orcid":"","institution":"Nanchong Center for Disease Control and Prevention","correspondingAuthor":false,"prefix":"","firstName":"Tianrong","middleName":"","lastName":"Li","suffix":""},{"id":407720752,"identity":"845d85fc-bad2-4a77-9e2a-39e54506c7ad","order_by":6,"name":"Wenbo Li","email":"","orcid":"","institution":"Sichuan Center for Disease Control and Prevention","correspondingAuthor":false,"prefix":"","firstName":"Wenbo","middleName":"","lastName":"Li","suffix":""},{"id":407720753,"identity":"6af63fe7-6932-4bcf-bd1c-302beeb3610d","order_by":7,"name":"Linzi Zeng","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA1klEQVRIiWNgGAWjYBAC9gYwJSEnz9584MCHCiK08BwAkQk2xoY9xxIPzjhDvJa0xIYbOcaHeVuI0cLe+/Dhzx+HjRkbcj4c4G1gkOcXO0BAC89xY2OehMNy7AxnNxyQ3MFgOHN2An4t9hJpbNIMCUBbGns3HDA8w5BgcJuAFh6JNPafPxIOJzYc5nlwILGNOC1sDDwg7x/jYThwkCgtPMeYpXnSQIHMZnCw4YwEYb/wsLcxfvxhA4xK+cePP/+psJHnlyagBR1IkKZ8FIyCUTAKRgF2AABPXEc0XK0N0QAAAABJRU5ErkJggg==","orcid":"","institution":"Sichuan Center for Disease Control and Prevention","correspondingAuthor":true,"prefix":"","firstName":"Linzi","middleName":"","lastName":"Zeng","suffix":""}],"badges":[],"createdAt":"2025-01-22 08:23:14","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5878875/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5878875/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":75001028,"identity":"5e37b960-b79e-46ef-ab62-81266a6a27b7","added_by":"auto","created_at":"2025-01-29 09:45:28","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":111308,"visible":true,"origin":"","legend":"\u003cp\u003eSerotypes distribution of 105 \u003cem\u003estreptococcus pneumoniae\u003c/em\u003e strains\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-5878875/v1/652a576351499c2d2fa9bb13.png"},{"id":75001030,"identity":"bf5d0ed2-a781-4412-9ba9-73eaffa178c9","added_by":"auto","created_at":"2025-01-29 09:45:28","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":161818,"visible":true,"origin":"","legend":"\u003cp\u003eMLSTs of 105 \u003cem\u003estreptococcus pneumoniae\u003c/em\u003e strains in Sichuan Province in 2023\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-5878875/v1/5f72dcc96bbd57b226217743.png"},{"id":75001031,"identity":"09eb4028-cc74-4e49-ae36-4dd5974bfef9","added_by":"auto","created_at":"2025-01-29 09:45:28","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":361747,"visible":true,"origin":"","legend":"\u003cp\u003eGPSCs of 105 \u003cem\u003estreptococcus pneumoniae\u003c/em\u003e strains\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-5878875/v1/9b626a891fdee44098aae32e.png"},{"id":79941613,"identity":"1c5c4bb7-678a-427d-94fb-d5312afab075","added_by":"auto","created_at":"2025-04-04 21:16:26","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2919339,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5878875/v1/bdcc9f9e-464d-4186-93bd-e363ff48e208.pdf"},{"id":75001708,"identity":"6bc0bf0b-86d0-4622-8b5e-1e9485ae9c64","added_by":"auto","created_at":"2025-01-29 09:53:28","extension":"xls","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":19298,"visible":true,"origin":"","legend":"\u003cp\u003eTable S1 Sensitivity information of 105 \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e strains to 14 antibiotics\u003c/p\u003e","description":"","filename":"TABLES1.xls","url":"https://assets-eu.researchsquare.com/files/rs-5878875/v1/06ece2ffa1886274c140e5aa.xls"},{"id":75001029,"identity":"4e181d48-ee3e-4b64-a5de-8a57e31ecc84","added_by":"auto","created_at":"2025-01-29 09:45:28","extension":"xls","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":17447,"visible":true,"origin":"","legend":"\u003cp\u003eTable S2 Typing characteristics based on whole-genome sequencing of 105 \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e strains\u003c/p\u003e","description":"","filename":"TABLES2.xls","url":"https://assets-eu.researchsquare.com/files/rs-5878875/v1/e259e0d8a74a9c05e4025abf.xls"}],"financialInterests":"No competing interests reported.","formattedTitle":"Molecular characterization based on whole-genome sequencing and antimicrobial susceptibility of Streptococcus pneumoniae in Sichuan Province, China in 2023","fulltext":[{"header":"Introduction","content":"\u003cp\u003e \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e (\u003cem\u003eS. pneumoniae\u003c/em\u003e) is a Gram-positive diplococcus, with humans as its sole host. It often colonizes in the nasopharynx of the human body and is a common opportunistic pathogen[\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. When the body's immune system is weakened, \u003cem\u003eS. pneumoniae\u003c/em\u003e can cause diseases such as pneumonia, bacteremia, otitis media, meningitis, etc. It has become the main pathogenic bacterium of community-acquired pneumonia (CAP)[\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. A global study on causes of death has also proved that more than half of the deaths caused by lower respiratory tract infections are attributed to infections with \u003cem\u003eS. pneumoniae\u003c/em\u003e[\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eCurrently, there are over one hundred serotypes of \u003cem\u003eS. pneumoniae\u003c/em\u003e[\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Although pneumococcal vaccines have a good protective effect against vaccine serotypes of invasive pneumococcal disease (IPD)[\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e], the current 'serotype replacement' has seriously undermined the protective effect of the vaccine[\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. Therefore, a long-term and continuous monitoring of pneumococcus is the basis for the prevention and control of pneumococcal disease, risk assessment, vaccine development and evaluation of vaccine effectiveness. With the abuse of antibiotics, the issue of antibiotic resistance in \u003cem\u003eS. pneumoniae\u003c/em\u003e cannot be ignored. According to the statistics of Global Antimicrobial Surveillance System (GLASS) of the World Health Organization (WHO), \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e is one of the four most commonly reported bacterial strains for antibiotic resistance[\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. According to the Bacterial Priority Pathogens List (BPPL) released by WHO in 2024, \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e is classified as a moderate priority pathogen due to its resistance to macrolide[\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e](\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.who.int/publications/i/item/9789240093461\u003c/span\u003e\u003cspan address=\"https://www.who.int/publications/i/item/9789240093461\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). A study published by the Global Burden of Disease Working Group also shows that \u003cem\u003eS. pneumoniae\u003c/em\u003e is one of the six major pathogens closely related to bacterial resistance[\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. Our study aims to explore the molecular typing and antibiotic resistance of \u003cem\u003eS. pneumoniae\u003c/em\u003e through whole-genome sequencing and antibiotics susceptibility test, providing a relevant reference for the epidemic prevention and control of \u003cem\u003eS. pneumoniae\u003c/em\u003e.