Unraveling genetic similarities of Klebsiella pneumoniae from poultry and poultry handlers in Punjab, India

Abstract

The study aimed to characterize K. pneumoniae isolates from poultry (broiler) farms of Ludhiana, Punjab, India. The Whole genome sequencing (WGS) of K. pneumoniae isolates (K. pneumoniae strain PF_L1_IN, K. pneumoniae strain PF_L2_IN, K. pneumoniae strain PHS_IN) using NovaSeq6000 (Illumina, USA) platform revealed the presence of several antimicrobial resistant genes (ARGs) on the genome of the isolates conferring potential resistance to antibiotics classified as critically important, highly important and important. The virulence factors (VFs) detected were Type I fimbriae, Type 3 fimbriae, AcrAB, Aerobactin, Enterobactin, Salmochelin, RcsAB, T6SS-I, II and III. The mobile genetic elements such as plasmid replicons (IncFIB and Col440I), integron elements (In0, CALIN), a unit transposon (Tn512) and insertion sequences (ISKpn24, ISEc9, ISKpn1, IS102, IS903, IS5075 and ISKpn38) were detected in the isolates. The plasmids carried ARGs for the important antibiotic classes such as aminoglycoside, macrolides, quinolones, tetracyclines, carbapenems and sulphonamides. However, none of the insertion sequences and transposons in the isolates was associated with any antimicrobial resistant gene. In multilocus sequence typing (MLST) analysis, the isolates belonged to sequence type (ST) ST-147 and ST-147 with double locus variation, while, in core-genome multilocus sequence typing (cgMLST) the isolates belonged to ST-25590 and ST-1508. The isolates from broiler (K. pneumoniae strain PF_L1_IN) and its handler (K. pneumoniae strain PHS_IN) showed clonal relationship. The present study suggested that the food animal's production environment could act as a reservoir of multidrug resistant (MDR) and Extended spectrum β-lactamases (ESBL) producing K. pneumoniae. These resistant isolates could easily be disseminated to human through shared environment and food.