Whole -genome sequencing and comparative genomics analysis of Klebsiella pneumoniae isolates from animal source foods

Abstract

The objective of the study was genome sequencing and comparative genomics analysis of Klebsiella pneumoniae isolates from animal source foods. We collected a total of 196 animal source food samples from three locations in Guwahati, Assam, India. The samples were screened for Klebsiella pneumoniae and the presumed Klebsiella spp. isolates were further confirmed by whole genome sequencing on the Illumina Miseq platform, and the reads obtained were assembled and utilized for the downstream analysis. Fourteen K. pneumoniae isolates could be recovered from 196 samples. The whole genome sequence analysis revealed that the virulence genes and antimicrobial resistant genes (ARGs) were located on different mobile genetic elements of these isolates. The isolates carried genes encoding resistance to quinolones (oqxA_1& oqxB_1), fosfomycin (fosA6_1 & fosA_3), beta-lactam antibiotics (bla_SHV-187, bla_SHV-172, bla_SHV-106, bla_DHA-1, blaOKP-B-8, bla_SHV-61, bla_SHV-220, bla_CTX-M-15, and bla_SHV-106), aminoglycosides (aph (6)-Id and aac(3)-IIe) and sulphonamides(sul1). Seven distinct sequence types were identified across the isolates, and the ST14 sequence type was most prevalent (n = 8). The most predominant serotypes identified were K16 and O1. All the isolates were predicted as human pathogens with an approximate mean probability of 89.2 %. This study highlighted K. pneumoniae as a potential foodborne pathogen as well as the significant reservoir of resistant and virulence genes, which in turn potentiate the transfer of these genes through horizontal gene transfer among microbial populations. Klebsiella pneumoniae is a leading cause of hospital acquired infections, and its prevalence in food is concerning because of the wide srepertoire of virulence and antimicrobial genes (ARGs) as well as their transfer among microbial populations in the same niche.