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Janezic S, Garneau JR, Monot M. Comparative Genomics of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:199-218. [PMID: 38175477 DOI: 10.1007/978-3-031-42108-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile, a Gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of nosocomial diarrhoea in hospitals. The availability of large numbers of genome sequences, mainly due to the use of next-generation sequencing methods, has undoubtedly shown their immense advantages in the determination of C. difficile population structure. The implementation of fine-scale comparative genomic approaches has paved the way for global transmission and recurrence studies, as well as more targeted studies, such as the PaLoc or CRISPR/Cas systems. In this chapter, we provide an overview of recent and significant findings on C. difficile using comparative genomic studies with implications for epidemiology, infection control and understanding of the evolution of C. difficile.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia.
- Faculty of Medicine, University of Maribor, Maribor, Slovenia.
| | - Julian R Garneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Paris, France
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Couturier J, Davies K, Barbut F. Ribotypes and New Virulent Strains Across Europe. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:151-168. [PMID: 38175475 DOI: 10.1007/978-3-031-42108-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides (formerly Clostridium) difficile is a major bacterial cause of post-antibiotic diarrhoea. The epidemiology of C. difficile infections (CDIs) has dramatically changed since the early 2000s, with an increasing incidence and severity across Europe. This trend is partly due to the emergence and rapid worldwide spread of the hypervirulent and epidemic PCR ribotype 027. Profiles of patients with CDI have also evolved, with description of community-acquired (CA) infections in patients with no traditional risk factors for CDI. However, epidemiological studies indicated that some European countries have successfully controlled the dissemination of the 027 clone whereas other countries reported the emergence of other virulent or unusual strains. The aims of this review are to summarize the current European CDI epidemiology and to describe the new virulent C. difficile strains circulating in Europe, as well as other potential emerging strains described elsewhere. Standardized typing methods and surveillance programmes are mandatory for a better understanding and monitoring of CDI in Europe.
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Affiliation(s)
- Jeanne Couturier
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France.
- Université Paris Cité, UMR INSERM 1139, Paris, France.
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Frédéric Barbut
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France
- Université Paris Cité, UMR INSERM 1139, Paris, France
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
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Dicks LMT. Biofilm Formation of Clostridioides difficile, Toxin Production and Alternatives to Conventional Antibiotics in the Treatment of CDI. Microorganisms 2023; 11:2161. [PMID: 37764005 PMCID: PMC10534356 DOI: 10.3390/microorganisms11092161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Clostridioides difficile is considered a nosocomial pathogen that flares up in patients exposed to antibiotic treatment. However, four out of ten patients diagnosed with C. difficile infection (CDI) acquired the infection from non-hospitalized individuals, many of whom have not been treated with antibiotics. Treatment of recurrent CDI (rCDI) with antibiotics, especially vancomycin (VAN) and metronidazole (MNZ), increases the risk of experiencing a relapse by as much as 70%. Fidaxomicin, on the other hand, proved more effective than VAN and MNZ by preventing the initial transcription of RNA toxin genes. Alternative forms of treatment include quorum quenching (QQ) that blocks toxin synthesis, binding of small anion molecules such as tolevamer to toxins, monoclonal antibodies, such as bezlotoxumab and actoxumab, bacteriophage therapy, probiotics, and fecal microbial transplants (FMTs). This review summarizes factors that affect the colonization of C. difficile and the pathogenicity of toxins TcdA and TcdB. The different approaches experimented with in the destruction of C. difficile and treatment of CDI are evaluated.
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Affiliation(s)
- Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
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Matsumoto A, Yamagishi Y, Miyamoto K, Higashi S, Oka K, Takahashi M, Mikamo H. Comparison of clinical severity, genotype and toxin gene expression of binary toxin-producing Clostridioides difficile clinical isolates in Japan. Access Microbiol 2022; 4:acmi000362. [PMID: 36415735 PMCID: PMC9675170 DOI: 10.1099/acmi.0.000362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/14/2022] [Indexed: 11/07/2023] Open
Abstract
The emerging Clostridioides difficile strain BI/NAP1/027 has been reported to be associated with more severe clinical symptoms and higher mortality rates, thought in part due to production of a novel binary toxin alongside conventional A and B toxins. However, recent studies suggest that this may not always be the case. Therefore, the purpose of this report was to investigate the correlation between clinical severity and microbiological characteristics of CDT-producing C. difficile isolates in Japan. Eight Japanese isolates of CDT producing C. difficile were investigated using genotyping, cytotoxic activity assays and toxin gene expression. Correlation with clinical severity was performed retrospectively using the patient record. Three of eight patients were assessed as having severe C. difficile infection (CDI). PCR ribotyping resolved six ribotypes including ribotype 027. No specific genes were identified determining severe compared with non-severe cases. Positive correlation of expression levels of tcdA, tcdB and cdtB were observed although these expression levels were not correlated with cytotoxicity. CDI severity index neither correlated with toxin gene expression level nor cytotoxicity. These data indicate that the possession of the CDT gene and toxin gene expression levels may not relate to C. difficile cytotoxicity or clinical severity.
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Affiliation(s)
- Asami Matsumoto
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- Department of Clinical Infectious Diseases, Kochi Medical School, 185-1, Kohasu, Oko-cho, Nankoku City, Kochi 783-8505, Japan
| | - Kentaro Miyamoto
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Seiya Higashi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Kentaro Oka
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Motomichi Takahashi
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, 1-1, Yazakokarimata, Nagakute City, Aichi, 480-1195, Japan
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Tsai BY, Chien CC, Huang SH, Zheng JY, Hsu CY, Tsai YS, Hung YP, Ko WC, Tsai PJ. The emergence of Clostridioides difficile PCR ribotype 127 at a hospital in northeastern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:896-909. [PMID: 35042668 DOI: 10.1016/j.jmii.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/27/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Several studies have highlighted the incidence of Clostridioides difficile infections (CDIs) in Taiwan and certain ribotypes have been related to severe clinical diseases. A study was conducted to investigate the polymerase chain reaction (PCR) ribotypes and genetic relatedness of clinical C. difficile strains collected from January 2009 to December 2015 at a hospital in northeastern Taiwan. MATERIAL AND METHODS A modified two-step typing algorithm for C. difficile was used by combining a modified 8-plex and 3'-truncated tcdA screening PCR. In addition, MLVA typing was adopted for investigation of bacterial clonality and transmission. RESULTS Among a total of 86 strains, 24 (28%) were nontoxigenic and 62 (72%) had both tcdA and tcdB (A + B+). No tcdA-negative and tcdB-positive (A-B+) strains were identified. Binary toxin (CDT)-producing (cdtA+/cdtB+) strains were started to be identified in 2013. The 21 (34%) A+B+ clinical strains with binary toxin and tcdC deletion were identified as RT127 strains, which contained both RT078-lineage markers and fluoroquinolone (FQ)-resistant mutations (Thr82Ile in gyrA). Multiple loci variable-number tandem repeat analysis (MLVA) for phylogenetic relatedness of RT127 strains indicated that 20 of 21 strains belonged to a clonal complex that was identical to a clinical strain collected from southern Taiwan in 2011, suggestive of a clonal expansion in Taiwan. CONCLUSION A two-step typing method could rapidly confirm species identification and define the toxin gene profile of C. difficile isolates. The clonal expansion of RT127 strains in Taiwan indicates monitoring and surveillance of toxigenic C. difficile isolates from human, animal, and environment are critical to develop One Health prevention strategies.
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Affiliation(s)
- Bo-Yang Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Chun-Chih Chien
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Kaohsiung, Kaohsiung, Taiwan.
| | - Shu-Huan Huang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Kee-Lung, Keelung, Taiwan.
| | - Jun-Yuan Zheng
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Kee-Lung, Kee-Lung, Taiwan.
| | - Chih-Yu Hsu
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
| | - Yau-Sheng Tsai
- Institute of Clinical Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Yuan-Pin Hung
- Departments of Internal Medicine, Tainan Hospital, Ministry of Health & Welfare, Tainan, Taiwan; Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Pei-Jane Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan; Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Gu W, Li W, Jia S, Zhou Y, Yin J, Wu Y, Fu X. Antibiotic resistance and genomic features of Clostridioides difficile in southwest China. PeerJ 2022; 10:e14016. [PMID: 36093337 PMCID: PMC9454788 DOI: 10.7717/peerj.14016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/15/2022] [Indexed: 01/19/2023] Open
Abstract
Background Clostridioides difficile infection (CDI) caused by toxigenic strains leads to antibiotic-related diarrhea, colitis, or even fatal pseudomembranous enteritis. Previously, we conducted a cross-sectional study on prevalence of CDI in southwest China. However, the antibiotics resistance and characteristics of genomes of these isolates are still unknown. Methods Antibiotic susceptibility testing with E-test strips and whole genome sequence analysis were used to characterize the features of these C. difficile isolates. Results Forty-nine strains of C. difficile were used in this study. Five isolates were non-toxigenic and the rest carried toxigenic genes. We have previously reported that ST35/RT046, ST3/RT001 and ST3/RT009 were the mostly distributed genotypes of strains in the children group. In this study, all the C. difficile isolates were sensitive to metronidazole, meropenem, amoxicillin/clavulanic acid and vancomycin. Most of the strains were resistant to erythromycin, gentamicin and clindamycin. The annotated resistant genes, such as macB, vanRA, vanRG, vanRM, arlR, and efrB were mostly identified related to macrolide, glycopeptide, and fluoroquinolone resistance. Interestingly, 77.55% of the strains were considered as multi-drug resistant (MDR). Phylogenetic analysis based on core genome of bacteria revealed all the strains were divided into clade 1 and clade 4. The characteristics of genome diversity for clade 1 could be found. None of the isolates showed 18-bp deletion of tcdC as RT027 strain as described before, and polymorphism of tcdB showed a high degree of conservation than tcdA gene. Conclusions Most of the C. difficile isolates in this study were resistant to macrolide and aminoglycoside antibiotics. Moreover, the MDR strains were commonly found. All the isolates belonged to clade 1 and clade 4 according to phylogenetic analysis of bacterial genome, and highly genomic diversity of clade 1 was identified for these strains.