\u003c/p\u003e"},{"header":"Materials and methods","content":"\u003cp\u003eIsolation and identification of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e strains\u003c/p\u003e \u003cp\u003eOur study collected 105 clinical \u003cem\u003eS. pneumoniae\u003c/em\u003e strains from ten cities of Sichuan Province, China in 2023, including Chengdu, Dazhou, Deyang, Guangyuan, Luzhou, Mianyang, Nanchong, Neijiang, Panzhihua and Ziyang. The cultured samples were blood (4 strains), cerebrospinal fluid (1 strain), and respiratory tract (100 strains), including sputum (96 strains) and bronchoalveolar lavage fluid (4 strains). The gender information of 1 patient was missing, and the remainder included 65 males and 39 females. Of these, 73 patients (69.52%) were \u0026le;\u0026thinsp;18-year-old children, 10 patients were 18\u0026thinsp;~\u0026thinsp;65 years old, and 22 patients (20.95%) were older than 65 years old. According to the \"National Guide to Clinical Laboratory Procedures\", the strains were inoculated onto Colombian blood plates and cultured at 37 ℃ in a 5% CO2-enriched atmosphere for 18\u0026ndash;20 hours. After cultivation the identification was confirmed by an automatic matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (EXS3000, Zybio). At the same time, ANI (Average Nucleotide Identity, \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://pubmlst.org/bigsdb?db=pubmlst_rmlst_seqdef_kiosk\u003c/span\u003e\u003cspan address=\"https://pubmlst.org/bigsdb?db=pubmlst_rmlst_seqdef_kiosk\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) was used to identify the species based on the results of whole-genome sequencing, in order to exclude non-pneumococcal pathogens. The \u003cem\u003eS. pneumoniae\u003c/em\u003e isolates are stored in skim milk culture storage tubes at -80\u0026deg;C for subsequent analysis.\u003c/p\u003e \u003cp\u003eAntimicrobial Susceptibility Test (AST)\u003c/p\u003e \u003cp\u003eSubcultured \u003cem\u003eS. pneumoniae\u003c/em\u003e strains on the Colombian blood plates were used for antibiotic susceptibility test by the Customized AST plate CHNSTRF from Thermo Fisher Scientific, using the following agents: penicilin (PEN), cefepime (FEP), cefotaxime (CTX), amoxicillin (AMX), erythromycin (ERY), meropenem (MEM), vancomycin (VAN), clindamycin (CLI), chloramphenicol (CHL), tetracycline (TCY), moxifloxacin (MFX), levofloxacin (LVX), trimethoprim / sulfamethoxazole (SXT) and linezolid (LNZ). The broth medium containing split horse blood CAMHB-LHB also comes from Thermo Fisher Scientific. After culturing for 18\u0026ndash;20 hours, the results were read using Thermo Scientific Sensititre Vizion. Minimum inhibitory concentrations (MICs) of the antimicrobial agents were interpreted according to the Clinical and Laboratory Standards Institute (CLSI) documents M100 34th edition. WHONET 2024 software recommended by WHO was used to input antimicrobial susceptibility testing data and conduct sensitivity analysis. The multiple-drug resistance (MDR) phenotype was defined as being resistant to three or more different classes of antimicrobial agents. \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e ATCC49619 was used as a quality control strain.\u003c/p\u003e \u003cp\u003eGenome Sequencing and Assembly\u003c/p\u003e \u003cp\u003eThe total DNA of \u003cem\u003eS. pneumoniae\u003c/em\u003e strains was extracted by using FastPure Bacterial DNA Isolation Mini Kit (Vazyme, China). Proteinase k and RNAse used in the laboratory are both from Vazyme. DNA purity quotient was tested by using spectrophotometer NanoDropTM 2000 (Thermo Fisher Scientific, Waltham, MA, United States). Purified DNA was simultaneously fragmented and tagged with adapters by using the TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, China). We used Illumina platform to sequence, and a series of data processing was carried out on the raw data, mainly including removing reads with 5 bp of ambiguous bases, removing reads with 20 bp of low quality (\u0026le;\u0026thinsp;Q20) bases, adapter contamination, and duplication contamination. Denovo was used to assemble bacterial genome sequencing data from scratch to obtain the optimal contig.\u003c/p\u003e \u003cp\u003eData Analysis Based on Whole Genome Sequencing\u003c/p\u003e \u003cp\u003eQualified reads were used to predict the capsular serotypes of the strains using PneumoKIty (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/CarmenSheppard/PneumoKITy\u003c/span\u003e\u003cspan address=\"https://github.com/CarmenSheppard/PneumoKITy\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e)[\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. And capsular serotypes and Global Pneumococcal Sequencing Cluster (GPSC) of these genomes were also determined using the global genomic surveillance platform PathogenWatch (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://pathogen.watch/\u003c/span\u003e\u003cspan address=\"https://pathogen.watch/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e)[\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. The genome sequence of each \u003cem\u003eS. pneumoniae\u003c/em\u003e isolate was submitted to 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)[\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e] \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e database and aligned to multilocus sequence typing (MLST) housekeeping genes aroE, gdh, gki, recP, spi, xpt, and ddl alleles to obtain the ST type of each strain, then the BioNumerics software was used to construct a phylogenetic tree of \u003cem\u003eS. pneumoniae\u003c/em\u003e isolates based on MLST. Upload the whole genome sequencing data to the online analyzing platform BacWGSTdb (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://bacdb.cn/BacWGSTdb/index.php\u003c/span\u003e\u003cspan address=\"http://bacdb.cn/BacWGSTdb/index.php\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e)[\u003cspan additionalcitationids=\"CR16\" citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e] to perform sequence alignment to obtain the carrying status of drug-resistance genes and virulence genes of our \u003cem\u003eS. pneumoniae\u003c/em\u003e strains.\u003c/p\u003e \u003cp\u003eDate Processing\u003c/p\u003e \u003cp\u003eThe data was processed with Microsoft Excel and Word. The figures were created by BioNumerics7.6 and Graphd Prism 8.0 software. Statistical analysis was conducted using SPSS 22.0 software. Count data is expressed as percentages (%), and inter group comparisons are conducted using the Chi-square test or Fisher's exact probability method, p\u0026thinsp;\u0026lt;\u0026thinsp;0.05 was considered as statistically significant.