Genetic characteristics of antimicrobial resistance in escherichia coli isolated from pigs, pork and humans in Thailand and Lao PDR border provinces

Abstract

The objectives of this study were to monitor the prevalence of antimicrobial resistance (AMR) among Escherichia coli isolated from pigs, pork and humans in Thailand-Laos border areas, characterize AMR of E. coli isolated from pigs, pork and humans in Thailand-Laos border areas, and compare the resistance to last-line antimicrobials of E. coli and Salmonella isolated from pigs and pork in Thailand-Laos and Thai-Cambodia border areas. Three study projects were conducted. Project 1 demonstrated the results of phenotypic and genotypic monitoring of AMR in E. coli in pigs, pork, and humans in Thailand and Lao PDR border provinces. A total of 847 E. coli isolates were obtained from pigs, pig carcasses, pork, and humans in Thailand and Lao PDR border provinces. Most isolates (67%) were multidrug resistance (MDR). Class 1 integrons carrying aadA1 gene cassette array were most observed (37.2%). The low percentage of ESBL-producing E. coli was observed in Thailand (3.4%) and Lao PDR (3.2%). The ESBLs genes found were blaCTX-M14, blaCTX-M27, and blaCTX-M55, of which blaCTX-M55 was the most common (58.6%). Amino acid substitutions, Ser-83-Leu and Asp-87-Asn were predominant in GyrA of ciprofloxacin resistant isolates. Plasmid-mediated quinolone resistance genes, qnrA and qnrB, was identified at low rate (0.1% each) but at higher rate for qnrS (23%). Class 1 integrons carrying aadA1 from pigs (n = 1) and ESBL genes (blaCTX-M55 and blaCTX-M14) from pigs (n = 2), pork (n = 1), and humans (n = 7) were located on conjugative plasmids. Most plasmid (29.3%) were in IncF group. Project 2 described colistin resistance and plasmid-mediated mcr genes in E. coli and Salmonella isolated from pigs, pig carcass and pork in Thailand, Lao PDR, and Cambodia border provinces. A total of 1,619 E. coli and Salmonella isolates from pigs, pig carcasses, and pork were obtained. Colistin resistance was more common in E. coli (8%) than Salmonella (1%) and the highest resistance rate was found in Cambodia (10.1%). Colistin-resistance genes mcr-1, mcr-3 and mcr-5 were identified, of which mcr-1 and mcr-3 were predominant. The E. coli and Salmonella isolates (n=7) contained mcr-1 or mcr-3 associated with IncF and/or IncI conjugative plasmids. The mcr-positive Salmonella from Thailand and Cambodia were categorized into two clusters. None of meropenem-resistant isolates were detected. Project 3 investigated the genomic characteristics of AMR in seven mcr-carrying ESBL producing E. coli from two pigs (TH2 and TH3) and two humans (TH8 and TH9) in Thailand, and three pigs from Lao PDR (LA1, LA2, and LA3) by Whole Genome Sequencing analysis. Four different sequence types/serotypes were found, including ST6833/H20 (TH2 and TH3), ST48/O160:H40 (TH8 and TH9), ST5708/H45 (LA1), and ST10562/O148:H30 (LA2 and LA3). The point mutation Ser-31-Thr in PmrA and His-2-Arg in PmrB were identified in all isolates (colistin MIC=4-8 µg/mL). LA1 contained up to five point mutations in PmrB (colistin MIC=8 µg/mL). All mcr-1.1 resided in ISApl1-mcr-1-pap2 region, whereas all mcr-3.1 located in TnAs2-mcr-3.1-dgkA-ISKpn40 element. Colocalization of mcr-3.1 and blaCTX-M55 on the same plasmids were detected in TH2, TH3, TH8, TH9, and LA1. All plasmids concurrently carry other resistance genes, including cml, qnrS1, and tmrB. The co-transmission of blaCTX-M55 and mcr-3.1 genes was found in LA1 under the selective pressure of either ampicillin or colistin. Only blaCTX-M55 could be transferred in TH8 and TH9, although the blaCTX-M55 was co-localized on the same plasmid with mcr-3.1. All E. coli isolates contained at least one virulence gene. In conclusion, our findings demonstrated the high prevalence of MDR E. coli and Salmonella and the circulation of their AMR determinants among these areas. Resistance to last line antibiotics, in particular new generation cephalosporins and colistin distributes in E. coli and Salmonella from pigs, pork and humans along Thailand, Lao PDR, and Cambodia. To contain AMR, the comprehensive collaborations based on One Health at nation, regional and global level is required.