Emerg Infect Dis. 2024 Jan;30(1):39-49. doi: 10.3201/eid3001.221927.
Streptococcus pneumoniae is an opportunistic pathogen that causes substantial illness and death among children worldwide. The genetic backgrounds of pneumococci that cause infection versus asymptomatic carriage vary substantially. To determine the evolutionary mechanisms of opportunistic pathogenicity, we conducted a genomic surveillance study in China. We collected 783 S. pneumoniae isolates from infected and asymptomatic children. By using a 2-stage genomewide association study process, we compared genomic differences between infection and carriage isolates to address genomic variation associated with pathogenicity. We identified 8 consensus k-mers associated with adherence, antimicrobial resistance, and immune modulation, which were unevenly distributed in the infection isolates. Classification accuracy of the best k-mer predictor for S. pneumoniae infection was good, giving a simple target for predicting pathogenic isolates. Our findings suggest that S. pneumoniae pathogenicity is complex and multifactorial, and we provide genetic evidence for precise targeted interventions.
肺炎链球菌是一种机会致病菌，可导致全球儿童罹患大量疾病和死亡。引起感染和无症状携带的肺炎链球菌的遗传背景有很大差异。为了确定机会性致病性的进化机制，我们在中国进行了一项基因组监测研究。我们收集了 783 株来自感染和无症状儿童的肺炎链球菌分离株。通过使用两阶段全基因组关联研究过程，我们比较了感染和携带分离株之间的基因组差异，以解决与致病性相关的基因组变异。我们确定了 8 个与黏附、抗菌药物耐药性和免疫调节相关的共识 k-mer，这些 k-mer 在感染分离株中分布不均匀。用于预测肺炎链球菌感染的最佳 k-mer 预测器的分类准确性较好，为预测致病性分离株提供了一个简单的目标。我们的研究结果表明，肺炎链球菌的致病性是复杂的、多因素的，我们为精确靶向干预提供了遗传证据。
