Carriage of three plasmids in a single human clinical isolate of Clostridioides difficile

Roseboom, Anna M.; Ducarmon, Quinten R; Hornung, Bastian; Harmanus, Céline; Crobach, Monique J. T.; Kuijper, Ed J.; Vossen, Rolf H. A. M.; Kloet, Susan L.; Smits, Wiep Klaas

doi:10.1016/j.plasmid.2022.102669

Cited by 2 publications

(4 citation statements)

References 37 publications

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“…The non-phage elements B1_2_phi4 and MA_2_phi4 yielded no significant BLAST hit against a phage but matched against C. difficile plasmids. Both matching plasmids belong to classes of C. difficile plasmids with similar organization that are present in diverse C. difficile strains ( Smits et al, 2018 ; Roseboom et al, 2023 ). All these plasmids might therefore likewise be inducible and particle-protected, which implies a different mechanism of HGT than currently assumed.…”

Section: Resultsmentioning

confidence: 99%

“…Prophage regions predicted by PHASTEST (Wishart et al, 2023) are highlighted (intact = green, incomplete = pink). Smits et al, 2018;Roseboom et al, 2023). All these plasmids might therefore likewise be inducible and particle-protected, which implies a different mechanism of HGT than currently assumed.…”

Section: Nucleotide Blast Analyses Assess Phage Prevalence and Noveltymentioning

confidence: 93%

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Novel insights into phage biology of the pathogen Clostridioides difficile based on the active virome

Schüler,

Daniel,

Poehlein

2024

Front. Microbiol.

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The global pathogen Clostridioides difficile is a well-studied organism, and researchers work on unraveling its fundamental virulence mechanisms and biology. Prophages have been demonstrated to influence C. difficile toxin expression and contribute to the distribution of advantageous genes. All these underline the importance of prophages in C. difficile virulence. Although several C. difficile prophages were sequenced and characterized, investigations on the entire active virome of a strain are still missing. Phages were mainly isolated after mitomycin C-induction, which does not resemble a natural stressor for C. difficile. We examined active prophages from different C. difficile strains after cultivation in the absence of mitomycin C by sequencing and characterization of particle-protected DNA. Phage particles were collected after standard cultivation, or after cultivation in the presence of the secondary bile salt deoxycholate (DCA). DCA is a natural stressor for C. difficile and a potential prophage-inducing agent. We also investigated differences in prophage activity between clinical and non-clinical C. difficile strains. Our experiments demonstrated that spontaneous prophage release is common in C. difficile and that DCA presence induces prophages. Fourteen different, active phages were identified by this experimental procedure. We could not identify a definitive connection between clinical background and phage activity. However, one phage exhibited distinctively higher activity upon DCA induction in the clinical strain than in the corresponding non-clinical strain, although the phage is identical in both strains. We recorded that enveloped DNA mapped to genome regions with characteristics of mobile genetic elements other than prophages. This pointed to mechanisms of DNA mobility that are not well-studied in C. difficile so far. We also detected phage-mediated lateral transduction of bacterial DNA, which is the first described case in C. difficile. This study significantly contributes to our knowledge of prophage activity in C. difficile and reveals novel aspects of C. difficile (phage) biology.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Nucleotide Blast Analyses Assess Phage Prevalence and Noveltymentioning

confidence: 93%

Novel insights into phage biology of the pathogen Clostridioides difficile based on the active virome

Schüler,

Daniel,

Poehlein

2024

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…The non-phage elements B1_2_phi4 and MA_2_phi4 yielded no significant BLAST hit against a phage, but matched against C. difficile plasmids. Both matching plasmids belong to classes of C. difficile plasmids with similar organization that are present in diverse C. difficile strains (73,74). All these plasmids might therefore likewise be inducible and particle-protected, which implies a different mechanism of HGT than currently assumed.…”

Section: Resultsmentioning

confidence: 99%

“…A nucleotide BLAST analysis (33) was performed on all active regions in Table 3 (73,74). All these plasmids might therefore likewise be inducible and particle-protected, which implies a different mechanism of HGT than currently assumed.…”

Section: Nucleotide Blast Analyses Assess Phage Prevalence and Noveltymentioning

confidence: 99%

Novel insights into phage biology of the pathogenClostridioides difficilebased on the active virome

Schüler,

Daniel,

Poehlein

2023

Preprint

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The global pathogenClostridioides difficileis a well-studied organism, and researchers work on unravelling its fundamental virulence mechanisms and biology. Prophages have been demonstrated to influenceC. difficiletoxin expression and contribute to the distribution of advantageous genes. All this underlines the importance of prophages inC. difficilevirulence. Although severalC. difficileprophages were sequenced and characterized, investigations on the entire active virome of a strain are still missing. Phages were mainly isolated after mitomycin C-induction, which does not resemble natural stressor forC. difficile.We examined active prophages from differentC. difficilestrains after cultivation in the absence of mitomycin C by sequencing and characterization of particle-protected DNA. Phage particles were collected after standard cultivation, or after cultivation in the presence of the secondary bile salt deoxycholate (DCA). DCA is a natural stressor forC. difficileand a potential prophage-inducing agent. We also investigated differences in prophage activity between clinical and non-clinicalC. difficilestrains. Our experiments demonstrated that spontaneous prophage release is common inC. difficile, and that DCA presence induces prophages. Fourteen different, active phages were identified by this experimental procedure. We could not identify a definitive connection between clinical background and phage activity. However, one phage exhibited distinctively higher activity upon DCA-induction in the clinical strain than in the corresponding non-clinical strain, although the phage is identical in both strains. We recorded that enveloped DNA mapped to genome regions with characteristics of mobile genetic elements other than prophages. This pointed to mechanisms of DNA mobility that are not well-studied inC. difficileso far. We also detected phage-mediated lateral transduction of bacterial DNA, which is the first described case inC. difficile. This study significantly contributes to our knowledge on prophage activity inC. difficileand revealed novel aspects onC. difficile(phage) biology.

show abstract

Carriage of three plasmids in a single human clinical isolate of Clostridioides difficile

Cited by 2 publications

References 37 publications

Novel insights into phage biology of the pathogen Clostridioides difficile based on the active virome

Novel insights into phage biology of the pathogen Clostridioides difficile based on the active virome

Novel insights into phage biology of the pathogenClostridioides difficilebased on the active virome

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