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Calderaro A, Buttrini M, Farina B, Montecchini S, Martinelli M, Arcangeletti MC, Chezzi C, De Conto F. Characterization of Clostridioides difficile Strains from an Outbreak Using MALDI-TOF Mass Spectrometry. Microorganisms 2022; 10:microorganisms10071477. [PMID: 35889196 PMCID: PMC9320467 DOI: 10.3390/microorganisms10071477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
The epidemiology of Clostridioides difficile infection (CDI) has changed over the last two decades, due to the emergence of C. difficile strains with clinical relevance and responsible for nosocomial outbreaks with severe outcomes. This study reports an outbreak occurred in a Long-term Care Unit from February to March 2022 and tracked by using a Matrix-Assisted Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) typing approach (T-MALDI); subsequently, a characterization of the toxigenic and antimicrobial susceptibility profiles of the C. difficile isolates was performed. A total of 143 faecal samples belonging to 112 patients was evaluated and C. difficile DNA was detected in 51 samples (46 patients). Twenty-nine C. difficile isolates were obtained, and three different clusters were revealed by T-MALDI. The most representative cluster accounted 22 strains and was considered to be epidemic, in agreement with PCR-Ribotyping. Such epidemic strains were susceptible to vancomycin (MIC ≤ 0.5 mg/mL) and metronidazole (MIC ≤ 1 mg/mL), but not to moxifloxacin (MIC > 32 mg/mL). Moreover, they produced only the Toxin A and, additionally, the binary toxin. To our knowledge, this is the first reported outbreak referable to a tcdA+/tcdB-/cdt+ genotypic profile. In light of these results, T-MALDI is a valid and rapid approach for discovering and tracking outbreaks.
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Affiliation(s)
- Adriana Calderaro
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
- Correspondence: ; Tel.: +39-0521-033499; Fax: +39-0521-993620
| | - Mirko Buttrini
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
| | - Benedetta Farina
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
| | - Sara Montecchini
- Unit of Clinical Virology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy;
| | - Monica Martinelli
- Unit of Clinical Microbiology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy;
| | - Maria Cristina Arcangeletti
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
| | - Carlo Chezzi
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
| | - Flora De Conto
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
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Choi MH, Kim D, Jeong SH, Lee HM, Kim H. Risk Factors of Severe Clostridioides difficile Infection; Sequential Organ Failure Assessment Score, Antibiotics, and Ribotypes. Front Microbiol 2022; 13:900681. [PMID: 35633677 PMCID: PMC9133954 DOI: 10.3389/fmicb.2022.900681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 12/14/2022] Open
Abstract
We aimed to determine whether the Sequential Organ Failure Assessment (SOFA) score predicts the prognosis of patients with Clostridioides difficile infection (CDI). In addition, the association between the type of antibiotic used and PCR ribotypes was analyzed. We conducted a propensity score (PS)-matched study and machine learning analysis using clinical data from all adult patients with confirmed CDI in three South Korean hospitals. A total of 5,337 adult patients with CDI were included in this study, and 828 (15.5%) were classified as having severe CDI. The top variables selected by the machine learning models were maximum body temperature, platelet count, eosinophil count, oxygen saturation, Glasgow Coma Scale, serum albumin, and respiratory rate. After propensity score-matching, the SOFA score, white blood cell (WBC) count, serum albumin level, and ventilator use were significantly associated with severe CDI (P < 0.001 for all). The log-rank test of SOFA score ≥ 4 significantly differentiated severe CDI patients from the non-severe group. The use of fluoroquinolone was more related to CDI patients with ribotype 018 strains than to ribotype 014/020 (P < 0.001). Even after controlling for other variables using propensity score matching analysis, we found that the SOFA score was a clinical predictor of severe CDI. We also demonstrated that the use of fluoroquinolones in hospital settings could be associated with the PCR ribotype in patients with CDI.
