Molecular characterization of IncFII plasmid carrying bla _NDM-5 in a Salmonella enterica serovar Typhimurium ST34 clinical isolate in China

Abstract

The detection rate of carbapenem-resistant nontyphoidal Salmonella (NTS) is relatively low. However, carbapenem-sensitive and carbapenem-resistant Salmonella enterica serovar Typhimurium ( S. enterica serovar Typhimurium) were isolated from a clinical outpatient within a span of 10 days, named 1104–65 and 1104–75. We aimed to reveal the mechanism of carbapenem resistance in S. enterica serovar Typhimurium isolates in this case. The resistance phenotype of S. enterica serovar Typhimurium was analyzed by the VITEK-2 Compact equipment and Kirby-Bauer disc diffusion method. Whole-genome sequencing was used to analyze the serotype, ST type, genetic relationship, resistance genes, plasmid replicon, the genetic environment of bla NDM-5 , and the characteristics of IncFII plasmid carrying bla NDM-5 in S. enterica serovar Typhimurium. The transferability of the IncFII plasmid carrying bla NDM-5 was verified by the conjugation assay and PCR. The serotypes of both NTS are S. enterica serovar Typhimurium, belonging to ST34. Single nucleotide polymorphisms analysis showed that they were the same clone. A conjugative IncFII plasmid pIncFII-NDM5 with transferability was detected in isolate 1104–75, which harboring the bla NDM-5 gene was the primary mechanism responsible for mediating carbapenem resistance in S. enterica serovar Typhimurium. The genetic environment of bla NDM-5 on pIncFII-NDM5 is “IS 26 -ΔIS 3000 -IS 5 -ΔIS Aba125-bla NDM-5 - ble MBL - trpF-dsbC -cutA -IS 26 ”, which was confirmed as a novel structure not previously reported in the NCBI database. Although the mechanism is rarely reported in NTS, the prevalence of IncFII plasmid pIncFII-NDM5 will pose a great threat to the clinical treatment of S. enterica serovar Typhimurium. Meanwhile, the coexistence of bla CTX-M-55 , qnrS1 , bla NDM-5 , and mph(A ) in S. enterica serovar Typhimurium ST34 warrants additional attention. IMPORTANCE In this study, an IncFII plasmid pIncFII-NDM5 carrying bla NDM-5 was found in carbapenem-resistant Salmonella enterica serovar Typhimurium ( S. enterica serovar Typhimurium), which has conjugative transferability and carried bla NDM-5 , ble MBL , mph(A ), and bla TEM-1 four resistance genes that can mediate resistance to multiple antibiotics including cephalosporins, beta-lactamase inhibitor combinations, carbapenems, and macrolides. Phylogenetic analysis showed that 1104–65 and 1104–75 were closely related to other S. enterica serovar Typhimurium in this area. The above-mentioned S. enterica serovar Typhimurium chromosome carries bla CTX-M-55 , qnrS1 , and tet(A ) genes, so the antibiotic resistance of isolates will be further enhanced after obtaining the pIncFII_NDM5-like plasmid. Meanwhile, we discovered a novel genetic structure of bla NDM-5 mediated by the IS 26 composite transposon, which will expand our understanding of the emergence and spread of carbapenem-resistance genes. Altogether, the presence of the IncFII plasmid pIncFII-NDM5 further underscores the need for vigilant surveillance and appropriate infection control measures to mitigate the impact of carbapenem-resistant S. enterica serovar Typhimurium in clinical settings.

Genomic Insights into the First Emergence of blaNDM-5-Carrying Carbapenem-Resistant Salmonella enterica Serovar London Strain in China

“…Previous reports in Salmonella have mainly identified bla NDM genes on IncX3 and IncFII plasmids. [38][39][40] Notably, our study represents the first documentation of bla NDM-5 located on a transmissible IncFIB plasmid of Salmonella. IncFIB plasmids, often referred to as ColV plasmids, have predominantly been associated with serovars Kentucky, Typhimurium, Heidelberg and Schwarzengrund.…”

“…Additionally, previous studies have reported bla NDM-5 gene in IncX3-type plasmids of Enterobacteriaceae, located in the roughly similar genetic context (IS3000-ISAba125Δ-IS5-ΔISAba125-bla NDM-5 -ble MBL -trpF-dsbC-cutA-IS26), with the bla NDM-5 gene flanked by IS elements and located adjacent to three other ARGs (ble MBL -trpF-dsbC). 39,40,44 Despite the presence or absence of other gene elements in the genetic context (such as ΔISAba125 and cutA which were not found in pA132-1-NDM), the combination of four ARGs (bla NDM-5 -ble MBL -trpF-dsb) were found to be conserved across all bla NDM-5 -harboring IncX3-and IncF-type plasmids reported thus far. These evidences together emphasize the conservation and significance of the four ARGs as a basic unit in the transmission and expression of carbapenemase, suggesting a potential pattern for the dissemination of bla NDM-5 gene.…”

“…These evidences together emphasize the conservation and significance of the four ARGs as a basic unit in the transmission and expression of carbapenemase, suggesting a potential pattern for the dissemination of bla NDM-5 gene. 40,45 Moreover, the location of bla NDM-5 gene in the vicinity of a class 1 integron seems to enhance its dissemination. The bla NDM-5 -containing ISCR1-IS26-flanked cassette in pA132-1-NDM was found to be linked to a complete class 1 integron via transposition of an ISCR1 element.…”

Rapid Dissemination of blaNDM-5 Gene among Carbapenem-Resistant Escherichia coli Isolates in a Yellow-Feather Broiler Farm via Multiple Plasmid Replicon

“…Plasmids Pathogens 2024, 13, 387 2 of 11 belonging to different incompatibility groups play an important role in the epidemiology of bla NDM genes. The bla NDM-5 gene is carried by a broad range of plasmids belonging to the IncX3, IncHI2, and IncF incompatibility groups [11,12]. E. coli sequence types (STs) ST48, ST167, and ST10 were identified as the main epidemiological clones of bla NDM-5 associated with human infections, which pose a potential threat to public health [5][6][7].…”