Monitoring of antibiogram and resistance gene profiles among Escherichia coli in pig production system

Abstract

The antimicrobial resistant (AMR) bacteria in pig farms have been believed as an important source in food chain with public health concern. While some studies suggested transmission of AMR from pigs to humans may occur, but there was still needing to combine high resolution genomic data analysis with systematically collected epidemiological evidence to reconstruct patterns of AMR transmission between pigs and humans. The objectives of this study were to determine the occurrence and characterization the AMR phenotypes against 18 antimicrobials in pig producing system in both cross-sectional from fattening and longitudinal studies from newborn to slaughtering pigs and to evaluate the effect of flavomycin to reduce AMR rate in pig farms. The commensal enteric Escherichia coli were used as a proxy to estimate the overall extent of AMR. Altogether, Multiple Drug Resistance (MDR) E. coli were highly found from fattening pigs. Interestingly, some resistant phenotypes (β-lactam resistance and tetracycline resistance) were commonly detected in the isolates either from farm with and without antimicrobial usage in feed however extended-spectrum β-lactamase producing (ESBLP) and aminoglycosides resistance were detected in farms with antimicrobial usage in feed (amoxicillin and tiamulin) while farm using only antimicrobial by injection for therapeutic purpose had ESBLP and aminoglycosides resistance in very low rate. All ESBLP E. coli relatively possessed blaCTX-M-1 and/or blaCTX-M-9 genes. For longitudinal study, AMR situations were monitored through pigs producing system in 5 periods; pre-weaning, nursery, growing, fattening and slaughtering periods. ESBLP E. coli and aminoglycosides resistance significantly increased in nursery and growing periods in the farm with antimicrobial usage in feed (amoxicillin and tiamulin) but the resistant rate decreased in slaughtering. For clonal typing analysis, the most common clonal type of E. coli in live pigs was ST10 that were non-ESBLP strain and could not find in all meat samples. ST44, 117 and 638 shared between both live pigs and meats but none was ESBLP or aminoglycosides resistant strains. The resistant isolates recovered from pig meat largely differed from those detected in the feces of the same live pigs sampled during the production period. In vitro, flavomycin at 8 μg/ml and 16 μg/ml concentrations could reduce the conjugative rates of the plasmids carrying blaCTX-M-1 and blaCTX-M-9 10 times. In vivo, use of flavomycin at 10 ppm in feed could reduce antimicrobial resistance rates of third generation cephalosporins resistance phenotypes and genotypes at 20.0-23.3% in nursery and growing periods. This study provided the insight of AMR type, distribution and their characteristics in pig farms in the relation of antimicrobial use and supported the indication of flavomycin mixed in feed. The molecular typing limited to identify a direct clonal relationship between critically important antimicrobial resistant strains, especially the third generation cephalosporins resistance and aminoglycosides resistance in meat and those found in the corresponding live animals during their production cycle. Further work is required to identify the source of resistant E. coli in pig meat following slaughter.