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Affiliation(s)
- Min Hyuk Choi
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Gangnam Severance Hospital, Seoul, South Korea
| | - Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Gangnam Severance Hospital, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Gangnam Severance Hospital, Seoul, South Korea
| | - Hyuk Min Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Severance Hospital, Seoul, South Korea
| | - Heejung Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Yongin Severance Hospital, Yongin, South Korea
- *Correspondence: Heejung Kim,
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Clostridium Difficile and COVID-19: General Data, Ribotype, Clinical Form, Treatment-Our Experience from the Largest Infectious Diseases Hospital in Western Romania. ACTA ACUST UNITED AC 2021; 57:medicina57101099. [PMID: 34684136 PMCID: PMC8539017 DOI: 10.3390/medicina57101099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022]
Abstract
Background and Objectives: In Coronavirus Disease 2019 (COVID-19), which is caused by the infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the clinical manifestations are primarily related to the pulmonary system. Under 10% of cases also develop gastrointestinal events such as diarrhea, nausea, vomiting and abdominal pain. Materials and Methods: We conducted an observational, retrospective study in the Infectious Diseases Clinic of "Victor Babes" Hospital, Timis County, in order to assess the incidence, outcome and risk factors for clostridium difficile infection (CDI) in COVID-19 patients. Results: Out of 2065 COVID-19 cases, hospitalized between 1st September 2020 and 30th April 2021, 40 cases of CDI were identified with 32 cases of hospital-onset of CDI and eight cases of community-onset and healthcare-associated CDI. By randomization, polymerase chain reaction ribotyping of Clostridium Difficile was performed in six cases. All the randomized cases tested positive for ribotype 027. The percentage of cases recovered with complications at discharge was higher among COVID-19 patients and CDI (p = 0.001). The in-hospital stay, 36 days versus 28 days, was longer among COVID-19 patients and CDI (p = 0.01). The presence of previous hospitalization (p = 0.004) and administration of antibiotics during the hospital stay, increased the risk of CDI among COVID-19 patients. The mean adjusted CCI at admission was lower among controls (p = 0.01). In two cases, exitus was strictly CDI-related, with one case positive for 027 ribotype. Conclusions: CDI has complicated the outcome of COVID-19 patients, especially for those with comorbidities or previously exposed to the healthcare system. In the face of the COVID-19 pandemic and the widespread, extensive use of antibiotics, clinicians should remain vigilant for possible CDI and SARS-CoV-2 co-infection.
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Li BY, Oh J, Young VB, Rao K, Wiens J. Using Machine Learning and the Electronic Health Record to Predict Complicated Clostridium difficile Infection. Open Forum Infect Dis 2019; 6:ofz186. [PMID: 31139672 PMCID: PMC6527086 DOI: 10.1093/ofid/ofz186] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/13/2019] [Indexed: 02/06/2023] Open
Abstract
Background Clostridium (Clostridioides) difficile infection (CDI) is a health care–associated infection that can lead to serious complications. Potential complications include intensive care unit (ICU) admission, development of toxic megacolon, need for colectomy, and death. However, identifying the patients most likely to develop complicated CDI is challenging. To this end, we explored the utility of a machine learning (ML) approach for patient risk stratification for complications using electronic health record (EHR) data. Methods We considered adult patients diagnosed with CDI between October 2010 and January 2013 at the University of Michigan hospitals. Cases were labeled complicated if the infection resulted in ICU admission, colectomy, or 30-day mortality. Leveraging EHR data, we trained a model to predict subsequent complications on each of the 3 days after diagnosis. We compared our EHR-based model to one based on a small set of manually curated features. We evaluated model performance using a held-out data set in terms of the area under the receiver operating characteristic curve (AUROC). Results Of 1118 cases of CDI, 8% became complicated. On the day of diagnosis, the model achieved an AUROC of 0.69 (95% confidence interval [CI], 0.55–0.83). Using data extracted 2 days after CDI diagnosis, performance increased (AUROC, 0.90; 95% CI, 0.83–0.95), outperforming a model based on a curated set of features (AUROC, 0.84; 95% CI, 0.75–0.91). Conclusions Using EHR data, we can accurately stratify CDI cases according to their risk of developing complications. Such an approach could be used to guide future clinical studies investigating interventions that could prevent or mitigate complicated CDI.
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Affiliation(s)
- Benjamin Y Li
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan
| | - Jeeheh Oh
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Krishna Rao
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Jenna Wiens
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan
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Carlucci C, Jones CS, Oliphant K, Yen S, Daigneault M, Carriero C, Robinson A, Petrof EO, Weese JS, Allen-Vercoe E. Effects of defined gut microbial ecosystem components on virulence determinants of Clostridioides difficile. Sci Rep 2019; 9:885. [PMID: 30696914 PMCID: PMC6351598 DOI: 10.1038/s41598-018-37547-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022] Open
Abstract
Many cases of Clostridioides difficile infection (CDI) are poorly responsive to standard antibiotic treatment strategies, and often patients suffer from recurrent infections characterized by severe diarrhea. Our group previously reported the successful cure of two patients with recurrent CDI using a standardized stool-derived microbial ecosystem therapeutic (MET-1). Using an in vitro model of the distal gut to support bacterial communities, we characterized the metabolite profiles of two defined microbial ecosystems derived from healthy donor stool (DEC58, and a subset community, MET-1), as well as an ecosystem representative of a dysbiotic state (ciprofloxacin-treated DEC58). The growth and virulence determinants of two C. difficile strains were then assessed in response to components derived from the ecosystems. CD186 (ribotype 027) and CD973 (ribotype 078) growth was decreased upon treatment with DEC58 metabolites compared to ciprofloxacin-treated DEC58 metabolites. Furthermore, CD186 TcdA and TcdB secretion was increased following treatment with ciprofloxacin-treated DEC58 spent medium compared to DEC58 spent medium alone. The net metabolic output of C. difficile was also modulated in response to spent media from defined microbial ecosystems, although several metabolite levels were divergent across the two strains examined. Further investigation of these antagonistic properties will guide the development of microbiota-based therapeutics for CDI.
