AUTHOR=Grakh Kushal , Mittal Dinesh , Prakash Anand , Kumar Ramesh , Jindal Naresh 

TITLE=uspA gene-based phylogenetic analysis and antigenic epitope prediction for Escherichia coli strains of avian origin

JOURNAL=Frontiers in Veterinary Science

VOLUME=10

YEAR=2023

URL=https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2023.1183048

DOI=10.3389/fvets.2023.1183048

ISSN=2297-1769

ABSTRACT=<p>Pathogenic <italic>Escherichia coli</italic> (<italic>E. coli</italic>) is responsible for various local and systemic infections in animal and human populations. Conventional methods for the detection and identification of <italic>E. coli</italic> are time-consuming and less reliable for atypical strains. The <italic>uspA</italic> gene has been widely used as a target for the detection of <italic>E. coli</italic>. The present study was aimed at phylogenetic analysis of the <italic>uspA</italic> gene sequences to determine the evolutionary relationships between the strains and other members of the <italic>Enterobacteriaceae</italic> family. In addition, the unique differences in the sequences of the current study with <italic>Salmonella</italic> and <italic>Shigella</italic> species were tested using Tajima’s molecular clock test. Antigenic epitope prediction was performed to locate the B-cell epitope region of the UspA protein. Two <italic>E. coli</italic> isolates of avian origin and strains from the National Center for Biotechnology Information (NCBI) database were used for prediction. The Immune Epitope Database (IEDB) server, Bepitope, ABCpred, SVMTrip, and ElliPro server were used to identify B-cell epitopes. The 3D structure was predicted using SWISS-MODEL. Phylogenetic analysis of the isolates from the current study revealed that both OM837340 and OM837341 sequences from the current study had maximum nucleotide homology (nt) of 99.87%–100% with <italic>E. coli</italic> isolates and minimum nt homology of 84.08% with <italic>Salmonella enteritidis</italic> and <italic>S</italic>. Hissar. The isolates in the current study had a homology of 98.87%, while the homology with <italic>Shigella</italic> species was 99.25%. Seven silent mutations were observed in the coding region of the UspA protein of ECO9LTBW (current study). Modeling of the UspA protein revealed a maximum homology of 67.86% with the Protein Data Bank in Europe (PDBe), also validated by the Ramachandran plot. No significant differences were found in the coding regions of <italic>usp</italic>A of <italic>Salmonella</italic>, <italic>Shigella</italic>, and <italic>E. coli</italic> with Tajima’s test. For the <italic>E. coli</italic> isolates, a total of 24 linear B-cell and seven discontinuous epitopes were predicted using <italic>in-silico</italic> analysis. When the results of the predicted peptides were compared, two peptides, namely ARPYNA and YSDLYTGLIDVNLGDMQKRISEE, were found suitable candidates. In conclusion, the <italic>usp</italic>A gene appears to be conserved among <italic>E. coli</italic> isolates and can be used for molecular detection.</p>