ISEcp1-associated dissemination of blaCTX-M/blaCMY-2 among cefotaxime-resistant non-typhoidal Salmonella from patients with diarrhea in Chongqing, China, 2022–2024

Abstract

CTX-resistant Salmonella infections threaten public health. This study aimed to characterize the genetic environments of bla CTX-M / bla CMY-2 in CTX-resistant non-typhoidal Salmonella from patients with diarrhea in Chongqing, China (2022–2024). Among 306 Salmonella isolates recovered from seven hospitals, 36 (11.8%) were confirmed as CTX-resistant. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), genetic structure analysis, conjugation experiments, and core-genome single nucleotide polymorphism (cgSNP) analysis were performed. All 36 CTX-resistant isolates were resistant to CTX and ampicillin; resistance rates to chloramphenicol (88.9%), tetracycline (86.1%), and ceftazidime (63.9%) were high. Thirteen serotypes were identified, with S . I 4,[5],12:i:- (30.6%), S. Goldcoast (16.7%), and S. Typhimurium (11.1%) being the most frequently identified. The most frequently detected ESBL genes were bla CTX-M-65 (17/36) and bla CTX-M-55 (11/36). bla CMY-2 occurred in five isolates. QnrS co-carriage was 72.2% (26/36). IS Ecp1 flanked bla CTX-M / bla CMY-2 in 94.4% (34/36) of isolates, highlighting its major role in mobilizing these resistance genes. IncHI2A was the most frequently identified plasmid (50.0%). In an S . I 4,[5],12:i:- isolate, a 96,117-bp IncI1 plasmid carrying IS Ecp1 - bla CMY-2 was 100% identical to a Botswana E. coli plasmid. In an S . Thompson isolate, a 152,834-bp IncC plasmid carrying the same transposition unit shared >99% identity with a plasmid from a Hefei clinical isolate. Notably, a novel 75,302-bp IS Ecp1 -mediated transposition unit carrying bla CTX-M-65 , together with the entire IncI plasmid backbone, was identified with 5-bp direct repeats. This unit is far larger than typical IS Ecp1 -mediated insertions (2.9–3.0 kb). Our findings suggest that ISEcp1 is associated with the dissemination of bla CTX-M / bla CMY-2 among CTX-resistant isolates in this regional collection, and suggest the potential to mobilize large DNA segments. Enhanced genomic surveillance of such mobile elements is urgently needed in this region.