ESBL and AmpC β-Lactamase Encoding Genes in E. coli From Pig and Pig Farm Workers in Vietnam and Their Association With Mobile Genetic Elements

Abstract

Animals are considered important sources of ESBL/AmpC-producing bacteria in humans. We analyzed indications of transfer of ESBL/AmpC genes between pigs and pig farmers in Vietnam by analyzing whole genome sequences of 114 ESBL/AmpC-producing E. coli isolated from the two hosts, and performed conjugation experiments and plasmid profiling to confirm that such transfer could have happened. ESBL-encoding genes detected in pigs and pig farmers included blaCTX–M-55, blaCTX-M-27, blaCTX-M-65, blaCTX-M-15, blaCTX-M-14, blaCTX-M-3, blaCTX-M-24, and blaCARB-2, and AmpC β-lactamases included blaCMY-2, blaDHA-1, and blaCMY-42. The most frequent ESBL gene, blaCTX-M-55, was carried on plasmid with replicons types IncF, IncX, IncH, IncN, IncR, and IncP. The insertion transposases downstream of the blaCTX-M-55 gene were different in plasmids carried by different strains. The second most detected gene, blaCTX-M-27, is found in a stable genetic arrangement with the same flanking transposons seen across strains, and the gene was located on similar conjugal IncF plasmid types, suggesting a horizontal spread of these plasmids. In three strains, we observed a novel blaCTX-M-27 harboring IncF type of plasmid which had not been reported before. Its closest reference in NCBI was the non-ESBL Salmonella Typhimurium plasmid pB71 that might have experienced an insertion of blaCTX-M-27. Our data also point to an emergence of plasmids co-carrying ESBL genes, mcr genes, quinolones and other antimicrobials resistance determinants, and such plasmids require special attention. Plasmids phylogeny confirmed that the blaCTX-M-55 encoding plasmids varied considerably, while those encoding blaCTX-M-27 were closely related. Plasmids harboring both ESBL genes were confirmed to be conjugative and not to differ in transfer efficacy. The isolates carrying the plasmids, even those with plasmids of similar types, showed wide genetic variation with high number of SNPs, suggesting horizontal spread of plasmids into different clonal lines. Their virulence profiles did not confirm to known pathotypes, suggesting that unrelated commensals are a main reservoir for ESBL and AmpC β-lactamases in both humans and pigs. Overall, despite evidence of transferability of plasmids in the analyzed strains, our findings do not support that ESBL-producing E. coli from pigs or their ESBL/AmpC encoding plasmids are commonly spread to workers in close contact with the animals.

Molecular Epidemiology and Characteristics of CTX-M-55 Extended-Spectrum β-Lactamase-Producing Escherichia coli From Guangzhou, China

“…Plasmids are known as an important reason for the rapid spread of bla CTX–M . Recently, CTX-M-55 has been reported to appear on the IncI1, IncF, IncP, and IncA/C plasmids ( Kim J. S. et al, 2017 ; Xia et al, 2017 ; Hounmanou et al, 2021 ). Additionally, the transmission of bla CTX–M is also related to many mobile genetic elements.…”

Genome-associations of extended-spectrum ß-lactamase producing (ESBL) or AmpC producing E. coli in small and medium pig farms from Khon Kaen province, Thailand

“…We identified that nearly 50% plasmids also harbored at least one other ARG conferring resistance to critically important antimicrobials. While we do not have access to the farming system, a Vietnamese study has also identified that several ESBL-carrying plasmids also co-carry ARGs conferring resistance to critically important antimicrobials [70]. Additionally, we identified that plasmids from small farms were more likely to co-carry these ARGs than those from medium farms.…”

“…These plasmids are known to be highly transmissible among E. coli, further stressing the importance of stopping the spread of plasmids that contain genes conferring resistance to extended-spectrum ß-lactams, fluoroquinolones and colistin [71]. IncF plasmids harboring CTX-M-55 and qnr have also been reported in other regions of Southeast Asia [70].…”

Genomic Characterization of a Uropathogenic Escherichia coli ST405 Isolate Harboring blaCTX-M-15-Encoding IncFIA-FIB Plasmid, blaCTX-M-24-Encoding IncI1 Plasmid, and Phage-Like Plasmid

“…Understanding the mechanisms underlying its increasing ability to cause outbreaks requires an in-depth knowledge of the genetic features of ST405. bla CTX-M-24 has been found in IncP1 ( Hounmanou et al, 2021 ), IncFII ( Yang et al, 2020 ), IncH1B-FIB ( Shen et al, 2019 ), and IncFI plasmids ( Nguyen et al, 2010 ). However, there are no complete sequences of IncI1 plasmids carrying bla CTX-M-24 in publicly available genome databases.…”