Characterization of the prophage content of Argentinean and global GBS strains by genomic analysis

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

Simposio; 2nd International Symposium on Streptococcus Agalactiae Disease (ISSAD); 2021

trabajo enviadoThe role of prophages in GBS epidemiology is still under study. We aimed to characterize theprophage content of 10 representative Argentinean human GBS strains and others publiclyavailable, in the context of GBS genomic and epidemiological data.Whole genome sequencing was performed using Illumina MiSeq v2 platform. De novoassemblies were obtained with SPAdes. In addition, 148 GBS assemblies from 18 countries (5continents), from human and animal hosts, were accessed from public databases. Allassemblies were annotated with Prokka. Roary, SNP-sites and RaxML were used to construct acore-SNPs phylogenetic tree. MLSTs were assigned with Pathogenwatch and serotypes weredetermined through a BLASTn search of reference capsular genes (Sheppard, 2016). Plasmidrep, virulence factors (VF) and antimicrobial resistance (AMR) genes were searched withABRicate. Prophages were screened and classified according to GBS-prophage group (A-F) (byin silico PCR; van der Mee-Marquet, 2018) and/or GBS-prophage-integrase (GBSint) type (byBLASTx against a GBSint database; Crestani, 2020).Argentinean strains were interspaced in the phylogeny related to human GBS from 4 continents.Thirteen prophages were found in 9/10 genomes (1-2 prophages/genome); most frequentprophage-types: A (3/13), B/GBSint9.2 (2/13), D/GBSint4 (2/13, found exclusively in Argentina)and E/GBSint3 (2/13). Globally, 1-4 prophages were found in 63% of strains; most frequenttypes: A (37%) and GBSint3 (20%), which co-infect 31% of strains with multiple prophages.Similar prophage content was detected within clades of the core-SNPs phylogenetic tree, inwhich clade distribution was related to clonal complex (CC) and serotype. Predominantprophage-types were found in some CCs (A: CC1, CC7, CC19; GBSint3: CC22, CC23;GBSint1: CC283). No relation between VF/AMR/rep genes presence and CC or phage contentwas found.Argentinean GBS are related to strains circulating globally. The implications in local GBSepidemiology of an exclusive prophage-type need to be studied. The relation between GBSdistribution in the core-genome phylogeny and prophage content implies an important role ofprophages in the spread of GBS strains.