Phenotypic and genotypic characterisation of Salmonella serovars from poultry in ilorin, Kwara state, Nigeria

Salmonellosis is a major foodborne illness globally; however, knowledge about Salmonella phenotypic and genomic characteristics in poultry is elusive in Nigeria. This study aimed to determine the detection rate, serovars distribution, virulence and resistance profiles, and multilocus sequence types (ST) of Salmonella serovars (using WGS) from poultry farms in Ilorin, Kwara State. In a cross-sectional study, 272 samples were collected from apparently healthy laying birds (n = 200) and dead birds (caecum, n = 20, intestine, n = 25, liver, n = 15, and spleen, n = 12) from ten randomly selected commercial layer farms (≥ 5000) in Ilorin, Kwara State. Salmonella was isolated and identified according to standard protocols. The isolates were characterised phenotypically and genotypically using whole genome sequencing (WGS). Salmonella was detected in 11 (4.04%) of the samples, with a significant rate of detection (8.3%) from dead birds (P < 0.05). Eight serovars were recovered, with Salmonella Duesseldorf (1.1%) being the most abundant. The highest resistance rate was observed against ciprofloxacin (58.0%). WGS revealed that the isolates Harboured varying resistance genes. Six aminoglycoside genes and three quinolone resistance genes were detected. There was 92% phenotypic-genotypic resistance concordance, and Salmonella Kentucky isolated exhibited multidrug-resistant phenotypes and genotypes. Seven different sequence types were observed among the isolates, ST-5317 (n = 3) and ST-413 (n = 3) being the most abundant. The data provide further insight into the epidemiology of Salmonella in Nigeria and could serve as the basis for further studies on antibiotic resistance mechanisms in foodborne bacterial pathogens.