Genetic context of bla CTX-M-55 and qnrS1 genes in a foodborne Salmonella enterica serotype Saintpaul isolate from China

Lili Li; Rikke Heidemann Olsen; Jian Xiao; Hecheng Meng; Shifu Peng; Lei Shi

doi:10.3389/fmicb.2022.899062

Genetic context of bla _CTX-M-55 and qnrS1 genes in a foodborne Salmonella enterica serotype Saintpaul isolate from China

Front Microbiol. 2022 Aug 9:13:899062. doi: 10.3389/fmicb.2022.899062. eCollection 2022.

Authors

Lili Li^{1

2}, Rikke Heidemann Olsen³, Jian Xiao⁴, Hecheng Meng², Shifu Peng⁵, Lei Shi¹

Affiliations

¹ Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.
² School of Food Science and Engineering, South China University of Technology, Guangzhou, China.
³ Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
⁴ Guangzhou Food Inspection Institute, Guangzhou, China.
⁵ Department of Environment and Health, Jiangsu Center for Disease Control and Prevention, Nanjing, China.

Abstract

Salmonella enterica resistant to fluoroquinolones (FQs) and extended-spectrum cephalosporins (ESCs) has been deemed a high-priority pathogen by the WHO. Salmonella enterica serovar Saintpaul (S. Saintpaul) co-resistant to ESCs and FQs and harboring corresponding resistance genes (bla _CTX-M-55 and qnrS1) have been previously reported. However, they have not been reported in China. Moreover, the genetic context and transferability of ESCs and FQs resistance genes in S. Saintpaul remain obscure. This study is the first study to characterize a multidrug-resistant (MDR) S. Saintpaul isolate (16Sal016) harboring plasmid-mediated bla _CTX-M-55 and qnrS1 genes recovered from weever fish in China. The whole genome short- and long-read sequencing results identified the presence of 15 acquired antibiotic resistance genes encoding resistance to nine classes of antibiotics, as well as abundant mobile genetic elements residing on a 259,529 bp IncHI2 plasmid. The bla _CTX-M-55 and qnrS1 genes were located in a 12,865 bp region, IS26-orf-orf-ISKpn19-qnrS1-IS3-Tn3-orf-bla _CTX-M-55-ISEc9-orf-IS26. Similar structures have been identified in various bacterial species, indicating a high transferability of bla _CTX-M-55 and qnrS1 genes within this gene cluster. The plasmid was found to be transferable to Escherichia coli (E. coli) J53 by conjugation and resulted in the acquisition of multiple resistances by the transconjugants. Genome sequence comparisons by core genome multilocus sequence typing (cgMLST) based on global 2,947 S. Saintpaul isolates indicated that strain 16Sal016 was epidemiologically linked with an isolate from the United Kingdom (UK). Our findings suggest that plasmids and IS26-mediated mobile genetic elements are carriers of bla _CTX-M-55 and qnrS1 genes in S. Saintpaul, and highlight their potential transmission, which needs continuous investigations.

Keywords: S. Saintpaul; blaCTX–M–55; fish; plasmid; qnrS1.