Supplementary Information for - Evolution of pneumococcal serotype 19A in Bangladesh: insights from genomic analysis

<b>Abstract</b><b>Background </b>Invasive pneumococcal disease (IPD), caused by <i>Streptococcus pneumoniae</i>, remains a major global health concern, particularly for children. Among more than 100 pneumococcal serotypes, 19A is known for its multidrug resistance and increased incidence following PCV7/PCV10 introduction in many countries. Bangladesh introduced PCV10 nationwide in 2015 considering the low burden of 19A, and hence, continuous monitoring of the serotype is required.<br><b>Methods</b>Utilizing the IPD surveillance data from 2004 to 2023 in Bangladesh, we investigated the incidence of serotype 19A before and after PCV10 introduction. Whole-genome sequencing was performed on 153 pneumococcal 19A isolates from IPD, otitis media, nasopharyngeal carriage, and urine samples. Using phylogenetic and BEAST analyses, we evaluated the population structure of 19A in Bangladesh, including circulating subtypes, global pneumococcal sequence clusters (GPSCs), sequence types (STs), and antimicrobial resistance (AMR) genes, and compared these findings with 19A genomes available from other countries.<br><b>Results</b>Our findings indicate no significant increase in hospital IPD incidence due to serotype 19A following the introduction of PCV10. The MDR 19A-ST320 lineage (GPSC1) remains absent in Bangladesh. ST12888 (GPSC84) appear to have become dominant after PCV10 introduction, rising from 15% (8/53) to 70% (70/100) in the post-PCV10 era. GPSC84 possesses a capsular locus of 19A subtype I (19A-I), which emerged independently from the standard 19A locus. Macrolide resistance within the 19A-I/GPSC84 lineage was also observed and is estimated to have originated between 2007-2011. The diverse distribution of GPSCs and STs detected in Bangladesh is distinct from other countries.<br><b>Conclusion</b>This study presents the first comprehensive genomic analysis of the serotype 19A population in Bangladesh, supporting the decision to introduce PCV10 in Bangladesh based on local pneumococcal serotype burden data. However, the rapid evolution within the local 19A population highlights the need for continuous epidemiological and genomic surveillance to support effective vaccination programs.

<b>摘要</b><b>背景</b> 侵袭性肺炎球菌病（invasive pneumococcal disease, IPD）由肺炎链球菌（Streptococcus pneumoniae）引发，仍是全球重大公共卫生负担，对儿童群体尤为突出。在逾100种肺炎球菌血清型中，19A血清型以多重耐药性著称，且在多国引入7价肺炎球菌结合疫苗（PCV7）/10价肺炎球菌结合疫苗（PCV10）后发病率有所上升。孟加拉国于2015年在全国范围内推广PCV10，当时考量到19A血清型的疾病负担较低，因此仍需对该血清型开展持续监测。<br><b>方法</b> 本研究利用孟加拉国2004年至2023年的IPD监测数据，分析了PCV10引入前后19A血清型的发病率情况。研究人员对源自IPD、中耳炎、鼻咽定植及尿液样本的153株肺炎球菌19A分离株开展了全基因组测序（whole-genome sequencing）。通过系统发育分析及BEAST分析，本研究评估了孟加拉国19A血清型的种群结构，包括流行亚型、全球肺炎球菌序列簇（global pneumococcal sequence clusters, GPSCs）、序列型（sequence types, STs）及抗菌药物耐药（antimicrobial resistance, AMR）基因，并将上述研究结果与其他国家公开的19A基因组数据进行了比对。<br><b>结果</b> 研究结果显示，PCV10引入后，由19A血清型引发的住院IPD发病率未出现显著上升。多重耐药19A-ST320谱系（GPSC1）在孟加拉国仍未出现。ST12888（GPSC84）似乎在PCV10引入后成为优势谱系，其占比从PCV10时代前的15%（8/53）升至后PCV10时代的70%（70/100）。GPSC84携带19A亚型I（19A-I）的荚膜基因座，该基因座独立于标准19A基因座演化而来。研究同时在19A-I/GPSC84谱系中检测到大环内酯类耐药性，经估算该耐药性起源于2007年至2011年之间。孟加拉国检出的GPSCs及STs分布具有多样性，与其他国家的分布特征存在显著差异。<br><b>结论</b> 本研究首次对孟加拉国19A血清型种群开展了全面的基因组分析，印证了孟加拉国基于本地肺炎球菌血清型疾病负担数据推广PCV10的决策合理性。但本地19A血清型种群的快速演化提示，仍需开展持续的流行病学及基因组监测，以支撑高效的疫苗接种计划。