Fusobacterium necrophorum lktA gene variants from cow foot rot lesions:molecular characterization, phylogeny and homology modelling analysis

Abstract

Foot rot is a necrotic, infectious, and debilitating disease of hooves in ruminants caused by theconcordant effect of Dichelobacter nodosus and Fusobacterium necrophorum. This work aimed foridentification and prevalence of leukotoxin gene, lktA, variant strains of F. necrophorum in cow foot rotlesions. A total of twenty samples were collected from the feet of foot rot-affected cattle. Bacterial DNA wasextracted and amplification of lktA was performed through polymerase chain reaction (PCR) followedby direct DNA sequencing. The sequencing data was subjected to homology search, multiple sequencealignment and phylogenetic tree reconstruction using respective software for taxonomic characterization.This study revealed the presence of JKS-F3, JKS-F2 and JKS-F1 in the foot rot-affected cattle in the localisolates of Punjab, Pakistan, with high prevalence of F. necrophorum JKS-F3 strain (80%) with a lesionscore of 3 and 4. The 3D structure of protein was performed using comparative homology modeling withI-TASSER. The accuracy of the predicted 3D structure was checked using Ramachandran plot analysisand showed that 85.4% amino acids were in the favored region i.e., extended conformation of β-sheetsare clustered in the right hand-region. These findings suggest that early and accurate identification andcharacterization of the causative agent of foot rot is a preliminary requirement to control the infection