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Affiliation(s)
- Christian Carlucci
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
| | - Carys S Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Sandi Yen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Michelle Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Charley Carriero
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Avery Robinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Elaine O Petrof
- Division of Infectious Diseases/Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Gupta SB, Dubberke ER. Reprint of: Overview and changing epidemiology of Clostridium difficile infection. SEMINARS IN COLON AND RECTAL SURGERY 2018. [DOI: 10.1053/j.scrs.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Hargreaves KR, Thanki AM, Jose BR, Oggioni MR, Clokie MRJ. Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078. BMC Genomics 2016; 17:1020. [PMID: 27964731 PMCID: PMC5154133 DOI: 10.1186/s12864-016-3346-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/25/2016] [Indexed: 01/20/2023] Open
Abstract
Background How the pathogen Clostridium difficile might survive, evolve and be transferred between reservoirs within the natural environment is poorly understood. Some ribotypes are found both in clinical and environmental settings. Whether these strains are distinct from each another and evolve in the specific environments is not established. The possession of a highly mobile genome has contributed to the genetic diversity and ongoing evolution of C. difficile. Interpretations of genetic diversity have been limited by fragmented assemblies resulting from short-read length sequencing approaches and by a limited understanding of epigenetic regulation of diversity. To address this, single molecule real time (SMRT) sequencing was used in this study as it produces high quality genome sequences, with resolution of repeat regions (including those found in mobile elements) and can generate data to determine methylation modifications across the sequence (the methylome). Results Chromosomal rearrangements and ribosomal operon duplications were observed in both genomes. The rearrangements occurred at insertion sites within two mobile genetic elements (MGEs), Tn6164 and Tn6293, present only in the M120 and CD105HS27 genomes, respectively. The gene content of these two transposons differ considerably which could impact upon horizontal gene transfer; differences include CDSs encoding methylases and a conjugative prophage only in Tn6164. To investigate mechanisms which could affect MGE transfer, the methylome, restriction modification (RM) and the CRISPR/Cas systems were characterised for each strain. Notably, the environmental isolate, CD105HS27, does not share a consensus motif for m4C methylation, but has one additional spacer when compared to the clinical isolate M120. Conclusions These findings show key differences between the two strains in terms of their genetic capacity for MGE transfer. The carriage of horizontally transferred genes appear to have genome wide effects based on two different methylation patterns. The CRISPR/Cas system appears active although perhaps slow to evolve. Data suggests that both mechanisms are functional and impact upon horizontal gene transfer and genome evolution within C. difficile. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3346-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine R Hargreaves
- Department Infection, Immunity and Inflammation, University of Leicester, Leicester, UK. .,Department Microbiology, The Ohio State University, Columbus, OH, USA.
| | - Anisha M Thanki
- Department Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Bethany R Jose
- Department Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | | | - Martha R J Clokie
- Department Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.
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Coinfection and Emergence of Rifamycin Resistance during a Recurrent Clostridium difficile Infection. J Clin Microbiol 2016; 54:2689-2694. [PMID: 27558181 DOI: 10.1128/jcm.01025-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/15/2016] [Indexed: 01/04/2023] Open
Abstract
Clostridium difficile (Peptoclostridium difficile) is a common health care-associated infection with a disproportionately high incidence in elderly patients. Disease symptoms range from mild diarrhea to life-threatening pseudomembranous colitis. Around 20% of patients may suffer recurrent disease, which often requires rehospitalization of patients. C. difficile was isolated from stool samples from a patient with two recurrent C. difficile infections. PCR ribotyping, whole-genome sequencing, and phenotypic assays were used to characterize these isolates. Genotypic and phenotypic screening of C. difficile isolates revealed multiple PCR ribotypes present and the emergence of rifamycin resistance during the infection cycle. Understanding both the clinical and bacterial factors that contribute to the course of recurrent infection could inform strategies to reduce recurrence. (This study has been registered at ClinicalTrials.gov under registration no. NCT01670149.).
