Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents

Cheleuitte-Nieves, Christopher; Gulvik, Christopher A.; McQuiston, John R.; Humrighouse, Ben W.; Bell, Melissa; Villarma, Aaron; Fischetti, Vincent A.; Westblade, Lars F.; Lipman, Neil S

doi:10.1371/journal.pone.0209231

Cited by 14 publications

(18 citation statements)

References 74 publications

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“…4A). In the COG analysis, “information storage and processing” includes RNA processing and modification, chromosome dynamics, translation, transcription, replication, recombination, and repair 35 . The function of COGs with “information storage and processing” might be associated with intracellular survival 36 .…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence

Liang¹,

Yang²,

Lai³

et al. 2019

Sci Rep

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Bacteria of the genus Elizabethkingia are emerging infectious agents that can cause infection in humans. The number of published whole-genome sequences of Elizabethkingia is rapidly increasing. In this study, we used comparative genomics to investigate the genomes of the six species in the Elizabethkingia genus, namely E. meningoseptica, E. anophelis, E. miricola, E. bruuniana, E. ursingii, and E. occulta. In silico DNA–DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, and clusters of orthologous groups were evaluated. Of the 86 whole-genome sequences available in GenBank, 21 were complete genome sequences and 65 were shotgun sequences. In silico DNA–DNA hybridization clearly delineated the six Elizabethkingia species. Phylogenetic analysis confirmed that E. bruuniana, E. ursingii, and E. occulta were closer to E. miricola than to E. meningoseptica and E. anophelis. A total of 2,609 clusters of orthologous groups were identified among the six type strains of the Elizabethkingia genus. Metabolism-related clusters of orthologous groups accounted for the majority of gene families in KEGG analysis. New genes were identified that substantially increased the total repertoire of the pan genome after the addition of 86 Elizabethkingia genomes, which suggests that Elizabethkingia has shown adaptive evolution to environmental change. This study presents a comparative genomic analysis of Elizabethkingia, and the results of this study provide knowledge that facilitates a better understanding of this microorganism.

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Section: Resultsmentioning

confidence: 99%

Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence

Liang¹,

Yang²,

Lai³

et al. 2019

Sci Rep

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“…2,18,49 Using whole-genome sequencing and comparative genomic analyses, we recently reported on the genetic diversity of 21 C. bovis isolates obtained from various hosts, geographical locations, and time points. 3,4,8,21,36,37,57,61 Genotypic differences between isolates, including the number of associated virulence factors, reflected the host from which they were obtaineds. 8,19 Analyses using the PHAST (Phage Search Tool) and PHASTER (Phage Search Tool Enhanced Release) algorithms failed to identify the presence of intact or true (completeness score greater than 90) or questionable (completeness score, 70 to 90) phage in any of the isolates.…”

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confidence: 99%

“…3,4,8,21,36,37,57,61 Genotypic differences between isolates, including the number of associated virulence factors, reflected the host from which they were obtaineds. 8,19 Analyses using the PHAST (Phage Search Tool) and PHASTER (Phage Search Tool Enhanced Release) algorithms failed to identify the presence of intact or true (completeness score greater than 90) or questionable (completeness score, 70 to 90) phage in any of the isolates. 1,64 Both PHAST and PHASTER are used to identify, annotate, and graphically display prophage sequences within bacterial genomes or plasmids.…”

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confidence: 99%

“…1 Furthermore, although no specific lysin sequences were found in our previous study, these methods did identify several incomplete phages in each isolate (completeness score of less than 70). 8 For these reasons, additional in vitro studies are necessary to definitively conclude that C. bovis lacks phages.…”

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confidence: 99%

“…22,49,54 In total, 8 lysins were screened against C. bovis, including PlyCf, which is a lysin derived from a prophage from the closely related Corynebacterium falsenii. 8 We hypothesized that lysins originating from non-C. bovis phage might exhibit nonspecific lytic activity against C. bovis. For example, the lysin from corynephage BFK20 obtained from Brevibacterium flavum has shown effective lytic activity against other bacterial species, including Corynebacterium glutamicum and Brevibacterium lactofermentum.…”

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confidence: 99%

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Searching for a Bacteriophage Lysin to Treat Corynebacterium bovis in Immunocompromised Mice

et al. 2020

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Corynebacterium bovis is the causative agent of Corynebacterium-associated hyperkeratosis in immunocompromised mice. The resulting skin pathology can be profound and can be associated with severe wasting, making the animals unsuitable for research. Although the administration of antibiotics is effective in resolving clinical symptoms, antibiotics do not eradicate the offending bacterium. Furthermore, antibiotic use may be contraindicated as it can affect tumor growth and is associated with Clostridioides difficile enterotoxemia in highly immunocompromised murine strains. Lysins, which are lytic enzymes obtained from bacteriophages, are novel antimicrobial agents for treating bacterial diseases. The advantage of lysins are its target specificity, with minimal off-target complications that could affect the host or the biology of the engrafted tumor. The aim of this study was to identify lysins active against C. bovis. Chemical activation of latent prophages by using mitomycin C in 3 C. bovis isolates did not cause bacteriophage induction as determined through plaque assays and transmission electron microscopy. As an alternative approach, 8 lysins associated with other bacterial species, including those from the closely related species C. falsenii, were tested for their lytic action against C. bovis but were unsuccessful. These findings were congruentwith the previously reported genomic analysis of 21 C. bovis isolates, which failed to reveal bacteriophage sequences by usingthe PHAST and PHASTER web server tools. From these results, we suggest C. bovis is among those rare bacterial species devoid of lysogenic bacteriophages, thus making the identification of C. bovis-specific lysins more challenging. However, C. bovis may be a useful model organism for studying the effects of antiphage systems.

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Novel configurations of type I-E CRISPR-Cas system in Corynebacterium striatum clinical isolates

Ramos

Baio²,

Veras

et al. 2022

Braz J Microbiol

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Clustered regularly interspaced short palindromic repeats (CRISPR) are a prokaryotic adaptive immune system that, through Cas proteins, promote the degradation of foreign nucleic acids such as phages and plasmids. We analyzed 10 genomes of Corynebacterium striatum clinical isolates from a public hospital in Rio de Janeiro, Brazil, the most emergent multidrug-resistant Corynebacterium species. All isolates were submitted to antimicrobial susceptibility testing. The occurrence and diversity of the CRISPR system were investigated by bioinformatics tools. Our analysis revealed that the isolates exhibited type I-E gene arrangements, and 3 more multidrug-resistant isolates, alternative type I-E gene arrangements, showing a divergent gene arrangement within the cas operon. Phylogenetic analysis of the cas1 gene of this type I-E CRISPR-Cas system alternative arrangement, termed here type I-E’, showed a cluster in a distinct clade of the type I-E CRISPR-Cas system. The systems’ guanine-cytosine (GC) content is lower than the genomic DNA’s GC content, and mobile genetic elements were found in some isolates near the CRISPR-Cas system. Most CRISPR spacers are unknown indicating that there is a reservoir of unexplored corynebacteriophages and plasmids. Some spacers showed perfect homologies with phage and plasmid sequences. Intact phage regions were found in 3 of our isolates, ranging from 9.1 to 43.8 kb, with regions showing similarity to Rhodococcus and Corynebacterium phages. Our results may contribute to research about the CRISPR-Cas system diversity in C. striatum, where there are no published data to date.

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Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents

Cited by 14 publications

References 74 publications

Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence

Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence

Searching for a Bacteriophage Lysin to Treat Corynebacterium bovis in Immunocompromised Mice

Novel configurations of type I-E CRISPR-Cas system in Corynebacterium striatum clinical isolates

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