Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical Klebsiella pneumoniae Strains

Baliga, Pallavi; Shekar, Malathi; Girisha, S.K.

doi:10.1007/s00284-021-02472-2

Cited by 5 publications

(5 citation statements)

References 45 publications

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“…Using an in silico approach, among the 104 intact prophages, we found Myoviridae to be the most represented family (59.6%), followed by Siphoviridae (38.5%) and Podoviridae (1.9%). The same distribution was observed in other studies [55,56]. Myoviridae, which are typically the largest phage family, had size genomes below average, while Siphoviridae had sizes slightly above the average.…”

Section: Discussionsupporting

confidence: 86%

“…The majority, 62 (59.6%) was assigned to the Myoviridae family, 40 (38.5%) to the Siphoviridae family, and 2 (1.9%) to the Podoviridae family (Figure 2). This is in accordance with the estimated distribution described in the literature [55,56]. Based on information on the Expansy website (http: //viralzone.expasy.org/, last accessed July 2021), Myoviridae are typically the largest phages with a high variability in their genome sizes, ranging from 33 to 244 kbp and coding for 40 to 415 proteins.…”

Section: Classification Of K Pneumoniae Prophagessupporting

confidence: 89%

“…Incomplete and questionable prophages often lack essential phage functions [73] and therefore our further analysis was focused on intact prophages. Only a few studies have characterized the prevalence of prophages in K. pneumoniae species, although they are genetic elements that significantly contribute to genome variability, evolution, and virulence of their bacterial hosts [32,55,56,72,73,75].…”

Section: Discussionmentioning

confidence: 99%

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Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates

et al. 2021

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Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.

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Section: Discussionsupporting

confidence: 86%

Section: Classification Of K Pneumoniae Prophagessupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

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Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates

et al. 2021

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“…Notably, all of the K. pneumoniae isolates in the study carried a significant load of prophages, and the number of prophages within an isolate varied from 3 to 13. The overall prophage diversity in K. pneumoniae is not well documented to date, and there are only a few recent studies on the topic ( 33 ), and thus, this finding warrants future research. The PHASTER tool ( 34 ) identifies the genes found in the prophage regions to be hits either against virus and prophage database or bacterial database.…”

Section: Discussionmentioning

confidence: 93%

Molecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing Klebsiella pneumoniae

Örmälä-Tiznado,

Allander,

Maatallah

et al. 2024

Microbiol Spectr

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Extensively drug-resistant (XDR) Klebsiella pneumoniae inflict a notable burden on healthcare worldwide. Of specific concern are strains producing carbapenem-hydrolyzing enzymes, as the therapeutic options for these strains are still very limited. Specific sequence types of K. pneumoniae have been noted for their epidemic occurrence globally, but the mechanisms behind the success of specific clones remain unclear. Herein, we have characterized 20 high-risk clones (HiRCs) and 10 non-HiRCs of XDR K. pneumoniae , exploring factors connected to the epidemiological success of some clones. Isolates were subjected to core genome multilocus sequence typing analysis to determine the clonal relationships of the isolates and subsequently characterized with regard to features known to be linked to overall bacterial fitness and virulence. The genomes were analyzed in silico for capsule types, O antigens, virulence factors, antimicrobial resistance genes, prophages, and CRISPR-Cas loci. In vitro growth experiments were conducted to retrieve proxies for absolute and relative fitness for 11 HiRC and 9 non-HiRC isolates selected based on the clonal groups they belonged to, and infections in a Galleria mellonella insect model were used to evaluate the virulence of the isolates in vivo . This study did not find evidence that virulence factors, prophages, CRISPR-Cas loci, or fitness measured in vitro alone would contribute to the global epidemiological success of specific clones of carbapenemase-producing XDR K. pneumoniae . However, this study did find the HiRC group to be more virulent than the non-HiRC group when measured in vivo in a model with G. mellonella . This suggests that the virulence and epidemiological success of certain clones of K. pneumoniae cannot be explained by individual traits investigated in this study and thus warrant further experiments in the future. IMPORTANCE Herein, we explored potential explanations for the successfulness of some epidemic or high-risk clones of carbapenemase-producing Klebsiella pneumoniae . We found differences in mortality in a larva model but found no clear genomic differences in known virulence markers. Most of the research on virulence in K. pneumoniae has been focused on hypervirulent strains, but here, we try to understand differences within the group of highly resistant strains. The results from the larva virulence model could be used to design experiments in higher animals. Moreover, the data could provide further support to a differentiated infection control approach against extensively drug-resistant strains, based on their classification as high-risk clones.

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“…At present, some studies on VF and AMR genes encoded by prophages have primarily focused on intact prophages [13], while the effect of questionable and incomplete types on host bacterial virulence and resistance seems to be less well studied. In fact, even degraded questionable or incomplete prophages can provide many benefits for the host to cope with adverse environmental conditions [14].…”

Section: The Classes and Proportions Of Vf And Amr Genes Encoded By P...mentioning

confidence: 99%

Characterization and Diversity of Klebsiella pneumoniae Prophages

F¹,

Chai²,

Li³

et al. 2023

IJMS

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Klebsiella pneumoniae is a common human commensal and opportunistic pathogen. In recent years, the clinical isolation and resistance rates of K. pneumoniae have shown a yearly increase, leading to a special interest in mobile genetic elements. Prophages are a representative class of mobile genetic elements that can carry host-friendly genes, transfer horizontally between strains, and coevolve with the host’s genome. In this study, we identified 15,946 prophages from the genomes of 1437 fully assembled K. pneumoniae deposited in the NCBI database, with 9755 prophages on chromosomes and 6191 prophages on plasmids. We found prophages to be notably diverse and widely disseminated in the K. pneumoniae genomes. The K. pneumoniae prophages encoded multiple putative virulence factors and antibiotic resistance genes. The comparison of strain types with prophage types suggests that the two may be related. The differences in GC content between the same type of prophages and the genomic region in which they were located indicates the alien properties of the prophages. The overall distribution of GC content suggests that prophages integrated on chromosomes and plasmids may have different evolutionary characteristics. These results suggest a high prevalence of prophages in the K. pneumoniae genome and highlight the effect of prophages on strain characterization.

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Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical Klebsiella pneumoniae Strains

Cited by 5 publications

References 45 publications

Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates

Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates

Molecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing Klebsiella pneumoniae

Characterization and Diversity of Klebsiella pneumoniae Prophages

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