Antimicrobial and Genomic Characterization of Salmonella Nigeria from Pigs and Poultry in Ilorin, North-central, Nigeria

Abstract

Introduction: Non-typhoidal Salmonella are major foodborne pathogens causing serious challenges to public health and food safety worldwide. This study aimed to determine the resistance, virulence genes, sequence type, using multi-locus sequence typing, plasmids and Single Nucleotide Polymorphisms (SNPs) of Salmonella enterica subsp. enterica serovar Nigeria (S. Nigeria) from livestock in Ilorin, North central Nigeria. Methodology: A total of 1,500 samples from pig (feces; n = 600) and poultry (feces, postmortem samples; n = 900) were collected and analyzed between 2014 to 2017. Presumptive Salmonella isolates were characterized by Whole Genome Sequencing (WGS). Results: We recovered nine S. Nigeria serovars. All the isolates harbored a single point mutation parC(T57S) in addition to qnrB19 and the tetA gene. Furthermore, two plasmids, Col(pHAD28) and IncQ1 predicted to encode qnrB19 and tetA genes, respectively, were detected in all the strains. All the isolates belonged to a single sequence type (ST) 4911, the SNP-based phylogeny showed all the isolates to be highly related, in addition two clinical isolates from the United Kingdom (UK) and Canada, collected outside of this study, also fell into this cluster. Twenty virulence genes were identified from Salmonella Pathogenicity Islands (SPI), chromosomal and fimbriae loci. Conclusions: This study highlights the roles of pig and poultry in the emergence and spread of S. Nigeria serovar in Nigeria, sub-Sahara Africa. It also highlighted the importance of WGS in clinical and epidemiological surveillance. There is the need for collaborative research studies to investigate the public health importance of Salmonella enterica serovar Nigeria.