101
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Cheng JW, Xiao M, Kudinha T, Xu ZP, Hou X, Sun LY, Zhang L, Fan X, Kong F, Xu YC. The First Two Clostridium difficile Ribotype 027/ST1 Isolates Identified in Beijing, China-an Emerging Problem or a Neglected Threat? Sci Rep 2016; 6:18834. [PMID: 26740150 PMCID: PMC4703979 DOI: 10.1038/srep18834] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/27/2015] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile hyper-virulent ribotype 027 strain has become a significant concern globally, but has rarely been reported in Asian countries including China. Recently, a retrospective single-center study in Beijing, China, detected two ribotype 027 C. difficile isolates from two patients coming for outpatient visits in 2012 and 2013. We performed a systematic investigation of the two isolates (and patients). Both C. difficile isolates had the typical PCR ribotype 027 profile; were positive for tcdA, tcdB and binary toxin genes; belonged to multilocus sequence type 1 (ST1); had typical ribotype 027 deletions in the tcdC gene; and were highly-resistant to fluoroquinolones; but had a different MLVA profile and were not genetically related to any previously reported international ribotype 027 clones. A review of the patients' medical records showed that neither received appropriate antimicrobial treatment and were lost to follow-up after outpatient visits. We propose that C. difficile infections caused by ribotype 027 are probably a neglected problem in China, and the subsequent impact of unawareness of this problem is worrying. Appropriate testing assays and multi-center or national level surveillance for C. difficile infections and specifically for ribotype 027 should be introduced to provide essential data and guide future clinical practice.
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Affiliation(s)
- Jing-Wei Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Timothy Kudinha
- Charles Sturt University, Leeds Parade, Orange, New South Wales 2687, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, University of Sydney, Darcy Road, Westmead, New South Wales 2145, Australia
| | - Zhi-Peng Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xin Hou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Lin-Ying Sun
- Teaching and Research Section of Clinical Laboratory, School of Public Health, Taishan Medical School, Taian, Shandong 271000, China
| | - Li Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xin Fan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, University of Sydney, Darcy Road, Westmead, New South Wales 2145, Australia
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
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102
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Bacteriophage Combinations Significantly Reduce Clostridium difficile Growth In Vitro and Proliferation In Vivo. Antimicrob Agents Chemother 2015; 60:968-81. [PMID: 26643348 PMCID: PMC4750681 DOI: 10.1128/aac.01774-15] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/15/2015] [Indexed: 12/17/2022] Open
Abstract
The microbiome dysbiosis caused by antibiotic treatment has been associated with both susceptibility to and relapse of Clostridium difficile infection (CDI). Bacteriophage (phage) therapy offers target specificity and dose amplification in situ, but few studies have focused on its use in CDI treatment. This mainly reflects the lack of strictly virulent phages that target this pathogen. While it is widely accepted that temperate phages are unsuitable for therapeutic purposes due to their transduction potential, analysis of seven C. difficile phages confirmed that this impact could be curtailed by the application of multiple phage types. Here, host range analysis of six myoviruses and one siphovirus was conducted on 80 strains representing 21 major epidemic and clinically severe ribotypes. The phages had complementary coverage, lysing 18 and 62 of the ribotypes and strains tested, respectively. Single-phage treatments of ribotype 076, 014/020, and 027 strains showed an initial reduction in the bacterial load followed by the emergence of phage-resistant colonies. However, these colonies remained susceptible to infection with an unrelated phage. In contrast, specific phage combinations caused the complete lysis of C. difficile in vitro and prevented the appearance of resistant/lysogenic clones. Using a hamster model, the oral delivery of optimized phage combinations resulted in reduced C. difficile colonization at 36 h postinfection. Interestingly, free phages were recovered from the bowel at this time. In a challenge model of the disease, phage treatment delayed the onset of symptoms by 33 h compared to the time of onset of symptoms in untreated animals. These data demonstrate the therapeutic potential of phage combinations to treat CDI.
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103
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Spigaglia P, Barbanti F, Morandi M, Moro ML, Mastrantonio P. Diagnostic testing for Clostridium difficile in Italian microbiological laboratories. Anaerobe 2015; 37:29-33. [PMID: 26555737 DOI: 10.1016/j.anaerobe.2015.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/02/2015] [Accepted: 11/02/2015] [Indexed: 12/15/2022]
Abstract
A laboratory diagnosis survey of Clostridium difficile infection (CDI) was performed in Italy in 2012-2013. Questionnaires from 278 healthcare settings from 15 regions of Italy were collected and analysed. Eighty seven percent of the laboratories declared to routinely perform CDI diagnosis, 99% of them only after the clinician's request. Among the 216 laboratories providing information on the size of the hospitals in which they were located, 65 had more than 500 beds (large hospitals), while 151 had less than 500 beds (small hospitals). The average percentage of positive tests for C. difficile toxins was 12.2%. Almost half of the laboratories (42%) used immunoenzymatic assay (EIA) for Tox A/B as a stand-alone method, while only 34% used an algorithm for CDI as indicated by the European guidelines. A low percentage of laboratories performed molecular assays or C. difficile culture, 25% and 29%, respectively. Most laboratories (161/278) declared to type C. difficile strains, the majority in collaboration with a reference laboratory. Among the 103 C. difficile clinical isolates collected during the study, 31 different PCR-ribotypes were identified. PCR-ribotype 356/607 (27%) was predominant, followed by 018 (12%). These two PCR-ribotypes show 87.5% of similarity in ribotyping profile. PCR-ribotypes 027 and 078 represented 8% and 4% of the strains, respectively. Four PCR-ribotypes (027, 033, 078 and 126) were positive for the binary toxin CDT. In particular, PCR-ribotype 033 produces only CDT, and it has recently been associated with symptomatic cases. The majority of strains were multidrug resistant. In particular, all strains PCR-ribotypes 356/607 and 018 were resistant to moxifloxacin, rifampicin, erythromycin and clindamycin. The results obtained highlight the need to raise awareness to the microbiological diagnosis of CDI among clinicians and to implement and harmonize diagnostic methods for CDI in Italian laboratories in the perspective of a future national surveillance.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Fabrizio Barbanti
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Matteo Morandi
- Agenzia Sanitaria e Sociale, Regione Emilia-Romagna, Bologna, Italy
| | - Maria Luisa Moro
- Agenzia Sanitaria e Sociale, Regione Emilia-Romagna, Bologna, Italy
| | - Paola Mastrantonio
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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104
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Seugendo M, Mshana SE, Hokororo A, Okamo B, Mirambo MM, von Müller L, Gunka K, Zimmermann O, Groß U. Clostridium difficile infections among adults and children in Mwanza/Tanzania: is it an underappreciated pathogen among immunocompromised patients in sub-Saharan Africa? New Microbes New Infect 2015; 8:99-102. [PMID: 26649183 PMCID: PMC4644260 DOI: 10.1016/j.nmni.2015.09.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/27/2015] [Accepted: 09/28/2015] [Indexed: 01/05/2023] Open
Abstract
Little is known regarding the epidemiology Clostridium difficile in developing countries. Fresh stool samples from patients with diarrhoea were cultured anaerobically. C. difficile was detected in nine (6.4%) of 141 (95% confidence interval 4.2–13.1), of which seven (77.8%) were from children. HIV infection, prolonged hospitalization and antibiotic use were independent factors associated with the occurrence of C. difficile in the gastrointestinal tract. Two of the toxigenic isolates were typed as ribotype 045, and the other two had unknown ribotype. All C. difficile isolates were susceptible to metronidazole, moxifloxacin and clarithromycin, while three isolates were resistant to clarithromycin. C. difficile may be an important pathogen causing diarrhoea in sub-Saharan Africa among immunocompromised patients.
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Affiliation(s)
- M Seugendo
- Department of Pediatric and Child Health, Weill Bugando School of Medicine, Mwanza, Tanzania
| | - S E Mshana
- Department of Microbiology, Weill Bugando School of Medicine, Mwanza, Tanzania
| | - A Hokororo
- Department of Pediatric and Child Health, Weill Bugando School of Medicine, Mwanza, Tanzania
| | - B Okamo
- Department of Biochemistry and Molecular Biology, Weill Bugando School of Medicine, Mwanza, Tanzania
| | - M M Mirambo
- Department of Microbiology, Weill Bugando School of Medicine, Mwanza, Tanzania
| | - L von Müller
- Institute for Medical Microbiology and Hygiene, German Reference Laboratory for Clostridium difficile Saarland University Medical Center, Germany
| | - K Gunka
- Institute of Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - O Zimmermann
- Institute of Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - U Groß
- Institute of Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
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105
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Gerding DN, Hecht DW, Louie T, Nord CE, Talbot GH, Cornely OA, Buitrago M, Best E, Sambol S, Osmolski JR, Kracker H, Locher HH, Charef P, Wilcox M. Susceptibility of Clostridium difficile isolates from a Phase 2 clinical trial of cadazolid and vancomycin in C. difficile infection. J Antimicrob Chemother 2015; 71:213-9. [PMID: 26433782 PMCID: PMC4681371 DOI: 10.1093/jac/dkv300] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/23/2015] [Indexed: 12/18/2022] Open
Abstract
Objectives The aim of this study was to evaluate the susceptibilities of Clostridium difficile isolates to cadazolid, a novel antibiotic for the treatment of C. difficile infection. Methods Ribotyping and susceptibilities were determined for C. difficile isolates from a multicentre, double-blind, Phase 2 study of oral cadazolid in patients with C. difficile infection (NCT01222702, ClinicalTrials.gov; EudraCT 2010-020941-29, European Clinical Trials Database). Patients were randomized to receive 250, 500 or 1000 mg of cadazolid twice daily or 125 mg of vancomycin four times daily, for 10 days. MICs of cadazolid, vancomycin, fidaxomicin, linezolid and moxifloxacin were determined at baseline for all patients and post-baseline for patients with clinical failure or recurrence, using the agar dilution method. Results Seventy-eight of 84 patients had an evaluable toxigenic C. difficile isolate at baseline. The most frequent PCR ribotype was 027 (15.4%). Cadazolid MICs for baseline isolates (including epidemic strain 027) ranged from 0.06 to 0.25 mg/L. Baseline cadazolid MICs were similar to those of fidaxomicin and lower than those of vancomycin, linezolid and moxifloxacin. For each clinical outcome group (clinical cure, clinical failure, sustained clinical response and clinical failure or recurrence), the baseline cadazolid MIC range was 0.06–0.25 mg/L. Mean (min–max) cadazolid faecal concentration (μg/g) on day 5 was 884 (101–2710), 1706 (204–4230) and 3226 (1481–12 600) for the doses 250, 500 and 1000 mg, respectively. Conclusions For all cadazolid doses, the faecal concentration was in excess of several thousand-fold the MIC90 for C. difficile. The MIC of cadazolid for all C. difficile isolates, including epidemic strains, was low and in the same narrow range regardless of treatment outcome.
