Draft genome sequences of 25 Salmonella enterica serovar Agona strains isolated from poultry and associated food products harbouring multiple antibiotic resistance genes

Abstract

Antimicrobial-resistant livestock-associated Salmonella enterica serovar Agona infection poses a significant public health threat worldwide. The present study aimed to identify antibiotic resistance genes in livestock-associated S. Agona strains isolated from chickens and associated food products (meat and eggs) in Pakistan via whole-genome sequencing. The genomic DNAs of S. Agona strains (n=25) were sequenced using an Illumina MiSeq platform. The generated reads were trimmed and de novo assembled using CLC Genomics Workbench v.7. The draft genomes were annotated using the National Centre for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline and were characterised by multilocus sequence typing (MLST). The antimicrobial-resistance genes (acquired and chromosomal mutations), extrachromosomal plasmids and Salmonella pathogenicity islands were predicted using ResFinder and CARD, PlasmidFinder and SPIFinder, respectively. The genome size of S. Agona ranges from 4.9 to 5.1 Mb with 52.1% GC contents. The strains belong to ST13 and harbour several antibiotic-resistance genes, including aac (6')-Iaa, aadA1, aadA2, bla OXA-10, qnrS1, cmlA, floR, tet(A), dfrA12 and point mutations in gyrB, gyrA, ParC conferring antibiotic resistance to fluoroquinolones. The strains also contain several plasmids and Salmonella pathogenicity islands. This study reports draft genomes of multidrug-resistant S. Agona from Pakistan isolated from chickens and associated food products. The data may help with understanding the antimicrobial resistance mechanisms and transmission dynamics of this serovar in poultry and associated food products and their possible transmission to humans.