Genome Sequencing and Comparative Genome Analysis of Multi drug Resistant Salmonella Infantis Isolated from Broiler Chicken in Pakistan

Abstract

Multi drug resistant Salmonella enterica is one of the most important foodborne pathogens and mainly associated with gastroenteritis infection both in humans and animals. The irrational use of antibiotics has developed potential antimicrobial resistance in non typhoidal S. enterica. Currently, the number of human infections caused by Salmonella enterica serovar Infantis has been rising worldwide as these strains have become multi drug resistant. Whole Genome Sequencing has become an important tool in the surveillance of antimicrobial resistance in S. enterica. The aim of this study was whole genome sequencing-based genome analysis of three indigenous strains of Salmonella Infantis and detection of genetic components responsible for antimicrobial resistance in them. Result revealed the genome size of all three strains, S. Infantis RW51, S. Infantis RW52, and S. Infantis SKR55 is approximately 4.8Mb with 52.0% GC content. These strains harbour resistance determinants; golA, sdiA, adeF. kpnE, rsmA, APH(3')-Iia, ANT(3'')-Iia, tet(A), gyrA and arr-2 that provide resistance to beta-lactams, aminoglycosides, tetracycline, macrolides, fluoroquinolones Chloramphenicol, sulfonamides and rifampicin. Several genetic factors such as mobile genetic elements, prophages and insertion sequences were also identified that influence the genetic and phenotypic diversity of antimicrobial resistance and virulence in them. Phylogenetic analysis inferred that RW51 and RW52 are evolutionarily related to strain S. Infantis 119944 reported from Israel while SKR55 is found to be closely related to strain VNCSE001 reported from Vietnam.