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003eAntibiotical susceptibility of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e isolates\u003c/p\u003e \u003cp\u003eThe susceptibilities of 105 \u003cem\u003eS. pneumoniae\u003c/em\u003e isolates to 14 antibiotics are shown in Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e. As we can see, in our experiment, all strains of \u003cem\u003eS. pneumoniae\u003c/em\u003e were sensitive to LNZ and VAN; The sensitivity to ERY, CLI, TCY and SXT is low, with resistance rates as high as 92.38%, 82.86%, 86.87%, and 60.95%; The resistance rate to PEN, FEP, CTX, AMX, MFX and LVX is low, while the sensitivity rate is high, at 84.73%, 74.28%, 86.87%, 70%, 96.19%, and 97.14%, respectively. It is worth noting that in our AST of 105 strains of \u003cem\u003eS. pneumoniae\u003c/em\u003e, a total of 90 strains were resistant to antibiotics of class 3 or above, with a MDR rate of 85.71%. These strains exhibited various resistance patterns, with CLI/ERY/TCY being the predominant resistance pattern. Moreover, the specific MDR combinations varied among different serotypes of \u003cem\u003eS. pneumoniae\u003c/em\u003e isolates. For instance, in serotypes 19F and 23F, the most common MDR combination was CHL/CLI/ERY/TCY, while in serotype 19A, the most common MDR combination was CHL/CLI/ERY/TCY/SXT (Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eResistance of 105 Streptococcus pneumoniae strains to 14 antibiotics, including penicilin (PEN), cefepime (FEP), cefotaxime (CTX), amoxicillin (AMX), erythromycin (ERY), meropenem (MEM), vancomycin (VAN), clindamycin (CLI), chloramphenicol (CHL), tetracycline (TCY), moxifloxacin (MFX), levofloxacin (LVX), trimethoprim / sulfamethoxazole (SXT) and linezolid (LNZ)\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\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 \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eAntimicrobial agent\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003eSusceptible\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eIntermediate\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c7\" namest=\"c6\"\u003e \u003cp\u003eResistant\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003en(%)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMIC(ug/mL)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003en(%)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMIC(ug/mL)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003en(%)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eMIC(ug/mL)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePenicilin Non-meningitis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e88(83.81)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e16(15.24)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;8\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePenicilin\u003c/p\u003e \u003cp\u003eMeningitis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;0.06\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;0.12\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCefepime\u003c/p\u003e \u003cp\u003eNon-meningitis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e77(73.33)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e27(25.71)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCefepime\u003c/p\u003e \u003cp\u003eMeningitis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCefotaxime\u003c/p\u003e \u003cp\u003eNon-meningitis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e94(89.52)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4(3.81)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e6(5.72)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCefotaxime\u003c/p\u003e \u003cp\u003eMeningitis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAmoxicillin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e73(70)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e32(30)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;8\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eErythromycin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e6(5.72)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;0.25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2(1.90)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e97(92.38)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMeropenem\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e52(49.52)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;0.25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e34(32.38)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e19(18.10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVancomycin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e105(100.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eClindamycin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e17(16.19)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;0.25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e87(82.86)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eChloramphenicol\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e56(53.33)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e49(46.67)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;8\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTetracycline\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e13(12.38)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e91(86.67)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMoxifloxacin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e101(96.19)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4(3.81)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLevofloxacin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e102(97.14)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3(2.86)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;8\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTrimethoprim / Sulfamethoxazole\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e25(23.81)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;0.5/9.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e16(15.24)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1/19\u0026thinsp;\u0026minus;\u0026thinsp;2/38\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e64(60.95)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ge;\u0026thinsp;4/76\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLinezolid\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e105(100.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026le;\u0026thinsp;2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0(0.00)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-\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 results of AST (including resistant and intermediate) of \u003cem\u003eS. pneumoniae\u003c/em\u003e strains isolated from patients of different ages are shown in Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e. The insensitivity rate of strains isolated from the children's group and the elderly group to trimethoprim/sulfamethoxazole was higher than that of the adult group, and the difference was statistically significant (χ\u003csup\u003e2\u003c/sup\u003e\u0026thinsp;=\u0026thinsp;12.143, p\u0026thinsp;=\u0026thinsp;0.002). There was no statistically significant difference in insensitivity to other antibiotics among the three age groups (p\u0026thinsp;\u0026gt;\u0026thinsp;0.05).