Background: Salmonella enterica (S. enterica) causes tens of thousands of cases of diarrheal disease worldwide each year. However, our understanding of the genome and transmission dynamics of S. enterica in Minhang District in Shanghai, China is still insufficient. This study is aimed to better understand the population structure, antibiotic resistance patterns, and evolution dynamics of local strains.
Methods: We sequenced 458 S. enterica strains from outpatients at Minhang District Central Hospital in Shanghai, China, from 2012 to 2021. Bioinformatics analyses on antibiotic resistance genes, virulence factors, mobile genetic elements, pathogenic islands, and phylogenetic relationships were performed.
Results: Here we show that two dominant serovars are S. Enteritidis and S. Typhimurium isolated from outpatients in Minhang District in Shanghai, China. A total of 40 serovars and 53 sequence types (STs) are identified, two S. Montevideo strains isolated in 2013 belong to a newly identified ST10844, which is firstly identified in Minhang District in Shanghai, China. More than half of the isolates show resistance to fluoroquinolones and beta-lactams. Notably, 259 (56.6%) of the 458 isolates exhibit a multidrug-resistant pattern. Third-generation cephalosporin resistance gene blaCTX-M-55 is identified in 15 (3.3%) isolates, and fluoroquinolone resistance gene qnrS1 is identified in 42 (9.2%) isolates, both of which are strongly correlated with IS26. Mutations of T57S in ParC and D87Y in GyrA are observed in 149 (32.5%) and 133 (29.0%) isolates, respectively. In addition, phylogenetic analysis confirms the presence of outbreaks caused by S. Enteritidis and S. Typhimurium, respectively.
Conclusions: These results suggest local expansion and evolution in Salmonella occurred in Shanghai, China, and the underlying emergence of the undefined multidrug-resistant clone. Our findings enlarge the knowledge of local epidemics of Salmonella, especially S. Enteritidis and S. Typhimurium in Shanghai, and provide a piece of useful baseline information for future whole-genome sequencing surveillance.
Plain language summary
Salmonella is a bacterium that can cause diarrhea in infected people. Non-typhoidal Salmonella is a combination of the types that do not cause typhoid, which is a particular type of bacterial infection. We looked at non-typhoidal Salmonella infections occurring in the Minhang District of Shanghai, China. We analyzed the types of Salmonella from fecal samples across over a 10-year period and identified the two most common types of non-typhoidal Salmonella responsible for infections. We found that the genetic sequences of the bacteria changed and spread within the local area over time. This study provides information that could help support future monitoring of Salmonella spread. This could help track development of bacteria that do not respond well to treatment and enable the development of better infection control strategies.
© 2025. The Author(s).
Keywords：genomic insights; minhang district
背景： 沙门氏菌（Salmonella enterica）每年在全球造成数万例腹泻病例。然而，我们对中国上海市闵行区沙门氏菌的基因组和传播动态的理解仍然不足。本研究旨在更好地了解当地菌株的人群结构、抗生素抗性模式及进化动力学。
方法： 我们在2012年至2021年间对上海市闵行区中心医院门诊患者采集的458株沙门氏菌进行了测序。我们对抗生素抗性基因、毒力因子、可移动遗传元件、致病岛和系统发育关系进行了生物信息学分析。
结果： 结果显示，两个主要血清型是分别从上海市闵行区门诊患者中分离出来的S. Enteritidis 和 S. Typhimurium。共鉴定出40个血清型和53种序列类型（STs），2013年分离的两株S. Montevideo属于新发现的ST10844，这是首次在中国上海闵行区被识别出来。超过一半的菌株对氟喹诺酮类和β-内酰胺类抗生素表现出耐药性。值得注意的是，在458个分离物中有259（56.6%）显示出多重耐药模式。第三代头孢菌素抗性基因blaCTX-M-55在15（3.3%）株中被鉴定，氟喹诺酮类抗性基因qnrS1在42（9.2%）株中被发现，两者均与IS26高度相关。我们在149（32.5%）和133（29.0%）分离物中分别观察到ParC的T57S突变及GyrA的D87Y突变。此外，系统发育分析证实了由S. Enteritidis 和 S. Typhimurium 引起的爆发。
结论： 这些结果表明，在中国上海发生了沙门氏菌在当地扩展和进化，并且未定义的多重耐药克隆逐渐出现。我们的发现扩大了对上海市当地流行的沙门氏菌，尤其是S. Enteritidis 和 S. Typhimurium 的了解，并为未来全基因组测序监测提供了一个有用的基线信息。
简易语言摘要
沙门氏菌是一种可以引起感染人群腹泻的细菌。非伤寒型沙门氏菌是由不引起伤寒这种特定类型细菌感染的各种类型的组合。我们研究了上海市闵行区发生的非伤寒型沙门氏菌感染情况。在超过10年的期间内，我们分析了粪便样本中的不同种类沙门氏菌，并确定了导致感染的两种最常见的非伤寒型沙门氏菌类型。我们发现细菌的遗传序列随着时间的变化在当地传播开来。这项研究提供了未来监测沙门氏菌传播的信息支持。这有助于追踪对治疗不敏感的细菌的发展并推动改进的感染控制策略。
© 2025. The Author(s).
