Genetic characteristics of antimicrobial resistance of salmonella enterica and escherichia coli isolated from broilers, pigs and their meat products in Sa Kaeo, banteay meanchey and Siem Reap provinces

Abstract

This research study aimed to investigate the incidence and characterize antimicrobial resistance (AMR) in Salmonella enterica and Escherichia coli isolated from broilers, pigs and their meat products in Thailand–Cambodia border provinces. Resistance to clinically importance antimicrobials was additionally examined in the E. coli isolates from other provinces with high pig production in Thailand. A total of 941 samples were collected from broilers and pigs at slaughterhouses and their carcasses at local fresh markets in Sa Kaeo, Thailand (n=554) and Banteay Meanchey and Siem Reap, Cambodia (n=387) during 2014-2015. Three hundred forty-five Salmonella isolates were collected from Thailand (n = 145; 23%) and Cambodia (n = 200; 47%). Serovars Typhimurium (29%) and Rissen (29%) were most frequently found among the Thai and Cambodian isolates, respectively. Multidrug resistance (MDR) was detected in 34% and 52% of the isolates from Thailand and Cambodia, respectively. Class 1 integrons containing dfrA12-aadA2 cassette array was most prevalent (61.1%). Six isolates were ESBL producers, of which blaTEM-1, blaCTX-M-55 and blaCMY-2 were found. A total of 667 commensal E. coli isolates were obtained from Sa Kaeo, Thailand (n=381) and Banteay Meanchey and Siem Reap, Cambodia (n=286). The prevalence of E. coli in pig and broiler carcasses from slaughterhouses and fresh markets was 57.1% in Thailand and 58.8% in Cambodia. The majority were MDR (75.3%). The dfrA12-aadA2 cassette array (41.5%) was predominant class 1 integrons-gene cassette in Thai isolates, whereas the dfrA1-aadA1 cassette array (70.8%) was most common in Cambodian isolates. Sixteen E. coli isolates were confirmed to be ESBL producers, of which blaCTX-M-15, blaTEM-1 and blaCMY-2 were detected. Four hundred fifty-four E. coli isolates from healthy pigs (n=354; piglets, n=83; fattening pigs, n=142 and sows, n=129) and sick pigs (n=100) collected in Thailand during 2007-2018 were determined for the prevalence and investigated for the molecular mechanisms underlying colistin resistance and ESBL production. The healthy pig (41%) and sick pig (73%) isolates were commonly resistant to colistin. The mcr-3 gene was most predominant in the healthy (37.9%) and sick pig (70%) isolates. Coexistence of mcr-1/mcr-3 and mcr-2/mcr-3 was observed and common in the piglet isolates (23%). The ESBL producers were more frequently detected in sick pig (44%) than healthy pig isolates (19.2%) (P<0.05). The blaCTX-M-14 (54.5%) and blaCTX-M-55 (42.9%) genes were the predominant ESBL gene in this study. Most ESBL producers (80.4%) additionally carried mcr and all were MDR. Co-transfer of ß-lactamase genes (blaTEM-1 and blaCTX-M-55) and mcr-3 was detected. Characterization of three E. coli co-harboring ESBL and mcr genes from sick pigs by using WGS approach revealed two mcr-1.1 gene cassettes that were located on IncI2 plasmid and had plasmid backbone identical to (98% identity) pHNSHP45. The mcr-2.1 gene carrying contig in fattening pig showed 100% identity to pKP37-BE. All three mcr.3.1 carrying contigs contained a core segment ∆TnAs2-mcr-3.1-dgkA and had high nucleotide similarity (85-100%) to the original plasmid pWJ1. In summary, the results demonstrated the high prevalence of MDR Salmonella and E. coli in broilers, pigs and their meat products in Thailand–Cambodia border provinces. Pigs are the important reservoirs of colistin-resistant and ESBL-producing strains. It indicates that the restrictive policies on prudent use of antimicrobials in pigs and other food animals should be encouraged. The implementation of national AMR monitoring and surveillance at phenotypic and genotypic level is required to elucidate the root causes and burden of AMR. The data can be combined for regional and global perspective.