\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 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eInsensitivity of 105 strains of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e isolated from patients of different ages\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=\"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 \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAntimicrobial agent\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eChildren/%\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult/%\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eElderly/%\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eX2\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003ep\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePenicilin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0(0/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCefepime\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0(0/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCefotaxime\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e5.48(4/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e9.09(2/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1.079\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.583\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAmoxicillin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0(0/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eErythromycin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e94.52(69/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e80.00(8/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e90.91(20/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2.720\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.257\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMeropenem\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e20.55(15/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e18.18(4/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2.506\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.286\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVancomycin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0(0/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eClindamycin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e80.82(59/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e90.00(9/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e86.36(19/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0.763\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.683\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eChloramphenicol\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e42.47(31/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e40.00(4/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e63.64(14/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3.242\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.198\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTetracycline\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e87.67(64/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e70.00(7/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e90.91(20/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2.810\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.245\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMoxifloxacin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0(0/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLevofloxacin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0(0/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTrimethoprim / Sulfamethoxazole\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e67.12(49/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e10.00(1/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e63.64(14/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e12.143\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.002\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLinezolid\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0(0/73)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0(0/10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0(0/22)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNA\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\u003eSerotype distribution of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e\u003c/p\u003e \u003cp\u003eA total of 24 serotypes were involved in 105 strains of \u003cem\u003eS. pneumoniae\u003c/em\u003e in this study, the main serotypes were 19F (34.29%), 19A (10.48%), 3 (7.62%) and 6E (7.62%). The serotype coverage rates for 7- and 10-pneumococcal conjugate vaccines (PCV7, PCV10) were both 45.71%. And there were 8 serotypes and 68 isolates (64.78%) were covered by 13-pneumococcal conjugate vaccine (PCV13), as well as 10 serotypes and 73 isolates (69.52%) were covered by 23-valent pneumococcal polysaccharide vaccine (PPV23). There were 6 cases of mucoid \u003cem\u003eS. pneumoniae\u003c/em\u003e strains in our experiment, all of which belonged to serotype 3(Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eGenotyping characteristics of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e strains\u003c/p\u003e \u003cp\u003eThe 105 \u003cem\u003eS. pneumoniae\u003c/em\u003e isolates were further molecular typed. As we can see from Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e, 45 different STs were classified, among which ST271 was the dominant type with 32 strains (30.48%), followed by ST320 type with 11 strains (10.48%), and the remaining 62 strains belongs to 43 different ST types. The black solid lines in this figure indicate that each MLST type has at least four or more identical alleles. And the MLST types with six or more identical alleles were classified as the same clonal complexes (CC) in our experiment (with black thick solid line). It can be seen that there are different genotypes in different cities, but they are also interrelated with each other. Eighteen STs were divided into 7 clone complexes, named CC230, CC271, CC338, CC505, CC902, CC7752 and CC11972, representing for 63.81% of all isolates (Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e), the rest 38 STs were ungrouped. CC271 (including ST271, ST320, ST1937, ST7962 and ST19441) is the most prevalent clonal complexe which accounted for 44.76% (n\u0026thinsp;=\u0026thinsp;47) of the strains, and its serotype belongs to 19F (n\u0026thinsp;=\u0026thinsp;36) and 19A (n\u0026thinsp;=\u0026thinsp;11) (Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e \u003cp\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\u003eDistribution of serotypes and STs in different CCs\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"4\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" 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=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCC\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eST\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSerotype\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003en (%)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e230\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e9396,230,709\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e23A,23F,24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e3 (2.86)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e271\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e271,320,1937,7962,19441\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e19A,19F,35C\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e47 (44.76)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e338\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e338,5242\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e23A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e2 (1.90)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e505\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e505,15272\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e5 (4.76)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e902\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e902,19393\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e6B\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e3 (2.86)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e7752\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e7752,2754\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e11B,35C\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e4 (3.81)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e11972\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e11972,14097\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e15A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e3 (2.86)\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\u003eAmong our \u003cem\u003eS. pneumoniae\u003c/em\u003e 105 strains belong to 28 GPSCs (6 strains were not assigned), the most prevalent GPSC was GPSC1 (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). GPSC1 contains 46 strains (35 strains of serotype 19F and 11 strains of serotype 19A), with MLST types including ST271 (n\u0026thinsp;=\u0026thinsp;31), ST320 (n\u0026thinsp;=\u0026thinsp;11), ST7962 (n\u0026thinsp;=\u0026thinsp;2), ST1937 (n\u0026thinsp;=\u0026thinsp;1), and ST19441 (n\u0026thinsp;=\u0026thinsp;1). GPSC23 contains 7 strains, all of serotype 6E, with MLST types including ST90 (n\u0026thinsp;=\u0026thinsp;6) and ST13962 (n\u0026thinsp;=\u0026thinsp;1) (Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eDrug resistance genes and virulence genes of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e\u003c/p\u003e \u003cp\u003eA total of 9 drug resistance genes were detected in 105 \u003cem\u003eS. pneumoniae\u003c/em\u003e strains, including macrolides (remB, mefA, msrD), tetracyclines (lsa (C), tetA (60), tetM), aminoalcohols (cat (pC194)) and aminoglycoside resistance genes (aph (3') -III, ant (6) -Ia) (Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). Among them, one isolate does not carry any resistance gene, which is consistent with its AST phenotype experiment. It is sensitive to all antibiotics in the experiment. 104 strains (99.05%) carry the ermB gene, 47 strains carry both mefA and msr(D), and 101 strains (96.19%) carry the tetM gene. Based on our drug susceptibility phenotype experiments, it was found that among the 96 strains exhibiting erythromycin resistance, 45.83% carried both ermB and mefA\u0026thinsp;+\u0026thinsp;msr (D) genes, while the rest carried ermB alone. Among the 88 strains exhibiting tetracycline resistance, all carry the resistance gene tetM.\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 4\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eThe drug resistance genes in the \u003cem\u003estreptococcus pneumoniae\u003c/em\u003e strains [n (%)]\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"3\"\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 \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eDrug resistance genes\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eStreptococcus pneumoniae (n\u0026thinsp;=\u0026thinsp;105)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eMacrolides\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eermB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e104(99.05)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003emefA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e47(44.76)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003emsrD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e47(44.76)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eTetracyclines\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003elsa(C)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003etetA(60)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003etetM\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e101(96.19)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAmphenicols\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ecat(pC194)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e6(5.71)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eAminoglycosides\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eaph(3')-III\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eant(6)-Ia\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1(0.95)\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\u003eBesides, our 105 \u003cem\u003eS. pneumoniae\u003c/em\u003e strains identified five classes of virulence factors, including adhesion genes (pspC, cbpG, pce, pavA, pfbA, piantB, sipA, rrgA, rrgB, rrgC, srtG1, srtG2, srtC1, srtC2, srtC3), exotoxin gene(ply), ectoenzyme genes (cbpD, lytA, lytB, hysA, nanA, nanB), immunomodulatory factors (cps4A) and nutritional metabolic factors (cps4B, cps4D, zmpC, psaA)(Table\u0026nbsp;\u003cspan refid=\"Tab5\" class=\"InternalRef\"\u003e5\u003c/span\u003e).Among these virulence genes, the carrier rates of pavA, ply, pytA, cps4a and psaA were all 99.05% (n\u0026thinsp;=\u0026thinsp;104).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab5\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 5\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eThe virulence genes in the \u003cem\u003estreptococcus pneumoniae\u003c/em\u003e strains [n (%)]\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"3\"\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 \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e \u003cp\u003eVirulence genes\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eStreptococcus pneumoniae (n\u0026thinsp;=\u0026thinsp;105)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"15\" rowspan=\"16\"\u003e \u003cp\u003eAdhesion genes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epspC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1(0.95)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ecbpG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e34(32.38)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epce\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e85(80.95)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epavA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e104(99.05)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epfbA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e61(58.1)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epitA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e45(42.86)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epitB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e45(42.86)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003esipA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e45(42.86)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003errgA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e45(42.86)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003errgB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e42(40)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003errgC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e52(49.52)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003esrtG1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e45(42.86)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003esrtG2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e45(42.86)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003esrtC1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e52(49.52)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003esrtC2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e52(49.52)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003esrtC3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e42(40)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eExotoxin