Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages
BackgroundClostridioides difficile is a significant cause of healthcare-associated infections, with rising antimicrobial resistance complicating treatment. This study offers a genomic analysis of C. difficile, focusing on sequence types (STs), global distribution, antibiotic resistance genes, and vi...
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Frontiers Media S.A.
2025-01-01
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| author | Mohammad Sholeh Mohammad Sholeh Masoumeh Beig Masoumeh Beig Ebrahim Kouhsari Mahdi Rohani Mohammad Katouli Farzad Badmasti |
| author_facet | Mohammad Sholeh Mohammad Sholeh Masoumeh Beig Masoumeh Beig Ebrahim Kouhsari Mahdi Rohani Mohammad Katouli Farzad Badmasti |
| author_sort | Mohammad Sholeh |
| collection | DOAJ |
| description | BackgroundClostridioides difficile is a significant cause of healthcare-associated infections, with rising antimicrobial resistance complicating treatment. This study offers a genomic analysis of C. difficile, focusing on sequence types (STs), global distribution, antibiotic resistance genes, and virulence factors in its chromosomal and plasmid DNA.MethodsA total of 19,711 C. difficile genomes were retrieved from GenBank. Prokka was used for genome annotation, and multi-locus sequence typing (MLST) identified STs. Pan-genome analysis with Roary identified core and accessory genes. Antibiotic resistance genes, virulence factors, and toxins were detected using the CARD and VFDB databases, and the ABRicate software. Statistical analyses and visualizations were performed in R.ResultsAmong 366 identified STs, ST1 (1,326 isolates), ST2 (1,141), ST11 (893), and ST42 (763) were predominant. Trends of genome streamlining included reductions in chromosomal length, gene count, protein-coding genes, and pseudogenes. Common antibiotic resistance genes—cdeA (99.46%), cplR (99.63%), and nimB (99.67%)—were nearly ubiquitous. Rare resistance genes like blaCTX-M-2, cfxA3, and blaZ appeared in only 0.005% of genomes. Vancomycin susceptibility-reducing vanG cluster genes were detected at low frequencies. Virulence factors showed variability, with highly prevalent genes such as zmp1 (99.62%), groEL (99.60%), and rpoB/rpoB2 (99.60%). Moderately distributed genes included cwp66 (54.61%) and slpA (79.02%). Toxin genes tcdE (91.26%), tcdC (89.67%), and tcdB (89.06%) were widespread, while binary toxin genes cdtA (26.19%) and cdtB (26.26%) were less common. Toxin gene prevalence, particularly tcdA and tcdB, showed a gradual decline over time, with sharper reductions for cdtA and cdtB. Gene presence patterns (GPP-1) for resistance, virulence, and toxin genes were primarily linked to ST2, ST42, and ST8.ConclusionThis study highlights C. difficile’s adaptability and genetic diversity. The decline in toxin genes reflects fewer toxigenic isolates, but the bacterium’s increasing preserved resistance factors and virulence genes enable its rapid evolution. ST2, ST42, and ST8 dominate globally, emphasizing the need for ongoing monitoring. |
| format | Article |
| id | doaj-art-8b64f9e413024e5092e616196dce831e |
| institution | DOAJ |
| issn | 2235-2988 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-8b64f9e413024e5092e616196dce831e2025-08-20T02:41:07ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-01-011410.3389/fcimb.2024.14932251493225Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineagesMohammad Sholeh0Mohammad Sholeh1Masoumeh Beig2Masoumeh Beig3Ebrahim Kouhsari4Mahdi Rohani5Mohammad Katouli6Farzad Badmasti7Department of Bacteriology, Pasteur Institute of Iran, Tehran, IranStudent Research Committee, Pasteur Institute of Iran, Tehran, IranDepartment of Bacteriology, Pasteur Institute of Iran, Tehran, IranStudent Research Committee, Pasteur Institute of Iran, Tehran, IranLaboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, IranDepartment of Bacteriology, Pasteur Institute of Iran, Tehran, IranGenecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, AustraliaDepartment of Bacteriology, Pasteur Institute of Iran, Tehran, IranBackgroundClostridioides difficile is a significant cause of healthcare-associated infections, with rising antimicrobial resistance complicating treatment. This study offers a genomic analysis of C. difficile, focusing on sequence types (STs), global distribution, antibiotic resistance genes, and virulence factors in its chromosomal and plasmid DNA.MethodsA total of 19,711 C. difficile genomes were retrieved from GenBank. Prokka was used for genome annotation, and multi-locus sequence typing (MLST) identified STs. Pan-genome analysis with Roary identified core and accessory genes. Antibiotic resistance genes, virulence factors, and toxins were detected using the CARD and VFDB databases, and the ABRicate software. Statistical analyses and visualizations were performed in R.ResultsAmong 366 identified STs, ST1 (1,326 isolates), ST2 (1,141), ST11 (893), and ST42 (763) were predominant. Trends of genome streamlining included reductions in chromosomal length, gene count, protein-coding genes, and pseudogenes. Common antibiotic resistance genes—cdeA (99.46%), cplR (99.63%), and nimB (99.67%)—were nearly ubiquitous. Rare resistance genes like blaCTX-M-2, cfxA3, and blaZ appeared in only 0.005% of genomes. Vancomycin susceptibility-reducing vanG cluster genes were detected at low frequencies. Virulence factors showed variability, with highly prevalent genes such as zmp1 (99.62%), groEL (99.60%), and rpoB/rpoB2 (99.60%). Moderately distributed genes included cwp66 (54.61%) and slpA (79.02%). Toxin genes tcdE (91.26%), tcdC (89.67%), and tcdB (89.06%) were widespread, while binary toxin genes cdtA (26.19%) and cdtB (26.26%) were less common. Toxin gene prevalence, particularly tcdA and tcdB, showed a gradual decline over time, with sharper reductions for cdtA and cdtB. Gene presence patterns (GPP-1) for resistance, virulence, and toxin genes were primarily linked to ST2, ST42, and ST8.ConclusionThis study highlights C. difficile’s adaptability and genetic diversity. The decline in toxin genes reflects fewer toxigenic isolates, but the bacterium’s increasing preserved resistance factors and virulence genes enable its rapid evolution. ST2, ST42, and ST8 dominate globally, emphasizing the need for ongoing monitoring.https://www.frontiersin.org/articles/10.3389/fcimb.2024.1493225/fullClostridioides difficilegenomicspan-genome analysissequence typingplasmidchromosome |
| spellingShingle | Mohammad Sholeh Mohammad Sholeh Masoumeh Beig Masoumeh Beig Ebrahim Kouhsari Mahdi Rohani Mohammad Katouli Farzad Badmasti Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages Frontiers in Cellular and Infection Microbiology Clostridioides difficile genomics pan-genome analysis sequence typing plasmid chromosome |
| title | Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages |
| title_full | Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages |
| title_fullStr | Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages |
| title_full_unstemmed | Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages |
| title_short | Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages |
| title_sort | global insights into the genome dynamics of clostridioides difficile associated with antimicrobial resistance virulence and genomic adaptations among clonal lineages |
| topic | Clostridioides difficile genomics pan-genome analysis sequence typing plasmid chromosome |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2024.1493225/full |
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