Predicted endolysins from phages with broad lytic activity against Shiga toxin producing Escherichia coli of diverse serogroups

Abstract

Shiga toxin-producing Escherichia coli are important causative agents of foodborne outbreaks.They can cause serious illnesses such as haemolytic uraemic syndrome. The use of phages andtheir enzymes are novel strategies which show a high antibacterial potential. Among theseenzymes are the endolysins, used by double-stranded DNA phages to degrade the cell wall atthe end of their virulent cycle. Endolysins can be classified according to their capacity to cleavelinkages in the peptidoglycan layer as glycosidases, amidases, and endopeptidases. In thiswork, phages isolated from the dairy environment and minced meat were chosen for genomecharacterization. Previous studies have shown the potential of these phages to lyse strainsbelonging to different relevant STEC serogroups. DNA was purified with a commercial kit fromhigh-titer stocks, and sequenced using Illumina technology. Ten contigs containing completephage genomes were characterized. Virus genera were assigned using the software Kraken.Genomes were annotated with RAST and putative endolysins were screened with BLAST,Interpro, Uniprot and HHpred. A molecular phylogenetic analysis of the predicted endolysinswas performed by maximum likelihood method conducted in Mega 7. Seven differentgenomes were further characterized corresponding to different genera: Tequatrovirus (3),Vequintavirus (2), Mosigvirus (1) and Gamaleyavirus (1). Predicted endolysins were analysedand showed to encode six different amino acid sequences. The enzymatically active domainsbelonged to the glycoside hydrolase family 24 (IPR002196) except one that corresponded tothe glycoside hydrolase family 108 (IPR008565). The phylogenetic tree grouped endolysins inaccordance to the phage genus. In conclusion, this work showed diversity in the phages weisolated against STEC and also in the endolysins they encode. Further studies will be performedto continue their characterization as antimicrobial agents against this pathogen.