gene\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eply\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e104(99.05)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"6\" rowspan=\"7\"\u003e \u003cp\u003eEctoenzyme genes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ecbpD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e97(92.38)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003elytA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e104(99.05)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003elytB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e28(26.67)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003elytC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100(95.24)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ehysA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e101(96.19)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003enanA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e82(78.1)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003enanB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e94(89.52)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmunomodulatory factors\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ecps4A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e104(99.05)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"3\" rowspan=\"4\"\u003e \u003cp\u003eNutritional metabolic factors\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ecps4B\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e103(98.1)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ecps4D\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e49(46.67)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ezmpC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2(1.9)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epsaA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e104(99.05)\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\u003eAnd the carrier rate of cps4B, hysA, lytC and cpbD was 98.1% (n\u0026thinsp;=\u0026thinsp;103), 96.19% (n\u0026thinsp;=\u0026thinsp;101), 95.24% (n\u0026thinsp;=\u0026thinsp;100) and 92.38% (n\u0026thinsp;=\u0026thinsp;97), respectively.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003e \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e, as an important human pathogen, is the main cause of community-acquired pneumonia, meningitis, sepsis, and other invasive pneumococcal diseases[\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. With the widespread use of antibiotics, the resistance of \u003cem\u003eS. pneumoniae\u003c/em\u003e to multiple antibiotics has become increasingly severe, posing a significant challenge to global public health[\u003cspan additionalcitationids=\"CR19\" citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. In this study, we utilized whole-genome sequencing data analysis and AST of \u003cem\u003eS. pneumoniae\u003c/em\u003e strains to analyze and assess the drug resistance characteristics, serotype distribution, and the presence of virulence and resistance genes in clinical isolates of \u003cem\u003eS. pneumoniae\u003c/em\u003e. This is aimed at providing guidance for clinical treatment and scientific basis for the optimization of pneumococcal vaccines.\u003c/p\u003e \u003cp\u003eIn recent years, the insensitivity rate of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e strains to antibiotics in China has remained at a high level. Fang Chao et al. found that the resistance rates of pneumococcal isolates from children in China to erythromycin, clindamycin, and tetracycline were as high as 97.9%, 95.9%, and 93.2%, respectively[\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. In our antimicrobial susceptibility testing of the 105 strains of pneumococcus this time, we found that the results were similar to the previously reported drug resistance of \u003cem\u003eS. pneumoniae\u003c/em\u003e. The strains showed high resistance rates to erythromycin and tetracycline, but high sensitivity to levofloxacin and moxifloxacin. No \u003cem\u003eS. pneumoniae\u003c/em\u003e strains resistant to vancomycin and linezolid were found[\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e]. In addition, we also observed the distribution patterns of the resistance genes in these strains. Although 104 strains contained the macrolide ermB gene, only 96 strains exhibited erythromycin resistance, among which 44 strains simultaneously contained the ermB\u0026thinsp;+\u0026thinsp;mef(A)\u0026thinsp;+\u0026thinsp;msr(D) genes. The ermB gene is widely present in \u003cem\u003estreptococcus pneumoniae\u003c/em\u003e and other bacteria worldwide and is one of the main genes causing resistance to macrolide. In some regions, the carrier rate of ermB gene is very high. For example, in Hebei Province, the carrier rate of ermB in \u003cem\u003eS. pneumoniae\u003c/em\u003e is as high as 96.00%. Bacteria carrying the ermB gene may be resistant to multiple antibiotics at the same time, which increases the difficulty of treatment and may lead to the emergence of multidrug-resistant bacteria[\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. Some \u003cem\u003eS. pneumoniae\u003c/em\u003e strains may simultaneously carry the mef(A) and ermB genes, showing resistance to macrolide and lincosamide antibiotics (MLSB type), and the msr(D) gene can be cotranscribed with mef(A), leading to bacterial resistance to antibiotics[\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e]. Although 101 strains were detected tet(M) gene, only 88 strains exhibited tetracycline resistance. It can be seen from this that the presence of these resistance genes does not directly lead to the emergence of a resistant phenotype in the strains, but may be related to the development of antibiotics resistance in \u003cem\u003eS. pneumoniae\u003c/em\u003e. At the same time, these data can remind us to use antibiotics more rationally in clinical treatment to reduce the further development of resistant strains. It also emphasizes the importance of continuously monitoring the changing trends of pneumococcus drug resistance, so as to provide timely guidance for clinical treatment.\u003c/p\u003e \u003cp\u003eWe identified a total of 29 virulence genes in 5 categories. Among them, the detection rates of Adhesion gene pavA, Exotoxin gene ply, Ectoenzyme genes lytA, hysA, lytC, Immunomodulatory genes cps4A, cps4B, and Nutritional metabolic gene psaA were relatively high. This is similar to the reports from Hebei Province and Shanghai, but contrary to the results reported in Ningbo[\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e, \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. This suggests that the positive detection rate of virulence genes varies by region. In pneumococcal isolates from China, lytA, ply, hysA, and nanA are the most common virulence genes, with positive rates ranging from 95\u0026ndash;100%. The pavA and psaA genes are significantly associated with the occurrence of pneumococcal bacteremia and meningitis[\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e, \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. Most isolates carried lytA, ply, psaA, nanA, pavA, and piaA, which is similar to other cities in China[\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. Based on the current research findings, we believe that these virulence factors, lytA, ply, psaA, nanA, pavA, and piaA, may become potential candidates for future vaccines.