Molecular characterization of Salmonella enterica from poultry farms in Ilorin, north-central Nigeria

Poultry salmonellosis caused by Salmonella enterica is one of the most important bacterial diseases posing serious challenges to poultry production and human health worldwide. This study investigated the occurrence, serotypes, multilocus sequence types (MLSTs), antimicrobial resistance, plasmids, and 12 selected virulence genes of non-typhoidal Salmonella from poultry layer farms using whole-genome sequencing (WGS) methods. Two hundred cloaca swab samples were aseptically collected from four commercial poultry farms (layers) and transferred in sterile universal bottles on ice to the laboratory for analysis. Presumptive Salmonella isolates were detected with selective media and conventional biochemical tests. Serovars were confirmed by serotyping using the slide agglutination and Seqsero methods. Seven samples were positive for Salmonella consisting of Salmonella Typhimurium (S. Typhimurium) (n = 4), S. Albany (n = 2), and S. Agama with an occurrence rate of 3.5 % (7/200). Overall, 3 isolates showed the parC mutation expected not to cause resistance. Similarly, one S. Typhimurium isolate carried plasmid replicons of IncFIB(S)/IncFII(S) type without antimicrobial resistance genes. Three sequence types (STs); 19 (S. Typhimurium), 5317 (S. Albany), and 467 (S. Agama) were obtained. Salmonella Agama harboured 12 virulence genes, while S. Typhimurium and S. Albany harboured 11 virulence genes each. This study highlights the importance of S. Typhimurium, S. Albany, and S. Agama as major pathogens associated with poultry farms in Ilorin, north-central Nigeria. It equally provided baseline information on the serovar distribution, STs, resistance and the virulence gene profiles of all the serovars. Therefore, chickens can serve as a potential source of Salmonella transmission to humans, and this constitutes a potential health risk to the human population. Hence, there is a need for a specific Salmonella control program to be instituted as part of a national food safety strategy.