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Pilate T, Verhaegen J, Van Ranst M, Saegeman V. Binary toxin and its clinical importance in Clostridium difficile infection, Belgium. Eur J Clin Microbiol Infect Dis 2016; 35:1741-1747. [PMID: 27393490 DOI: 10.1007/s10096-016-2719-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/27/2016] [Indexed: 12/18/2022]
Abstract
Binary toxin-producing Clostridium difficile strains such as ribotypes 027 and 078 have been associated with increased Clostridium difficile infection (CDI) severity. Our objective was to investigate the association between presence of the binary toxin gene and CDI severity and recurrence. We performed a laboratory-based retrospective study including patients between January 2013 and March 2015 whose fecal samples were analyzed by polymerase chain reaction (PCR) for the presence of the genes for toxin B and binary toxin and a deletion in the tcdC gene, specific for ribotype 027. Clinical and epidemiological characteristics were compared between 33 binary toxin-positive CDI patients and 33 binary toxin-negative CDI patients. Subsequently, the characteristics of 66 CDI patients were compared to those of 66 diarrhea patients who were carriers of non-toxigenic C. difficile strains. Fifty-nine of 1034 (5.7 %) fecal samples analyzed by PCR were binary toxin-positive, belonging to 33 different patients. No samples were positive for ribotype 027. Binary toxin-positive CDI patients did not differ from binary toxin-negative CDI patients in terms of disease recurrence, morbidity, or mortality, except for a higher peripheral leukocytosis in the binary toxin-positive group (16.30 × 109/L vs. 11.65 × 109/L; p = 0.02). The second part of our study showed that CDI patients had more severe disease, but not a higher 30-day mortality rate than diarrhea patients with a non-toxicogenic C. difficile strain. In our setting with a low prevalence of ribotype 027, the presence of the binary toxin gene is not associated with poor outcome.
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Affiliation(s)
- T Pilate
- Department of Laboratory Medicine, UH Leuven, Herestraat 49, Leuven, Belgium.
| | - J Verhaegen
- Department of Laboratory Medicine, UH Leuven, Herestraat 49, Leuven, Belgium
| | - M Van Ranst
- Department of Laboratory Medicine, UH Leuven, Herestraat 49, Leuven, Belgium
| | - V Saegeman
- Department of Laboratory Medicine, UH Leuven, Herestraat 49, Leuven, Belgium
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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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Clostridium difficile PCR Ribotype 018, a Successful Epidemic Genotype. J Clin Microbiol 2015; 53:2575-80. [PMID: 26041894 DOI: 10.1128/jcm.00533-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/26/2015] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile infection (CDI) became a public health problem for the global spreading of the so-called hypervirulent PCR ribotypes (RTs) 027 and 078, associated with increases in the transmission and severity of the disease. However, especially in Europe, several RTs are prevalent, and the concept of hypervirulence is currently debated. We investigated the toxin and resistance profiles and the genetic relatedness of 312 C. difficile strains isolated in a large Italian teaching hospital during a 5-year period. We evaluated the role of CDI-related antibiotic consumption and infection control practices on the RT predominance in association with their molecular features and transmission capacity. Excluding secondary cases due to nosocomial transmission, RT018 was the predominant genotype (42.4%) followed by RT078 (13.6%), while RT027 accounted for 0.8% of the strains. RT078 was most frequently isolated from patients in intensive care units. Its prevalence significantly increased over time, but its transmission capacity was very low. In contrast, RT018 was highly transmissible and accounted for 95.7% of the secondary cases. Patients with the RT018 genotype were significantly older than those with RT078 and other RTs, indicating an association between epidemic RT and age. We provide here the first epidemiological evidence to consider RT018 as a successful epidemic genotype that deserves more attention in clinical practice.
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Gupta SB, Dubberke ER. Overview and changing epidemiology of Clostridium difficile infection. SEMINARS IN COLON AND RECTAL SURGERY 2014. [DOI: 10.1053/j.scrs.2014.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Abstract
There has been dramatic change in the epidemiology of Clostridium difficile infection (CDI) since the turn of the 21st century noted by a marked increase in incidence and severity, occurring at a disproportionately higher frequency in older patients. Historically considered a nosocomial infection associated with antibiotic exposure, CDI has now also emerged in the community in populations previously considered low risk. Emerging risk factors and disease recurrence represent continued challenges in the management of CDI. The increased incidence and severity associated with CDI has coincided with the emergence and rapid spread of a previously rare strain, ribotype 027. Recent data from the United States and Europe suggest that the incidence of CDI may have reached a crescendo in the recent years and is perhaps beginning to plateau. The acute care direct costs of CDI were estimated to be US$4.8 billion in 2008. However, nearly all the published studies have focused on CDI diagnosed and treated in the acute care hospital setting and fail to measure the burden outside the hospital, including recently discharged patients, outpatients, and those in long-term care facilities. Enhanced surveillance methods are needed to monitor the incidence, to identify populations at risk, and to characterize the molecular epidemiology of strains causing CDI.
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Characterization of temperate phages infecting Clostridium difficile isolates of human and animal origins. Appl Environ Microbiol 2014; 80:2555-63. [PMID: 24532062 DOI: 10.1128/aem.00237-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Clostridium difficile is a Gram-positive pathogen infecting humans and animals. Recent studies suggest that animals could represent potential reservoirs of C. difficile that could then transfer to humans. Temperate phages contribute to the evolution of most bacteria, for example, by promoting the transduction of virulence, fitness, and antibiotic resistance genes. In C. difficile, little is known about their role, mainly because suitable propagating hosts and conditions are lacking. Here we report the isolation, propagation, and preliminary characterization of nine temperate phages from animal and human C. difficile isolates. Prophages were induced by UV light from 58 C. difficile isolates of animal and human origins. Using soft agar overlays with 27 different C. difficile test strains, we isolated and further propagated nine temperate phages: two from horse isolates (ΦCD481-1 and ΦCD481-2), three from dog isolates (ΦCD505, ΦCD506, and ΦCD508), and four from human isolates (ΦCD24-2, ΦCD111, ΦCD146, and ΦCD526). Two phages are members of the Siphoviridae family (ΦCD111 and ΦCD146), while the others are Myoviridae phages. Pulsed-field gel electrophoresis and restriction enzyme analyses showed that all of the phages had unique double-stranded DNA genomes of 30 to 60 kb. Phages induced from human C. difficile isolates, especially the members of the Siphoviridae family, had a broader host range than phages from animal C. difficile isolates. Nevertheless, most of the phages could infect both human and animal strains. Phage transduction of antibiotic resistance was recently reported in C. difficile. Our findings therefore call for further investigation of the potential risk of transduction between animal and human C. difficile isolates.
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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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Boone JH, Archbald-Pannone LR, Wickham KN, Carman RJ, Guerrant RL, Franck CT, Lyerly DM. Ribotype 027 Clostridium difficile infections with measurable stool toxin have increased lactoferrin and are associated with a higher mortality. Eur J Clin Microbiol Infect Dis 2014; 33:1045-51. [PMID: 24449345 PMCID: PMC4013447 DOI: 10.1007/s10096-013-2043-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/20/2013] [Indexed: 12/18/2022]
Abstract
We evaluated clinical and diagnostic indicators of severe C. difficile infection (CDI) and their association with poor clinical outcome. A total of 210 patients positive according to PCR (toxin B: tcdB) were included, with patients having a median age of 62 years and a Charlson co-morbidity index (CI) score of 5. Ninety-one percent (n = 191) were positive by toxigenic culture and 61 % (n = 129) had stool toxin. Toxin-positive patients had significantly higher fecal lactoferrin (mean 316 μg/g versus 106 μg/g stool; p < 0.0001). Forty percent of patients (n = 85) were infected with ribotype 027 and significantly more of these patients had measurable stool toxin (79 % vs. 50 %; p < 0.0001). The mean fecal lactoferrin was significantly higher for toxin-positive 027 CDI compared with the 027 toxin-negative group (317 vs 60 μg/g; p = 0.0014). Ribotype 027 CDI with stool toxin showed a higher all-cause, 100-day mortality compared with non-027 with stool toxin (36 % vs 18 %; p = 0.017). Logistic regression univariate analysis for odds ratio (OR) and p values revealed that age (OR = 1.1), intensive care unit treatment (OR = 2.7), CI (OR = 1.2), 027 CDI (OR = 2.1), white blood cell count (OR = 1.0), albumin level (OR = 0.1), and stool toxin-positive 027 CDI (OR = 2.5) were significantly associated with 100-day mortality (p < 0.05). In conclusion, CDI PCR-positive patients with 027 infection and stool toxin have increased lactoferrin and are at an increased risk of death.
