Transmissible antibiotic resistance genes present in Escherichia coli from USA and Thailand poultry

Conventional poultry production has used sub-therapeutic levels of antibiotics in the diet to prevent disease and stimulate growth for many decades. Health concerns over the potential of antibiotic resistant bacteria in the food supply has resulted in consumer demand and regulatory changes limiting the use of antibiotics, thereby making alternatives to antibiotics part of the mainstream in most poultry markets today. One of the expected benefits of using antibiotic alternatives is a reduction in antibiotic resistance genes in the environment. In 2014, <5% of broilers in the USA were “Raised without Antibiotics” and this increased to >40% by 2018. To determine the prevalence and type of antibiotic resistance genes present in the USA poultry industry before the concerted push to raise poultry without antibiotics, we sequenced the genomes of 111 Escherichia coli strains from broilers and turkeys collected in 2014 and 2015 and analyzed them for acquired antibiotic resistance genes. Transmissible resistance genes to aminoglycosides, tetracyclines, sulfonamides, and beta-lactams were the most prevalent. A multiplex PCR was developed to detect seven of the antibiotic resistance genes. This assay was used to determine the presence of antibiotic resistance genes in poultry E. coli isolates from the USA and Thailand. The average number of antibiotic resistance genes detected per isolate was 1.7 in both countries with a maximum of five of the seven genes in any one isolate, but different genes were predominant in each county. Over 30% of the USA isolates possessed aminoglycoside resistance gene aac3VIa, compared to only 1% of the Thailand isolates. Beta-lactam resistance gene, blaTEM1, and tetracycline resistance gene, tetA, were the most prevalent in Thailand isolates at 70% and 60% compared to 25% and 27% in the USA isolates. Over time there was a significant decrease in the number of antibiotic genes per isolate in the USA. The average number was 2.2 genes in 2015 and 2016 which dropped significantly to 1.2, 1.3 and 1.4 in 2017, 2018 and 2019 respectively. This multiplex assay will be used for continuous monitoring of transmissible antibiotic resistance genes in avian E. coli across countries and time.

Keywords: transmissible antibiotic resistance genes, Escherichia coli.

Abstract presented at the 3rd International Symposium on Alternatives to Antibiotics 2019.