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Affiliation(s)
- D N Gerding
- Loyola University, Maywood, IL, USA Edward Hines Jr VA Hospital, Hines, IL, USA
| | - D W Hecht
- Loyola University, Maywood, IL, USA Edward Hines Jr VA Hospital, Hines, IL, USA
| | - T Louie
- University of Calgary, Calgary, Alberta, Canada
| | - C E Nord
- Karolinska Institute, Stockholm, Sweden
| | | | - O A Cornely
- Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany Clinical Trials Centre Cologne, University of Cologne, Cologne, Germany Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - M Buitrago
- Idaho Falls Infectious Diseases, Idaho Falls, ID, USA
| | - E Best
- Leeds General Infirmary, Leeds, UK
| | - S Sambol
- Loyola University, Maywood, IL, USA Edward Hines Jr VA Hospital, Hines, IL, USA
| | - J R Osmolski
- Loyola University, Maywood, IL, USA Edward Hines Jr VA Hospital, Hines, IL, USA
| | - H Kracker
- Actelion Pharmaceuticals Ltd, Allschwil, Switzerland
| | - H H Locher
- Actelion Pharmaceuticals Ltd, Allschwil, Switzerland
| | - P Charef
- Actelion Pharmaceuticals Ltd, Allschwil, Switzerland
| | - M Wilcox
- Leeds General Infirmary, Leeds, UK
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106
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Spigaglia P, Barbanti F, Castagnola E, Bandettini R. Clostridium difficile infection (CDI) in children due to hypervirulent strains PCR-ribotype 027: An emblematic report of two cases. Anaerobe 2015; 36:91-3. [PMID: 26385433 DOI: 10.1016/j.anaerobe.2015.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/10/2015] [Accepted: 09/15/2015] [Indexed: 02/08/2023]
Abstract
In this report, the first two cases of pediatric Clostridium difficile infection (CDI) due to the hypervirulent PCR-ribotype 027 in Italy are described as emblematic of the role of both the infecting C. difficile strain and patient status in the occurrence and clinical manifestation of CDI in children.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Fabrizio Barbanti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Elio Castagnola
- Infectious Diseases Unit, Istituto Giannina Gaslini, Genoa, Italy
| | - Roberto Bandettini
- Clinical Pathology Laboratory Unit, Istituto Giannina Gaslini, Genoa, Italy
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107
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von Müller L, Mock M, Halfmann A, Stahlmann J, Simon A, Herrmann M. Epidemiology of Clostridium difficile in Germany based on a single center long-term surveillance and German-wide genotyping of recent isolates provided to the advisory laboratory for diagnostic reasons. Int J Med Microbiol 2015; 305:807-13. [PMID: 26341328 DOI: 10.1016/j.ijmm.2015.08.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epidemiology of Clostridium difficile is characterized by worldwide increase of C. difficile infections (CDI) and the emergence of new epidemic outbreak strains with the capacity for global spreading. Long-term local surveillance at the University of Saarland Medical Center between 2000 and 2013 shows that the incidence rate of laboratory-confirmed CDI was influenced by local epidemiology as well as by testing strategies. Since 2008, molecular typing of C. difficile was regularly performed for symptomatic hospitalized patients by surface-layer protein A sequence typing (slpAST), which is an established highly standardized technique for genotyping of C. difficile. The results were assigned to known ribotypes for better comparison to international data. It could be demonstrated that distribution of genotypes was different between age groups. Older patients were predominantly infected with ribotype 001 and 027, whereas ribotype 027 was not detected in the pediatric population. Molecular typing of German isolates sent to the advisory laboratory between 2011 and 2013 revealed that ribotype 027 is present with high percentages in most German regions except for the very North. In conclusion, optimized testing of all hospitalized patients with diarrhea should be generally implemented to avoid under-diagnosis of C. difficile infection. Ribotype 027 is highly prevalent in Germany, but its infections are restricted to older patients, while absent in children. Molecular typing of suspected hospital outbreaks and of patients with severe or recurrent disease may help to better understand virulence and epidemic spreading of C. difficile.
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Affiliation(s)
- Lutz von Müller
- Institute of Medical Microbiology and Hygiene, State of Saarland Laboratory of Hygiene, Consultant Laboratory for Clostridium difficile, University of Saarland Medical Center, Kirrberger Straße, Building 43, Homburg D-66421 Saarland, Germany.
| | - Markus Mock
- Institute of Medical Microbiology and Hygiene, State of Saarland Laboratory of Hygiene, Consultant Laboratory for Clostridium difficile, University of Saarland Medical Center, Kirrberger Straße, Building 43, Homburg D-66421 Saarland, Germany
| | - Alexander Halfmann
- Institute of Medical Microbiology and Hygiene, State of Saarland Laboratory of Hygiene, Consultant Laboratory for Clostridium difficile, University of Saarland Medical Center, Kirrberger Straße, Building 43, Homburg D-66421 Saarland, Germany
| | - Julia Stahlmann
- Institute of Medical Microbiology and Hygiene, State of Saarland Laboratory of Hygiene, Consultant Laboratory for Clostridium difficile, University of Saarland Medical Center, Kirrberger Straße, Building 43, Homburg D-66421 Saarland, Germany
| | - Arne Simon
- Paediatric Hematology and Oncology, Children's Hospital Medical Center, University Hospital of Saarland, Kirrberger Straße, Building 9, Homburg, Saarland, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, State of Saarland Laboratory of Hygiene, Consultant Laboratory for Clostridium difficile, University of Saarland Medical Center, Kirrberger Straße, Building 43, Homburg D-66421 Saarland, Germany
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108
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Indra A, Schmid D, Huhulescu S, Simons E, Hell M, Stickler K, Allerberger F. Clostridium difficile ribotypes in Austria: a multicenter, hospital-based survey. Wien Klin Wochenschr 2015; 127:587-93. [PMID: 26156942 PMCID: PMC4536264 DOI: 10.1007/s00508-015-0808-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/13/2015] [Indexed: 12/18/2022]
Abstract
A prospective, noninterventional survey was conducted among Clostridium difficile positive patients identified in the time period of July until October 2012 in 18 hospitals distributed across all nine Austrian provinces. Participating hospitals were asked to send stool samples or isolates from ten successive patients with C.difficile infection to the National Clostridium difficile Reference Laboratory at the Austrian Agency for Health and Food Safety for PCR-ribotyping and in vitro susceptibility testing. A total of 171 eligible patients were identified, including 73 patients with toxin-positive stool specimens and 98 patients from which C. difficile isolates were provided. Of the 159 patients with known age, 127 (74.3 %) were 65 years or older, the median age was 76 years (range: 9–97 years), and the male to female ratio 2.2. Among these patients, 73 % had health care-associated and 20 % community-acquired C. difficile infection (indeterminable 7 %). The all-cause, 30-day mortality was 8.8 % (15/171). Stool samples yielded 46 different PCR-ribotypes, of which ribotypes 027 (20 %), 014 (15.8 %), 053 (10.5 %), 078 (5.3 %), and 002 (4.7 %) were the five most prevalent. Ribotype 027 was found only in the provinces Vienna, Burgenland, and Lower Austria. Severe outcome of C. difficile infection was found to be associated with ribotype 053 (prevalence ratio: 3.04; 95 % CI: 1.24, 7.44), not with the so-called hypervirulent ribotypes 027 and 078. All 027 and 053 isolates exhibited in vitro resistance against moxifloxacin. Fluoroquinolone use in the health care setting must be considered as a factor favoring the spread of these fluoroquinolone resistant C. difficile clones.
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Affiliation(s)
- Alexander Indra
- Institute for Medical Microbiology and Hygiene, National Clostridium difficile Reference Laboratory, Austrian Agency for Health and Food Safety (AGES), Waehringerstr. 25a, 1090, Vienna, Austria
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109
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Nyc O, Krutova M, Liskova A, Matejkova J, Drabek J, Kuijper EJ. The emergence of Clostridium difficile PCR-ribotype 001 in Slovakia. Eur J Clin Microbiol Infect Dis 2015; 34:1701-8. [DOI: 10.1007/s10096-015-2407-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/06/2015] [Indexed: 12/14/2022]
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110
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Troiano T, Harmanus C, Sanders IMJG, Pasquale V, Dumontet S, Capuano F, Romano V, Kuijper EJ. Toxigenic Clostridium difficile PCR ribotypes in edible marine bivalve molluscs in Italy. Int J Food Microbiol 2015; 208:30-4. [PMID: 26022983 DOI: 10.1016/j.ijfoodmicro.2015.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 01/05/2023]
Abstract
Even though food of animal sources and different foodstuffs are well known to be potentially carrier of Clostridium difficile, few data are available on the occurrence of C. difficile in seafood. This work investigated the occurrence of C. difficile in edible bivalve molluscs in southern Italy. Out of the 925 investigated samples, 3.9% contained C. difficile. Eighteen strains harboured both genes for toxins A and B whereas 1 only had toxin B gene. Binary toxin genes were found in 22.2% of the isolates. The most frequently ribotypes found were 078/126 (22.2%), 010 (19.4%), and 001 (8.3%). All isolates were susceptible to metronidazole, vancomycin, fidaxomicin, and to the new semisynthetic thiopeptide antibiotic LFF571, whereas 19.4% of them were resistant to moxifloxacin, 30.5% to clindamycin, 38.8% to erythromycin, and 100% to ciprofloxacin. This study points out that edible molluscs could be a potential source of toxigenic C. difficile ribotypes and a potential risk for human health.
