Genome Analysis of Multidrug-Resistant Isolated from Poultry in Nigeria.

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 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 from food animals from Nigeria, multidrug-resistant 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 β-lactamase (ESBL) genes, and , whereas one isolate harbored an additional ESBL, . All of the tetracycline-resistant isolates carried (A). The genes and , conferring resistance to aminoglycosides, were identified in an isolate resistant to gentamicin and tobramycin. In two isolates, , , and , were detected conferring resistance to trimethoprim, fluoroquinolones, and sulfonamides, respectively. The third isolate carried , no fluoroquinolone resistance gene, an additional gene, and a chloramphenicol resistance gene, Mutations in candidate genes conferring resistance to fosfomycin and fluoroquinolones were also detected. Several efflux systems were detected in all the isolates and virulence-associated genes related to serum resistance, motility, and adhesion. and non- origin prophages were also identified in the isolates. The results underline the higher resolution power of whole-genome sequencing for investigation of antimicrobial resistance, virulence, and phage in .