Complete Genome Sequence of Carbapenemase-Producing Klebsiella pneumoniae Myophage Matisse

Provasek, Vincent E.; Lessor, Lauren; Cahill, Jesse; Rasche, Eric; Everett, Gabriel F. Kuty

doi:10.1128/genomea.01136-15

Cited by 10 publications

(9 citation statements)

References 16 publications

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“…The presence of the ndd gene ( orf276 ), the deduced amino acid sequence of which shared 100% identity with the nucleoid disruption protein of Klebsiella phage KP15, suggested a lytic lifestyle for vB_EaeM_φEap-3 ( Kesik-Szeloch et al, 2013 ). Comparative analysis of the whole genome sequence of vB_EaeM_φEap-3 against those of phages retrieved from the NCBI databases revealed that vB_EaeM_φEap-3 is most closely related to coliphages RB16 (NC_014467; Petrov et al, 2006 ) and RB43 (NC_007023; Petrov et al, 2006 ), Klebsiella phages KP15 (GU295964; Kesik-Szeloch et al, 2013 ), KP27 (HQ918180; Kesik-Szeloch et al, 2013 ), Matisse (KT001918; Provasek et al, 2015 ), and Miro (KT001919; Mijalis et al, 2015 ), Cronobacter phage vB_CsaM_GAP161 (JN882287; Abbasifar et al, 2012 ), and members of the myoviral subfamily Tevenvirinae, belonging to a genus of T4-like viruses ( Adriaenssens and Brister, 2017 ; Figure 6 ). A large percentage of the putative proteins that could be assigned a metabolic function were devoted to DNA metabolism and, replication ( Figure 7 ).…”

Section: Resultsmentioning

confidence: 99%

Characterizing the Biology of Lytic Bacteriophage vB_EaeM_φEap-3 Infecting Multidrug-Resistant Enterobacter aerogenes

et al. 2019

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Carbapenem-resistant Enterobacter aerogenes strains are a major clinical problem because of the lack of effective alternative antibiotics. However, viruses that lyze bacteria, called bacteriophages, have potential therapeutic applications in the control of antibiotic-resistant bacteria. In the present study, a lytic bacteriophage specific for E. aerogenes isolates, designated vB_EaeM_φEap-3, was characterized. Based on transmission electron microscopy analysis, phage vB_EaeM_φEap-3 was classified as a member of the family Myoviridae (order, Caudovirales). Host range determination revealed that vB_EaeM_φEap-3 lyzed 18 of the 28 E. aerogenes strains tested, while a one-step growth curve showed a short latent period and a moderate burst size. The stability of vB_EaeM_φEap-3 at various temperatures and pH levels was also examined. Genomic sequencing and bioinformatics analysis revealed that vB_EaeM_φEap-3 has a 175,814-bp double-stranded DNA genome that does not contain any genes considered undesirable for the development of therapeutics (e.g., antibiotic resistance genes, toxin-encoding genes, integrase). The phage genome contained 278 putative protein-coding genes and one tRNA gene, tRNA-Met (AUG). Phylogenetic analysis based on large terminase subunit and major capsid protein sequences suggested that vB_EaeM_φEap-3 belongs to novel genus “Kp15 virus” within the T4-like virus subfamily. Based on host range, genomic, and physiological parameters, we propose that phage vB_EaeM_φEap-3 is a suitable candidate for phage therapy applications.

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Section: Resultsmentioning

confidence: 99%

Characterizing the Biology of Lytic Bacteriophage vB_EaeM_φEap-3 Infecting Multidrug-Resistant Enterobacter aerogenes

et al. 2019

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“…Nowadays, the interest of the scientific community is more and more focussed on alternative antibacterials such as bacterial predators—bacteriophages and phage-encoded endolysins. There is an increasing number of Klebsiella phages propagating on especially extended spectrum beta-lactamase (ESBL) and carbapenemase (KPC) producing isolates (Drulis-Kawa et al 2011; Kęsik-Szeloch et al 2013; Mijalis et al 2015; Provasek et al 2015; Wangkahad et al 2015; Jamal et al 2015), which enables analysis of homology and particular properties of this specific clade of phages. The proposed new Kp15virus genus within the subfamily Tevenvirinae groups five phages: Klebsiella phages vB_KpnM_KP15 and vB_KpnM_KP27 from the Polish collection; Klebsiella phages Matisse and Miro isolated in TX, USA; and Enterobacter phage phiEap-3 originating from Beijing, China.…”

Section: Discussionmentioning

confidence: 99%

Klebsiella phages representing a novel clade of viruses with an unknown DNA modification and biotechnologically interesting enzymes