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Affiliation(s)
- Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Senquan Jia
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Yongming Zhou
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Jianwen Yin
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
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Karpiński P, Wultańska D, Piotrowski M, Brajerova M, Mikucka A, Pituch H, Krutova M. Motility and the genotype diversity of the flagellin genes fliC and fliD among Clostridioides difficile ribotypes. Anaerobe 2022; 73:102476. [PMID: 34780914 DOI: 10.1016/j.anaerobe.2021.102476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVE The motility and genotype of the flagellin fliC and fliD genes were investigated in 82 Clostridioides difficile isolates belonging to the ribotypes (RTs): 027 (n = 41), 176 (n = 17), 023 (n = 8), 017 (n = 6) and 046 (n = 10). The reference C. difficile strains 630 and M120 were included as controls for the motility assay. METHODS A Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) was used to exclude the genetic relatedness of C. difficile isolates belonging to the same RT. The variability of the fliC and fliD genes was determined by PCR-restriction fragment length polymorphism (RFLP) analysis and Sanger sequencing. The motility assay was carried out with 0.175% BHI agar tubes and BHI solid media plates with 0.4% agar. RESULTS The highest motility was observed in C. difficile RT023 isolates (p < 0.01), followed by RTs 027 and 176. C. difficile isolates of RTs 017 and 046 were less motile than RTs 027, 176 and 023 (p < 0.01). The fliC and fliD genes were present in all clinical isolates irrespective of the motility results. In the fliC gene analysis, four different RFLP groups were identified (I, II, VII, X). The fliC group VII was identified in two RTs (027 and 176), whereas the remaining three groups (I, II and X) belonged to a single RT 046, 017 and 023, respectively. The fliD gene analysis identified four new RFLP groups (a, b, c and d). CONCLUSIONS C. difficile RT023 is highly motile and its motility is comparable to the hypervirulent RT027 and its genetic relative RT176.
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Affiliation(s)
- Paweł Karpiński
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Dorota Wultańska
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Michał Piotrowski
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; The member of European Society of Clinical Microbiology and Infectious Disease (ESCMID) Study group for Clostridioides difficile (ESGCD), Poland
| | - Marie Brajerova
- Department of Medical Microbiology, Charles University 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic; The member of European Society of Clinical Microbiology and Infectious Disease (ESCMID) Study group for Clostridioides difficile (ESGCD), Poland
| | - Agnieszka Mikucka
- Dr Antoni Jurasz University Hospital No. 1 Bydgoszcz, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Poland
| | - Hanna Pituch
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; The member of European Society of Clinical Microbiology and Infectious Disease (ESCMID) Study group for Clostridioides difficile (ESGCD), Poland.
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic; The member of European Society of Clinical Microbiology and Infectious Disease (ESCMID) Study group for Clostridioides difficile (ESGCD), Poland
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Richards SJG, Udayasiri DK, Jones IT, Hastie IA, Chandra R, McCormick JJ, Chittleborough TJ, Read DJ, Hayes IP. Delayed ileostomy closure increases the odds of Clostridium difficile infection. Colorectal Dis 2021; 23:3213-3219. [PMID: 34351046 DOI: 10.1111/codi.15858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/30/2021] [Accepted: 07/31/2021] [Indexed: 01/06/2023]
Abstract
AIM A diverting ileostomy is typically performed to divert intestinal contents in high-risk colorectal anastomoses. Ileostomy closure is associated with high rates of postoperative Clostridium difficile infection (CDI). Risk factors for the development of CDI are unclear; however, a correlation has been observed with delayed closure. This study aimed to assess the odds of developing CDI in patients who had a delay to reversal of ileostomy, compared to those who had no delay. METHODS A retrospective cohort study was conducted of patients undergoing reversal of ileostomy between 2010 and 2019 at a single tertiary centre. A delay to reversal of ileostomy was defined if the procedure was performed at >365 days following the index procedure. CDI was defined as the presence of Clostridium difficile toxin associated with diarrhoea. Univariable logistic regression analysis was performed to estimate odds of CDI for each covariable, comparing patients who had a delay to reversal of ileostomy with those who did not. Multivariable logistic regression analysis was used to adjust for the potential confounding effects of covariables. RESULTS Of 195 patients, 11 (5.6%), developed postoperative CDI. Multivariable analysis showed that delay to reversal of ileostomy was associated with a nearly 7-fold increase in odds of CDI (OR = 6.95, CI: 1.06-81.6; p-value = 0.03). CONCLUSION A delay to reversal of ileostomy of >365 days was associated with a higher incidence of CDI postoperatively. Careful consideration should be given to the timing of reversal and appropriate preoperative counselling of patients.
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Affiliation(s)
- Simon J G Richards
- Colorectal Surgical Unit, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Dilshan K Udayasiri
- Colorectal Surgical Unit, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian T Jones
- Colorectal Surgical Unit, Department of Surgery, The Royal Melbourne Hospital and University of Melbourne, Melbourne, Victoria, Australia
| | - Ian A Hastie
- Colorectal Surgical Unit, Department of Surgery, The Royal Melbourne Hospital and University of Melbourne, Melbourne, Victoria, Australia
| | - Raaj Chandra
- Colorectal Surgical Unit, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Colorectal Surgical Unit, Department of Surgery, Box Hill Hospital Melbourne, Monash University, Melbourne, Victoria, Australia
| | - Jacob J McCormick
- Colorectal Surgical Unit, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Colorectal Surgical Unit, Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Timothy J Chittleborough
- Colorectal Surgical Unit, Department of Surgery, The Royal Melbourne Hospital and University of Melbourne, Melbourne, Victoria, Australia
| | - David J Read
- Colorectal Surgical Unit, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian P Hayes
- Colorectal Surgical Unit, Department of Surgery, The Royal Melbourne Hospital and University of Melbourne, Melbourne, Victoria, Australia
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Harrison MA, Kaur H, Wren BW, Dawson LF. Production of p-cresol by Decarboxylation of p-HPA by All Five Lineages of Clostridioides difficile Provides a Growth Advantage. Front Cell Infect Microbiol 2021; 11:757599. [PMID: 34778108 PMCID: PMC8588808 DOI: 10.3389/fcimb.2021.757599] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and is capable of causing severe symptoms, such as pseudomembranous colitis and toxic megacolon. An unusual feature of C. difficile is the distinctive production of high levels of the antimicrobial compound para-cresol. p-Cresol production provides C. difficile with a competitive colonization advantage over gut commensal species, in particular, Gram-negative species. p-Cresol is produced by the conversion of para-hydroxyphenylacetic acid (p-HPA) via the actions of HpdBCA decarboxylase coded by the hpdBCA operon. Host cells and certain bacterial species produce p-HPA; however, the effects of p-HPA on the viability of C. difficile and other gut microbiota are unknown. Here we show that representative strains from all five C. difficile clades are able to produce p-cresol by two distinct mechanisms: (i) via fermentation of p-tyrosine and (ii) via uptake and turnover of exogenous p-HPA. We observed strain-specific differences in p-cresol production, resulting from differential efficiency of p-tyrosine fermentation; representatives of clade 3 (CD305) and clade 5 (M120) produced the highest levels of p-cresol via tyrosine metabolism, whereas the toxin A-/B+ isolate from clade 4 (M68) produced the lowest level of p-cresol. All five lineages share at least 97.3% homology across the hpdBCA operon, responsible for decarboxylation of p-HPA to p-cresol, suggesting that the limiting step in p-cresol production may result from tyrosine to p-HPA conversion. We identified that elevated intracellular p-HPA, modulated indirectly via CodY, controls p-cresol production via inducing the expression of HpdBCA decarboxylase ubiquitously in C. difficile populations. Efficient turnover of p-HPA is advantageous to C. difficile as p-HPA has a deleterious effect on the growth of C. difficile and other representative Gram-negative gut bacteria, transduced potentially by the disruption of membrane permeability and release of intracellular phosphate. This study provides insights into the importance of HpdBCA decarboxylase in C. difficile pathogenesis, both in terms of p-cresol production and detoxification of p-HPA, highlighting its importance to cell survival and as a highly specific therapeutic target for the inhibition of p-cresol production across C. difficile species.
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Affiliation(s)
- Mark A. Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harparkash Kaur
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lisa F. Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Effect of Restriction of Fluoroquinolone Antibiotics on Clostridioides difficile Infections in the University Hospital Hradec Králové. Antibiotics (Basel) 2021; 10:antibiotics10050519. [PMID: 34063201 PMCID: PMC8147471 DOI: 10.3390/antibiotics10050519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/19/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022] Open
Abstract
Clostridioides difficile is the most common pathogen responsible for hospital-acquired diarrhea. This complication of antibiotic treatment mainly endangers the health of elder patients. Preventing the development of C. difficile infections (CDI) is still a challenge that needs to be addressed. In our study, the results of 872 C. difficile positive stool samples were used to describe the epidemiological situation affected by a change in the prescription of fluoroquinolone antibiotics. In a total, 93 of strains were typed by polymerase chain reaction (PCR) and capillary gel electrophoresis. Between years 2014 and 2018 the decline in the fluoroquinolones consumption was 69.3 defined daily dose (DDD) per 1000 patient-days (from 103.3 to 34.0), in same period CDI incidence declined by 1.3 cases per 10,000 patient-bed days (from 5.6 to 4.3). Results of epidemiologic and statistical analysis shows that decline in fluoroquinolones consumption has significant influence on CDI incidence and prevalence of hypervirulent strains. In the University Hospital Hradec Králové properly managed antibiotic stewardship policy has reduced CDI incidence by 23.2% and lowered rate of hypervirulent ribotypes 001 and 176.
