Genomic analysis of multidrug resistant non-typhoidal Salmonella enterica strains isolated from broiler chicken in Pakistan

Abstract

Multidrug resistant non-typhoidal Salmonella enterica is zoonotic pathogenic bacteria that poses threat to public and animal health. This study represents first whole genome sequencing based analysis of multidrug resistant S. enterica strains isolated from broiler chicken in Pakistan for identification of anti-microbial resistance determinants and genomic components like virulence factors, plasmids, phages, pathogenicity islands and mobile genetic elements. Based on genome assembly quality report, 2 out of 5, S. enterica strains (S. Enteritidis RW50 and S. Enteritidis KHR57) were used for these assessments. Both genomes were of approximately 4.8 Mb having 52% GC content. A variety of resistance determinants like QnrS1, golS, Tet(A), AAC (6')-Iy, KpnF, cmlA1, Arr-3 were identified in them that confer resistance to fluoroquinolone, beta-lactam, tetracycline, aminoglycoside, macrolide, chloramphenicol and rifampin antibiotics. Resistance determinants were most common to fluoroquinolones, followed by tetracycline and cephalosporins. Mismatches between phenotypic and genotypic resistance profiles were observed in S. Enteritidis KHR57, which was phenotypically susceptible against beta-lactams and chloramphenicols despite harboring golS and cmlA1 genes. Similarly, S. Enteritidis RW50 showed phenotypic susceptibility for carbapenems despite having golS and mdsA. A large number of mobile elements, insertion sequences, pathogenicity islands and prophages were observed that can enhance genomic mobility and antimicrobial resistance in these S. Enteritidis isolates. Virulence factors including type three secretion systems and effector proteins (Sips, Sops) were identified in both isolates that are known to increase the entero pathogenicity and zoonotic potential of Salmonella strains