Genomic insights into antibiotic-resistant non-typhoidal Salmonella isolates from outpatients in Minhang District in Shanghai.

Abstract

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 bla_CTX-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.