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Badilla-Lobo A, Rodríguez C. Microbiological features, epidemiology, and clinical presentation of Clostridioidesdifficile strains from MLST Clade 2: A narrative review. Anaerobe 2021; 69:102355. [PMID: 33711422 DOI: 10.1016/j.anaerobe.2021.102355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile is an emerging One Health pathogen and a common etiologic agent of diarrhea, both in healthcare settings and the community. This bacterial species is highly diverse, and its global population has been classified in eight clades by multilocus sequence typing (MLST). The C. difficile MLST Clade 2 includes the NAP1/RT027/ST01 strain, which is highly recognized due to its epidemicity and association with severe disease presentation and mortality. By contrast, the remaining 83 sequence types (STs) that compose this clade have received much less attention. In response to this shortcoming, we reviewed articles published in English between 1999 and 2020 and collected information for 27 Clade 2 STs, with an emphasis on STs 01, 67, 41 and 188/231/365. Our analysis provides evidence of large phenotypic differences that preclude support of the rather widespread notion that ST01 and Clade 2 strains are "hypervirulent". Moreover, it revealed a profound lack of (meta)data for nearly 70% of the Clade 2 STs that have been identified in surveillance efforts. Targeted studies aiming to relate wet-lab and bioinformatics results to patient and clinical parameters should be performed to gain a more in-depth insight into the biology of this intriguing group of C. difficile isolates.
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Affiliation(s)
- Adriana Badilla-Lobo
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, and Master's Program in Microbiology, Parasitology, Clinical Chemistry and Immunology, Universidad de Costa Rica, Costa Rica
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, and Master's Program in Microbiology, Parasitology, Clinical Chemistry and Immunology, Universidad de Costa Rica, Costa Rica.
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Dawson LF, Peltier J, Hall CL, Harrison MA, Derakhshan M, Shaw HA, Fairweather NF, Wren BW. Extracellular DNA, cell surface proteins and c-di-GMP promote biofilm formation in Clostridioides difficile. Sci Rep 2021; 11:3244. [PMID: 33547340 PMCID: PMC7865049 DOI: 10.1038/s41598-020-78437-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Clostridioides difficile is the leading cause of nosocomial antibiotic-associated diarrhoea worldwide, yet there is little insight into intestinal tract colonisation and relapse. In many bacterial species, the secondary messenger cyclic-di-GMP mediates switching between planktonic phase, sessile growth and biofilm formation. We demonstrate that c-di-GMP promotes early biofilm formation in C. difficile and that four cell surface proteins contribute to biofilm formation, including two c-di-GMP regulated; CD2831 and CD3246, and two c-di-GMP-independent; CD3392 and CD0183. We demonstrate that C. difficile biofilms are composed of extracellular DNA (eDNA), cell surface and intracellular proteins, which form a protective matrix around C. difficile vegetative cells and spores, as shown by a protective effect against the antibiotic vancomycin. We demonstrate a positive correlation between biofilm biomass, sporulation frequency and eDNA abundance in all five C. difficile lineages. Strains 630 (RT012), CD305 (RT023) and M120 (RT078) contain significantly more eDNA in their biofilm matrix than strains R20291 (RT027) and M68 (RT017). DNase has a profound effect on biofilm integrity, resulting in complete disassembly of the biofilm matrix, inhibition of biofilm formation and reduced spore germination. The addition of exogenous DNase could be exploited in treatment of C. difficile infection and relapse, to improve antibiotic efficacy.
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Affiliation(s)
- Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Johann Peltier
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Catherine L Hall
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark A Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Maria Derakhshan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Helen A Shaw
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- National Institute for Biological Standards and Control, Potters Bar, UK
| | - Neil F Fairweather
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
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Marujo V, Arvand M. The largely unnoticed spread of Clostridioides difficile PCR ribotype 027 in Germany after 2010. Infect Prev Pract 2020; 2:100102. [PMID: 34368730 PMCID: PMC8336157 DOI: 10.1016/j.infpip.2020.100102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 02/04/2023] Open
Abstract
In recent decades, incidence and severity of Clostridioides difficile infection (CDI) has increased dramatically, coinciding with the emergence of hypervirulent strains such as PCR ribotype 027 (RT027). Data on prevalence of distinct C. difficile strains in random CDI cases in Germany are scarce. The aim of this review was to obtain an overview of prevalence and geographical distribution of RT027 among clinical C. difficile isolates from random cases in non-outbreak settings in hospitals in Germany. For this purpose, we performed a literature review on reported cases of C. difficile RT027 in Germany between 2007 and 2019 in three databases (PubMed, Embase and LIVIVO) and conference proceedings. Studies with selection bias for RT027 (e.g. clinical severity, outbreak reports) were excluded. A total of 304 records were screened, from which 21 were included in this analysis. The nationwide prevalence of RT027 in Germany was <1% prior to 2010 but increased continuously thereafter, reaching 21.7% in 2013. The regional prevalence varied markedly between federal states, higher prevalence was reported from North Rhine-Westphalia (37.4%) and Saxony (31.8%) in 2013-2015. However, data on C. difficile RT027 were not available from almost half of the federal states and were scarce at the national level. Our data suggest a remarkable spread of RT027 in Germany during the past decade, which has remained rather unnoticed so far. A national program for molecular surveillance of C. difficile is required to monitor the changing epidemiology of CDI and to adjust the prevention and control measures.
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Affiliation(s)
- Vanda Marujo
- Robert Koch Institute, Department of Infectious Diseases, Unit for Hospital Hygiene, Infection Prevention and Control, Berlin, Germany
| | - Mardjan Arvand
- Robert Koch Institute, Department of Infectious Diseases, Unit for Hospital Hygiene, Infection Prevention and Control, Berlin, Germany
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14
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Cheknis A, Devaris D, Chesnel L, Dale SE, Nary J, Sambol SP, Citron DM, Goering RV, Johnson S. Characterization of Clostridioides difficile isolates recovered from two Phase 3 surotomycin treatment trials by restriction endonuclease analysis, PCR ribotyping and antimicrobial susceptibilities. J Antimicrob Chemother 2020; 75:3120-3125. [PMID: 32747931 DOI: 10.1093/jac/dkaa297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To investigate the molecular epidemiology and antimicrobial susceptibility of Clostridioides difficile isolates from patients with C. difficile infection (CDI) from two Phase 3 clinical trials of surotomycin. METHODS In both trials [Protocol MK-4261-005 (NCT01597505) conducted across Europe, North America and Israel; and Protocol MK-4261-006 (NCT01598311) conducted across North America, Asia-Pacific and South America], patients with CDI were randomized (1:1) to receive oral surotomycin (250 mg twice daily) or oral vancomycin (125 mg four times per day) for 10 days. Stool samples were collected at baseline and C. difficile isolates were characterized by restriction endonuclease analysis (REA) and PCR ribotyping. Susceptibility testing was performed by agar dilution, according to CLSI recommendations. RESULTS In total, 1147 patients were included in the microbiological modified ITT population. Of 992 recovered isolates, 922 (92.9%) were typed. There was a high association between REA groups and their corresponding predominant PCR ribotype (RT) for BI, DH, G and CF strains. REA group A showed more diverse PCR RTs. Overall, the most common strain was BI/RT027 (20.3%) followed by Y/RT014/020 (15.0%) and DH/RT106 (7.2%). The BI/RT027 strain was particularly prevalent in Europe (29.9%) and Canada (23.6%), with lower prevalence in the USA (16.8%) and Australia/New Zealand (3.4%). Resistance was most prevalent in the BI/RT027 strain, particularly to metronidazole, vancomycin and moxifloxacin. CONCLUSIONS A wide variation in C. difficile strains, both within and across different geographical regions, was documented by both REA and ribotyping, which showed overall good correlation.
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Affiliation(s)
| | | | | | | | - Julia Nary
- ACM Global Laboratories, Rochester, NY, USA
| | | | | | | | - Stuart Johnson
- Edward Hines, Jr. VA Hospital, Hines, IL, USA.,Loyola University Medical Center, Maywood, IL, USA
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An outbreak of Clostridioides difficile infections due to a 027-like PCR ribotype 181 in a rehabilitation centre: Epidemiological and microbiological characteristics. Anaerobe 2020; 65:102252. [PMID: 32781108 DOI: 10.1016/j.anaerobe.2020.102252] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
Clostridioides difficile is one of the most important healthcare-associated pathogens. Recently, several new 027-like types have been found that all belong to the multilocus sequence typing (MLST) Clade 2. We report a rapidly spreading outbreak of C. difficile infections (CDI) due to a newly identified PCR ribotype (RT) 181 in a Rehabilitation Centre (RC). Genomic analysis revealed the outbreak strain, not previously identified in Greece, belonged to clade 2, sequence type (ST) 1 and had a 18bp deletion in tcdC at position 311 together with a single nucleotide deletion at position 117, similarly to RT 027. The presence of a clonal outbreak was confirmed by whole genome sequencing, yet the source of this ribotype remained unclear. The emergence and rapid spread of new C. difficile ribotypes highlights the need for ongoing C. difficile surveillance and better understanding of overall Clade 2 phylogeny.
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Wu Y, Wang L, Bian Y, Zhou Z, Wang Y, Cao L, Gu S. Production and characteristics of high quality vinegar from Cornus officinalis produced by a two-stage fermentative process. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2020. [DOI: 10.1007/s11694-020-00473-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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17
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Johnson S, Citron DM, Gerding DN, Wilcox MH, Goldstein EJC, Sambol SP, Best EL, Eves K, Jansen E, Dorr MB. Efficacy of bezlotoxumab in trial participants infected with Clostridioides difficile strain BI associated with poor outcomes. Clin Infect Dis 2020; 73:e2616-e2624. [PMID: 32735653 DOI: 10.1093/cid/ciaa1035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Bezlotoxumab reduced rates of recurrent Clostridioides difficile infection (rCDI) versus placebo in MODIFY I/II trial participants receiving antibacterial drug treatment for CDI. A secondary objective of MODIFY I/II was to assess bezlotoxumab's efficacy against C. difficile strains associated with increased rates of morbidity and mortality. METHODS In this post-hoc analysis of pooled MODIFY I/II data, efficacy endpoints were assessed in participants infected with restriction endonuclease analysis (REA) BI and non-BI strains of C. difficile at study entry. Treatment outcomes were compared between participants receiving bezlotoxumab (alone or with actoxumab: B, B+A) and those receiving no bezlotoxumab (placebo or actoxumab: P, A). RESULTS From 2559 randomized participants, C. difficile was isolated from 1588 (67.2%) baseline stool samples. Participants with BI strains (n=328) were older and had more risk factors for rCDI than non-BI strain participants (n=1260). There were no differences in initial clinical cure rate between BI and non-BI strains in either group. The rCDI rates for BI strains treated with bezlotoxumab was lower than for the no bezlotoxumab group (B, B+A vs P, A: 23.6% vs 43.9%) and was also lower for the non-BI strains (B, B+A vs P, A: 21.4% vs 36.1%). Rates of 30-day CDI-associated re-hospitalization were greater with BI versus non-BI strains in both groups. CONCLUSIONS Infection with BI strains of C. difficile predicted poor outcomes in the MODIFY I/II trials. Bezlotoxumab (B, B+A) treatment was effective both in BI and non-BI subpopulations.
