Complete Genome Sequence of Klebsiella pneumoniae Jumbo Phage Miami

Mora, Daniel; Lessor, Lauren; Le, Tram; Clark, James; Gill, Jason J.; Liu, Mei

doi:10.1128/mra.01404-20

Cited by 4 publications

(4 citation statements)

References 19 publications

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“…Annotations were attributed to 141 CDSs (shown in colour in Figure 3) leaving a total of 393 (73.6%) CDSs of unknown function. GBH019 shows high similarity to previously described jumbo phage Muenster (Mora et al, 2021), K64-1 (Pan et al, 2017) and vB_KleM-RaK2 (Sǐmoliunas et al, 2013) with DNA similarity values calculated using MASH of 98.2-98.4% but with highly dissimilar gene organisation (Supplementary Figure 1). Examination of the pangenome of these four phage using Roary 3.13 (Page et al, 2015) showed that 384 genes were common to all genomes (BLASTP > 90%).…”

Section: Jumbo Phage Gbh019supporting

confidence: 54%

“…Three K51-selective phage displayed non-identical genomes of 348 kb and consequently fell into the category of jumbo (Yuan and Gao, 2017) also known as huge (Al-Shayeb et al, 2020) phage characterised by genomes of >200 kb. As isolation-based methods select against large phage (Yuan and Gao, 2017), only 94 jumbo phage have been described following isolation and only three of these, with a high degree of sequence similarity, are Klebsiella spp virions (Sǐmoliunas et al, 2013;Pan et al, 2017;Mora et al, 2021): these have genomes of 345.8 kb, making phage GBH019, GBH020 and GBH023 (Table 2) amongst the largest Klebsiella phage described and sequenced to date.…”

Section: Phage Isolationmentioning

confidence: 99%

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Characterisation of Bacteriophage-Encoded Depolymerases Selective for Key Klebsiella pneumoniae Capsular Exopolysaccharides

Blundell‐Hunter

Enright

Negus

et al. 2021

Front. Cell. Infect. Microbiol.

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Capsular polysaccharides enable clinically important clones of Klebsiella pneumoniae to cause severe systemic infections in susceptible hosts. Phage-encoded capsule depolymerases have the potential to provide an alternative treatment paradigm in patients when multiple drug resistance has eroded the efficacy of conventional antibiotic chemotherapy. An investigation of 164 K. pneumoniae from intensive care patients in Thailand revealed a large number of distinct K types in low abundance but four (K2, K51, K1, K10) with a frequency of at least 5%. To identify depolymerases with the capacity to degrade capsules associated with these common K-types, 62 lytic phage were isolated from Thai hospital sewage water using K1, K2 and K51 isolates as hosts; phage plaques, without exception, displayed halos indicative of the presence of capsule-degrading enzymes. Phage genomes ranged in size from 41–348 kb with between 50 and 535 predicted coding sequences (CDSs). Using a custom phage protein database we were successful in applying annotation to 30 - 70% (mean = 58%) of these CDSs. The largest genomes, of so-called jumbo phage, carried multiple tRNAs as well as CRISPR repeat and spacer sequences. One of the smaller phage genomes was found to contain a putative Cas type 1E gene, indicating a history of host DNA acquisition in these obligate lytic phage. Whole-genome sequencing (WGS) indicated that some phage displayed an extended host range due to the presence of multiple depolymerase genes; in total, 42 candidate depolymerase genes were identified with up to eight in a single genome. Seven distinct virions were selected for further investigation on the basis of host range, phage morphology and WGS. Candidate genes for K1, K2 and K51 depolymerases were expressed and purified as his6-tagged soluble protein and enzymatic activity demonstrated against K. pneumoniae capsular polysaccharides by gel electrophoresis and Anton-Paar rolling ball viscometry. Depolymerases completely removed the capsule in K-type-specific fashion from K. pneumoniae cells. We conclude that broad-host range phage carry multiple enzymes, each with the capacity to degrade a single K-type, and any future use of these enzymes as therapeutic agents will require enzyme cocktails for utility against a range of K. pneumoniae infections.

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Section: Jumbo Phage Gbh019supporting

confidence: 54%

Section: Phage Isolationmentioning

confidence: 99%

Characterisation of Bacteriophage-Encoded Depolymerases Selective for Key Klebsiella pneumoniae Capsular Exopolysaccharides

Blundell‐Hunter

Enright

Negus

et al. 2021

Front. Cell. Infect. Microbiol.

