Table_1_Molecular Characterization Based on Whole-Genome Sequencing of Streptococcus pneumoniae in Children Living in Southwest China During 2017-2019.xlsx

BackgroundStreptococcus pneumoniae is an important pathogen causing high morbidity and high mortality in children and undergoes frequent recombination for capsule switching to neutralize the 13-valent pneumococcal conjugate vaccine (PCV13). This study aimed to investigate the prevalence, and molecular characteristics including serotypes and antibiotic susceptibility of S. pneumoniae isolated from children living in Southwest China from 2017 to 2019 to facilitate the selection of effective vaccine formulations and appropriate antibiotic treatment regimens.MethodsThis study was conducted at West China Second University Hospital (Chengdu, Sichuan Province, China), Zunyi Medical University Third Affiliated Hospital/First People’s Hospital of Zunyi (Zunyi, Guizhou Province, China) and Chengdu Jinjiang District Maternal and Child Healthcare Hospital (Chengdu, Sichuan Province, China). Demographic and clinical characteristics of children infected with S. pneumoniae were collected and analysed. Next-generation sequencing and sequence analysis were used to determine the serotypes, sequence types, antibiotic resistance and potential protein vaccine target genes of the pneumococcal isolates. The coverage rate provided by PCV13 was estimated by calculating the percentage of the specific serotypes that were specifically the PCV13-included serotypes. Antimicrobial susceptibility was determined by the microdilution broth method.ResultsThe most prevalent pneumococcal serotypes were 19F (25.8%), 19A (14.1%), 6B (12.5%), 6A (9.4%) and 14 (7.8%). The predominant STs were ST271 (23.3%), ST320 (15.5%) and ST90 (8.6%), dominated by the clonal complex Taiwan19F-14 (39.1%). The coverage rate of PCV13 was 77.3% in all the isolates, with relatively higher values in invasive isolates (86.4%). Over the decade, the rates of resistance to penicillin, amoxicillin and cefotaxime were 5.6%, 5.3% and 5.1%, respectively, with significantly higher values in invasive isolates (22.4%, 14.9% and 11.9%). Almost all the isolates were resistant to erythromycin (99.1%) and clindamycin (95.9%). All isolates carried virulence-related genes, including ply, psaA, piaA, piuA, phtE, nanA, pepO, danJ, pvaA, clpP, pcsB, stkP, potD, and strH. The carriage of virulence and resistance genes varied among serotypes and clades, with serotype 19F/ST271 showing higher resistance to antibiotics and being more likely to carry pilus genes and other virulence genes.ConclusionThese data provide valuable information for the understanding of pneumococcal pathogenesis, antimicrobial resistance and the development of protein-based vaccines against pneumococcal infection.背景肺炎链球菌作为一种重要的病原体，在儿童中引起高发病率和死亡率，且其常发生重组以切换荚膜，从而中和13价肺炎球菌结合疫苗（PCV13）。本研究旨在调查2017年至2019年期间居住于中国西南地区的肺炎链球菌分离株的流行情况及分子特征，包括血清型及抗生素敏感性，以促进有效疫苗配方和适宜抗生素治疗方案的选择。方法本研究在四川成都的华西第二医院、贵州遵义的遵义医科大学第三附属医院/遵义市第一人民医院以及四川成都金堂区妇女儿童保健医院进行。收集并分析了感染肺炎链球菌的儿童的流行病学和临床特征。采用下一代测序和序列分析技术，确定肺炎链球菌分离株的血清型、序列型、抗生素耐药性和潜在的蛋白疫苗靶基因。通过计算特定血清型中PCV13所包含血清型的百分比，估算PCV13的覆盖率。通过微量稀释法确定抗菌药物的敏感性。结果最常见的肺炎链球菌血清型为19F（25.8%）、19A（14.1%）、6B（12.5%）、6A（9.4%）和14（7.8%）。最主要的序列型为ST271（23.3%）、ST320（15.5%）和ST90（8.6%），以台湾19F-14克隆复合体为主（39.1%）。在所有分离株中，PCV13的覆盖率为77.3%，在侵袭性分离株中相对较高（86.4%）。在过去十年中，对青霉素、阿莫西林和头孢噻肟的耐药率分别为5.6%、5.3%和5.1%，在侵袭性分离株中的值显著较高（22.4%、14.9%和11.9%）。几乎所有分离株都对红霉素（99.1%）和克林霉素（95.9%）耐药。所有分离株均携带与致病性相关的基因，包括ply、psaA、piaA、piuA、phtE、nanA、pepO、danJ、pvaA、clpP、pcsB、stkP、potD和strH。致病性和耐药基因的携带情况在不同血清型和分支群中存在差异，其中血清型19F/ST271对抗生素的耐药性较高，且更可能携带毛菌素基因和其他致病性基因。结论这些数据为理解肺炎链球菌的致病机制、抗菌药物耐药性以及针对肺炎链球菌感染开发基于蛋白的疫苗提供了宝贵信息。