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.

Keywords: Antimicrobial resistance; Chicken; Escherichia coli; Genetic relatedness; Multidrug resistance; Nigeria; One health; Prevalence.

Fig. 1

Antimicrobial resistance pattern of E. coli strains from humans, chickens, and poultry farm or market environment in Abuja-Nigeria, 2019. *DR means drug resistance; 1DR means the E. coli isolate was only resistant to one antimicrobial agent while > 10DR means the E. coli isolate was resistant to more than ten different antimicrobial drugs tested. The minimum number of antimicrobial drugs the human and chicken E. coli isolates were resistant to was one while the poultry environmental E. coli isolates were resistant to a minimum of three antimicrobial agents. Hence, all the poultry environmental E. coli isolates were multidrug-resistant

Fig. 2

Distribution of MDR E. coli isolates based on isolation sources. The bars represent the number of MDR E. coli isolates from humans working on the poultry farm or selling chickens at the live bird market (LBM); the number of MDR E. coli isolates from chickens at the poultry farm or LBM and the number of MDR E. coli isolates from poultry farm or LBM environment

Fig. 3

Multilocus Sequence Types for E. coli isolates from humans, chickens, and poultry farm/market environment, Abuja-Nigeria, 2019. Each bar represents the various E. coli sequence types for isolates obtained from humans, chickens, and poultry farm/LBM environments

Fig. 4

Phylogenetic classification of E. coli isolates from humans, chickens and poultry farm/market environments, Abuja-Nigeria, 2019. The peak of the blue triangle denotes the highest frequency of human E. coli isolates in phylogroup A. The orange triangle denotes the highest frequency of chicken E. coli isolates in phylogroup B1. The black triangle peaks in the same direction as the blue triangle indicating that the phylogroup A has the highest frequency for the E. coli isolates from the poultry farm/LBM environment

Fig. 5

SNP-based phylogeny of MDR E. coli isolates from humans, chickens, and poultry environments in Abuja, 2019. SNP-based maximum likelihood phylogeny of E. coli isolates visualized in iterative Tree of life tool (iTol). The tree was rooted in a reference isolate E. coli strain NCTC11129. Clustering of isolates was found to be following the core genome and SNP-based phylogenies. The clustering of isolates belonging to the same phylogenetic group and sequence type was consistent. Shown for each isolate is the source/origin: farm (F) or live bird market (LBM) and phylogroup. AMR genes cluster for 110 E. coli strains are displayed on the phylogenetic tree. The presence (orange) and absence (white) of 12 AMR genes that were most prevalent are represented in the image while the presence (gray) and absence (white) of 10 prevalent plasmid replicons are also represented in the image

Fig. 6

a Phylogenetic SNP-based maximum likelihood tree for E. coli isolates with Novel ST from humans, chickens and poultry farm or market environments. The phylogenetic SNP-based maximum likelihood tree was rooted in a reference isolate E. coli strain NCTC11129. For each isolate, the source and origin: farm (F) or live bird market (LBM) as well as the phylogenetic group is displayed. The phylogenetic tree has several clades with a common ancestor however the red clade has two isolates from the same farm belonging to the same phylogroup and sharing a novel ST. These two isolates from human and poultry farm environments although quite diverse had similar plasmid replicons harbouring AMR genes. b Phylogenetic maximum likelihood tree for E. coli isolates with ST 1638. The SNP-based maximum likelihood tree was rooted in a reference isolate E. coli strain NCTC11129. Two isolates of human and avian origin although not clonally related acquired similar AMR genes