Genomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Serovars from Poultry in Nigeria.

Antimicrobial resistance is a global public health concern, and resistance genes in , especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included , , , , , , and a variety of aminoglycoside-modifying genes, in addition to point mutations in the and genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of Schwarzengrund and Muenster, and most genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of Kentucky strains carried multidrug ARGs located in two distinct variants of genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential