Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments

Abstract

Background Inappropriate use of antimicrobial agents in animal production has led to the development of antimicrobial resistance (AMR) in foodborne pathogens. Transmission of AMR foodborne pathogens from reservoirs, particularly chickens to the human population does occur. Recently, we reported that occupational exposure was a risk factor for multidrug-resistant (MDR) Escherichia coli (E. coli) among poultry-workers. Here we determined the prevalence and genetic relatedness among MDR E. coli isolated from poultry-workers, chickens, and poultry environments in Abuja, Nigeria. This study was conducted to address the gaps identified by the Nigerian AMR situation analysis. Methods We conducted a cross-sectional study among poultry-workers, chickens, and poultry farm/live bird market (LBM) environments. The isolates were tested phenotypically for their antimicrobial susceptibility profiles, genotypically characterized using whole-genome sequencing (WGS) and in silico multilocus sequence types (MLST). We conducted a phylogenetic single nucleotide polymorphism (SNPs) analysis to determine relatedness and clonality among the isolates. Results A total of 115 (26.8%) out of 429 samples were positive for E. coli. Of these, 110 isolates were viable for phenotypic and genotypic characterization. The selection comprised 47 (42.7%) isolates from poultry-workers, 36 (32.7%) from chickens, and 27 (24.5%) from poultry-farm or LBM environments. Overall, 101 (91.8%) of the isolates were MDR conferring resistance to at least three drug classes. High frequency of resistance was observed for tetracycline (n = 102; 92.7%), trimethoprim/sulfamethoxazole (n = 93; 84.5%), streptomycin (n = 87; 79.1%) and ampicillin (n = 88; 80%). Two plasmid-mediated colistin genes—mcr-1.1 harboured on IncX4 plasmids were detected in environmental isolates. The most prevalent sequence types (ST) were ST-155 (n = 8), ST-48 (n = 8) and ST-10 (n = 6). Two isolates of human and environmental sources with a SNPs difference of 6161 originating from the same farm shared a novel ST. The isolates had similar AMR genes and plasmid replicons. Conclusion MDR E.coli isolates were prevalent amongst poultry-workers, poultry, and the poultry farm/LBM environment. The emergence of MDR E. coli with novel ST in two isolates may be plasmid-mediated. Competent authorities should enforce AMR regulations to ensure prudent use of antimicrobials to limit the risk of transmission along the food chain.

Multi-Drug and β-Lactam Resistance in Escherichia coli and Food-Borne Pathogens from Animals and Food in Portugal, 2014–2019

“…In line with our observations, other studies have reported high MDR levels in E. coli through the food chain [ 13 , 17 , 18 , 19 , 20 ]. Overall, E. coli MDR levels were reported at 76% for pig production in South Africa; 75% on farms and 50% in slaughterhouses; 72% from pig and chicken samples in Malaysia; 78% in broiler products from retail in Bangladesh with AMR above 80% to PEN, TET, and MAC; and 92% from chicken samples in Nigeria with resistance in more than two thirds to AMN, F(Q), PEN, TET, and SLP/TMP [ 17 , 18 , 19 , 20 ]. E. coli MDR was observed to differ considerably across EU member states, ranging from 3% to 85% in pigs, 0% to 87% in broilers, and 0% to 78% in turkeys.…”

“…In line with our observations, other studies have reported high MDR levels in E. coli through the food chain [13,[17][18][19][20]. Overall, E. coli MDR levels were reported at 76% for pig production in South Africa; 75% on farms and 50% in slaughterhouses; 72% from pig and chicken samples in Malaysia; 78% in broiler products from retail in Bangladesh with AMR above 80% to PEN, TET, and MAC; and 92% from chicken samples in Nigeria with resistance in more than two thirds to AMN, F(Q), PEN, TET, and SLP/TMP [17][18][19][20]. E. coli MDR was observed to differ considerably across EU member states, ranging from 3% to 85% in pigs, 0% to 87% in broilers, and 0% to 78% in turkeys.…”

Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019

“…High resistance rates were observed in all isolates, especially to aminoglycosides, cephalosporins, penicillins, quinolones, and trimethoprim + sulfamethoxazole. Two isolates were also resistant to carbapenems, which was also observed recently in Nigeria ( Aworh et al, 2021 ), and four were resistant to amphenicol. The high degree of AMR in our study is not surprising, as these antibiotics (ceftriaxone, ciprofloxacin, and beta-lactamases) are easily accessible and commonly used in Benin for therapeutic purposes and very few antimicrobial stewardship programs are in place.…”

Multi-Drug Resistant Escherichia coli, Biosecurity and Anti-Microbial Use in Live Bird Markets, Abeokuta, Nigeria

“…The presence and persistence of resistance in commensal E. coli is a significant biomarker for the selective pressure enforced by antibiotic use and subsequent resistance predicted in other potentially pathogenic bacteria [ 20 ]. The high prevalence of MDR E. coli in poultry has been evaluated and reported in several countries including Nigeria [ 5 , 21 , 22 , 23 , 24 , 25 ]. However, only a few studies on MDR E. coli among chickens in LBMs in the country exist.…”