Genomic analysis of GBS prophages from Argentinean strains: lysins as potential treatment to fight AMR.

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

Cambrige

Conferencia; Antimicrobial Resistance ? Genomes, Big Data and Emerging Technologies (Virtual Conference); 2020

Wellcome Trust Sanger Institute

The increase in antimicrobial resistance (AMR) is a global concern and Streptococcus agalactiae (GBS) is not the exception. The absence of a vaccine leads efforts towards the development of new alternatives, such as the employment of phage lysins for the control of these infections.Within the framework of an Argentinean Multicenter Study, we selected 10 GBS strains with different serotype, clinical origin and AMR profile to perform WGS analysis. The aim of this work was to detect and characterize prophages and their lysins in the selected GBS genomes and others publicly available. This will allow us to select lysins that could prevent and treat GBS infections.Total genomic DNA was extracted using a commercial kit and WGS was performed using Illumina MiSeq v2 platform. The quality of the reads was controlled with FastQC and Kraken. De novo assemblies were obtained with SPAdes and quality checked with Quast. Genomes were annotated with RAST.The detection of prophages was performed with PhiSpy and manual inspection. The viral family was determined with VIRFAM. AMR determinants and virulence genes within prophages were searched with ABRicate (using ResFinder, NCBI, CARD, ARGANNOT and VFDB databases).Alignments were used to construct a Maximum Likelihood phylogenetic tree using IQTree and 100 bootstrap replicates. To provide a wider context, we included in the phylogenetic analysis 50 publicly available GBS prophages and their lysins.Thirteen prophages from the Siphoviridae family were found in 9/10 EGB genomes, having 32-49kb, 35-44% GC, 88-96% coding genome (41-84 ORFs, 42-70% with assigned putative function) and modular organization of genes. No AMR determinants were detected. In 12/13 prophages ORFs encoding putative proteins related to: toxin-antitoxin systems, bacterial fitness and/or virulence were found. Lysins were found in all 13 prophages.Phylogenetic analysis of the prophages revealed three clusters, one containing exclusively three Argentinean phages, the remaining phages insterspread on the other clusters.No relationship between clinical origin, serotype and AMR profile of GBS strains and their prophage content was established.Lysin phylogenetic analysis showed four clusters, Argentinian sequences were present in all of them.Our results indicate that some prophages present in Argentinean GBS strains are not clonally related, but most of them (and their lysins) share similarities with prophages from other regions. Lysins isolated locallycould be useful for the treatment of GBS infections not only in Argentina but in other regions, regardless of their antimicrobial resistance profile.