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Affiliation(s)
- Tiziana Troiano
- Department of Science and Technology, Parthenope University of Naples, 80143 Naples, Italy
| | - Celine Harmanus
- Department of Medical Microbiology, National Reference Laboratory for Clostridium difficile, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Ingrid M J G Sanders
- Department of Medical Microbiology, National Reference Laboratory for Clostridium difficile, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Vincenzo Pasquale
- Department of Science and Technology, Parthenope University of Naples, 80143 Naples, Italy.
| | - Stefano Dumontet
- Department of Science and Technology, Parthenope University of Naples, 80143 Naples, Italy
| | - Federico Capuano
- Department of Food Inspection, Istituto Zooprofilattico Sperimentale per il Mezzogiorno di Portici, 80055 Portici (Naples), Italy
| | - Vincenza Romano
- Department of Science and Technology, Parthenope University of Naples, 80143 Naples, Italy
| | - Ed J Kuijper
- Department of Medical Microbiology, National Reference Laboratory for Clostridium difficile, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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111
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Nyc O, Krutova M, Kriz J, Matejkova J, Bebrova E, Hysperska V, Kuijper EJ. Clostridium difficile ribotype 078 cultured from post-surgical non-healing wound in a patient carrying ribotype 014 in the intestinal tract. Folia Microbiol (Praha) 2015; 60:541-4. [PMID: 25935201 DOI: 10.1007/s12223-015-0392-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/02/2015] [Indexed: 11/29/2022]
Abstract
Extra-intestinal infections caused by Clostridium difficile are rare. The risk of extra-intestinal infections associated with C. difficile may be particularly relevant in environments contaminated with C. difficile spores. This paper describes the case of a non-diarrheic patient colonized with C. difficile ribotype 014 in the intestinal tract who developed a post-surgical wound infection by C. difficile ribotype 078. The infection responded to metronidazole administered first intravenously and then orally. This case indicates that C. difficile may not only be related to diarrheic diseases, but also to infections of non-healing wounds, especially in situations when C. difficile is the only isolated pathogen.
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Affiliation(s)
- Otakar Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84, 150 06, Prague 5, Czech Republic
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84, 150 06, Prague 5, Czech Republic. .,DNA Laboratory, Department of Child Neurology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.
| | - Jiri Kriz
- Spinal Cord Unit, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jana Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84, 150 06, Prague 5, Czech Republic
| | - Eliska Bebrova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84, 150 06, Prague 5, Czech Republic
| | - Veronika Hysperska
- Spinal Cord Unit, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands
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112
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Nagar A, Yew P, Fairley D, Hanrahan M, Cooke S, Thompson I, Elbaz W. Report of an outbreak of Clostridium difficile infection caused by ribotype 053 in a neurosurgery unit. J Infect Prev 2015; 16:126-130. [PMID: 28989415 DOI: 10.1177/1757177414560250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 10/19/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND We describe an outbreak of Clostridium difficile infection (CDI) with ribotype 053, a possible hypervirulent strain that causes outbreaks, in a neurosurgical unit. OUTBREAK INVESTIGATION The outbreak was investigated by creating a timeline of all toxin positive patients with root cause analysis, supplemented with ribotyping results, hand hygiene and environmental audits. There were five cases of CDI, three caused by ribotype 053 indicating transmission. INFECTION PREVENTION MEASURES These included a short period of ward closure to allow enhanced cleaning, including use of vaporised hydrogen peroxide, isolation of infected patients, reinforcement of hand hygiene, education of all staff on C. difficile, reduction of shared bay occupancy from six to four, and addressing staffing levels. DISCUSSION The patients with ribotype 053 all had long inpatient stays and had required several courses of broad-spectrum antibiotics for aspiration pneumonia. They also required enteral feeding, which can cause diarrhoea, and during long inpatient stays they had multiple toxin negative faecal samples making clinical diagnosis of CDI difficult. Hence they were not isolated promptly, leading to transmission. This is the first reported outbreak of C. difficile ribotype 053 in the UK and highlights the unique aspects of an outbreak in neurosurgical patients.
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Affiliation(s)
- Aaron Nagar
- Microbiology Department, Royal Victoria Hospital, Belfast, Northern Ireland
| | - Peter Yew
- Microbiology Department, Royal Victoria Hospital, Belfast, Northern Ireland
| | - Derek Fairley
- Virology Department, Royal Victoria Hospital, Belfast Health & Social Care Trust, Belfast, Northern Ireland
| | - Mary Hanrahan
- Infection Prevention and Control, Royal Victoria Hospital, Belfast Health & Social Care Trust, Belfast, Northern Ireland
| | - Stephen Cooke
- Neurosurgery Department, Royal Victoria Hospital, Belfast Health & Social Care Trust, Northern Ireland
| | - Irene Thompson
- Infection Prevention and Control, Royal Victoria Hospital, Belfast Health & Social Care Trust, Belfast, Northern Ireland
| | - Wesam Elbaz
- Microbiology Department, Royal Victoria Hospital, Belfast, Northern Ireland
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Rizzardi K, Åkerlund T. High Molecular Weight Typing with MALDI-TOF MS - A Novel Method for Rapid Typing of Clostridium difficile. PLoS One 2015; 10:e0122457. [PMID: 25923527 PMCID: PMC4414534 DOI: 10.1371/journal.pone.0122457] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/11/2015] [Indexed: 11/19/2022] Open
Abstract
Clostridium difficile strains were typed by a newly developed MALDI-TOF method, high molecular weight typing, and compared to PCR ribotyping. Among 500 isolates representing 59 PCR ribotypes a total of 35 high molecular weight types could be resolved. Although less discriminatory than PCR ribotyping, the method is extremely fast and simple, and supports for cost-effective screening of isolates during outbreak situations.
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Affiliation(s)
- Kristina Rizzardi
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Thomas Åkerlund
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
- * E-mail:
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114
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Martinson JNV, Broadaway S, Lohman E, Johnson C, Alam MJ, Khaleduzzaman M, Garey KW, Schlackman J, Young VB, Santhosh K, Rao K, Lyons RH, Walk ST. Evaluation of portability and cost of a fluorescent PCR ribotyping protocol for Clostridium difficile epidemiology. J Clin Microbiol 2015; 53:1192-7. [PMID: 25631804 PMCID: PMC4365229 DOI: 10.1128/jcm.03591-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/22/2015] [Indexed: 11/20/2022] Open
Abstract
Clostridium difficile is the most commonly identified pathogen among health care-associated infections in the United States. There is a need for accurate and low-cost typing tools that produce comparable data across studies (i.e., portable data) to help characterize isolates during epidemiologic investigations of C. difficile outbreaks and sporadic cases of disease. The most popular C. difficile-typing technique is PCR ribotyping, and we previously developed methods using fluorescent PCR primers and amplicon sizing on a Sanger-style sequencer to generate fluorescent PCR ribotyping data. This technique has been used to characterize tens of thousands of C. difficile isolates from cases of disease. Here, we present validation of a protocol for the cost-effective generation of fluorescent PCR ribotyping data. A key component of this protocol is the ability to accurately identify PCR ribotypes against an online database (http://walklab.rcg.montana.edu) at no cost. We present results from a blinded multicenter study to address data portability across four different laboratories and three different sequencing centers. Our standardized protocol and centralized database for typing of C. difficile pathogens will increase comparability between studies so that important epidemiologic linkages between cases of disease and patterns of emergence can be rapidly identified.
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Affiliation(s)
- Jonathan N V Martinson
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Susan Broadaway
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Egan Lohman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Christina Johnson
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - M Jahangir Alam
- College of Pharmacy, University of Houston, Houston, Texas, USA
| | | | - Kevin W Garey
- College of Pharmacy, University of Houston, Houston, Texas, USA
| | - Jessica Schlackman
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA Division of Infectious Diseases, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Kavitha Santhosh
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA Division of Infectious Diseases, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Robert H Lyons
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Seth T Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
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116
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Containment of Clostridium difficile infection without reduction in antimicrobial use in Hong Kong. Eur J Clin Microbiol Infect Dis 2015; 34:1381-6. [DOI: 10.1007/s10096-015-2362-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/06/2015] [Indexed: 02/05/2023]
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117
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Rapid spread of Clostridium difficile NAP1/027/ST1 in Chile confirms the emergence of the epidemic strain in Latin America. Epidemiol Infect 2015; 143:3069-73. [PMID: 25687254 DOI: 10.1017/s0950268815000023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clostridium difficile infection has gained importance in recent years as a result of the rapid spread of epidemic strains, including hypervirulent strains. This study reports the molecular epidemiology of C. difficile obtained from hospitalized patients in Chile. Seven hundred and nineteen isolates of toxigenic C. difficile from 45 hospitals across the country were characterized through toxin profile, pulsed-field gel electrophoresis (PFGE), and sequencing of the tcdC gene. In addition, polymerase chain reaction (PCR) ribotyping and multilocus sequence typing (MLST) were performed on a subset of selected strains. PFGE typing of 719 isolates of C. difficile produced 60 PFGE patterns (subtypes). Subtype 1 was predominant (79% of isolates) and related to the hypervirulent strain (NAP1). Subtype 1 showed 73% relatedness with nine other subtypes, which had a similar tcdC deletion. Subtype 1 corresponded to ribotype 027 and ST1. This report shows the wide dissemination of the hypervirulent strain NAP1/027/ST1 in Chile.
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118
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Fawley WN, Knetsch CW, MacCannell DR, Harmanus C, Du T, Mulvey MR, Paulick A, Anderson L, Kuijper EJ, Wilcox MH. Development and validation of an internationally-standardized, high-resolution capillary gel-based electrophoresis PCR-ribotyping protocol for Clostridium difficile. PLoS One 2015; 10:e0118150. [PMID: 25679978 PMCID: PMC4332677 DOI: 10.1371/journal.pone.0118150] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/05/2015] [Indexed: 01/08/2023] Open
Abstract
PCR-ribotyping has been adopted in many laboratories as the method of choice for C. difficile typing and surveillance. However, issues with the conventional agarose gel-based technique, including inter-laboratory variation and interpretation of banding patterns have impeded progress. The method has recently been adapted to incorporate high-resolution capillary gel-based electrophoresis (CE-ribotyping), so improving discrimination, accuracy and reproducibility. However, reports to date have all represented single-centre studies and inter-laboratory variability has not been formally measured or assessed. Here, we achieved in a multi-centre setting a high level of reproducibility, accuracy and portability associated with a consensus CE-ribotyping protocol. Local databases were built at four participating laboratories using a distributed set of 70 known PCR-ribotypes. A panel of 50 isolates and 60 electronic profiles (blinded and randomized) were distributed to each testing centre for PCR-ribotype identification based on local databases generated using the standard set of 70 PCR-ribotypes, and the performance of the consensus protocol assessed. A maximum standard deviation of only ±3.8bp was recorded in individual fragment sizes, and PCR-ribotypes from 98.2% of anonymised strains were successfully discriminated across four ribotyping centres spanning Europe and North America (98.8% after analysing discrepancies). Consensus CE-ribotyping increases comparability of typing data between centres and thereby facilitates the rapid and accurate transfer of standardized typing data to support future national and international C. difficile surveillance programs.