Maciejewska

Roszniowski

Espaillat

et al. 2016

Appl Microbiol Biotechnol

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Lytic bacteriophages and phage-encoded endolysins (peptidoglycan hydrolases) provide a source for the development of novel antimicrobial strategies. In the present study, we focus on the closely related (96 % DNA sequence identity) environmental myoviruses vB_KpnM_KP15 (KP15) and vB_KpnM_KP27 (KP27) infecting multidrug-resistant Klebsiella pneumoniae and Klebsiella oxytoca strains. Their genome organisation and evolutionary relationship are compared to Enterobacter phage phiEap-3 and Klebsiella phages Matisse and Miro. Due to the shared and distinct evolutionary history of these phages, we propose to create a new phage genus “Kp15virus” within the Tevenvirinae subfamily. In silico genome analysis reveals two unique putative homing endonucleases of KP27 phage, probably involved in unrevealed mechanism of DNA modification and resistance to restriction digestion, resulting in a broader host spectrum. Additionally, we identified in KP15 and KP27 a complete set of lysis genes, containing holin, antiholin, spanin and endolysin. By turbidimetric assays on permeabilized Gram-negative strains, we verified the ability of the KP27 endolysin to destroy the bacterial peptidoglycan. We confirmed high stability, absence of toxicity on a human epithelial cell line and the enzymatic specificity of endolysin, which was found to possess endopeptidase activity, cleaving the peptide stem between l-alanine and d-glutamic acid.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-016-7928-3) contains supplementary material, which is available to authorized users.

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“…The genome of phage P-KP2 is a linear double-stranded DNA that is comprised of 172,138 bp with a G + C content of 41.9%, and the termini of the phage genome is located at 38,590 bp (Supplementary Figure 2). Comparative analysis of the complete nucleotide sequence indicates that several phages show high similarity to P-KP2, including Enterobacter phage phiEap-3 (Zhao et al, 2019), Klebsiella phage Matisse (Provasek et al, 2015), Klebsiella phage KP27, Klebsiella phage KP15, Klebsiella phage PMBT1 (Koberg et al, 2017), Klebsiella phage KOX10, Klebsiella phage Miro (Mijalis et al, 2015), Escherichia phage phT4A (Pereira et al, 2017), and Klebsiella phage KOX8 (Table 1), which can be classified as a member of pseudo-Teven myophages which belong to "KP15likevirus" genus. Multiple genome alignment confirmed that these phages have parallel gene functional modules (Figure 3).…”

Section: Bioinformatics Analyses Of P-kp2 Genomementioning

confidence: 99%

Combination Therapy of Phage vB_KpnM_P-KP2 and Gentamicin Combats Acute Pneumonia Caused by K47 Serotype Klebsiella pneumoniae

et al. 2021

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Klebsiella pneumoniae (K. pneumoniae) is an important nosocomial and community acquired opportunistic pathogen which causes various infections. The emergence of multi-drug resistant (MDR) K. pneumoniae and carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) has brought more severe challenge to the treatment of K. pneumoniae infection. In this study, a novel bacteriophage that specifically infects K. pneumoniae was isolated and named as vB_KpnM_P-KP2 (abbreviated as P-KP2). The biological characteristics of P-KP2 and the bioinformatics of its genome were analyzed, and then the therapeutic effect of P-KP2 was tested by animal experiments. P-KP2 presents high lysis efficiency in vitro. The genome of P-KP2 shows homology with nine phages which belong to “KP15 virus” family and its genome comprises 172,138 bp and 264 ORFs. Besides, P-KP2 was comparable to gentamicin in the treatment of lethal pneumonia caused by K. pneumoniae W-KP2 (K47 serotype). Furthermore, the combined treatment of P-KP2 and gentamicin completely rescued the infected mice. Therefore, this study not only introduces a new member to the phage therapeutic library, but also serves as a reference for other phage-antibiotic combinations to combat MDR pathogens.

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Complete Genome Sequence of Carbapenemase-Producing Klebsiella pneumoniae Myophage Matisse

Cited by 10 publications

References 16 publications

Characterizing the Biology of Lytic Bacteriophage vB_EaeM_φEap-3 Infecting Multidrug-Resistant Enterobacter aerogenes

Characterizing the Biology of Lytic Bacteriophage vB_EaeM_φEap-3 Infecting Multidrug-Resistant Enterobacter aerogenes

Klebsiella phages representing a novel clade of viruses with an unknown DNA modification and biotechnologically interesting enzymes

Combination Therapy of Phage vB_KpnM_P-KP2 and Gentamicin Combats Acute Pneumonia Caused by K47 Serotype Klebsiella pneumoniae

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