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Non-typhoidal salmonella (TS) remains a significant health burden worldwide. In Vietnam, pork accounts for 70% of the total meat consumed, and contamination with Salmonella is high. High levels of antimicrobial resistance (AMR) have emerged among porcine NTS and of particular concern is the emergence of colistin resistance, a "last defense" antibioic against multi-drug resistant (MDR) Gram-negative pathogens. This study aimed to investigate the antibiotic susceptibility of 69 NTS isolates collected from the pork retail outlets and slaughterhouses in Vietnam during 2014 a nd 2018/19. Phenotypic testing and whole genome sequencing was used to assess the serotype and AMR gene profiles of the 69 NTS isolates. Seventeen different serotypes were identified, of which S. enterica subsp enterica serotype Typhimurium was the most common followed by S . ser. Rissen, S . ser. London, S . ser. Anatum, and S . ser. Derby. Phenotype AMR was common with 41 (59.4%) isolates deemed MDR. MDR strains were most common in slaughterhouses (83%) and supermarkets (75%) and lowest in traditional markets (38%) and convenience stores (40%). Colistin resistance was identified in 18 strains (15 resistant, three intermediate) with mcr-1 identified in seven isolates ( S . ser. Meleagridis, S . Rissen, S . Derby) and mcr-3 in two isolates ( S . Typhimurium). This includes the first mcr positive S . Meleagridis to our knowledge. Surprisingly, boutique stores had high levels (60%) of MDR isolates including 5/20 isolates with mcr -1. This study demonstrates that pork from modern retail stores classed as supermarkets or boutique (with pork claiming to be high quality, traceable, environmentally friendly marketed toward higher income consumers) still contained NTS with high levels of AMR., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Holohan, Wallat, Hai Yen Luu, Clark, Truong, Xuan, Vu, Van Truong, Tran Huy, Nguyen-Viet, Unger, Thi Thanh Dang and Stabler.)

We analyzed and compared genomes of Extended Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli from pigs and pig farm workers at 116 farms in Vietnam. Analyses revealed the presence of bla CTX-M-55 , bla CTX-M-27 ,  bla CTX-M-15 ,  bla CTX-M-14 ,  bla CTX-M-3 ,  bla CTX-M-65 ,  bla CTX-M-24 , bla DHA-1 , and bla CMY2 in both hosts. Most strains from pigs contained quinolones ( qnr ) and colistin resistance genes ( mcr -1 and mcr -3). Isolates predominantly harbored more than one plasmid replicon and some harbored plasmid replicons on the same contigs as the ESBL genes. Five strains from farm workers of ST38 (2), ST69 (1), and ST1722 (2) were classified as either uropathogenic E. coli (UPEC HM )/extraintestinal pathogenic E. coli (ExPEC JJ ) or UPEC HM , and the remaining were genetically distinct commensals. A high heterogeneity was found among the ESBL-producing E. coli from pigs and workers, with most isolates belonging to unrelated phylogroups, serogroups, and sequence types with >4046 Single-Nucleotide Polymorphisms-(SNPs). In comparing the genomes of pig isolates to those from humans, it appeared that ESBL-producing E. coli in workers did not predominantly originate from pigs but were rather host-specific. Nevertheless, the occurrence of ESBL-producing E. coli carrying plasmid-mediated colistin and quinolone resistance genes in pigs could represent a potential source for horizontal transmission to humans through food rather than direct contact.

WHO considers colistin as a highest priority critically important drug for human health, and occurrence of colistin-resistant bacteria in livestock is of health concern. The current study determined occurrence of colistin-resistant Escherichia coli in pigs and workers at pig farms in Vietnam, and investigated the genetic background for resistance. Colistin-resistant E. coli were detected from pigs in 53/116 (45.7%) farms, and from workers taking care of the pigs in 21/94 (22.3%) farms. Colistin-resistant isolates showed MIC to colistin between 4-16 mg/L, they were multidrug resistant (99%) and resistance was caused by the presence of mcr-1 genes in 97/102 (95.1%) E. coli from pigs and in 31/34 (91.1%) isolates from humans. mcr-1 is considered a plasmid-encoded gene, but this was not confirmed in the current investigation. In total, one pig isolate carried both mcr-1 and mcr-3 genes, whereas mcr-2, mcr-4 and mcr-5 genes were not detected. Shared resistance profiles between pig and human isolates on the same farm was only observed in four farms. The study showed that commensal E. coli from pigs in Vietnam constitute a reservoir for colistin-resitant E. coli , however, further studies are needed to confirm that mcr genes are associated with plasmids and their importance for human health., Competing Interests: None declared., (© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.)