\u003c/p\u003e \u003cp\u003eA total of 53 serotypes of \u003cem\u003eS. pneumoniae\u003c/em\u003e have been reported in China, with the most common serotype being 19F[\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. In our current experiment, the most common serotypes were 19F (36 strains, 34.29%) and 19A (11 strains, 10.48%). For the 19F serotype strains, there were 4 ST types, among which ST271 was the predominant MLST type (32 strains, 88.89%). For the 19A serotype strains, there was only one ST320 type, which is similar to the report from Zhongjiang County, Sichuan Province previously[\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. The CC271 is one of the most important clonal complexes of \u003cem\u003eS. pneumoniae\u003c/em\u003e in China at present, and the two dominant clones are 19F ST271-B and 19A ST320[\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. Similarly, in our experiment, CC271 was the most popular CC. GPSC1, which was the most frequent in our study, was associated with serotypes 19F and 19A, and the isolates were mostly multidrug-resistant. Studies have confirmed that pneumococcal vaccination can significantly reduce pneumonia caused by vaccine-covered serotypes (VT). Understanding the distribution of pneumococcal serotypes is a key factor in formulating vaccination strategies. In China, PCV13 was launched in June 2017 and quickly replaced PCV7 as the main pneumococcal conjugate vaccine for children due to its broader serotype coverage and better cost-effectiveness. However, according to the data reported by the Chinese Center for Disease Control and Prevention, although the vaccination rate of pneumococcal vaccine in Sichuan Province increased year by year from 2019 to 2021, by 2021, the full-course vaccination completion rate in Sichuan Province was still only 16.45%, far lower than that of the eastern regions during the same period[\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. In this study, the vaccine-covered serotypes of PCV7 and PCV10 accounted for 45.71%, the vaccine-covered serotypes of PCV13 accounted for 64.76%, and the vaccine-covered serotypes of PPV23 accounted for 69.52%. It can be seen that pneumococcal vaccination not only reduces the risk of individual illness and the severity of the disease, and reduces the use of antimicrobial drugs; but also reduces the carriage rate of pneumococcus, effectively reducing the spread of the disease among the population.\u003c/p\u003e \u003cp\u003eIn summary, the antibiotic resistance of \u003cem\u003estreptococcus pneumoniae\u003c/em\u003e is a complex and serious issue. It requires in-depth understanding of its resistance mechanisms through molecular typing, detection of resistance genes, and research on serotype distribution, in order to guide the rational use of drugs in clinical practice and vaccination strategies. At the same time, continuous monitoring of antibiotic resistance is crucial for controlling and preventing the development of antibiotic resistance in pneumococcus.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThe leading serotypes of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e were 19F, 19A, 3 and 6E in Sichuan, with CC271 and GPSC1 being the predominant complex types. The overall coverage rates of PCV7, PCV10, PCV13 and PPV23 were 45.71%, 45.71%, 64.78% and 69.52%, respectively. The most of the \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e isolates were resistant to erythromycin, clindamycin, tetracycline and trimethoprim/sulfamethoxazole, with a multidrug resistance rate of 85.71%, and CLI/EY/TCY was the main resistance mode. Timely vaccination with pneumococcal vaccine and control of antibiotics abuse are crucial for controlling the infection of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003e\u003cem\u003eS. Pneumonia: Streptococcus pneumoniae\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003eCAP: community-acquired pneumonia\u003c/p\u003e\n\u003cp\u003eIPD: invasive pneumococcal disease\u003c/p\u003e\n\u003cp\u003eGLASS: Global Antimicrobial Surveillance System\u003c/p\u003e\n\u003cp\u003eWHO: World Health Organization\u003c/p\u003e\n\u003cp\u003eBPPL: Bacterial Priority Pathogens List\u003c/p\u003e\n\u003cp\u003eANI: Average Nucleotide Identity\u003c/p\u003e\n\u003cp\u003ePEN: penicilin\u003c/p\u003e\n\u003cp\u003eFEP: cefepime\u003c/p\u003e\n\u003cp\u003eCTX: cefotaxime\u003c/p\u003e\n\u003cp\u003eAMX: amoxicillin\u003c/p\u003e\n\u003cp\u003eERY: erythromycin\u003c/p\u003e\n\u003cp\u003eMEM: meropenem\u003c/p\u003e\n\u003cp\u003eVAN: vancomycin\u003c/p\u003e\n\u003cp\u003eCLI: clindamycin\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eCHL: chloramphenicol\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eTCY: tetracycline\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eMFX: moxifloxacin\u003c/p\u003e\n\u003cp\u003eLVX: levofloxacin\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eSXT: trimethoprim / sulfamethoxazole\u003c/p\u003e\n\u003cp\u003eLNZ: linezolid\u003c/p\u003e\n\u003cp\u003eMIC: Minimum inhibitory concentration\u003c/p\u003e\n\u003cp\u003eCLSI: Clinical and Laboratory Standards Institute\u003c/p\u003e\n\u003cp\u003eMDR: multiple-drug resistance\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eMLST: multilocus sequence typing\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eCC: clonal complexe\u003c/p\u003e\n\u003cp\u003eVT: vaccine-covered serotype\u003c/p\u003e\n\u003cp\u003ePCV7/PCV10/PCV13: 7-, 10-, 13-valent pneumococcal conjugate vaccines\u003c/p\u003e\n\u003cp\u003ePPV23: \u0026nbsp;23-valent pneumococcal polysaccharide vaccine\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003eEthics approval and consent to participate: This study was conducted according to the principles of the Declaration of Helsinki. The research protocol was reviewed and approved by the Ethics Committee of the Sichuan Provincial Center for Disease Control and Prevention (No. SCCDCIRB2023-001). The study was conducted in accordance with the local legislation and institutional requirements.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eConsent for publication: Not applicable.\u003c/p\u003e\n\u003cp\u003eAvailability of data and materials: The data that supports the findings of this study are available in the supplementary material.\u003c/p\u003e\n\u003cp\u003eCompeting interests: The authors declare no competing interests in this study.\u003c/p\u003e\n\u003cp\u003eFunding: This study was supported by Sichuan Science and Technology Program (No. 2022ZDZX0017). The funders played no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.\u003c/p\u003e\n\u003cp\u003eAuthors' contributions:\u003c/p\u003e\n\u003cp\u003eHS and SLH contributed equally to this work.