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Affiliation(s)
- Warren N Fawley
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - C W Knetsch
- Department of Medical Microbiology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | - Duncan R MacCannell
- Centers for Disease Control and Prevention (CDC), Atlanta, United States of America
| | - Celine Harmanus
- Department of Medical Microbiology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | - Tim Du
- Public Health Agency of Canada (PHAC), Winnipeg, Canada
| | | | - Ashley Paulick
- Centers for Disease Control and Prevention (CDC), Atlanta, United States of America
| | - Lydia Anderson
- Centers for Disease Control and Prevention (CDC), Atlanta, United States of America
| | - E J Kuijper
- Department of Medical Microbiology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom; Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
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119
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Dingle TC, MacCannell DR. Molecular Strain Typing and Characterisation of Toxigenic Clostridium difficile. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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120
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Krutova M, Nyc O, Kuijper EJ, Geigerova L, Matejkova J, Bergerova T, Arvand M. A case of imported Clostridium difficile PCR-ribotype 027 infection within the Czech Republic which has a high prevalence of C. difficile ribotype 176. Anaerobe 2014; 30:153-5. [DOI: 10.1016/j.anaerobe.2014.09.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 09/23/2014] [Accepted: 09/29/2014] [Indexed: 11/24/2022]
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121
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Abstract
This study presents a DNA microarray-based assay for fast and simple PCR ribotyping of Clostridium difficile strains. Hybridization probes were designed to query the modularly structured intergenic spacer region (ISR), which is also the template for conventional and PCR ribotyping with subsequent capillary gel electrophoresis (seq-PCR) ribotyping. The probes were derived from sequences available in GenBank as well as from theoretical ISR module combinations. A database of reference hybridization patterns was set up from a collection of 142 well-characterized C. difficile isolates representing 48 seq-PCR ribotypes. The reference hybridization patterns calculated by the arithmetic mean were compared using a similarity matrix analysis. The 48 investigated seq-PCR ribotypes revealed 27 array profiles that were clearly distinguishable. The most frequent human-pathogenic ribotypes 001, 014/020, 027, and 078/126 were discriminated by the microarray. C. difficile strains related to 078/126 (033, 045/FLI01, 078, 126, 126/FLI01, 413, 413/FLI01, 598, 620, 652, and 660) and 014/020 (014, 020, and 449) showed similar hybridization patterns, confirming their genetic relatedness, which was previously reported. A panel of 50 C. difficile field isolates was tested by seq-PCR ribotyping and the DNA microarray-based assay in parallel. Taking into account that the current version of the microarray does not discriminate some closely related seq-PCR ribotypes, all isolates were typed correctly. Moreover, seq-PCR ribotypes without reference profiles available in the database (ribotype 009 and 5 new types) were correctly recognized as new ribotypes, confirming the performance and expansion potential of the microarray.
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122
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Spigaglia P, Drigo I, Barbanti F, Mastrantonio P, Bano L, Bacchin C, Puiatti C, Tonon E, Berto G, Agnoletti F. Antibiotic resistance patterns and PCR-ribotyping of Clostridium difficile strains isolated from swine and dogs in Italy. Anaerobe 2014; 31:42-6. [PMID: 25316022 DOI: 10.1016/j.anaerobe.2014.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/24/2014] [Accepted: 10/05/2014] [Indexed: 01/05/2023]
Abstract
Recent studies suggest animals, in particular farm and companion animals, as possible reservoir for Clostridium difficile human pathogenic strains. The aim of this study was to give a first characterization of C. difficile isolates from Italian swine and dogs. In total, 10 different PCR-ribotypes were identified among porcine strains and six among canine strains. The predominant type found among porcine strains was 078 (50%), whereas the most frequently detected among canine strains was the non-toxinogenic 010 (64%). Considering the CLSI breakpoints, 60% of porcine isolates was resistant to ERY, 35% to MXF, 15% to CLI, 5% to RIF, and none to MTZ or VAN. Among dogs, 51% of strains was resistant to CLI, 46% to ERY, 21% to MTZ and 5% to MXF or RIF, and none to VAN. Five porcine strains (10%) and 9 canine isolates (41%) were MDR. Interestingly, 8 MDR canine strains were highly resistant to MTZ, with MICs ≥32 mg/L. Considering the EUCAST cut-off for MTZ (MIC >2 mg/L), 13 canine isolates and one porcine strain were found with reduced susceptibility to MTZ (MICs ranging from 3 to ≥256 mg/L). Swine and canine strains showing resistance or reduced susceptibility to MTZ belonged to PCR-ribotype 010 and 078. These PCR-ribotypes have been associated to reduced susceptibility to MTZ also in human, suggesting a potential risk for the emergence of C. difficile strains resistant to the current first-line antibiotic for CDI treatment. The agar incorporation method (AIM) was confirmed as the best method to detect C. difficile strains with this phenotype also after strains manipulations. The results obtained add further evidences about the possible role of animals as source of MDR C. difficile strains and reservoir of antibiotic resistance determinants.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Ilenia Drigo
- Special Bacteriology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Treviso, Italy
| | - Fabrizio Barbanti
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Mastrantonio
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Luca Bano
- Special Bacteriology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Treviso, Italy
| | - Cosetta Bacchin
- Special Bacteriology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Treviso, Italy
| | - Cinzia Puiatti
- Special Bacteriology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Treviso, Italy
| | - Elena Tonon
- Special Bacteriology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Treviso, Italy
| | - Giacomo Berto
- Special Bacteriology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Treviso, Italy
| | - Fabrizio Agnoletti
- Special Bacteriology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Treviso, Italy
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Performance assessment of the BD MAX Cdiff assay in comparison to Xpert C. difficile assay in a setting with very low prevalence of toxigenic Clostridium difficile PCR ribotype 027. Anaerobe 2014; 30:156-8. [PMID: 25305151 DOI: 10.1016/j.anaerobe.2014.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 01/05/2023]
Abstract
In a clinical setting with low prevalence of 'epidemic' PCR ribotype 027, the BD MAX Cdiff assay was found to be a suitable alternative to the Xpert C. difficile assay for the detection of toxigenic Clostridium difficile in samples which are reflex PCR tested after obtaining a discrepant immunoassay result. There was no significant difference between the sensitivities and specificities of both commercial molecular assays.
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124
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Fang WJ, Jing DZ, Luo Y, Fu CY, Zhao P, Qian J, Tian BR, Chen XG, Zheng YL, Zheng Y, Deng J, Zou WH, Feng XR, Liu FL, Mou XZ, Zheng SS. Clostridium difficile carriage in hospitalized cancer patients: a prospective investigation in eastern China. BMC Infect Dis 2014; 14:523. [PMID: 25267108 PMCID: PMC4261591 DOI: 10.1186/1471-2334-14-523] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/25/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Clostridium difficile carriage has been considered as a potential source for the deadly infection, but its role in cancer patients is still unclear. We aimed to identify the clinical and immunological factors that are related to C. difficile carriage in Chinese cancer patients. METHODS A total of 400 stool samples were collected from cancer patients who received chemotherapy in three hospitals of eastern China. Bacterial genomic DNA was extracted and two toxin genes (tcdA and tcdB) were detected. PCR ribotyping was performed using capillary gel electrophoresis. Concentrations of prostaglandin E2 (PGE2), transforming growth factor beta (TGF-β) and interleukin-10 (IL-10) were measured using enzyme-linked immunosorbent assay (ELISA) kits. RESULTS Eighty-two (20.5%) samples were confirmed to be C. difficile-positive and positive for tpi, tcdA, and tcdB genes. The C. difficile-positive rates in patients with diarrhea and no diarrhea were 35% and 19.7%, respectively (p = 0.09). Patients who were younger than 50 years old and were hospitalized for at least 10 days had a C. difficile-positive rate as high as 35%. In contrast, patients who were older than 50 years old and were hospitalized for less than 10 days had a C. difficile-positive rate of only 12.7% (p = 0.0009). No association was found between C. difficile carriage and chemotherapy regimen, antibiotic drug use, or immunosuppressive mediators, such as prostaglandin E2 (PGE2), transforming growth factor beta (TGF-β), or interleukin-10 (IL-10). Twelve ribotypes of C. difficile were identified, but none of them belonged to ribotype 027. CONCLUSIONS We conclude that younger patients and those with longer hospitalization stays may be more prone to C. difficile carriage. Studies of larger populations are warranted to clarify the exact role of C. difficile carriage in hospitalized cancer patients in China.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Shu-Sen Zheng
- First Affiliated Hospital, School of Medicine, ZheJiang University, 79 Qinchun Road, Hangzhou 310006, China.
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Isolation and Characterization of a New Clostridium difficile Ribotype During a Prospective Study in a Hospital in Italy. Curr Microbiol 2014; 70:151-3. [DOI: 10.1007/s00284-014-0697-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/06/2014] [Indexed: 10/24/2022]
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126
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Janezic S, Indra A, Rattei T, Weinmaier T, Rupnik M. Recombination drives evolution of the Clostridium difficile 16S-23S rRNA intergenic spacer region. PLoS One 2014; 9:e106545. [PMID: 25222120 PMCID: PMC4164361 DOI: 10.1371/journal.pone.0106545] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/05/2014] [Indexed: 12/18/2022] Open
Abstract
PCR-ribotyping, a typing method based on size variation in 16S-23S rRNA intergenic spacer region (ISR), has been used widely for molecular epidemiological investigations of C. difficile infections. In the present study, we describe the sequence diversity of ISRs from 43 C. difficile strains, representing different PCR-ribotypes and suggest homologous recombination as a possible mechanism driving the evolution of 16S-23S rRNA ISRs. ISRs of 45 different lengths (ranging from 185 bp to 564 bp) were found among 458 ISRs. All ISRs could be described with one of the 22 different structural groups defined by the presence or absence of different sequence modules; tRNAAla genes and different combinations of spacers of different lengths (33 bp, 53 bp or 20 bp) and 9 bp direct repeats separating the spacers. The ISR structural group, in most cases, coincided with the sequence length. ISRs that were of the same lengths had also very similar nucleotide sequence, suggesting that ISRs were not suitable for discriminating between different strains based only on the ISR sequence. Despite large variations in the length, the alignment of ISR sequences, based on the primary sequence and secondary structure information, revealed many conserved regions which were mainly involved in maturation of pre-rRNA. Phylogenetic analysis of the ISR alignment yielded strong evidence for intra- and inter-homologous recombination which could be one of the mechanisms driving the evolution of C. difficile 16S-23S ISRs. The modular structure of the ISR, the high sequence similarities of ISRs of the same sizes and the presence of homologous recombination also suggest that different copies of C. difficile 16S-23S rRNA ISR are evolving in concert.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | - Alexander Indra
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Thomas Rattei
- Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | | | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
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Novak A, Spigaglia P, Barbanti F, Goic-Barisic I, Tonkic M. First clinical and microbiological characterization of Clostridium difficile infection in a Croatian University Hospital. Anaerobe 2014; 30:18-23. [PMID: 25079669 DOI: 10.1016/j.anaerobe.2014.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 01/16/2023]
Abstract
Clinical background and molecular epidemiology of Clostridium difficile infection (CDI) in the University Hospital Centre Split were investigated from January 2010 to December 2011. In total, 54 patients with first episode of CDI were consecutively included in the study based on the positive EIA test specific for A and B toxins. Demographic and clinical data were prospectively analyzed from medical records. CDI incidence rate was 0.6 per 10,000 patient-days. Thirty six cases (70.6%) were healthcare-associated, twelve cases (23.5%) were community-associated and three (5.9%) were indeterminate. Six patients (11.7%) had suffered one or more recurrences and 37 patients (72.5%) showed severe CDI. Prior therapy with third generation cephalosporin was significantly associated with severe CDI (P<0.021). Fifty four toxigenic C. difficile strains were isolated and 50 of them were available for PCR-ribotyping. Sixteen different PCR-ribotypes were identified. The most prevalent were PCR-ribotype 001 (27.8%) and 014/020 (24.1%). Twenty three strains were resistant to at least one of the antibiotics tested. Among resistant strains, three (13.0%)--all PCR-ribotype 001--were multi-resistant. Resistance to fluoroquinolones was significantly higher in strains that caused infection after previous use of fluoroquinolones (P=0.04).
