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Volume 6, Issue 5

Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Open Access

Abstract

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

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bioinformatics , comparative genomics , genomic analysis , Klebsiella pneumoniae , phylogeny and prophages
Funding
This study was supported by the:
  • Instituto de Salud Carlos III, http://dx.doi.org/10.13039/501100004587 (Award PI19/00878)
  • Instituto de Salud Carlos III, http://dx.doi.org/10.13039/501100004587 (Award PI16/01163)
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2020-04-29
2024-05-05
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Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae
M Gen 6, e000369 (2020); https://doi.org/10.1099/mgen.0.000369
/content/journal/mgen/10.1099/mgen.0.000369
/content/journal/mgen/10.1099/mgen.0.000369
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