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Affiliation(s)
- J H Boone
- Research and Development, TechLab, Inc., 2001 Kraft Drive, Blacksburg, VA, 24060, USA,
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17
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Gerding DN, Johnson S, Rupnik M, Aktories K. Clostridium difficile binary toxin CDT: mechanism, epidemiology, and potential clinical importance. Gut Microbes 2014; 5:15-27. [PMID: 24253566 PMCID: PMC4049931 DOI: 10.4161/gmic.26854] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Binary toxin (CDT) is frequently observed in Clostridium difficile strains associated with increased severity of C. difficile infection (CDI). CDT belongs to the family of binary ADP-ribosylating toxins consisting of two separate toxin components: CDTa, the enzymatic ADP-ribosyltransferase which modifies actin, and CDTb which binds to host cells and translocates CDTa into the cytosol. CDTb is activated by serine proteases and binds to lipolysis stimulated lipoprotein receptor. ADP-ribosylation induces depolymerization of the actin cytoskeleton. Toxin-induced actin depolymerization also produces microtubule-based membrane protrusions which form a network on epithelial cells and increase bacterial adherence. Multiple clinical studies indicate an association between binary toxin genes in C. difficile and increased 30-d CDI mortality independent of PCR ribotype. Further studies including measures of binary toxin in stool, analyses of CDI mortality caused by CDT-producing strains, and examination of the relationship of CDT expression to TcdA and TcdB toxin variants and PCR ribotypes are needed.
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Affiliation(s)
- Dale N Gerding
- Loyola University Chicago Stritch School of Medicine; Hines Veterans Affairs Hospital; Hines, IL USA,Correspondence to: Dale N Gerding,
| | - Stuart Johnson
- Loyola University Chicago Stritch School of Medicine; Hines Veterans Affairs Hospital; Hines, IL USA
| | - Maja Rupnik
- Institute of Public Health Maribor; University of Maribor, Medical Faculty, and Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins; Ljubljana, Slovenia
| | - Klaus Aktories
- Institute of Experimental and Clinical Pharmacology and Toxicology; Albert-Ludwigs-University Freiburg; Freiburg, Germany
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18
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19
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El Feghaly RE, Stauber JL, Tarr PI, Haslam DB. Intestinal inflammatory biomarkers and outcome in pediatric Clostridium difficile infections. J Pediatr 2013; 163:1697-1704.e2. [PMID: 24011765 PMCID: PMC4098967 DOI: 10.1016/j.jpeds.2013.07.029] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/25/2013] [Accepted: 07/19/2013] [Indexed: 01/05/2023]
Abstract
OBJECTIVES To identify specific fecal biomarkers for symptomatic Clostridium difficile infection and predictors of poor outcomes. STUDY DESIGN We enrolled 65 children with positive C difficile testing (cases) and 37 symptomatic controls. We also analyzed stool samples from colonized and non-colonized asymptomatic children. We performed enzyme immunoassays to determine fecal interleukin (IL)-8, lactoferrin, and phosphorylated-p38 protein concentrations, and quantitative polymerase chain reaction to determine IL-8 and chemokine ligand (CXCL)-5 RNA relative transcript abundances, and C difficile bacterial burden. RESULTS Of 68 asymptomatic controls, 16 were colonized with C difficile. Phosphorylated-p38 was specific for C difficile infection but lacked sensitivity. Fecal cytokines were elevated in samples from symptomatic children, whether cases or controls. In children with C difficile infection, fecal CXCL-5 and IL-8 messenger RNA abundances at diagnosis correlated with persistent diarrhea after 5 days of C difficile infection therapy and with treatment with vancomycin. When children with concomitant viral gastroenteritis were excluded, these correlations persisted. Time-to-diarrhea resolution was significantly longer in patients with elevated fecal cytokines at diagnosis. A logistic regression model identified high CXCL-5 messenger RNA abundance as the only predictor of persistent diarrhea. Conversely, fecal C difficile bacterial burden was not different in symptomatic and asymptomatic children and did not correlate with any clinical outcome measure. CONCLUSIONS Fecal inflammatory cytokines may be useful in distinguishing C difficile colonization from disease and identifying children with C difficile infection likely to have prolonged diarrhea.