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Affiliation(s)
- Stuart Johnson
- Edward Hines, Jr. VA Hospital, Hines, IL, USA.,Loyola University, Maywood, IL, USA
| | | | | | - Mark H Wilcox
- Leeds Teaching Hospital, Leeds, UK.,University of Leeds, Leeds, UK
| | | | - Susan P Sambol
- Edward Hines, Jr. VA Hospital, Hines, IL, USA.,Loyola University, Maywood, IL, USA
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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Induction of a Specific Humoral Immune Response by Nasal Delivery of Bcla2 ctd of Clostridioides difficile. Int J Mol Sci 2020; 21:ijms21041277. [PMID: 32074955 PMCID: PMC7072882 DOI: 10.3390/ijms21041277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/21/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile, formerly known as Clostridium difficile, is a spore-forming bacterium considered as the most common cause of nosocomial infections in developed countries. The spore of C. difficile is involved in the transmission of the pathogen and in its first interaction with the host; therefore, a therapeutic approach able to control C. difficile spores would improve the clearance of the infection. The C-terminal (CTD) end of BclA2, a spore surface protein of C. difficile responsible of the interaction with the host intestinal cells, was selected as a putative mucosal antigen. The BclA2 fragment, BclA2CTD, was purified and used to nasally immunize mice both as a free protein and after adsorption to the spore of Bacillus subtilis, a well-established mucosal delivery vehicle. While the adsorption to spores increased the in vitro stability of BclA2CTD, in vivo both free and spore-adsorbed BclA2CTD were able to induce a similar, specific humoral immune response in a murine model. Although in the experimental conditions utilized the immune response was not protective, the induction of specific IgG indicates that free or spore-bound BclA2CTD could act as a putative mucosal antigen targeting C. difficile spores.
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Archambault M, Rubin JE. Antimicrobial Resistance in Clostridium and Brachyspira spp. and Other Anaerobes. Microbiol Spectr 2020; 8:10.1128/microbiolspec.arba-0020-2017. [PMID: 31971162 PMCID: PMC10773235 DOI: 10.1128/microbiolspec.arba-0020-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Indexed: 01/26/2023] Open
Abstract
This article describes the antimicrobial resistance to date of the most frequently encountered anaerobic bacterial pathogens of animals. The different sections show that antimicrobial resistance can vary depending on the antimicrobial, the anaerobe, and the resistance mechanism. The variability in antimicrobial resistance patterns is also associated with other factors such as geographic region and local antimicrobial usage. On occasion, the same resistance gene was observed in many anaerobes, whereas some were limited to certain anaerobes. This article focuses on antimicrobial resistance data of veterinary origin.
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Affiliation(s)
- Marie Archambault
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatchewan S7N 5B4, Canada
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21
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Courson DS, Pokhrel A, Scott C, Madrill M, Rinehold AJ, Tamayo R, Cheney RE, Purcell EB. Single cell analysis of nutrient regulation of Clostridioides (Clostridium) difficile motility. Anaerobe 2019; 59:205-211. [PMID: 31386902 PMCID: PMC6785396 DOI: 10.1016/j.anaerobe.2019.102080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/10/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Regulation of bacterial motility to maximize nutrient acquisition or minimize exposure to harmful substances plays an important role in microbial proliferation and host colonization. The technical difficulties of performing high-resolution live microscopy on anaerobes have hindered mechanistic studies of motility in Clostridioides (formerly Clostridium) difficile. Here, we present a widely applicable protocol for live cell imaging of anaerobic bacteria that has allowed us to characterize C. difficile swimming at the single-cell level. This accessible method for anaerobic live cell microscopy enables inquiry into previously inaccessible aspects of C. difficile physiology and behavior. We present the first report that vegetative C. difficile are capable of regulated motility in the presence of different nutrients. We demonstrate that the epidemic C. difficile strain R20291 exhibits regulated motility in the presence of multiple nutrient sources by modulating its swimming velocity. This is a powerful illustration of the ability of single-cell studies to explain population-wide phenomena such as dispersal through the environment.
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Affiliation(s)
- David S Courson
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Astha Pokhrel
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Cody Scott
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Melissa Madrill
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Alden J Rinehold
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Richard E Cheney
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Erin B Purcell
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA.
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Eyre DW, Didelot X, Buckley AM, Freeman J, Moura IB, Crook DW, Peto TEA, Walker AS, Wilcox MH, Dingle KE. Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage. EBioMedicine 2019; 43:347-355. [PMID: 31036529 PMCID: PMC6558026 DOI: 10.1016/j.ebiom.2019.04.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Clostridium difficile ribotype-027, ribotype-078, and ribotype-017 are virulent and epidemic lineages. Trehalose metabolism variants in these ribotypes, combined with increased human trehalose consumption, have been hypothesised to have contributed to their emergence and virulence. METHODS 5232 previously whole-genome sequenced C. difficile isolates were analysed. Clinical isolates were used to investigate the impact of trehalose metabolism variants on mortality. Import data were used to estimate changes in dietary trehalose. Ribotype-027 virulence was investigated in a clinically reflective gut model. FINDINGS Trehalose metabolism variants found in ribotype-027 and ribotype-017 were widely distributed throughout C. difficile clade-2 and clade-4 in 24/29 (83%) and 10/11 (91%) of sequence types (STs), respectively. The four-gene trehalose metabolism cluster described in ribotype-078 was common in genomes from all five clinically-important C. difficile clades (40/167 [24%] STs). The four-gene cluster was variably present in 208 ribotype-015 infections (98 [47%]); 27/208 (13%) of these patients died within 30-days of diagnosis. Adjusting for age, sex, and infecting ST, there was no association between 30-day all-cause mortality and the four-gene cluster (OR 0.36 [95%CI 0.09-1.34, p = 0.13]). Synthetic trehalose imports in the USA, UK, Germany and the EU were < 1 g/capita/year during 2000-2006, and < 9 g/capita/year 2007-2012, compared with dietary trehalose from natural sources of ~100 g/capita/year. Trehalose supplementation did not increase ribotype-027 virulence in a clinically-validated gut model. INTERPRETATION Trehalose metabolism variants are common in C. difficile. Increases in total dietary trehalose during the early-mid 2000s C. difficile epidemic were likely relatively minimal. Alternative explanations are required to explain why ribotype-027, ribotype-078 and ribotype-017 have been successful. FUNDING National Institute for Health Research. Gut model experiments only: Hayashibara Co. Ltd.
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Affiliation(s)
- David W Eyre
- Big Data Institute, University of Oxford, UK; Nuffield Department of Medicine, University of Oxford, UK.
| | - Xavier Didelot
- School of Life Sciences, Department of Statistics, University of Warwick, UK
| | - Anthony M Buckley
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Jane Freeman
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Ines B Moura
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Kate E Dingle
- Nuffield Department of Medicine, University of Oxford, UK
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PCR based detection of tcdCΔ117 in Clostridium difficile infection identifies patients at risk for recurrence - A hospital-based prospective observational study. Anaerobe 2019; 57:39-44. [PMID: 30878603 DOI: 10.1016/j.anaerobe.2019.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Increasing incidence and severity of Clostridium difficile infection (CDI) in the last decades has been attributed to the emergence of hypervirulent C. difficile strain PCR-ribotype 027 (RT027). Commercial multiplex real-time PCR tests allow the presumptive identification of RT027 by detecting a single-base deletion at nt117 in the tcdC gene (tcdCΔ117). The clinical usefulness of the detection of tcdCΔ117 is unclear. Therefore, we evaluated test performance and clinical association of the detection of tcdCΔ117 in patients with CDI in a prospective observational study conducted in a tertiary care hospital in Germany. METHODS From June to October 2015, stool from all patients with suspected CDI was tested for C. difficile according to ESCMID guidelines. C. difficile was cultured from positive samples and ribotyping was performed. Clinical data were collected prospectively from all C. difficile positive patients. RESULTS From 1121 tested stool samples 107 patients with CDI were included in the study. TcdCΔ117 was detected in 18 (16.8%) of these patients. Multivariable logistic regression analysis revealed an independent association of detection of tcdCΔ117 with a further episode of CDI (OR 14.6; 95% CI 3.6-58.3; p < 0.001) and death within 30 days of the positive test (OR 5.1; 95% CI 1.0-25.7; p = 0.046). As follow up data are limited, it remains unclear, whether the further episode of CDI was due to tcdCΔ117 (recurrence) or another type. CONCLUSION In our setting, PCR-based detection of tcdCΔ117 identified patients at risk for recurrent CDI and increased mortality and thus may guide therapeutic choices in CDI patients at the time of diagnosis.
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Kokai-Kun JF, Sarver JL, Carman RJ. Characterization of Clostridium difficile isolates collected during a phase 2b clinical study with SYN-004 (ribaxamase) for the prevention of C. difficile infection. Anaerobe 2018; 53:30-33. [PMID: 29981838 DOI: 10.1016/j.anaerobe.2018.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/30/2018] [Accepted: 07/02/2018] [Indexed: 10/28/2022]
Abstract
During a Phase 2b study with SYN-004 (ribaxamase) for prevention of Clostridium difficile infection (CDI) conducted in North America and Eastern Europe, 45 C. difficile isolates from subjects with laboratory-confirmed CDI and or colonized with C. difficile were collected and characterized. Several C. difficile PCR ribotypes, including 027 and 198, were identified.