\u003c/p\u003e\n\u003cp\u003eHS, YRM, LHY, LWB, SLH, CG and LTR performed the strains culture and DNA extraction; HS, YRM, LHY and ZLZ performed data analysis and plotting of figures, and drafted the manuscript; HS and ZLZ participated in the design of the study; HS, YRM, LHY and ZLZ critically reviewed the manuscript.\u003c/p\u003e\n\u003cp\u003eAcknowledgements: Not applicable.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eLewnard JA, Tahtinen PA, Laine MK, Lindholm L, Jalava J, Huovinen P, Lipsitch M, Ruohola A: \u003cstrong\u003eImpact of Antimicrobial Treatment for Acute Otitis Media on Carriage Dynamics of Penicillin-Susceptible and Penicillin-Nonsusceptible Streptococcus pneumoniae\u003c/strong\u003e. \u003cem\u003eJ Infect Dis \u003c/em\u003e2018, \u003cstrong\u003e218\u003c/strong\u003e(9):1356-1366.\u003c/li\u003e\n\u003cli\u003eMusher DM, Thorner AR: \u003cstrong\u003eCommunity-acquired pneumonia\u003c/strong\u003e. \u003cem\u003eN Engl J Med \u003c/em\u003e2014, \u003cstrong\u003e371\u003c/strong\u003e(17):1619-1628.\u003c/li\u003e\n\u003cli\u003eCollaborators GBDCoD: \u003cstrong\u003eGlobal, regional, and national age-sex specific mortality for 264 causes of death, 1980-2016: a systematic analysis for the Global Burden of Disease Study 2016\u003c/strong\u003e. \u003cem\u003eLancet \u003c/em\u003e2017, \u003cstrong\u003e390\u003c/strong\u003e(10100):1151-1210.\u003c/li\u003e\n\u003cli\u003eRodrigo C, Lim WS: \u003cstrong\u003eThe relevance of pneumococcal serotypes\u003c/strong\u003e. \u003cem\u003eCurr Infect Dis Rep \u003c/em\u003e2014, \u003cstrong\u003e16\u003c/strong\u003e(4):403.\u003c/li\u003e\n\u003cli\u003eChapman TJ, Olarte L, Dbaibo G, Houston AM, Tamms G, Lupinacci R, Feemster K, Buchwald UK, Banniettis N: \u003cstrong\u003ePCV15, a pneumococcal conjugate vaccine, for the prevention of invasive pneumococcal disease in infants and children\u003c/strong\u003e. \u003cem\u003eExpert Rev Vaccines \u003c/em\u003e2024, \u003cstrong\u003e23\u003c/strong\u003e(1):137-147.\u003c/li\u003e\n\u003cli\u003eBriles DE, Paton JC, Mukerji R, Swiatlo E, Crain MJ: \u003cstrong\u003ePneumococcal Vaccines\u003c/strong\u003e. \u003cem\u003eMicrobiol Spectr \u003c/em\u003e2019, \u003cstrong\u003e7\u003c/strong\u003e(6).\u003c/li\u003e\n\u003cli\u003eWeinberger DM, Warren JL, Dalby T, Shapiro ED, Valentiner-Branth P, Slotved HC, Harboe ZB: \u003cstrong\u003eDifferences in the Impact of Pneumococcal Serotype Replacement in Individuals With and Without Underlying Medical Conditions\u003c/strong\u003e. \u003cem\u003eClin Infect Dis \u003c/em\u003e2019, \u003cstrong\u003e69\u003c/strong\u003e(1):100-106.\u003c/li\u003e\n\u003cli\u003eNurhonen M, Auranen K: \u003cstrong\u003eOptimal serotype compositions for Pneumococcal conjugate vaccination under serotype replacement\u003c/strong\u003e. \u003cem\u003ePLoS Comput Biol \u003c/em\u003e2014, \u003cstrong\u003e10\u003c/strong\u003e(2):e1003477.\u003c/li\u003e\n\u003cli\u003eAjulo S, Awosile B: \u003cstrong\u003eGlobal antimicrobial resistance and use surveillance system (GLASS 2022): Investigating the relationship between antimicrobial resistance and antimicrobial consumption data across the participating countries\u003c/strong\u003e. \u003cem\u003ePLoS One \u003c/em\u003e2024, \u003cstrong\u003e19\u003c/strong\u003e(2):e0297921.\u003c/li\u003e\n\u003cli\u003eWorld Health Organization\u003cstrong\u003e. 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(in Chinese)\u003c/li\u003e\n\u003cli\u003eZeng Y, Song Y, Cui L, Wu Q, Wang C, Coelho AC, Zhang G, Wei D, Li C, Zhang J\u003cem\u003e et al\u003c/em\u003e: \u003cstrong\u003ePhylogenomic insights into evolutionary trajectories of multidrug resistant S. pneumoniae CC271 over a period of 14 years in China\u003c/strong\u003e. \u003cem\u003eGenome Med \u003c/em\u003e2023, \u003cstrong\u003e15\u003c/strong\u003e(1):46. (in Chinese)\u003c/li\u003e\n\u003cli\u003eLiu L, Zhang Z, Zhang X, Xu C, Song Y, Li L, Ye J: \u003cstrong\u003eCoverage of 13-Valent Pneumococcal Conjugate Vaccine Among Children 0-15 Months of Age - 9 Provinces, China, 2019-2021\u003c/strong\u003e. \u003cem\u003eCHINA CDC WEEKLY \u003c/em\u003e2023, \u003cstrong\u003e5\u003c/strong\u003e(17):6.(in Chinese)\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Streptococcus pneumoniae, serotype, molecular characterization, antibiotics sensitivity, whole-genome sequencing","lastPublishedDoi":"10.21203/rs.3.rs-5878875/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5878875/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e is a major cause of pneumonia, meningitis and other invasive diseases resulting in high mortality and morbidity among children. In recent years, the issue of drug resistance in \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e has become increasingly prominent, posing challenges to clinical treatment. Besides, the typing of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e is important information for evaluating the value of pneumococcal vaccines and developing immunization strategies. A total of 105 \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e isolates were collected from ten cities in Sichuan Province in 2023. The leading serotypes were 19F (34.29%), 19A (10.48%), 3 (7.62%) and 6E (7.62%), with CC271 and GPSC1 being the predominant types. The overall coverage rates of 7-, 10-, 13-valent pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) and 23-valent pneumococcal polysaccharide vaccine (PPV23) were 45.71%, 45.71%, 64.78% and 69.52%, respectively. The antimicrobial susceptibility test of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e showed that most strains were resistant to erythromycin (ERY), clindamycin (CLI), tetracycline (TCY), and trimethoprim/sulfamethoxazole (SXT), with a multidrug resistance rate of 85.71%, and CLI/EY/TCY was the main resistance mode. The resistance rate of strains isolated from the children's group and the elderly group to SXT was higher than that of the adult group, and the difference was statistically significant (χ 2\u0026thinsp;=\u0026thinsp;12.143, p\u0026thinsp;=\u0026thinsp;0.002). In summary, continuous monitoring of the antibiotic resistance of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e is crucial for controlling and preventing the development of antibiotic resistance in pneumococcal bacteria. Our research is beneficial for understanding the type distribution of \u003cem\u003eStreptococcus pneumoniae\u003c/em\u003e in Sichuan province and guiding the rational use of drugs and adjustment of vaccination strategies in clinical practice.\u003c/p\u003e","manuscriptTitle":"Molecular characterization based on whole-genome sequencing and antimicrobial susceptibility of Streptococcus pneumoniae in Sichuan Province, China in 2023","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-01-29 09:45:24","doi":"10.21203/rs.3.rs-5878875/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":"ce9de0a7-c6f4-4ed6-b36f-c57a87937309","owner":[],"postedDate":"January 29th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-04-04T21:08:18+00:00","versionOfRecord":[],"versionCreatedAt":"2025-01-29 09:45:24","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-5878875","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5878875","identity":"rs-5878875","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}