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Affiliation(s)
- Rana E. El Feghaly
- Department of Pediatrics, Washington University School of Medicine. 660 S. Euclid Ave, St Louis, MO, United States 63110
| | - Jennifer L. Stauber
- Department of Pediatrics, Washington University School of Medicine. 660 S. Euclid Ave, St Louis, MO, United States 63110
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine. 660 S. Euclid Ave, St Louis, MO, United States 63110,Department of Molecular Microbiology, Washington University School of Medicine. 660 S. Euclid Ave, St Louis, MO, United States 63110
| | - David B. Haslam
- Department of Pediatrics, Washington University School of Medicine. 660 S. Euclid Ave, St Louis, MO, United States 63110,Department of Molecular Microbiology, Washington University School of Medicine. 660 S. Euclid Ave, St Louis, MO, United States 63110,Corresponding author: David B. Haslam, M.D. 3333 Burnet Ave., MLC 7017 Cincinnati, OH 45229-3039 Phone : 513 803 1170 Fax : 513 803 2057
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20
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Abstract
There has been dramatic change in the epidemiology of Clostridium difficile infection (CDI) since the turn of the 21st century noted by a marked increase in incidence and severity, occurring at a disproportionately higher frequency in older patients. Historically considered a nosocomial infection associated with antibiotic exposure, CDI has now also emerged in the community in populations previously considered low risk. Emerging risk factors and disease recurrence represent continued challenges in the management of CDI. The increased incidence and severity associated with CDI has coincided with the emergence and rapid spread of a previously rare strain, ribotype 027. Recent data from the United States and Europe suggest that the incidence of CDI may have reached a crescendo in the recent years and is perhaps beginning to plateau. The acute care direct costs of CDI were estimated to be US$4.8 billion in 2008. However, nearly all the published studies have focused on CDI diagnosed and treated in the acute care hospital setting and fail to measure the burden outside the hospital, including recently discharged patients, outpatients, and those in long-term care facilities. Enhanced surveillance methods are needed to monitor the incidence, to identify populations at risk, and to characterize the molecular epidemiology of strains causing CDI.
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Affiliation(s)
- Daryl D. DePestel
- Clinical Scientific Director, Medical Affairs, Cubist Pharmaceuticals, Inc., 65 Hayden Ave, Lexington, MA 02421
| | - David M. Aronoff
- Division of Infectious Diseases, Department of Internal Medicine, Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109
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21
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Biazzo M, Cioncada R, Fiaschi L, Tedde V, Spigaglia P, Mastrantonio P, Pizza M, Barocchi MA, Scarselli M, Galeotti CL. Diversity of cwp loci in clinical isolates of Clostridium difficile. J Med Microbiol 2013; 62:1444-1452. [DOI: 10.1099/jmm.0.058719-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An increased incidence of Clostridium difficile infection (CDI) is associated with the emergence of epidemic strains characterized by high genetic diversity. Among the factors that may have a role in CDI is a family of 29 paralogues, the cell-wall proteins (CWPs), which compose the outer layer of the bacterial cell and are likely to be involved in colonization. Previous studies have shown that 12 of the 29 cwp genes are clustered in the same region, named after slpA (cwp1), the slpA locus, whereas the remaining 17 paralogues are distributed throughout the genome. The variability of 14 of these 17 cwp paralogues was determined in 40 C. difficile clinical isolates belonging to six of the currently prevailing PCR ribotypes. Based on sequence conservation, these cwp genes were divided into two groups, one comprising nine cwp loci having highly conserved sequences in all isolates, and the other five loci showing low genetic conservation among isolates of the same PCR ribotype, as well as between different PCR ribotypes. Three conserved CWPs, Cwp16, Cwp18 and Cwp25, and two variable ones, Cwp26 and Cwp27, were characterized further by Western blot analysis of total cell extracts or surface-layer preparations of the C. difficile clinical isolates. Expression of genetically invariable CWPs was well conserved in all isolates, whilst genetically variable CWPs were not always expressed at comparable levels, even in strains containing identical sequences but belonging to different PCR ribotypes. This is the first report on the distribution and variability of a number of genes encoding CWPs in C. difficile.
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Affiliation(s)
| | | | | | | | - Patrizia Spigaglia
- 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
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Butt E, Foster JAH, Keedwell E, Bell JEA, Titball RW, Bhangu A, Michell SL, Sheridan R. Derivation and validation of a simple, accurate and robust prediction rule for risk of mortality in patients with Clostridium difficile infection. BMC Infect Dis 2013; 13:316. [PMID: 23849267 PMCID: PMC3733667 DOI: 10.1186/1471-2334-13-316] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 07/10/2013] [Indexed: 12/18/2022] Open
Abstract
Background Clostridium difficile infection poses a significant healthcare burden. However, the derivation of a simple, evidence based prediction rule to assist patient management has not yet been described. This study aimed to identify such a prediction rule to stratify hospital inpatients according to risk of all-cause mortality, at initial diagnosis of infection. Method Univariate, multivariate and decision tree procedures were used to deduce a prediction rule from over 186 variables; retrospectively collated from clinical data for 213 patients. The resulting prediction rule was validated on independent data from a cohort of 158 patients described by Bhangu et al. (Colorectal Disease, 12(3):241-246, 2010). Results Serum albumin levels (g/L) (P = 0.001), respiratory rate (resps /min) (P = 0.002), C-reactive protein (mg/L) (P = 0.034) and white cell count (mcL) (P = 0.049) were predictors of all-cause mortality. Threshold levels of serum albumin ≤ 24.5 g/L, C- reactive protein >228 mg/L, respiratory rate >17 resps/min and white cell count >12 × 103 mcL were associated with an increased risk of all-cause mortality. A simple four variable prediction rule was devised based on these threshold levels and when tested on the initial data, yield an area under the curve score of 0.754 (P < 0.001) using receiver operating characteristics. The prediction rule was then evaluated using independent data, and yield an area under the curve score of 0.653 (P = 0.001). Conclusions Four easily measurable clinical variables can be used to assess the risk of mortality of patients with Clostridium difficile infection and remains robust with respect to independent data.