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Affiliation(s)
- Anita Novak
- University Hospital Centre Split, Croatia; University of Split School of Medicine, Split, Croatia.
| | - Patrizia Spigaglia
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Fabrizio Barbanti
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Ivana Goic-Barisic
- University Hospital Centre Split, Croatia; University of Split School of Medicine, Split, Croatia
| | - Marija Tonkic
- University Hospital Centre Split, Croatia; University of Split School of Medicine, Split, Croatia
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Gray TJ, Kong F, Jelfs P, Sintchenko V, Chen SCA. Improved identification of rapidly growing mycobacteria by a 16S-23S internal transcribed spacer region PCR and capillary gel electrophoresis. PLoS One 2014; 9:e102290. [PMID: 25013955 PMCID: PMC4094492 DOI: 10.1371/journal.pone.0102290] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 06/17/2014] [Indexed: 01/04/2023] Open
Abstract
The identification of rapidly growing mycobacteria (RGM) remains problematic because of evolving taxonomy, limitations of current phenotypic methods and absence of a universal gene target for reliable speciation. This study evaluated a novel method of identification of RGM by amplification of the mycobacterial 16S–23S rRNA internal transcribed spacer (ITS) followed by resolution of amplified fragments by capillary gel electrophoresis (CGE). Nineteen American Type Culture Collection (ATCC) Mycobacterium strains and 178 clinical isolates of RGM (12 species) were studied. All RGM ATCC strains generated unique electropherograms with no overlap with slowly growing mycobacteria species, including M. tuberculosis. A total of 47 electropherograms for the 178 clinical isolates were observed allowing the speciation of 175/178 (98.3%) isolates, including the differentiation of the closely related species, M. massiliense (M. abscessus subspecies bolletii) and M. abscessus (M. abscessus sensu stricto). ITS fragment size ranged from 332 to 534 bp and 33.7% of clinical isolates generated electropherograms with two distinct peaks, while the remainder where characterized with a single peak. Unique peaks (fragment lengths) were identified for 11/12 (92%) RGM species with only M. moriokaense having an indistinguishable electropherogram from a rarely encountered CGE subtype of M. fortuitum. We conclude that amplification of the 16S–23S ITS gene region followed by resolution of fragments by CGE is a simple, rapid, accurate and reproducible method for species identification and characterization of the RGM.
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Affiliation(s)
- Timothy J. Gray
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
- * E-mail:
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Peter Jelfs
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead, New South Wales, Australia
- Marie Bashir Institute for Emerging Infections and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharon C-A. Chen
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead, New South Wales, Australia
- Marie Bashir Institute for Emerging Infections and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
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129
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Janezic S, Zidaric V, Pardon B, Indra A, Kokotovic B, Blanco JL, Seyboldt C, Diaz CR, Poxton IR, Perreten V, Drigo I, Jiraskova A, Ocepek M, Weese JS, Songer JG, Wilcox MH, Rupnik M. International Clostridium difficile animal strain collection and large diversity of animal associated strains. BMC Microbiol 2014; 14:173. [PMID: 24972659 PMCID: PMC4100527 DOI: 10.1186/1471-2180-14-173] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/19/2014] [Indexed: 01/08/2023] Open
Abstract
Background Clostridium difficile is an important cause of intestinal infections in some animal species and animals might be a reservoir for community associated human infections. Here we describe a collection of animal associated C. difficile strains from 12 countries based on inclusion criteria of one strain (PCR ribotype) per animal species per laboratory. Results Altogether 112 isolates were collected and distributed into 38 PCR ribotypes with agarose based approach and 50 PCR ribotypes with sequencer based approach. Four PCR ribotypes were most prevalent in terms of number of isolates as well as in terms of number of different host species: 078 (14.3% of isolates; 4 hosts), 014/020 (11.6%; 8 hosts); 002 (5.4%; 4 hosts) and 012 (5.4%; 5 hosts). Two animal hosts were best represented; cattle with 31 isolates (20 PCR ribotypes; 7 countries) and pigs with 31 isolates (16 PCR ribotypes; 10 countries). Conclusions This results show that although PCR ribotype 078 is often reported as the major animal C. difficile type, especially in pigs, the variability of strains in pigs and other animal hosts is substantial. Most common human PCR ribotypes (014/020 and 002) are also among most prevalent animal associated C. difficile strains worldwide. The widespread dissemination of toxigenic C. difficile and the considerable overlap in strain distribution between species furthers concerns about interspecies, including zoonotic, transmission of this critically important pathogen.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.
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130
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Krutova M, Matejkova J, Nyc O. C. difficile ribotype 027 or 176? Folia Microbiol (Praha) 2014; 59:523-6. [PMID: 24970104 DOI: 10.1007/s12223-014-0323-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 05/13/2014] [Indexed: 12/18/2022]
Abstract
Clostridium difficile is a major nosocomial pathogen of present times. The analysis of 624 C. difficile strains from 11 hospitals in the Czech Republic in 2013 revealed that 40% of isolates belonged to ribotype 176. These results suggest that the incidence of CDI (C. difficile infection) in the Czech Republic has increased probably in connection with C. difficile ribotype 176. The molecular systems Xpert C. difficile Epi assay (Cepheid Inc., Sunnyvale, CA) diagnoses toxigenic strains and supports C. difficile ribotype 027 determination based on three specific target places in the toxigenic C. difficile genome. Twenty-nine strains cultivated from stool specimens were evaluated by the Xpert systems as presumed C. difficile PCR ribotype 027 were confirmed as a C. difficile ribotype 176 based on ribotyping. A further 120 C. difficile strains of ribotype 176 were examined for the presence of genes tcdB, cdtB and deletion in position 117 in the tcdC gene. Our experience shows that due to the correspondence of the target places, C. difficile ribotype 176 may be interpreted as ribotype 027 by Xpert C. difficile Epi assay (Cepheid Inc., Sunnyvale, CA). Further molecular analysis as ribotyping based on capillary electrophoresis is needed to differentiate between C. difficile ribotypes 027 and 176 for appropriate epidemiological situation control on local and national levels.
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Affiliation(s)
- Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic,
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131
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Eyre DW, Walker AS. Clostridium difficile surveillance: harnessing new technologies to control transmission. Expert Rev Anti Infect Ther 2014; 11:1193-205. [PMID: 24151834 DOI: 10.1586/14787210.2013.845987] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Clostridium difficile surveillance allows outbreaks of cases clustered in time and space to be identified and further transmission prevented. Traditionally, manual detection of groups of cases diagnosed in the same ward or hospital, often followed by retrospective reference laboratory genotyping, has been used to identify outbreaks. However, integrated healthcare databases offer the prospect of automated real-time outbreak detection based on statistically robust methods, and accounting for contacts between cases, including those distant to the ward of diagnosis. Complementary to this, rapid benchtop whole genome sequencing, and other highly discriminatory genotyping, has the potential to distinguish which cases are part of an outbreak with high precision and in clinically relevant timescales. These new technologies are likely to shape future surveillance.
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Affiliation(s)
- David W Eyre
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
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132
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Starzengruber P, Segagni Lusignani L, Wrba T, Mitteregger D, Indra A, Graninger W, Presterl E, Diab-Elschahawi M. Severe Clostridium difficile infection: incidence and risk factors at a tertiary care university hospital in Vienna, Austria. Wien Klin Wochenschr 2014; 126:427-30. [PMID: 24903143 DOI: 10.1007/s00508-014-0549-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/13/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Clostridium difficile infection (CDI) is the major cause of hospital-acquired bacterial diarrhoea. The incidence of CDI has been increasing in Canada, the US and Europe and severe cases are becoming more common. METHODS A retrospective cohort study investigating all patients with an episode of CDI present at the Vienna University Hospital between 01 January 2012 and 31 December 2012 was conducted. All microbiologically confirmed C. difficile toxin positive cases were included, ribotyped and analysed regarding their clinical course. RESULTS A total of 278 patients with CDI were recorded, with an overall CDI incidence of 5.23 per 10,000 patients-days. Around 84,5 % (235/278) of CDI cases would have been classified as severe CDI according to European Society of Clinical Microbiology and Infectious Diseases (ESCMID) if all criteria were used. According to Society for Healthcare Epidemiology of America and the Infectious Diseases Society of America (SHEA/IDSA) guidelines only 16.5 % (46/278) could be classified as severe; with a severe CDI incidence of 4.41 and 0.86 per 10,000 patient-days, respectively. Multivariate analysis showed only a co-morbidity index of ≥ 3 (p = 0.013) as independent risk factor for severe CDI. No link between ribotype 027 and severity or clustering was observed in our study population. CONCLUSIONS Special attention in terms of restrictive antibiotic prescription should be given to patients having a Charlson co-morbidity ≥ 3 at the time of hospital admission. SHEA/IDSA guidelines were more accurate than ESCMID criteria in predicting severe CDI in our collective, of mostly severely ill patients, in a tertiary care hospital setting.