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“…S2C) in the NCBI taxonomic database. øKp_32 exhibits 95.9% nucleotide identity with Klebsiella phage Miami ( 30 ) (Fig. S2C).…”

Section: Resultsmentioning

confidence: 99%

Characterization of 29 newly isolated bacteriophages as a potential therapeutic agent against IMP-6-producing Klebsiella pneumoniae from clinical specimens

Kondo,

Nakano,

Hisatsune

et al. 2023

Microbiol Spectr

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Carbapenemase-producing Enterobacteriaceae (CPE) are one of the most detrimental species of antibiotic-resistant bacteria globally. Phage therapy has emerged as an effective strategy for the treatment of CPE infections. In western Japan, the rise of Klebsiella pneumoniae strains harboring the pKPI-6 plasmid encoding bla IMP-6 is of increasing concern. To address this challenge, we isolated 29 phages from Japanese sewage, specifically targeting 31 K . pneumoniae strains and one Escherichia coli strain harboring the pKPI-6 plasmid. Electron microscopy analysis revealed that among the 29 isolated phages, 21 (72.4%), 5 (17.2%), and 3 (10.3%) phages belonged to myovirus, siphovirus, and podovirus morphotypes, respectively. Host range analysis showed that 18 Slopekvirus strains within the isolated phages infected 25–26 K . pneumoniae strains, indicating that most of the isolated phages have a broad host range. Notably, K. pneumoniae strain Kp21 was exclusively susceptible to phage øKp_21, whereas Kp22 exhibited susceptibility to over 20 phages. Upon administering a phage cocktail composed of 10 phages, we observed delayed emergence of phage-resistant bacteria in Kp21 but not in Kp22. Intriguingly, phage-resistant Kp21 exhibited heightened sensitivity to other bacteriophages, indicating a “trade-off” for resistance to phage øKp_21. Our proposed phage set has an adequate number of phages to combat the K. pneumoniae strain prevalent in Japan, underscoring the potential of a well-designed phage cocktail in mitigating the occurrence of phage-resistant bacteria. IMPORTANCE The emergence of Klebsiella pneumoniae harboring the bla IMP-6 plasmid poses an escalating threat in Japan. In this study, we found 29 newly isolated bacteriophages that infect K. pneumoniae strains carrying the pKPI-6 plasmid from clinical settings in western Japan. Our phages exhibited a broad host range. We applied a phage cocktail treatment composed of 10 phages against two host strains, Kp21 and Kp22, which displayed varying phage susceptibility patterns. Although the phage cocktail delayed the emergence of phage-resistant Kp21, it was unable to hinder the emergence of phage-resistant Kp22. Moreover, the phage-resistant Kp21 became sensitive to other phages that were originally non-infective to the wild-type Kp21 strains. Our study highlights the potential of a well-tailored phage cocktail in reducing the occurrence of phage-resistant bacteria.

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“…Whole genome NCBI nucleotide BLAST for the bacteriophage KPN8 could not be completed due to its large size. However, many sections of its genome were found to BLAST to the previously reported novel Klebsiella jumbo phage Miami (MT701590) [41]. When analysed in a phylogenetic tree of putative capsid proteins, these two jumbo bacteriophages clustered together in a clade (Figure 2A).…”

Section: Phylogeny Of Klebsiella Bacteriophages Kpn7 and Kpn8mentioning

confidence: 94%

Effects of Klebsiella pneumoniae Bacteriophages on IRAK3 Knockdown/Knockout THP-1 Monocyte Cell Lines

Schubert

Kabwe

et al. 2022

Viruses

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Bacterial sepsis characterised by an immunosuppressive and cytokine storm state is a challenge to treat clinically. While conventional antibiotics have been associated with exacerbating the cytokine storm, the role that bacteriophages may play in immune modulation of sepsis remains unclear. Bacteriophages are bacterial viruses that have the capacity to lyse specific bacteria and hence provide a natural alternative to antibiotics. K. pneumoniae is known to cause sepsis in humans, and in this study we isolated two lytic bacteriophages against this pathogen, one of which was a novel jumbo bacteriophage. We employed THP-1 monocyte cell lines, with different functional phenotypes for the interleukin-1 receptor associated kinase 3 (IRAK3- a cytoplasmic homeostatic mediator and prognostic marker of inflammation), to evaluate the role of the K. pneumoniae bacteriophages in modulating the immune response in-vitro. We showed for the first time that bacteriophages did not stimulate excessive production of tumour necrosis factor alpha, or interleukin-6, in THP-1 monocyte cell lines which displayed varying levels of IRAK3 expression.

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Complete Genome Sequence of Klebsiella pneumoniae Jumbo Phage Miami

Abstract: Bacteriophage Miami infects Klebsiella pneumoniae, a Gram-negative pathogen that is becoming an increasing threat to public health due to its multidrug resistance. Here, we describe the annotation of the 253,383-bp jumbo phage Miami genome sequence and its similarity to other myophages.

Cited by 4 publications

References 19 publications

Characterisation of Bacteriophage-Encoded Depolymerases Selective for Key Klebsiella pneumoniae Capsular Exopolysaccharides

Characterisation of Bacteriophage-Encoded Depolymerases Selective for Key Klebsiella pneumoniae Capsular Exopolysaccharides

Characterization of 29 newly isolated bacteriophages as a potential therapeutic agent against IMP-6-producing Klebsiella pneumoniae from clinical specimens

Effects of Klebsiella pneumoniae Bacteriophages on IRAK3 Knockdown/Knockout THP-1 Monocyte Cell Lines

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