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Boone JH, DiPersio JR, Tan MJ, Salstrom SJ, Wickham KN, Carman RJ, Totty HR, Albert RE, Lyerly DM. Elevated lactoferrin is associated with moderate to severe Clostridium difficile disease, stool toxin, and 027 infection. Eur J Clin Microbiol Infect Dis 2013; 32:1517-23. [PMID: 23771554 PMCID: PMC3825630 DOI: 10.1007/s10096-013-1905-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/27/2013] [Indexed: 12/18/2022]
Abstract
We evaluated blood and fecal biomarkers as indicators of severity in symptomatic patients with confirmed Clostridium difficile infection (CDI). Recruitment included patients with CDI based on clinical symptoms and supporting laboratory findings. Disease severity was defined by physician’s assessment and blood and fecal biomarkers were measured. Toxigenic culture done using spore enrichment and toxin B detected by tissue culture were done as confirmatory tests. Polymerase chain reaction (PCR) ribotyping was performed on each isolate. There were 98 patients recruited, with 85 (87 %) confirmed cases of toxigenic CDI (21 severe, 57 moderate, and seven mild), of which 68 (80 %) were also stool toxin-positive. Elevated lactoferrin (p = 0.01), increased white blood cell (WBC) count (p = 0.08), and low serum albumin (p = 0.03) were all associated with the more severe cases of CDI. Ribotype 027 infection accounted for 71 % of severe cases (p < 0.01) and patients with stool toxin had significantly higher lactoferrin levels and WBC counts (p < 0.05). Our findings show that elevated fecal lactoferrin, along with increased WBC count and low serum albumin, were associated with more severe CDI. In addition, patients infected with ribotype 027 and those with stool toxin had significantly higher fecal lactoferrin and WBC counts.
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Affiliation(s)
- J H Boone
- Research and Development, TechLab, Inc., 2001 Kraft Drive, Blacksburg, VA, 24060, USA,
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Gerding DN, Johnson S. Does infection with specific Clostridium difficile strains or clades influence clinical outcome? Clin Infect Dis 2013; 56:1601-3. [PMID: 23463642 DOI: 10.1093/cid/cit133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gut microbiota patterns associated with colonization of different Clostridium difficile ribotypes. PLoS One 2013; 8:e58005. [PMID: 23469128 PMCID: PMC3585249 DOI: 10.1371/journal.pone.0058005] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/29/2013] [Indexed: 12/15/2022] Open
Abstract
C. difficile infection is associated with disturbed gut microbiota and changes in relative frequencies and abundance of individual bacterial taxons have been described. In this study we have analysed bacterial, fungal and archaeal microbiota by denaturing high pressure liquid chromatography (DHPLC) and with machine learning methods in 208 faecal samples from healthy volunteers and in routine samples with requested C. difficile testing. The latter were further divided according to stool consistency, C. difficile presence or absence and C. difficile ribotype (027 or non-027). Lower microbiota diversity was a common trait of all routine samples and not necessarily connected only to C. difficile colonisation. Differences between the healthy donors and C. difficile positive routine samples were detected in bacterial, fungal and archaeal components. Bifidobacterium longum was the single most important species associated with C. difficile negative samples. However, by machine learning approaches we have identified patterns of microbiota composition predictive for C. difficile colonization. Those patterns also differed between samples with C. difficile ribotype 027 and other C. difficile ribotypes. The results indicate that not only the presence of a single species/group is important but that certain combinations of gut microbes are associated with C. difficile carriage and that some ribotypes (027) might be associated with more disturbed microbiota than the others.
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26
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McDonald LC. Virulence and clinical outcomes in Clostridium difficile infection: a complex business. Clin Infect Dis 2012. [PMID: 23196956 DOI: 10.1093/cid/cis1001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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