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Krehelova M, Nyč O, Sinajová E, Krutova M. The predominance and clustering of Clostridioides (Clostridium) difficile PCR ribotype 001 isolates in three hospitals in Eastern Slovakia, 2017. Folia Microbiol (Praha) 2018; 64:49-54. [PMID: 29971567 DOI: 10.1007/s12223-018-0629-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/27/2018] [Indexed: 12/20/2022]
Abstract
This study aimed to implement a toxigenic culture as an optional third diagnostic step for glutamate dehydrogenase (GDH)-positive and toxin A/B-negative diarrheal stool samples into a diagnostic algorithm for Clostridioides (Clostridium) difficile infection (CDI), and to characterise C. difficile isolates for epidemiological purposes. During the 5-month study, 481 diarrhoeal stool samples from three Slovak hospitals were investigated and 66 non-duplicated GDH-positive stool samples were found. Of them, 36 were also toxin A/B-positive. Twenty-three GDH-positive and toxin A/B-negative stool samples were shown subsequently to be positive following toxigenic culture (TC). Molecular characterisation of C. difficile isolates showed the predominance of PCR ribotype (RT) 001 (n = 37, 56.1%) and the occurrence of RT 176 (n = 3, 4.5%). C. difficile RT 001 isolates clustered to eight clonal complexes (CCs) using multiple-locus variable-number tandem repeats analysis (MLVA). Interestingly, one third of RT 001 isolates clustering in these CCs were cultured from toxin A/B-negative stool samples. Our observations highlight the need of use multiple step diagnostic algorithm in CDI diagnosis in order to detect all CDI cases and to avoid the spread of C. difficile in healthcare settings.
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Affiliation(s)
| | - Otakar Nyč
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic
| | - Eva Sinajová
- Department of Microbiology, Medirex Group, Kosice, Slovakia
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic.
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Comparative Genomics of Clostridium difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1050:59-75. [PMID: 29383664 DOI: 10.1007/978-3-319-72799-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clostridium difficile, a gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of nosocomial diarrhoea in hospitals. The availability of genome sequences in large numbers, mainly due to the use of next-generation sequencing methods, have undoubtedly shown their immense advantages in the determination of the C. difficile population structure. The implementation of fine-scale comparative genomic approaches have paved the way to global transmission and recurrence studies, but also more targeted studies such as the PaLoc or the CRISPR/Cas systems. In this chapter, we provide an overview of the recent and significant findings on C. difficile using comparative genomics studies with implication for the epidemiology, infection control and understanding of the evolution of C. difficile.
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Couturier J, Davies K, Gateau C, Barbut F. Ribotypes and New Virulent Strains Across Europe. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1050:45-58. [PMID: 29383663 DOI: 10.1007/978-3-319-72799-8_4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Clostridium difficile is a major bacterial cause of post-antibiotic diarrhoea. The epidemiology of C. difficile infections (CDI) has dramatically changed since the early 2000s, with an increasing incidence and severity across Europe. This trend is partly due to the emergence and rapid worldwide spread of the hypervirulent and epidemic PCR ribotype 027. Profiles of patients with CDI have also evolved, with description of community-acquired (CA) infections in patients with no traditional risk factors for CDI. However, recent epidemiological studies indicated that some European countries have successfully controlled the dissemination of the 027 clone whereas other countries recently reported the emergence of other virulent or unusual strains. The aims of this review are to summarize the current European CDI epidemiology and to describe the new virulent C. difficile strains circulating in Europe, as well as other potential emerging strains described elsewhere. Standardized typing methods and surveillance programmes are mandatory for a better understanding and monitoring of CDI in Europe.
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Affiliation(s)
- Jeanne Couturier
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France. .,Université Paris Descartes, Faculté de Pharmacie, Paris, France.
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Cécile Gateau
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France
| | - Frédéric Barbut
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France.,Université Paris Descartes, Faculté de Pharmacie, Paris, France
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Couturier J, Eckert C, Barbut F. Spatio-temporal variability of the epidemic 027 Clostridium difficile strains in France based on MLVA typing. Anaerobe 2017; 48:179-183. [DOI: 10.1016/j.anaerobe.2017.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/02/2017] [Accepted: 08/08/2017] [Indexed: 11/15/2022]
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Dresler J, Krutova M, Fucikova A, Klimentova J, Hruzova V, Duracova M, Houdkova K, Salovska B, Matejkova J, Hubalek M, Pajer P, Pisa L, Nyc O. Analysis of proteomes released from in vitro cultured eight Clostridium difficile PCR ribotypes revealed specific expression in PCR ribotypes 027 and 176 confirming their genetic relatedness and clinical importance at the proteomic level. Gut Pathog 2017; 9:45. [PMID: 28814976 PMCID: PMC5556371 DOI: 10.1186/s13099-017-0194-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/28/2017] [Indexed: 01/22/2023] Open
Abstract
Background Clostridium difficile is the causative agent of C. difficile infection (CDI) that could be manifested by diarrhea, pseudomembranous colitis or life-threatening toxic megacolon. The spread of certain strains represents a significant economic burden for health-care. The epidemic successful strains are also associated with severe clinical features of CDI. Therefore, a proteomic study has been conducted that comprises proteomes released from in vitro cultured panel of eight different PCR ribotypes (RTs) and employs the combination of shotgun proteomics and label-free quantification (LFQ) approach. Results The comparative semi-quantitative analyses enabled investigation of a total of 662 proteins. Both hierarchical clustering and principal component analysis (PCA) created eight distinctive groups. From these quantifiable proteins, 27 were significantly increased in functional annotations. Among them, several known factors connected with virulence were identified, such as toxin A, B, binary toxin, flagellar proteins, and proteins associated with Pro–Pro endopeptidase (PPEP-1) functional complex. Comparative analysis of protein expression showed a higher expression or unique expression of proteins linked to pathogenicity or iron metabolism in RTs 027 and 176 supporting their genetic relatedness and clinical importance at the proteomic level. Moreover, the absence of putative nitroreductase and the abundance of the Abc-type fe3+ transport system protein were observed as biomarkers for the RTs possessing binary toxin genes (027, 176 and 078). Higher expression of selected flagellar proteins clearly distinguished RTs 027, 176, 005 and 012, confirming the pathogenic role of the assembly in CDI. Finally, the histidine synthesis pathway regulating protein complex HisG/HisZ was observed only in isolates possessing the genes for toxin A and B. Conclusions This study showed the applicability of the LFQ approach and provided the first semi-quantitative insight into the proteomes released from in vitro cultured panel of eight RTs. The observed differences pointed to a new direction for studies focused on the elucidation of the mechanisms underlining the CDI nature. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0194-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiri Dresler
- Military Health Institute, Military Medical Agency, Tychonova 1, Prague, Czech Republic
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Alena Fucikova
- Faculty of Military Health Sciences, UoD, Hradec Kralove, Czech Republic
| | - Jana Klimentova
- Faculty of Military Health Sciences, UoD, Hradec Kralove, Czech Republic
| | - Veronika Hruzova
- Military Health Institute, Military Medical Agency, Tychonova 1, Prague, Czech Republic
| | - Miloslava Duracova
- Faculty of Military Health Sciences, UoD, Hradec Kralove, Czech Republic
| | - Katerina Houdkova
- Military Health Institute, Military Medical Agency, Tychonova 1, Prague, Czech Republic
| | - Barbora Salovska
- Military Health Institute, Military Medical Agency, Tychonova 1, Prague, Czech Republic
| | - Jana Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry, Academy of Science, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, Prague, Czech Republic
| | - Libor Pisa
- Military Health Institute, Military Medical Agency, Tychonova 1, Prague, Czech Republic
| | - Otakar Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
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Krutova M, Nyc O, Matejkova J, Kuijper EJ, Jalava J, Mentula S. The recognition and characterisation of Finnish Clostridium difficile isolates resembling PCR-ribotype 027. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:344-351. [PMID: 28583353 DOI: 10.1016/j.jmii.2017.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/03/2017] [Accepted: 02/06/2017] [Indexed: 02/08/2023]
Abstract
PURPOSE To characterise and compare twenty-eight Finnish Clostridium difficile RT027-like isolates, selected based on the presence of 18 bp deletion in the tcdC gene and toxin gene profile (A, B, binary), with eleven RT027 isolates from different Finnish geographical areas and time periods. METHODS Twenty-eight C. difficile RT027-like isolates and 11 RT027 comparative strains were characterised by capillary-electrophoresis (CE) ribotyping, multi-locus variable tandem-repeats analysis (MLVA), multi-locus sequence typing (MLST), and sequencing of tcdC and gyrA gene fragments. Susceptibility to moxifloxacin was determined by E-test. RESULTS Of 28 RT027-like isolates, seven RTs (016, 034, 075, 080, 153, 176 and 328), three WEBRIBO types (411, 475, AI-78) and three new profiles (F1-F3) were identified. MLVA revealed six clonal complexes (RTs 016, 027, 176 and F3). MLST showed eleven sequence types (1, 41, 47, 67, 95, 191,192, 223, 229, 264 and new ST). Twenty-two isolates (RTs 016, 080, 176, 328, F1, F2, F3 and WRTAI-78) carried Δ117 in the tcdC gene. Isolates of RTs 016, 027 and 176 were moxifloxacin resistant and harboured Thr82Ile in the GyrA. CONCLUSION Our results show a high diversity within 28 Finnish RT027-like C. difficile isolates, with twelve CE-ribotyping profiles and eleven STs. MLVA revealed the regional spread of RTs 016, 027, 176 and F3. The presence of Δ117 in the tcdC gene in eight non-027 RTs highlights the importance of careful interpretation of the results from molecular systems targeting this site in the genome of C. difficile and the need of strain typing for epidemiological purposes.
