Genome analysis of multidrug resistant Escherichia coli isolated from poultry in Nigeria

Authors: SHARMA, POONAM - Orise Fellow; GUPTA, SUSHIM - Orise Fellow; ADENIPEKUN, EYITAYO - University Of Lagos; Barrett, John; Hiott, Lari; Woodley, Tiffanie; IWALOKUN, BAMIDELE - Nigerian Institute Of Medical Research; OLUWADUN, AFOLABI - Olabisi Onabanjo University; RAMADAN, HAZEM - Mansoura University; Frye, Jonathan; Jackson, Charlene

Submitted to: Foodborne Pathogens and Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2019
Publication Date: 9/11/2019
Citation: Sharma, P., Gupta, S., Adenipekun, E., Barrett, J.B., Hiott, L.M., Woodley, T.A., Iwalokun, B., Oluwadun, A., Ramadan, H., Frye, J.G., Jackson, C.R. 2019. Genome analysis of multidrug resistant Escherichia coli isolated from poultry in Nigeria. Foodborne Pathogens and Disease. https://doi.org/10.1089/fpd.2019.2659.
DOI: https://doi.org/10.1089/fpd.2019.2659

Interpretive Summary: Escherichia coli is a common commensal of the intestinal tract of humans and animals, but can also be an opportunist pathogen associated with illnesses caused by food-producing animals. In order to effectively treat these infections, it is important to understand the mechanisms of resistance in E. coli. In this study, three multidrug-resistant (MDR) E. coli isolated from chicken fecal samples from Lagos, Nigeria were sequenced and analyzed for the presence of antimicrobial resistance genes, plasmid replicons, virulence genes, and phage. The isolates harbored genes conferring resistance to aminoglycosides, extended-spectrum beta-lactamases, tetracycline, trimethoprim, sulfonamides, fluoroquinolones, and chloramphenicol. Some genes were located on plasmids capable of transferring among bacteria. Data from this study highlights the role of chickens as a potential reservoir of mobile antimicrobial resistance genes as well as virulence genes and phage. Increased efforts of antibiotic surveillance to control and regulate the use of antimicrobial agents is required to reduce risk factors associated with the acquisition of these MDR isolates. This information is useful for policy makers and scientists as they develop prevention and control strategies to inhibit spread of resistant bacteria to humans and the environment, especially in underfunded countries.

Technical Abstract: Escherichia coli is one of the most common commensal bacteria of the gastrointestinal tract of humans and warm-blooded animals. Contaminated poultry can lead to disease outbreaks in consumers causing massive economic losses in the poultry industry. Additionally, commensal E. coli can harbor antibiotic resistance genes that can be transferred to other bacteria, including pathogens, in a colonized human host. In a previous study on antimicrobial resistance of E. coli from food animals from Nigeria, multidrug resistant E. coli were detected. Three of those isolates were selected for further study using whole-genome sequencing due to the extensive drug-resistance exhibited. All of the isolates carried the Extended Spectrum Beta-Lactamase (ESBL) genes, blaCTX-M15 and blaTEM-1, whereas one isolate harbored an additional ESBL, blaOXA-1. All of the tetracycline resistant isolates carried tet(A). The genes aac3-IIa and aacA4, conferring resistance to aminoglycosides, were identified in an E. coli isolate resistant to gentamicin and tobramycin. In two E. coli isolates, dfrA14, qnrS1, and sulII, were detected conferring resistance to trimethoprim, fluoroquinolones, and sulfonamides, respectively. The third isolate carried dfrA17, no fluoroquinolone resistance gene, an additional sulI gene, and a chloramphenicol resistance gene, catB3. Mutations in candidate genes conferring resistance to fosfomycin and fluoroquinolones were also detected. Several efflux systems were detected in all the E. coli isolates as well as virulence-associated genes related to serum resistance, motility, and adhesion. E. coli and non-E. coli origin prophage were also identified in the isolates. The results underline the higher resolution power of WGS for investigation of antimicrobial resistance, virulence, and phage in E. coli.