Characterization of Salmonella spp. in a tertiary hospital in 2019-2021 in Nanjing, China: Focusing on the clonal dissemination of Salmonella Enteritidis ST11

Abstract Background To characterize clinical Salmonella spp. by whole genome sequencing (WGS) Methods Totally, 38 clinical Salmonella enterica isolates were subjected to antimicrobial susceptibility testing (AST), slide agglutination tests, and multi-locus sequence typing (MLST). Whole-genome sequencing (WGS) was performed to analyze the serovars, antibiotic-resistance genes (ARGs), virulence factors (VFs), sequence types (STs), and plasmid replicons. A phylogenetic tree was constructed to investigate the underlying genetic relationships. Results Thirteen serovars were identified, with Enteritidis (n = 19, 50.0%) being the most common, followed by Typhimurium (n = 4, 10.5%). High resistance against ampicillin (n = 27, 71.1%) and ampicillin/sulbactam (n = 24, 63.2%) was observed, and seven (18.4%) isolates were multidrug resistant (MDR). In total, 36 types of ARGs were detected, among which bla TEM-1B (n = 25, 65.8%) was the most frequent, and mutations in gyrA and/or parC were identified in 34 (89.5%) strains. Notably, 333 different VFs were detected, of which 177 were shared by all the strains. Fifteen distinct STs were identified, with ST11 being the most predominant, and a close genetic relationship between them can be observed in the phylogenetic tree. Ten different plasmid replicons were found, with the dominant ones being IncFIB(S), IncFII(S), and IncX1 in S. Enteritidis (94.7%). Conclusions More Salmonella serovars have been identified with the development of new molecular detection techniques. In addition to the high resistance and potential pathogenicity displayed by Salmonella spp., the clonal dissemination of S. Enteritidis ST11 highlights the urgent need to implement infection and control measures.