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Affiliation(s)
- Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic; DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic.
| | - Otakar Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Jana Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Ed J Kuijper
- Leiden University Medical Centre, Leiden, The Netherlands
| | - Jari Jalava
- Bacterial Infections Unit, Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Silja Mentula
- Bacterial Infections Unit, Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
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31
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Molecular typing and antimicrobial susceptibility testing to six antimicrobials of Clostridium difficile isolates from three Czech hospitals in Eastern Bohemia in 2011–2012. Folia Microbiol (Praha) 2017; 62:445-451. [DOI: 10.1007/s12223-017-0515-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 03/06/2017] [Indexed: 01/05/2023]
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Survival of Clostridium difficile spores at low water activity. Food Microbiol 2017; 65:274-278. [PMID: 28400013 DOI: 10.1016/j.fm.2017.03.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/28/2017] [Accepted: 03/15/2017] [Indexed: 02/03/2023]
Abstract
Clostridium difficile is frequently found in meat and meat products. Germination efficiency, defined as colony formation, was previously investigated at temperatures found in meat handling and processing for spores of strain M120 (animal isolate), R20291 (human isolate), and DK1 (beef isolate). In this study, germination efficiency of these spore strains was assessed in phosphate buffered saline (PBS, aw ∼1.00), commercial beef jerky (aw ∼0.82/0.72), and aw-adjusted PBS (aw ∼0.82/0.72). Surface hydrophobicity was followed for spores stored in PBS. After three months and for all PBS aw levels tested, M120 and DK1 spores showed a ∼1 decimal reduction in colony formation but this was not the case when kept in beef jerky suggesting a protective food matrix effect. During storage, and with no significant aw effect, an increase in colony formation was observed for R20291 spores kept in PBS (∼2 decimal log increase) and beef jerky (∼1 decimal log increase) suggesting a loss of spore superdormancy. For all strains, no significant changes in spore surface hydrophobicity were observed after storage. Collectively, these results indicate that depending on the germination properties of C. difficile spores and the media properties, their germination efficiency may increase or decrease during long term food storage.
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Anjuwon-Foster BR, Tamayo R. A genetic switch controls the production of flagella and toxins in Clostridium difficile. PLoS Genet 2017; 13:e1006701. [PMID: 28346491 PMCID: PMC5386303 DOI: 10.1371/journal.pgen.1006701] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 04/10/2017] [Accepted: 03/16/2017] [Indexed: 12/15/2022] Open
Abstract
In the human intestinal pathogen Clostridium difficile, flagella promote adherence to intestinal epithelial cells. Flagellar gene expression also indirectly impacts production of the glucosylating toxins, which are essential to diarrheal disease development. Thus, factors that regulate the expression of the flgB operon will likely impact toxin production in addition to flagellar motility. Here, we report the identification a "flagellar switch" that controls the phase variable production of flagella and glucosylating toxins. The flagellar switch, located upstream of the flgB operon containing the early stage flagellar genes, is a 154 bp invertible sequence flanked by 21 bp inverted repeats. Bacteria with the sequence in one orientation expressed flagellum and toxin genes, produced flagella, and secreted the toxins ("flg phase ON"). Bacteria with the sequence in the inverse orientation were attenuated for flagellar and toxin gene expression, were aflagellate, and showed decreased toxin secretion ("flg phase OFF"). The orientation of the flagellar switch is reversible during growth in vitro. We provide evidence that gene regulation via the flagellar switch occurs post-transcription initiation and requires a C. difficile-specific regulatory factor to destabilize or degrade the early flagellar gene mRNA when the flagellar switch is in the OFF orientation. Lastly, through mutagenesis and characterization of flagellar phase locked isolates, we determined that the tyrosine recombinase RecV, which catalyzes inversion at the cwpV switch, is also responsible for inversion at the flagellar switch in both directions. Phase variable flagellar motility and toxin production suggests that these important virulence factors have both advantageous and detrimental effects during the course of infection.
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Affiliation(s)
- Brandon R. Anjuwon-Foster
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
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Winston JA, Thanissery R, Montgomery SA, Theriot CM. Cefoperazone-treated Mouse Model of Clinically-relevant Clostridium difficile Strain R20291. J Vis Exp 2016. [PMID: 28060346 DOI: 10.3791/54850] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Clostridium difficile is an anaerobic, gram-positive, spore-forming enteric pathogen that is associated with increasing morbidity and mortality and consequently poses an urgent threat to public health. Recurrence of a C. difficile infection (CDI) after successful treatment with antibiotics is high, occurring in 20-30% of patients, thus necessitating the discovery of novel therapeutics against this pathogen. Current animal models of CDI result in high mortality rates and thus do not approximate the chronic, insidious disease manifestations seen in humans with CDI. To evaluate therapeutics against C. difficile, a mouse model approximating human disease utilizing a clinically-relevant strain is needed. This protocol outlines the cefoperazone mouse model of CDI using a clinically-relevant and genetically-tractable strain, R20291. Techniques for clinical disease monitoring, C. difficile bacterial enumeration, toxin cytotoxicity, and histopathological changes throughout CDI in a mouse model are detailed in the protocol. Compared to other mouse models of CDI, this model is not uniformly lethal at the dose administered, allowing for the observation of a prolonged clinical course of infection concordant with the human disease. Therefore, this cefoperazone mouse model of CDI proves a valuable experimental platform to assess the effects of novel therapeutics on the amelioration of clinical disease and on the restoration of colonization resistance against C. difficile.
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Affiliation(s)
- Jenessa A Winston
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine
| | - Rajani Thanissery
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine
| | - Casey M Theriot
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine;
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Tóth J, Urbán E, Osztie H, Benczik M, Indra A, Nagy E, Allerberger F. Distribution of PCR ribotypes among recent Clostridium difficile isolates collected in two districts of Hungary using capillary gel electrophoresis and review of changes in the circulating ribotypes over time. J Med Microbiol 2016; 65:1158-1163. [DOI: 10.1099/jmm.0.000334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Judith Tóth
- Synlab Budapest Diagnostic Center, Microbiology Laboratory, Budapest, Hungary
| | - Edith Urbán
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Hilda Osztie
- Synlab Budapest Diagnostic Center, Microbiology Laboratory, Budapest, Hungary
| | - Márta Benczik
- Synlab Budapest Diagnostic Center, GenoID Molecular Diagnostic Laboratory, Budapest, Hungary
| | - Alexander Indra
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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Thabit AK, Alam MJ, Burnham CAD, Nicolau DP. Clinical use comparison of a semiautomated PCR with fluorescent ribotyping for typing of Clostridium difficile. Arch Microbiol 2016; 199:317-323. [PMID: 27730251 DOI: 10.1007/s00203-016-1305-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/11/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022]
Abstract
Molecular typing of Clostridium difficile is performed to assess strain relatedness or place strains within an epidemiological context. Different C. difficile ribotyping systems are available. However, a common strain library does not exist. We aimed to compare ribotyping results of 29 clinical C. difficile isolates by two methods: semiautomated PCR-ribotyping and fluorescent PCR-ribotyping. For certain ribotypes (n = 16/29; 55.2 %), the inter-laboratory reproducibility was consistent among multiple samples from individual subjects, while 54.8 % (n = 14/29) were discordant. Additionally, 11/29 ribotypes (38 %) and 12/29 ribotypes (41 %) did not match with known reference strains in the semiautomated PCR-fluorescent ribotyping systems' libraries, respectively. The identification of 027 ribotype by both systems was consistent for 75 % of the isolates. Discriminatory indices for the semiautomated PCR-ribotyping and fluorescent PCR-ribotyping systems are 0.906 and 0.886, respectively. Although ribotyping provides important epidemiologic insights, the lack of a common strain library makes interpretation of results using different ribotyping protocols difficult.
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Affiliation(s)
- Abrar K Thabit
- Center for Anti-infective Research and Development, Hartford Hospital, 80 Seymour Street, Hartford, CT, 06102, USA
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - David P Nicolau
- Center for Anti-infective Research and Development, Hartford Hospital, 80 Seymour Street, Hartford, CT, 06102, USA.
- Division of Infectious Diseases, Hartford Hospital, Hartford, CT, USA.
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Krutova M, Nyc O, Matejkova J, Allerberger F, Wilcox MH, Kuijper EJ. Molecular characterisation of Czech Clostridium difficile isolates collected in 2013-2015. Int J Med Microbiol 2016; 306:479-485. [PMID: 27519407 DOI: 10.1016/j.ijmm.2016.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/27/2016] [Accepted: 07/31/2016] [Indexed: 12/16/2022] Open
Abstract
Clostridium difficile is a leading nosocomial pathogen and molecular typing is a crucial part of monitoring its occurrence and spread. Over a three-year period (2013-2015), clinical C. difficile isolates from 32 Czech hospitals were collected for molecular characterisation. Of 2201 C. difficile isolates, 177 (8%) were non-toxigenic, 2024 (92%) were toxigenic (tcdA and tcdB) and of these, 677 (33.5%) carried genes for binary toxin production (cdtA, cdtB). Capillary-electrophoresis (CE) ribotyping of the 2201 isolates yielded 166 different CE-ribotyping profiles, of which 53 were represented by at least two isolates for each profile. Of these, 29 CE-ribotyping patterns were common to the Leeds-Leiden C. difficile reference strain library and the WEBRIBO database (83.7% isolates), and 24 patterns were recognized only by the WEBRIBO database (11.2% isolates). Isolates belonging to these 53 CE-ribotyping profiles comprised 94.9% of all isolates. The ten most frequent CE-ribotyping profiles were 176 (n=588, 26.7%), 001 (n=456, 20.7%), 014 (n=176, 8%), 012 (n=127, 5.8%), 017 (n=85, 3.9%), 020 (n=68, 3.1%), 596 (n=55, 2.5%), 002-like (n=45, 2.1%), 010 (n=35, 1.6%) and 078 (n=34, 1.6%). Multi-locus sequence typing (MLST) of seven housekeeping genes performed in one isolate of each of 53 different CE-ribotyping profiles revealed 40 different sequence types (STs). We conclude that molecular characterisation of Czech C. difficile isolates revealed a high diversity of CE-ribotyping profiles; the prevailing RTs were 001 (20.7%) and 176 (027-like, 26.7%).