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Affiliation(s)
- Peter Starzengruber
- Department of Hospital Hygiene and Infection Control, Vienna General Hospital, Medical University Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
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133
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Sathyendran V, McAuliffe GN, Swager T, Freeman JT, Taylor SL, Roberts SA. Clostridium difficile as a cause of healthcare-associated diarrhoea among children in Auckland, New Zealand: clinical and molecular epidemiology. Eur J Clin Microbiol Infect Dis 2014; 33:1741-7. [PMID: 24810967 DOI: 10.1007/s10096-014-2139-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/23/2014] [Indexed: 12/18/2022]
Abstract
We aimed to determine the incidence of Clostridium difficile infection (CDI), the molecular epidemiology of circulating C. difficile strains and risk factors for CDI among hospitalised children in the Auckland region. A cross-sectional study was undertaken of hospitalised children <15 years of age in two hospitals investigated for healthcare-associated diarrhoea between November 2011 and June 2012. Stool specimens were analysed for the presence of C. difficile using a two-step testing algorithm including polymerase chain reaction (PCR). C. difficile was cultured and PCR ribotyping performed. Demographic data, illness characteristics and risk factors were compared between children with and without CDI. Non-duplicate stool specimens were collected from 320 children with a median age of 1.2 years (range 3 days to 15 years). Forty-six patients (14 %) tested met the definition for CDI. The overall incidence of CDI was 2.0 per 10,000 bed days. The percentage of positive tests among neonates was only 2.6 %. PCR ribotyping showed a range of strains, with ribotype 014 being the most common. Significant risk factors for CDI were treatment with proton pump inhibitors [risk ratio (RR) 1.74, 95 % confidence interval (CI) 1.09-5.59; p = 0.002], presence of underlying malignancy (RR 2.71, 95 % CI 1.65-4.62; p = 0.001), receiving chemotherapy (RR 2.70, 95 % CI 1.41-4.83; p = 0.003) and exposure to antibiotics (RR 1.17, 95 % CI 0.99-1.17; p = 0.03). C. difficile is an important cause of healthcare-associated diarrhoea in this paediatric population. The notion that neonatal populations will always have high rates of colonisation with C. difficile may not be correct. Several risk factors associated with CDI among adults were also found to be significant.
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Affiliation(s)
- V Sathyendran
- Department of Microbiology, LabPlus, Auckland City Hospital, Auckland, New Zealand
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134
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Oleastro M, Coelho M, Gião M, Coutinho S, Mota S, Santos A, Rodrigues J, Faria D. Outbreak of Clostridium difficile PCR ribotype 027--the recent experience of a regional hospital. BMC Infect Dis 2014; 14:209. [PMID: 24739945 PMCID: PMC3998949 DOI: 10.1186/1471-2334-14-209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 04/08/2014] [Indexed: 12/18/2022] Open
Abstract
Background Clostridium difficile infection (CDI) is the leading cause of healthcare-associated diarrhea, and several outbreaks with increased severity and mortality have been reported. In this study we report a C. difficile PCR ribotype 027 outbreak in Portugal, aiming to contribute to a better knowledge of the epidemiology of this agent in Europe. Methods Outbreak report with retrospective study of medical records and active surveillance data of all inpatients with the diagnosis of CDI, from 1st January to 31th December 2012, in a Portuguese hospital. C. difficile isolates were characterized regarding ribotype, toxin genes and moxifloxin resistance. Outbreak control measures were taken, concerning communication, education, reinforcement of infection control measures, optimization of diagnosis and treatment of CDI, and antibiotic stewardship. Results Fifty-three inpatients met the case definition of C. difficile-associated infection: 55% males, median age was 78.0 years (interquartile range: 71.0-86.0), 75% had co-morbidities, only 15% had a nonfatal condition, 68% had at least one criteria of severe disease at diagnosis, 89% received prior antibiotherapy, 79% of episodes were nosocomial. CDI rate peak was 13.89/10,000 bed days. Crude mortality rate at 6 months was 64.2% while CDI attributable cause was 11.3%. Worse outcome was related to older age (P = 0.022), severity criteria at diagnosis (leukocytosis (P = 0.008) and renal failure), and presence of fatal underlying condition (P = 0.025). PCR ribotype 027 was identified in 16 of 22 studied samples. Conclusions This is the first report of a 027-CDI outbreak in Portugal. We emphasize the relevance of the measures taken to control the outbreak and highlight the importance of implementing a close and active surveillance of CDI.
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Affiliation(s)
- Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr, Ricardo Jorge, Av, Padre Cruz, 1649-016 Lisbon, Portugal.
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135
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Kurka H, Ehrenreich A, Ludwig W, Monot M, Rupnik M, Barbut F, Indra A, Dupuy B, Liebl W. Sequence similarity of Clostridium difficile strains by analysis of conserved genes and genome content is reflected by their ribotype affiliation. PLoS One 2014; 9:e86535. [PMID: 24482682 PMCID: PMC3902958 DOI: 10.1371/journal.pone.0086535] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 12/10/2013] [Indexed: 12/18/2022] Open
Abstract
PCR-ribotyping is a broadly used method for the classification of isolates of Clostridium difficile, an emerging intestinal pathogen, causing infections with increased disease severity and incidence in several European and North American countries. We have now carried out clustering analysis with selected genes of numerous C. difficile strains as well as gene content comparisons of their genomes in order to broaden our view of the relatedness of strains assigned to different ribotypes. We analyzed the genomic content of 48 C. difficile strains representing 21 different ribotypes. The calculation of distance matrix-based dendrograms using the neighbor joining method for 14 conserved genes (standard phylogenetic marker genes) from the genomes of the C. difficile strains demonstrated that the genes from strains with the same ribotype generally clustered together. Further, certain ribotypes always clustered together and formed ribotype groups, i.e. ribotypes 078, 033 and 126, as well as ribotypes 002 and 017, indicating their relatedness. Comparisons of the gene contents of the genomes of ribotypes that clustered according to the conserved gene analysis revealed that the number of common genes of the ribotypes belonging to each of these three ribotype groups were very similar for the 078/033/126 group (at most 69 specific genes between the different strains with the same ribotype) but less similar for the 002/017 group (86 genes difference). It appears that the ribotype is indicative not only of a specific pattern of the amplified 16S–23S rRNA intergenic spacer but also reflects specific differences in the nucleotide sequences of the conserved genes studied here. It can be anticipated that the sequence deviations of more genes of C. difficile strains are correlated with their PCR-ribotype. In conclusion, the results of this study corroborate and extend the concept of clonal C. difficile lineages, which correlate with ribotypes affiliation.
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Affiliation(s)
- Hedwig Kurka
- Technische Universität München, Department of Microbiology, Freising, Germany
| | - Armin Ehrenreich
- Technische Universität München, Department of Microbiology, Freising, Germany
| | - Wolfgang Ludwig
- Technische Universität München, Department of Microbiology, Freising, Germany
| | - Marc Monot
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institute Pasteur, Paris, France
| | - Maja Rupnik
- Institute of Public Health Maribor and University of Maribor, Faculty of Medicine and Centre of excellence Cipkebip, Ljubljana, Slovenia
| | - Frederic Barbut
- National Reference Laboratory for Clostridium difficile, Faculté de Médecine Pierre et Marie Curie and Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alexander Indra
- Institute for Medical Microbiology and Hygiene, AGES – Austrian Agency for Health & Food Safety, Vienna, Austria
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institute Pasteur, Paris, France
| | - Wolfgang Liebl
- Technische Universität München, Department of Microbiology, Freising, Germany
- * E-mail:
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136
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Diagnosis of Clostridium difficile infection: an ongoing conundrum for clinicians and for clinical laboratories. Clin Microbiol Rev 2014; 26:604-30. [PMID: 23824374 DOI: 10.1128/cmr.00016-13] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Clostridium difficile is a formidable nosocomial and community-acquired pathogen, causing clinical presentations ranging from asymptomatic colonization to self-limiting diarrhea to toxic megacolon and fulminant colitis. Since the early 2000s, the incidence of C. difficile disease has increased dramatically, and this is thought to be due to the emergence of new strain types. For many years, the mainstay of C. difficile disease diagnosis was enzyme immunoassays for detection of the C. difficile toxin(s), although it is now generally accepted that these assays lack sensitivity. A number of molecular assays are commercially available for the detection of C. difficile. This review covers the history and biology of C. difficile and provides an in-depth discussion of the laboratory methods used for the diagnosis of C. difficile infection (CDI). In addition, strain typing methods for C. difficile and the evolving epidemiology of colonization and infection with this organism are discussed. Finally, considerations for diagnosing C. difficile disease in special patient populations, such as children, oncology patients, transplant patients, and patients with inflammatory bowel disease, are described. As detection of C. difficile in clinical specimens does not always equate with disease, the diagnosis of C. difficile infection continues to be a challenge for both laboratories and clinicians.
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137
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Phage ϕC2 mediates transduction of Tn6215, encoding erythromycin resistance, between Clostridium difficile strains. mBio 2013; 4:e00840-13. [PMID: 24255122 PMCID: PMC3870246 DOI: 10.1128/mbio.00840-13] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In this work, we show that Clostridium difficile phage ϕC2 transduces erm(B), which confers erythromycin resistance, from a donor to a recipient strain at a frequency of 10−6 per PFU. The transductants were lysogenic for ϕC2 and contained the erm(B) gene in a novel transposon, Tn6215. This element is 13,008 bp in length and contains 17 putative open reading frames (ORFs). It could also be transferred at a lower frequency by filter mating. Clostridium difficile is a major human pathogen that causes diarrhea that can be persistent and difficult to resolve using antibiotics. C. difficile is potentially zoonotic and has been detected in animals, food, and environmental samples. C. difficile genomes contain large portions of horizontally acquired genetic elements. The conjugative elements have been reasonably well studied, but transduction has not yet been demonstrated. Here, we show for the first time transduction as a mechanism for the transfer of a novel genetic element in C. difficile. Transduction may also be a useful tool for the genetic manipulation of C. difficile.
