Bioinformatic analysis of prophages and their lysins found in Streptococcus agalactiae genomes isolated in Argentina.

KOVACEC V; DI GREGORIO S; POKLEPOVICH T; CAMPOS J; MOLLERACH M; BONOFIGLIO L

Congreso; 1st Congress of Women in Bioinformatics and Data science LA,; 2020

Red Latinoamericana de Mujeres en Bioinformatica

Streptococcus agalactiae (GBS) causes severe infections in neonates, pregnant women and adults with comorbidities. Little is known about the contribution of prophages to GBS epidemiology. Phage lysins are promising agents to fight antimicrobial resistance. The aim of this work was to detect and characterize prophages and their lysins in the genomes of 10 representative GBS strains, selected within an Argentinean Multicenter Study. Whole genome sequencing was performed using Illumina MiSeq v2 platform. De novo assemblies were obtained with SPAdes. Genomes were annotated with RAST. Prophages detection was accomplished with PhiSpy and manual inspection. Antimicrobial resistance and virulence determinants were searched with ABRicate. Comparative analysis of prophage genomes was conducted with ACT. Phylogeny of selected proteins (integrase, helicase, terminase-large-subunit, major-tail-protein, lysin, toxin) was performed with IQTree. Lysins were analyzed with Expasy and NCBI tools. Thirteen Siphoviridae prophages were found in 9/10 GBS genomes, with similar features to phages we have previously communicated. In 12/13 prophages ORFs encoding putative proteins related to: bacterial defence systems, adaptation to challenging environments and/or virulence were found. Comparative analysis of genomes and phylogeny of selected proteins revealed 4 groups of prophages with 85-100% sequence identity. Prophages within the same integrase phylogenetic group shared the same GBS genome insertion site. Lysins were found in all prophages (n=16, distributed mainly within 5 phylogenetic clusters), being encoded by 2 genes in 3/13 phages, 15/16 showed at least one catalytic domain, 6/16 with cell-wall-binding domain. The lysins were classified, according to their cleavage site, into three of the four major endolysin classes. One group of lysins was bifunctional. The role of these prophages in the epidemiology of Argentinean GBS strains will continue to be studied. The variety of lysin classes found is encouraging as these lysins could potentially be used against the diversity of GBS strains circulating locally and internationally.