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Affiliation(s)
- M Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic; DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic.
| | - O Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - J Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - F Allerberger
- Austrian Agency for Health and Food Safety (AGES), Wien, Austria
| | - M H Wilcox
- Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - E J Kuijper
- Leiden University Medical Centre, Leiden, The Netherlands
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Krutova M, Matejkova J, Kuijper EJ, Drevinek P, Nyc O. Clostridium difficile PCR ribotypes 001 and 176 – the common denominator of C. difficile infection epidemiology in the Czech Republic, 2014. Euro Surveill 2016; 21:30296. [DOI: 10.2807/1560-7917.es.2016.21.29.30296] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/27/2015] [Indexed: 12/16/2022] Open
Abstract
In 2014, 18 hospitals in the Czech Republic participated in a survey of the incidence of Clostridium difficile infections (CDI) in the country. The mean CDI incidence was 6.1 (standard deviation (SD):7.2) cases per 10,000 patient bed-days and 37.8 cases (SD: 41.4) per 10,000 admissions. The mean CDI testing frequency was 39.5 tests (SD: 25.4) per 10,000 patient bed-days and 255.8 tests (SD: 164.0) per 10,000 admissions. A total of 774 C. difficile isolates were investigated, of which 225 (29%) belonged to PCR ribotype 176, and 184 isolates (24%) belonged to PCR ribotype 001. Multilocus variable-number tandem repeat analysis (MLVA) revealed 27 clonal complexes formed by 84% (190/225) of PCR ribotype 176 isolates, and 14 clonal complexes formed by 77% (141/184) of PCR ribotype 001 isolates. Clonal clusters of PCR ribotypes 176 and 001 were observed in 11 and 7 hospitals, respectively. Our data demonstrate the spread of two C. difficile PCR ribotypes within 18 hospitals in the Czech Republic, stressing the importance of standardising CDI testing protocols and implementing mandatory CDI surveillance in the country.
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Affiliation(s)
- Marcela Krutova
- DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Jana Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Otakar Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
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Davies KA, Ashwin H, Longshaw CM, Burns DA, Davis GL, Wilcox MH. Diversity of Clostridium difficile PCR ribotypes in Europe: results from the European, multicentre, prospective, biannual, point-prevalence study of Clostridium difficile infection in hospitalised patients with diarrhoea (EUCLID), 2012 and 2013. Euro Surveill 2016; 21:30294. [DOI: 10.2807/1560-7917.es.2016.21.29.30294] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/04/2015] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile infection (CDI) is the major cause of infective diarrhoea in healthcare environments. As part of the European, multicentre, prospective, biannual, point-prevalence study of Clostridium difficile infection in hospitalised patients with diarrhoea (EUCLID), the largest C. difficile epidemiological study of its type, PCR ribotype distribution of C. difficile isolates in Europe was investigated. PCR ribotyping was performed on 1,196 C. difficile isolates from diarrhoeal samples sent to the European coordinating laboratory in 2012–13 and 2013 (from two sampling days) by 482 participating hospitals from 19 European countries. A total of 125 ribotypes were identified, of which ribotypes 027 (19%, n =222), 001/072 (11%, n = 134) and 014/020 (10%, n = 119) were the most prevalent. Distinct regional patterns of ribotype distribution were noted. Of 596 isolates from patients with toxin-positive stools (CDI cases), ribotype 027 accounted for 22% (32/144) of infections in cases aged from 18 to less than 65 years, but the prevalence decreased in those aged ≥ 65 years (14% (59/412)) and further decreased in those aged ≥ 81 years (9% (18/195)). The prevalence of ribotype 027 and 176, but not other epidemic strains, was inversely proportional to overall ribotype diversity (R2 = 0.717). This study highlights an increased diversity of C. difficile ribotypes across Europe compared with previous studies, with considerable intercountry variation in ribotype distribution. Continuous surveillance programmes are necessary to monitor the changing epidemiology of C. difficile.
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Affiliation(s)
- Kerrie A Davies
- Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Helen Ashwin
- Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | | | | | - Georgina L Davis
- Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Mark H Wilcox
- Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
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Tsai BY, Ko WC, Chen TH, Wu YC, Lan PH, Chen YH, Hung YP, Tsai PJ. Zoonotic potential of the Clostridium difficile RT078 family in Taiwan. Anaerobe 2016; 41:125-130. [PMID: 27292030 DOI: 10.1016/j.anaerobe.2016.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 02/08/2023]
Abstract
Clostridium difficile is the major cause of nosocomial diarrhea. We have previously demonstrated that in southern Taiwan, severe C. difficile-associated diarrhea (CDAD) cases were due to the C. difficile RT 126 strain infection, indicating the arrival of an epidemic C. difficile clone in southern Taiwan. RT126 has a close genetic relationship with RT078. However, the RT078 family is the predominant strain of C. difficile in animals worldwide, particularly in swine. In this study, we surveyed C. difficile strains isolated from swine at several farms in Taiwan from August 2011 to March 2015. We found that all swine strains, namely RT078 (32.5%, 37 of 114), RT126 (28.9%, 33 of 114) and RT127 (37.7%, 43 of 114), belonged to the toxigenic RT078 family. All strains had high gyrA mutation rate (57.9%, 66/114), which was linked to quinolone resistance. Notably, Rep-PCR revealed that 3 RT078 animal strains had the same fingerprint as human RT078 clinical isolates; their phylogenic relationship was closely related to the whole gene sequences of tcdB, thus suggesting zoonotic potential for C. difficile infection in Taiwan.
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Affiliation(s)
- Bo-Yang Tsai
- Department of Microbiology and Immunology, National Cheng Kung University, Medical College, Tainan, Taiwan.
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Center for Infection Control, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Medicine, National Cheng Kung University Medical College, Tainan, Taiwan.
| | - Ter-Hsin Chen
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan.
| | - Ying-Chen Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan.
| | - Po-Han Lan
- Kaohsiung American School, Kaohsiung, Taiwan.
| | - Yi-Hsuan Chen
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Medical College, Tainan, Taiwan.
| | - Yuan-Pin Hung
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, Tainan, Taiwan.
| | - Pei-Jane Tsai
- Department of Microbiology and Immunology, National Cheng Kung University, Medical College, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Medical College, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.
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41
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Polivkova S, Krutova M, Petrlova K, Benes J, Nyc O. Clostridium difficile ribotype 176 - A predictor for high mortality and risk of nosocomial spread? Anaerobe 2016; 40:35-40. [PMID: 27155489 DOI: 10.1016/j.anaerobe.2016.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 05/01/2016] [Accepted: 05/02/2016] [Indexed: 12/19/2022]
Abstract
PURPOSE The objective of this survey was to determine the incidence of Clostridium difficile infections (CDI) at the Department of Infectious Diseases, Bulovka Hospital, and to evaluate clinical and epidemiological data on CDI patients together with a detailed molecular characterisation of C. difficile isolates. The patient outcomes were correlated to causative C. difficile PCR-ribotype. METHODS The twelve-month study (2013) comprised patients two years of age and older with CDI. CDI severity was estimated using ESCMID criteria and ATLAS scoring. C. difficile isolates were further characterized using ribotyping, Multiple-Locus Variable Tandem-Repeats analysis (MLVA) and investigation of antibiotic-resistance determinants (gyrA, gyrB, rpoB, ermB). RESULTS A total of 619 diarrhoeal stools were investigated. Seventy-two stool samples were GDH and toxin A/B positive, and 39 samples were GDH positive only and subsequently toxigenic C. difficile was cultured. In total, 111 C. difficile isolates were characterized, of which 64 (57.7%) belonged to PCR-ribotype 176. MLVA analysis of PCR-ribotype 176 isolates revealed 11 clonal complexes. Seventy-two isolates (64.9%) showed amino acid substitution Thr82Ile in the GyrA, and sixty-two isolates (55.9%) showed amino acid substitutions Arg505Lys together with His502Asn, or Asp492Glu together with Arg505Lys in the RpoB. Twelve isolates (10.8%) were ermB positive. Severe CDI according to the ESCMID criteria was recorded in forty-two patients (37.8%), and sixteen patients (14.4%) had ATLAS score ≥ 6. Twenty-nine patients (26.1%) had recurrent CDI and twenty-four patients (21.6%) died during the study period. CONCLUSIONS A higher rate of severe CDI, recurrences and mortality in association with PCR-ribotype 176 infections were observed. The high incidence of PCR-ribotype 176 in the study, and the presence of clonal relatedness between PCR-ribotype 176 isolates, indicate its higher capacity to spread in a hospital setting, which in turn highlights the need to implement strict epidemic measures when PCR-ribotype 176 occurs.
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Affiliation(s)
- Sylvia Polivkova
- Department of Infectious Diseases, 3rd Faculty of Medicine, Bulovka Teaching Hospital, Prague, Czech Republic
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic; DNA Laboratory, Department of Paediatric Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.
| | - Katarina Petrlova
- Department of Clinical Microbiology, Bulovka Teaching Hospital, Prague, Czech Republic
| | - Jiri Benes
- Department of Infectious Diseases, 3rd Faculty of Medicine, Bulovka Teaching Hospital, Prague, Czech Republic
| | - Otakar Nyc
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
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42
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Spigaglia P. Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection. Ther Adv Infect Dis 2016; 3:23-42. [PMID: 26862400 DOI: 10.1177/2049936115622891] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clostridium difficile epidemiology has changed in recent years, with the emergence of highly virulent types associated with severe infections, high rates of recurrences and mortality. Antibiotic resistance plays an important role in driving these epidemiological changes and the emergence of new types. While clindamycin resistance was driving historical endemic types, new types are associated with resistance to fluoroquinolones. Furthermore, resistance to multiple antibiotics is a common feature of the newly emergent strains and, in general, of many epidemic isolates. A reduced susceptibility to antibiotics used for C. difficile infection (CDI) treatment, in particular to metronidazole, has recently been described in several studies. Furthermore, an increased number of strains show resistance to rifamycins, used for the treatment of relapsing CDI. Several mechanisms of resistance have been identified in C. difficile, including acquisition of genetic elements and alterations of the antibiotic target sites. The C. difficile genome contains a plethora of mobile genetic elements, many of them involved in antibiotic resistance. Transfer of genetic elements among C. difficile strains or between C. difficile and other bacterial species can occur through different mechanisms that facilitate their spread. Investigations of the fitness cost in C. difficile indicate that both genetic elements and mutations in the molecular targets of antibiotics can be maintained regardless of the burden imposed on fitness, suggesting that resistances may persist in the C. difficile population also in absence of antibiotic selective pressure. The rapid evolution of antibiotic resistance and its composite nature complicate strategies in the treatment and prevention of CDI. The rapid identification of new phenotypic and genotypic traits, the implementation of effective antimicrobial stewardship and infection control programs, and the development of alternative therapies are needed to prevent and contain the spread of resistance and to ensure an efficacious therapy for CDI.