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138
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Gürtler V, Grando D. Reprint of New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes. METHODS IN MICROBIOLOGY 2013; 95:425-40. [PMID: 24050948 DOI: 10.1016/j.mimet.2013.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 11/24/2022]
Abstract
Clostridium difficile causes outbreaks of infectious diarrhoea, most commonly occurring in healthcare institutions. Recently, concern has been raised with reports of C. difficile disease in those traditionally thought to be at low risk i.e. community acquired rather than healthcare acquired. This has increased awareness for the need to track outbreaks and PCR-ribotyping has found widespread use to elucidate epidemiologically linked isolates. PCR-ribotyping uses conserved regions of the 16S rRNA gene and 23S rRNA gene as primer binding sites to produce varying PCR products due to the intergenic spacer (ITS1) regions of the multiple operons. With the explosion of whole genome sequence data it became possible to analyse the start of the 23S rRNA gene for a more accurate selection of regions closer to the end of the ITS1. However the following questions must still be asked: (i) Does the chromosomal organisation of the rrn operon vary between C. difficile strains? and (ii) just how conserved are the primer binding regions? Eight published C. difficile genomes have been aligned to produce a detailed database of indels of the ITS1's from the rrn operon sets. An iPad Filemaker Go App has been constructed and named RiboTyping (RT). It contains detail such as sequences, ribotypes, strain numbers, GenBank numbers and genome position numbers. Access to various levels of the database is provided so that details can be printed. There are three main regions of the rrn operon that have been analysed by the database and related to each other by strain, ribotype and operon: (1) 16S gene (2) ITS1 indels (3) 23S gene. This has enabled direct intra- and inter-genomic comparisons at the strain, ribotype and operon (allele) levels in each of the three genomic regions. This is the first time that such an analysis has been done. By using the RT App with search criteria it will be possible to select probe combinations for specific strains/ribotypes/rrn operons for experiments to do with diagnostics, typing and recombination of operons. Many more incomplete C. difficile whole genome sequencing projects are recorded in GenBank as underway and the rrn operon information from these can also be added to the RT App when available. The RT App will help simplify probe selection because of the complexity of the ITS1 in C. difficile even in a single genome and because other allele-specific regions (16S and 23S genes) of variability can be relationally compared to design extra probes to increase sensitivity.
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Affiliation(s)
- Volker Gürtler
- School of Applied Sciences, Building 223, Level 1, Bundoora Campus RMIT University, PO Box 71, Bundoora 3083, Australia.
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139
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Abstract
Clostridium difficile was isolated from 147 of 201 (73%) rectal swabs of piglets from 15 farms of Lower Saxony and North Rhine-Westphalia. In 14 farms, 14 to 100% (mean, 78%) of the animals tested were culture positive. The rate of isolation was 68% postpartum, increased to 94% in animals 2 to 14 days of age, and declined to 0% for animals 49 days of age and older. There was no link between isolation and antibiotic treatment or diarrhea of piglets. Strains were assigned to 10 PCR ribotypes, and up to 4 PCR ribotypes were found to be present at the same time on a farm. The closely related PCR ribotypes 078 (55%) and 126 (20%) were most frequently recovered and were present in 13 of the 14 positive farms. The comparison of multilocus VNTR (variable number of tandem repeats) analysis (MLVA) data from this study and previously published data on human, porcine, and bovine PCR ribotype 078 isolates from 5 European countries revealed genetic differences between strains of different geographic origin and confirmed the relatedness of human and porcine C. difficile isolates. This study demonstrated that the human-pathogenic PCR ribotypes 078 and 126 are predominant in piglets in Germany. The results suggest that presence of C. difficile is correlated with animal age but not with antibiotic treatment or clinical disease. MLVA indicated that strains of the same geographical origin are often genetically related and corroborated the hypothesis of a close epidemiological connection between human and porcine C. difficile isolates.
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140
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Schumann P, Pukall R. The discriminatory power of ribotyping as automatable technique for differentiation of bacteria. Syst Appl Microbiol 2013; 36:369-75. [DOI: 10.1016/j.syapm.2013.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 05/17/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
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Genetically diverse Clostridium difficile strains harboring abundant prophages in an estuarine environment. Appl Environ Microbiol 2013; 79:6236-43. [PMID: 23913427 DOI: 10.1128/aem.01849-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Clostridium difficile is the leading cause of antibiotic-associated diarrheal disease in health care settings across the world. Despite its pathogenic capacity, it can be carried asymptomatically and has been found in terrestrial and marine ecosystems outside hospital environments. Little is known about these environmental strains, and few studies have been conducted on estuarine systems. Although prophage abundance and diversity are known to occur within clinical strains, prophage carriage within environmental strains of C. difficile has not previously been explored. In this study, we isolated C. difficile from sites sampled in two consecutive years in an English estuarine system. Isolates were characterized by PCR ribotype, antibiotic resistance, and motility. The prevalence and diversity of prophages were detected by transmission electron microscopy (TEM) and a phage-specific PCR assay. We show that a dynamic and diverse population of C. difficile exists within these sediments and that it includes isolates of ribotypes which are associated with severe clinical infections and those which are more frequently isolated from outside the hospital environment. Prophage carriage was found to be high (75%), demonstrating that phages play a role in the biology of these strains.
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142
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Schneeberg A, Neubauer H, Schmoock G, Grossmann E, Seyboldt C. Presence of Clostridium difficile PCR ribotype clusters related to 033, 078 and 045 in diarrhoeic calves in Germany. J Med Microbiol 2013; 62:1190-1198. [DOI: 10.1099/jmm.0.056473-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
This study provides data on the distribution and relationship of C. difficile PCR ribotypes in diarrhoeic calves in Germany. C. difficile was isolated from 176 of 999 (17.6 %) faecal samples or swabs of diarrhoeic calves from 603 farms collected between January 2010 and August 2012 by eight federal laboratories of six states. Strains were assigned to 17 PCR ribotypes. PCR ribotypes 033 (57 %), 078 (17 %) and 045/FLI01 (closest match to 045 in the WEBRIBO database; 9 %) were found the most frequently. Nine per cent of all culture-positive tested animals shed more than one multiple locus variable number tandem repeat analysis (MLVA) or PCR ribotype. Eight PCR ribotypes with related profiles (including 033, 078 and 045/FLI01) representing 92 % of all isolates were grouped into three clusters. Molecular relatedness was supported by the absence of the MLVA locus A6
Cd
only in clustered strains and identical toxin gene profiles for strains within each cluster. Previously reported mulitilocus sequence typing analysis for PCR ribotypes that were also recovered in this study found identical sequence types and a tcdC deletion (Δ39 bp) for 033, 045, 078 and 126 (ST-11), confirming this clustering. A different geographical occurrence of PCR ribotypes was shown for cluster 033 (found more frequently in southern Germany) and 045 (found more frequently in northern Germany). This study showed that clusters of C. difficile PCR ribotypes related to 033, 078 and 045 are predominant in diarrhoeic calves in Germany. The high number of strains belonging to PCR ribotype 078 demonstrated that diarrhoeic calves are also potential reservoirs for human pathogenic C. difficile strains.
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Affiliation(s)
- Alexander Schneeberg
- Institute of Bacterial Infections and Zoonoses at the Federal Research Institute for Animal Health (Friedrich-Loeffler-Institut), Naumburger Strasse 96a, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses at the Federal Research Institute for Animal Health (Friedrich-Loeffler-Institut), Naumburger Strasse 96a, 07743 Jena, Germany
| | - Gernot Schmoock
- Institute of Bacterial Infections and Zoonoses at the Federal Research Institute for Animal Health (Friedrich-Loeffler-Institut), Naumburger Strasse 96a, 07743 Jena, Germany
| | - Ernst Grossmann
- Aulendorf State Veterinary Diagnostic Centre, Löwenbreitestrasse 18/20, 88326 Aulendorf, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses at the Federal Research Institute for Animal Health (Friedrich-Loeffler-Institut), Naumburger Strasse 96a, 07743 Jena, Germany
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143
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Leis JA, Gold WL, Ng J, Hirji Z, Pillai DR, Broukhanski G, Raggiunti P, Hota S, McGeer A, Poutanen SM. Indeterminate tcdB using a Clostridium difficile PCR assay: a retrospective cohort study. BMC Infect Dis 2013; 13:324. [PMID: 23865713 PMCID: PMC3718660 DOI: 10.1186/1471-2334-13-324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 07/08/2013] [Indexed: 01/05/2023] Open
Abstract
Background C. difficile (CD) real-time polymerase chain reaction (PCR) for toxin B gene (tcdB) is more sensitive, and reduces turnaround time when compared to toxin immunoassay. We noted typical amplification curves with high tcdB cycle thresholds (Ct) and low endpoints (Ept) that are labeled negative by the Xpert® C. difficile assay (Cepheid) and undertook this study to determine their significance. Methods We defined an indeterminate CD assay result as detection of a typical PCR amplification curve with an Ept >10 that was interpreted as negative by the Xpert® assay. Samples with indeterminate Xpert® result were collected for 5 months and retested by Xpert®, cultured for toxigenic CD, and isolates subjected to PCR ribotyping, detection of toxin genes and multilocus variable-number tandem repeat analysis (MLVA) typing. Chart reviews were completed to assess if patients met the Society of Healthcare Epidemiology of America and the Infectious Diseases Society of America CD infection (CDI) clinical case definition. Illness severity was compared with tcdB Ct and culture results. Results During the 5-month study period, 48/3620 (1%) of specimens were indeterminate and 387/3620 (11%) were positive. Of the 48 patients with indeterminate results, 39 (81%) met the clinical case definition of CDI, and 7 of these (18%) met criteria for severe CDI. Toxigenic stool cultures were positive for 86% (6/7) of patients with severe CDI, 19% (6/32) of patients with non-severe CDI, and 44% (4/9) of patients who did not meet the clinical case definition of CDI (p = 0.002). Lower tcdB Ct and higher Ept were associated with greater likelihood of toxigenic culture positivity (p = 0.03) and more severe symptoms (p = 0.06). Indeterminate results were not associated with a particular technologist or instrument module, or CD strain type. Conclusions A subset of specimens (1%) using the Xpert® C. difficile assay have typical amplification curves and are interpreted as negative. At least one-third of these results are associated with positive CD culture. The mechanism of these indeterminate results is not technique-related, equipment-related, or due to particular CD strains. Clinicians should be aware that even PCR testing has the potential to miss CDI cases and further highlights the importance of clinical context when interpreting results.
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Affiliation(s)
- Jerome A Leis
- Division of Infectious Diseases, Department of Medicine, University Health Network/Mount Sinai Hospital, Toronto, ON, Canada.
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144
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Behroozian AA, Chludzinski JP, Lo ES, Ewing SA, Waslawski S, Newton DW, Young VB, Aronoff DM, Walk ST. Detection of mixed populations of Clostridium difficile from symptomatic patients using capillary-based polymerase chain reaction ribotyping. Infect Control Hosp Epidemiol 2013; 34:961-966. [PMID: 23917911 DOI: 10.1086/671728] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To investigate the simultaneous occurrence of more than 1 Clostridium difficile ribotype in patients' stool samples at the time of diagnostic testing. METHODS Stool samples submitted for diagnostic testing for the presence of toxigenic C. difficile were obtained for 102 unique patients. A total of 95 single colonies of C. difficile per stool sample were isolated on selective media, subcultured alongside negative (uninoculated) controls, and polymerase chain reaction (PCR) ribotyped using capillary gel electrophoresis. RESULTS Capillary-based PCR ribotyping was successful for 9,335 C. difficile isolates, yielding a median of 93 characterized isolates per stool sample (range, 69-95). More than 1 C. difficile ribotype was present in 16 of 102 (16%) C. difficile infection (CDI) cases; 2 of the 16 mixtures were composed of at least 3 ribotypes, while the remaining 14 were composed of at least 2. CONCLUSIONS Deep sampling of patient stool samples coupled with capillary-based PCR ribotyping identified a high rate of mixed CDI cases compared with previous estimates. Studies seeking to quantify the clinical significance of particular C. difficile ribotypes should account for mixed cases of disease.
