Isolation and genomic characterization of “unassigned” Salmonella enterica serovars from poultry in Ilorin, north-central Nigeria

Abstract

Salmonellosis is an important global foodborne disease caused by Salmonella enterica (S. enterica). Strains that are resistant to a variety of antibiotics were known to constitute major hazard to public health. The objectives of this study are to determine the serovar distributions, genomic antimicrobial resistance, prediction of genes conferring resistance to selected antibiotics, the multi-locus sequence typing (MLST), and plasmid replicon typing of “unassigned” S. enterica isolated from poultry. A total of 300 samples comprised of: post-mortem tissues (n = 150), cloacal swabs (n = 30), and poultry environment (n = 120) were aseptically collected and analyzed between January and June, 2017. Presumptive S. enterica isolates were characterized using conventional cultural methods, biochemical tests, and serotyping. The isolates were characterized, using Whole Genome Sequencing (WGS) Method. Five “unassigned” S. enterica serovars were recovered from four matrices (liver, n = 1; water, n = 1; cloacal swab, n = 2; poultry feed, n = 1). Prediction of point mutation in parC (T57S) was reported in two strains which confer resistance to nalidixic acid; in addition to this, prediction of fosA7 that confers resistance to fosfomycin was identified in one of these strains. Three isolates each encoded plasmid mediated quinolone resistance (PMQR) qnrB69 and bla_-CMY-98 genes expected to confer decreased susceptibility to ciprofloxacin and resistance to ampicillin, amoxicillin-clavulanic acid, cefoxitin, and ceftriaxone, respectively. Three sequence types, ST-6111, 6114 and 7073 were detected. None of the isolates harbored plasmid replicon. This study highlights the importance of “unassigned” S. enterica serovars in the emergence and spread of S. enterica in poultry. There is a need for the establishment of national collaborative Salmonella program to further investigate the pathogenic and public health risk to humans, of “unassigned” S. enterica serovars in Nigeria.