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Drabek J, Nyc O, Krutova M, Stovicek J, Matejkova J, Keil R. Clinical features and characteristics of Clostridium difficile PCR-ribotype 176 infection: results from a 1-year university hospital internal ward study. Ann Clin Microbiol Antimicrob 2015; 14:55. [PMID: 26698842 PMCID: PMC4690340 DOI: 10.1186/s12941-015-0114-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/22/2015] [Indexed: 02/04/2023] Open
Abstract
Background Clostridium difficile infection (CDI) is a major cause of antibiotic-associated diarrhoea. Given an increasing CDI incidence and global spread of epidemic ribotypes, a 1-year study was performed to analyse the molecular characteristics of C. difficile isolates and associated clinical outcomes from patients diagnosed with CDI in the Internal Medicine department at University Hospital Motol, Prague from February 2013 to February 2014. Results A total of 85 unformed stool samples were analysed and CDI was laboratory confirmed in 30 patients (6.8 CDI cases per 10,000 patient bed days and 50.6 CDI cases per 10,000 admissions). The CDI recurrence rate within 3 months of treatment discontinuation was 13.3% (4/30). Mortality within 3 months after first CDI episode was 26.7% (8/30), with CDI the cause of death in two cases. 51.9% of C. difficile isolates belonged to PCR-ribotype 176. MLVA of ribotype 176 isolates revealed two clonal complexes formed by 10/14 isolates. ATLAS scores and Horn’s index were higher in patients with ribotype 176 infections than with non-ribotype 176 infections. Conclusion This study highlights the clinical relevance of C. difficile PCR-ribotype 176 and its capacity to spread within a healthcare facility.
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Affiliation(s)
- Jiri Drabek
- Department of Internal Medicine, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06, V Uvalu 84, Praha 5, Prague, Czech Republic.
| | - Otakar Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic.
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic. .,DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic.
| | - Jan Stovicek
- Department of Internal Medicine, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06, V Uvalu 84, Praha 5, Prague, Czech Republic.
| | - Jana Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic.
| | - Radan Keil
- Department of Internal Medicine, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06, V Uvalu 84, Praha 5, Prague, Czech Republic.
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Abstract
Clostridium difficile infection (CDI) is the leading cause of antimicrobial and health care-associated diarrhea in humans, presenting a significant burden to global health care systems. In the last 2 decades, PCR- and sequence-based techniques, particularly whole-genome sequencing (WGS), have significantly furthered our knowledge of the genetic diversity, evolution, epidemiology, and pathogenicity of this once enigmatic pathogen. C. difficile is taxonomically distinct from many other well-known clostridia, with a diverse population structure comprising hundreds of strain types spread across at least 6 phylogenetic clades. The C. difficile species is defined by a large diverse pangenome with extreme levels of evolutionary plasticity that has been shaped over long time periods by gene flux and recombination, often between divergent lineages. These evolutionary events are in response to environmental and anthropogenic activities and have led to the rapid emergence and worldwide dissemination of virulent clonal lineages. Moreover, genome analysis of large clinically relevant data sets has improved our understanding of CDI outbreaks, transmission, and recurrence. The epidemiology of CDI has changed dramatically over the last 15 years, and CDI may have a foodborne or zoonotic etiology. The WGS era promises to continue to redefine our view of this significant pathogen.
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45
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Beacher N, Sweeney MP, Bagg J. Dentists, antibiotics and Clostridium difficile-associated disease. Br Dent J 2015; 219:275-9. [DOI: 10.1038/sj.bdj.2015.720] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2015] [Indexed: 01/07/2023]
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Antibiotic profiling of Clostridium difficile ribotype 176--A multidrug resistant relative to C. difficile ribotype 027. Anaerobe 2015; 36:88-90. [PMID: 26256807 DOI: 10.1016/j.anaerobe.2015.07.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/22/2022]
Abstract
Antibiotic profiling of twenty Czech Clostridium difficile PCR-ribotype 176 isolates revealed a high level of resistance to erythromycin, ciprofloxacin and moxifloxacin (n = 20) and to rifampicin (n = 13). Accumulation of resistance mechanisms to multiple antibiotics highlight that PCR-ribotype 176 belong to problematic epidemic strains.
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47
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Mentula S, Laakso S, Lyytikäinen O, Kirveskari J. Differentiating virulent 027 and non-027 Clostridium difficile strains by molecular methods. Expert Rev Mol Diagn 2015; 15:1225-9. [PMID: 26289601 DOI: 10.1586/14737159.2015.1069710] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Hypervirulent Clostridium difficile clade has been shown to include several lineages of ribotype 027 and also other ribotypes. We present data on additional non-027 strains, identified as presumptive 027 by two commercial molecular C. difficile assays. METHODS The tested clinical isolates were selected from the national reference laboratory collection on the basis of toxin gene profile similarities with ribotype 027 and tested with XpertC. difficile/Epi and Amplidiag C. difficile+027 assay. RESULT Xpert misclassified five ribotypes (016, 019, 080, 176 and variant of type 046) as presumptive 027 and Amplidiag two ribotypes (016, 176). The misclassified strains were rare, covering 1.6% of reference laboratory strain collection. CONCLUSION Our findings confirm the concept that there are closely related outliers to hypervirulent 027 clones that can be misclassified as 027, and that these comprise numerous ribotypes, including previously reported four ribotypes (198, 176, 244, 019), and additional three (016, v046, 080) identified in the present study.
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Affiliation(s)
- Silja Mentula
- a 1 National Institute for Health and Welfare - Infectious Diseases, P.O. Box 30, Helsinki 00271, Finland
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48
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Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England. J Clin Microbiol 2015; 53:3141-7. [PMID: 26179308 PMCID: PMC4572532 DOI: 10.1128/jcm.00648-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/17/2015] [Indexed: 12/26/2022] Open
Abstract
Clostridium difficile remains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulent C. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients with C. difficile infection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates. De novo assembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages of C. difficile RT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified.
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49
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Carlson PE, Kaiser AM, McColm SA, Bauer JM, Young VB, Aronoff DM, Hanna PC. Variation in germination of Clostridium difficile clinical isolates correlates to disease severity. Anaerobe 2015; 33:64-70. [PMID: 25681667 PMCID: PMC4467518 DOI: 10.1016/j.anaerobe.2015.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/02/2015] [Accepted: 02/10/2015] [Indexed: 01/05/2023]
Abstract
Over the past two decades, Clostridium difficile infections have been increasing in both number and severity throughout the world. As with other spore forming bacteria, germination is a vital step in the life cycle of this pathogen. Studies have examined differences in sporulation and toxin production among a number of C. difficile clinical isolates; however, few have examined differences in germination and the relationship between this phenotype and disease severity. Here, over 100 C. difficile isolates from the University of Michigan Health System were examined for overall germination in response to various combinations of known germinants (taurocholate) and co-germinants (glycine and histidine). Significant variation was observed among isolates under all conditions tested. Isolates representing ribotype 014-020, which was the most frequently isolated ribotype at our hospital, exhibited increased germination in the presence of taurocholate and glycine when compared to isolates representing other ribotypes. Interestingly, isolates that caused severe disease exhibited significantly lower germination in response to minimal germination conditions (taurocholate only), indicating increased control over germination in these isolates. These data provide a broad picture of C. difficile isolate germination and indicate a role for precise control of germination in disease severity.
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Affiliation(s)
- Paul E Carlson
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alyssa M Kaiser
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah A McColm
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jessica M Bauer
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - David M Aronoff
- Division of Infectious Diseases, Department of Medicine, Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Philip C Hanna
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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Hargreaves KR, Otieno JR, Thanki A, Blades MJ, Millard AD, Browne HP, Lawley TD, Clokie MRJ. As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile. Genome Biol Evol 2015; 7:1842-55. [PMID: 26019165 PMCID: PMC4524475 DOI: 10.1093/gbe/evv094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The bacterium Clostridium difficile is a significant cause of nosocomial infections worldwide. The pathogenic success of this organism can be attributed to its flexible genome which is characterized by the exchange of mobile genetic elements, and by ongoing genome evolution. Despite its pathogenic status, C. difficile can also be carried asymptomatically, and has been isolated from natural environments such as water and sediments where multiple strain types (ribotypes) are found in close proximity. These include ribotypes which are associated with disease, as well as those that are less commonly isolated from patients. Little is known about the genomic content of strains in such reservoirs in the natural environment. In this study, draft genomes have been generated for 13 C. difficile isolates from estuarine sediments including clinically relevant and environmental associated types. To identify the genetic diversity within this strain collection, whole-genome comparisons were performed using the assemblies. The strains are highly genetically diverse with regards to the C. difficile “mobilome,” which includes transposons and prophage elements. We identified a novel transposon-like element in two R078 isolates. Multiple, related and unrelated, prophages were detected in isolates across ribotype groups, including two novel prophage elements and those related to the transducing phage φC2. The susceptibility of these isolates to lytic phage infection was tested using a panel of characterized phages found from the same locality. In conclusion, estuarine sediments are a source of genetically diverse C. difficile strains with a complex network of prophages, which could contribute to the emergence of new strains in clinics.
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Affiliation(s)
- Katherine R Hargreaves
- Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom Department of Ecology and Evolutionary Biology, University of Arizona
| | - James R Otieno
- Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anisha Thanki
- Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom
| | - Matthew J Blades
- Bioinformatics and Biostatistics Analysis Support Hub (BBASH), Core Biotechnology Services, University of Leicester, United Kingdom
| | - Andrew D Millard
- Microbiology & Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Hilary P Browne
- Microbial Pathogenesis Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Trevor D Lawley
- Microbial Pathogenesis Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom
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