Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae
Por:
Bleriot, I, Trastoy, R, Blasco, L, Fernandez-Cuenca, F, Ambroa, A, Fernandez-Garcia, L, Perez-Nadales, E, Torre-Cisneros, J, Oteo-Iglesias, J, Navarro, F, Miro, E, Pascual, A, Bou, G, Martinez-Martinez, L, Tomas, M
Publicada:
1 may 2020
Resumen:
Klebsiella pneumoniae is the clinically most important species within the genus Klebsiella 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 K. pneumoniae belonging to different sequence types, previously identified by multilocus sequence typing. These prophages were grouped into the three families in the order Caudovirales (27 prophages belonging to the family Myoviridae, 10 prophages belonging to the family Siphoviridae and 3 prophages belonging to the family Podoviridae). 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 terZABCDE operon) and methyltransferase proteins.
Filiaciones:
Bleriot, I:
Univ A Coruna UDC, Microbiol Dept, Res Inst Biomed A Coruna INIBIC, Hosp A Coruna CHUAC, La Coruna, Spain
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Trastoy, R:
Univ A Coruna UDC, Microbiol Dept, Res Inst Biomed A Coruna INIBIC, Hosp A Coruna CHUAC, La Coruna, Spain
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Blasco, L:
Univ A Coruna UDC, Microbiol Dept, Res Inst Biomed A Coruna INIBIC, Hosp A Coruna CHUAC, La Coruna, Spain
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Fernandez-Cuenca, F:
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Univ Seville, Dept Microbiol & Med, Clin Unit Infect Dis Microbiol & Prevent Med, Hosp Univ Virgen Macarena, Seville, Spain
REIPI, Spanish Network Res Infect Dis, Seville, Spain
Ambroa, A:
Univ A Coruna UDC, Microbiol Dept, Res Inst Biomed A Coruna INIBIC, Hosp A Coruna CHUAC, La Coruna, Spain
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Fernandez-Garcia, L:
Univ A Coruna UDC, Microbiol Dept, Res Inst Biomed A Coruna INIBIC, Hosp A Coruna CHUAC, La Coruna, Spain
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Perez-Nadales, E:
REIPI, Spanish Network Res Infect Dis, Seville, Spain
Univ Cordoba, Univ Hosp Reina Sofia, Maimonides Biomed Res Inst Cordoba IMIBIC, Microbiol Unit, Cordoba, Spain
Torre-Cisneros, J:
REIPI, Spanish Network Res Infect Dis, Seville, Spain
Univ Cordoba, Univ Hosp Reina Sofia, Maimonides Biomed Res Inst Cordoba IMIBIC, Microbiol Unit, Cordoba, Spain
Oteo-Iglesias, J:
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
REIPI, Spanish Network Res Infect Dis, Seville, Spain
Inst Hlth Carlos III, Reference & Res Lab Antibiot Resistance & Hlth Ca, Natl Ctr Microbiol, Madrid, Spain
Navarro, F:
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Autonomous Univ Barcelona Bellaterra, St Pau Hosp, Microbiol Dept, Barcelona, Spain
Miro, E:
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Autonomous Univ Barcelona Bellaterra, St Pau Hosp, Microbiol Dept, Barcelona, Spain
Pascual, A:
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
Univ Seville, Dept Microbiol & Med, Clin Unit Infect Dis Microbiol & Prevent Med, Hosp Univ Virgen Macarena, Seville, Spain
REIPI, Spanish Network Res Infect Dis, Seville, Spain
Bou, G:
Univ A Coruna UDC, Microbiol Dept, Res Inst Biomed A Coruna INIBIC, Hosp A Coruna CHUAC, La Coruna, Spain
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
REIPI, Spanish Network Res Infect Dis, Seville, Spain
Martinez-Martinez, L:
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
REIPI, Spanish Network Res Infect Dis, Seville, Spain
Univ Cordoba, Univ Hosp Reina Sofia, Maimonides Biomed Res Inst Cordoba IMIBIC, Microbiol Unit, Cordoba, Spain
Tomas, M:
Univ A Coruna UDC, Microbiol Dept, Res Inst Biomed A Coruna INIBIC, Hosp A Coruna CHUAC, La Coruna, Spain
Spanish Soc Infect Dis & Clin Microbiol SEIMC, Study Grp Mech Act & Resistance Antimicrobials GE, Madrid, Spain
REIPI, Spanish Network Res Infect Dis, Seville, Spain
Green Published, gold
|