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
