Genetic context of blaCTX–M–55 and qnrS1 genes in a foodborne Salmonella enterica serotype Saintpaul isolate from China

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, IS 26 - orf - orf -IS Kpn19-qnrS1 -IS 3 -Tn 3 - orf - bla CTX–M–55 -IS Ec9 - orf -IS 26 . 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 IS 26 -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.