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Affiliation(s)
- Adam A Behroozian
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Health System, Ann Arbor, Michigan
| | - Jeffrey P Chludzinski
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Health System, Ann Arbor, Michigan
| | - Eugene S Lo
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Health System, Ann Arbor, Michigan
| | - Sarah A Ewing
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Health System, Ann Arbor, Michigan
| | - Sheila Waslawski
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Health System, Ann Arbor, Michigan
| | - Duane W Newton
- Clinical Microbiology Laboratories, Department of Pathology, University of Michigan Health System, Ann Arbor, Michigan
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Health System, Ann Arbor, Michigan.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - David M Aronoff
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Health System, Ann Arbor, Michigan.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Seth T Walk
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Health System, Ann Arbor, Michigan.,Department of Microbiology, Montana State University, Bozeman, Montana
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145
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Abstract
Typing of Clostridium difficile facilitates understanding of the epidemiology of the infection. Some evaluations have shown that certain strain types (for example, ribotype 027) are more virulent than others and are associated with worse clinical outcomes. Although restriction endonuclease analysis (REA) and pulsed-field gel electrophoresis have been widely used in the past, PCR ribotyping is the current method of choice for typing of C. difficile. However, global standardization of ribotyping results is urgently needed. Whole-genome sequencing of C. difficile has the potential to provide even greater epidemiologic information than ribotyping.
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146
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Gürtler V, Grando D. New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes. J Microbiol Methods 2013; 93:257-72. [PMID: 23545446 DOI: 10.1016/j.mimet.2013.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
Abstract
Clostridium difficile causes outbreaks of infectious diarrhoea, most commonly occurring in healthcare institutions. Recently, concern has been raised with reports of C. difficile disease in those traditionally thought to be at low risk i.e. community acquired rather than healthcare acquired. This has increased awareness for the need to track outbreaks and PCR-ribotyping has found widespread use to elucidate epidemiologically linked isolates. PCR-ribotyping uses conserved regions of the 16S rRNA gene and 23S rRNA gene as primer binding sites to produce varying PCR products due to the intergenic spacer (ITS1) regions of the multiple operons. With the explosion of whole genome sequence data it became possible to analyse the start of the 23S rRNA gene for a more accurate selection of regions closer to the end of the ITS1. However the following questions must still be asked: (i) Does the chromosomal organisation of the rrn operon vary between C. difficile strains? and (ii) just how conserved are the primer binding regions? Eight published C. difficile genomes have been aligned to produce a detailed database of indels of the ITS1's from the rrn operon sets. An iPad Filemaker Go App has been constructed and named RiboTyping (RT). It contains detail such as sequences, ribotypes, strain numbers, GenBank numbers and genome position numbers. Access to various levels of the database is provided so that details can be printed. There are three main regions of the rrn operon that have been analysed by the database and related to each other by strain, ribotype and operon: (1) 16S gene (2) ITS1 indels (3) 23S gene. This has enabled direct intra- and inter-genomic comparisons at the strain, ribotype and operon (allele) levels in each of the three genomic regions. This is the first time that such an analysis has been done. By using the RT App with search criteria it will be possible to select probe combinations for specific strains/ribotypes/rrn operons for experiments to do with diagnostics, typing and recombination of operons. Many more incomplete C. difficile whole genome sequencing projects are recorded in GenBank as underway and the rrn operon information from these can also be added to the RT App when available. The RT App will help simplify probe selection because of the complexity of the ITS1 in C. difficile even in a single genome and because other allele-specific regions (16S and 23S genes) of variability can be relationally compared to design extra probes to increase sensitivity.
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Affiliation(s)
- Volker Gürtler
- School of Applied Sciences, Building 223, Level 1, Bundoora Campus RMIT University, PO Box 71, Bundoora 3083, Australia.
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147
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Epidemiology of Clostridium difficile infection and risk factors for unfavorable clinical outcomes: results of a hospital-based study in Barcelona, Spain. J Clin Microbiol 2013; 51:1465-73. [PMID: 23447638 DOI: 10.1128/jcm.03352-12] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Prospective hospital-based surveillance for Clostridium difficile-associated disease (CDAD) was conducted in Barcelona (Spain) to describe the epidemiology of this condition and investigate the risk factors for an unfavorable outcome. All patients diagnosed with CDAD during 2009 were included. Using logistic regression modeling, we analyzed the potential risk factors associated with recurrent and complicated CDAD, defined as a need for colectomy or death within 30 days. There were 365 episodes of CDAD, yielding an incidence of 22.5 cases/10(5) person-years, 1.22 cases/10(3) hospital discharges, and 1.93 cases/10(4) patient-days. The main PCR ribotypes identified were 241 (26%), 126 (18%), 078 (7%), and 020 (5%). PCR ribotype 027 was not detected. Among the 348 cases analyzed, 232 (67%) patients were cured, 63 (18%) had a recurrence of CDAD, and 53 (15%) developed complicated CDAD. Predictors of complicated CDAD were continued use of antibiotics following CDAD diagnosis (odds ratio [OR], 2.009; 95% confidence interval [CI], 1.012 to 3.988; P = 0.046), Charlson comorbidity index score (OR, 1.265; 95% CI, 1.105 to 1.449; P = 0.001), and age (OR, 1.028; 95% CI, 1.005 to 1.053; P = 0.019). A leukocyte count of >15 × 10(3) cells/ml (OR, 2.277; 95% CI, 1.189 to 4.362; P = 0.013), continuation of proton pump inhibitor (PPI) use after CDAD diagnosis (OR, 2.168; 95% CI, 1.081 to 4.347; P = 0.029), and age (OR, 1.021; 95% CI, 1.001 to 1.041; P = 0.036) were independently associated with higher odds of recurrence. The incidence of CDAD in Barcelona during 2009 was on the lower end of the previously described range for all of Europe. Our analysis suggests that the continuation of non-C. difficile antibiotics and use of PPIs in patients diagnosed with CDAD are associated with unfavorable clinical outcomes.
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148
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Schneeberg A, Rupnik M, Neubauer H, Seyboldt C. Prevalence and distribution of Clostridium difficile PCR ribotypes in cats and dogs from animal shelters in Thuringia, Germany. Anaerobe 2012; 18:484-8. [DOI: 10.1016/j.anaerobe.2012.08.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 06/22/2012] [Accepted: 08/12/2012] [Indexed: 01/05/2023]
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Walk ST, Micic D, Jain R, Lo ES, Trivedi I, Liu EW, Almassalha LM, Ewing SA, Ring C, Galecki AT, Rogers MAM, Washer L, Newton DW, Malani PN, Young VB, Aronoff DM. Clostridium difficile ribotype does not predict severe infection. Clin Infect Dis 2012; 55:1661-8. [PMID: 22972866 DOI: 10.1093/cid/cis786] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Studies of Clostridium difficile outbreaks suggested that certain ribotypes (eg, 027 and 078) cause more severe disease than other ribotypes. A growing number of studies challenge the validity of this hypothesis. METHODS We conducted a cross-sectional study of C. difficile infection (CDI) to test whether ribotype predicted clinical severity when adjusted for the influence of other predictors. Toxigenic C. difficile isolates were cultured from stool samples, screened for genes encoding virulence factors by polymerase chain reaction (PCR) and ribotyped using high-throughput, fluorescent PCR ribotyping. We collected data for 15 covariates (microbiologic, epidemiologic, and laboratory variables) and determined their individual and cumulative influence on the association between C. difficile ribotype and severe disease. We then validated this influence using an independent data set. RESULTS A total of 34 severe CDI cases were identified among 310 independent cases of disease (11.0%). Eleven covariates, including C. difficile ribotype, were significant predictors of severe CDI in unadjusted analysis. However, the association between ribotypes 027 and 078 and severe CDI was not significant after adjustment for any of the other covariates. After full adjustment, severe cases were significantly predicted only by patients' white blood cell count and albumin level. This result was supported by analysis of a validation data set containing 433 independent CDI cases (45 severe cases; 10.4%). CONCLUSIONS Ribotype is not a significant predictor of severe CDI when adjusted for the influence of any other variables separately or in combination. White blood cell count and albumin level are the most clinically relevant predictors of severe CDI cases.
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Affiliation(s)
- Seth T Walk
- Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan, USA
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A PCR-based intergenic spacer region-capillary gel electrophoresis typing method for identification and subtyping of Nocardia species. J Clin Microbiol 2012; 50:3478-84. [PMID: 22875897 DOI: 10.1128/jcm.01311-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
While 16S rRNA sequence-based identification of Nocardia species has become the gold standard, it is not without its limitations. We evaluated a novel approach encompassing the amplification of the Nocardia 16S-23S rRNA intergenic spacer (IGS) region followed by fragment analysis by capillary gel electrophoresis (CGE) of the amplified product for species identification of Nocardia. One hundred forty-five Nocardia isolates (19 species) and four non-Nocardia aerobic actinomycetes were studied. Reproducibility testing was performed in a subset (21%) of isolates. Ninety-five different electropherograms were identified, with heterogeneity within species being a general observation. Among common Nocardia species (e.g., Nocardia cyriacigeorgica, N. nova, N. farcinica), 2 or 3 dominant electropherogram subgroups were typical. While only a minority (8/19; 42%) of the different Nocardia species contained isolates displaying unique fragment sizes that were predictive of a particular species, virtually all isolates (142/145; 98%) could be assigned to the correct species using IGS-CGE typing based on the number and size of amplified fragments. The median number of fragments for each isolate was 2 (range, 1 to 5) with only a minority (17%) having a single fragment detected. The majority (93%) of amplified fragments were between 408 and 461 bp. The technique was also non-operator dependent, highly reproducible, and quicker and less expensive than 16S sequencing. In summary, PCR-based IGS-CGE typing is relatively simple, accurate, reproducible, and cost-effective and offers a potential alternative to 16S rRNA sequencing for identifying and subtyping Nocardia isolates.
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