Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae

• DOI: 10.1099/mgen.0.000369
• Publication Date: 2020-05-07T07:38:13Z
• Authors: Ines Bleriot; Rocío Trastoy; Lucia Blasco; Felipe Fernández-...; Antón Ambroa; Laura Fernández-G...; Olga Pacios; Elena Perez-Nadales; Julian Torre-Cisn...; Jesús Oteo-Iglesias; Ferran Navarro; Elisenda Miró; Alvaro Pascual; German Bou; Luis Martínez-Mar...; Maria Tomas
• Keywords: Prophage; Siphoviridae; Multilocus sequence typing

Klebsiella pneumoniae is the clinically most important species within genus and, as a result of continuous emergence multi-drug resistant (MDR) strains, cause severe nosocomial infections. The decline in effectiveness antibiotic treatments for infections caused by MDR bacteria has generated particular interest study bacteriophages. In this study, we characterized total 40 temperate bacteriophages (prophages) with genome range 11.454-84.199 kb, predicted from 16 carbapenemase-producing clinical strains K. belonging to different sequence types, previously identified multilocus typing. These prophages were grouped into three families order Caudovirales (27 family Myoviridae, 10 Siphoviridae and 3 Podoviridae). Genomic comparison prophage genomes led identification four isolated sizes around 33.3, 36.1, 39.6 42.6 kb. showed similarities (query cover >90 %, identity >99.9 %) international Microbe Versus Phage (MVP) (http://mvp.medgenius.info/home) clusters 4762, 4901, 3499 4280, respectively. Phylogenetic analysis revealed evolutionary proximity among members groups frequently bacterial studied (33.3, kb), bootstrap values 100 %. This allowed be classified clusters: A, B C. Interestingly, these did not infect highest number indicated host-range assay, results could explained development superinfection exclusion mechanisms. addition, bioinformatic presence 2363 proteins. total, 59.7 % proteins had function, mainly involving viral structure, transcription, replication regulation (lysogenic/lysis). some putative functions associated virulence (toxin expression efflux pump regulators), phage defence profiles such toxin-antitoxin modules, an anti-CRISPR/Cas9 protein, TerB protein (from terZABCDE operon) methyltransferase