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Adukauskienė D, Mickus R, Dambrauskienė A, Vanagas T, Adukauskaitė A. Improving Clostridioides difficile Infectious Disease Treatment Response via Adherence to Clinical Practice Guidelines. Antibiotics (Basel) 2024; 13:51. [PMID: 38247610 PMCID: PMC10812669 DOI: 10.3390/antibiotics13010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Clostridioides difficile (C. difficile) is a predominant nosocomial infection, and guidelines for improving diagnosis and treatment were published in 2017. We conducted a single-center, retrospective 10-year cohort study of patients with primary C. difficile infectious disease (CDID) at the largest referral Lithuanian university hospital, aiming to evaluate the clinical and laboratory characteristics of CDID and their association with the outcomes, as well as implication of concordance with current Clinical Practice Guidelines. The study enrolled a total of 370 patients. Cases with non-concordant CDID treatment resulted in more CDID-related Intensive Care Unit (ICU) admissions (7.5 vs. 1.8%) and higher CDID-related mortality (13.0 vs. 1.8%) as well as 30-day all-cause mortality (61.0 vs. 36.1%) and a lower 30-day survival compared with CDID cases with concordant treatment (p < 0.05). Among cases defined by two criteria for severe CDID, only patients with non-concordant metronidazole treatment had refractory CDID (68.8 vs. 0.0%) compared with concordant vancomycin treatment. In the presence of non-concordant metronidazole treatment for severe CDID, only cases defined by two severity criteria had more CDID-related ICU admissions (18.8 vs. 0.0%) and higher CDID-related mortality (25.0 vs. 2.0%, p < 0.05) compared with cases defined by one criterion. Severe comorbidities and the continuation of concomitant antibiotics administered at CDID onset reduced (p < 0.05) the 30-day survival and increased (p = 0.053) 30-day all-cause mortality, with 57.6 vs. 10.7% and 52.0 vs. 25.0%, respectively. Conclusions: CDID treatment non-concordant with the guidelines was associated with various adverse outcomes. In CDID with leukocytes ≥ 15 × 109/L and serum creatinine level > 133 µmol/L (>1.5 mg/dL), enteral vancomycin should be used to avoid refractory response, as metronidazole use was associated with CDID-related ICU admission and CDID-related mortality. Severe comorbidities worsened the outcomes as they were associated with reduced 30-day survival. The continuation of concomitant antibiotic therapy increased 30-day all-cause mortality; thus, it needs to be reasonably justified, deescalated or stopped.
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Affiliation(s)
- Dalia Adukauskienė
- Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (A.D.); (T.V.)
| | - Rytis Mickus
- Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (A.D.); (T.V.)
| | - Asta Dambrauskienė
- Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (A.D.); (T.V.)
| | - Tomas Vanagas
- Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (A.D.); (T.V.)
| | - Agnė Adukauskaitė
- Department of Cardiology and Angiology, University Hospital of Innsbruck, 6020 Innsbruck, Austria;
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Janezic S, Garneau JR, Monot M. Comparative Genomics of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:199-218. [PMID: 38175477 DOI: 10.1007/978-3-031-42108-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile, a Gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of nosocomial diarrhoea in hospitals. The availability of large numbers of genome sequences, mainly due to the use of next-generation sequencing methods, has undoubtedly shown their immense advantages in the determination of C. difficile population structure. The implementation of fine-scale comparative genomic approaches has paved the way for global transmission and recurrence studies, as well as more targeted studies, such as the PaLoc or CRISPR/Cas systems. In this chapter, we provide an overview of recent and significant findings on C. difficile using comparative genomic studies with implications for epidemiology, infection control and understanding of the evolution of C. difficile.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia.
- Faculty of Medicine, University of Maribor, Maribor, Slovenia.
| | - Julian R Garneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Paris, France
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Anwar F, Clark M, Lindsey J, Claus-Walker R, Mansoor A, Nguyen E, Billy J, Lainhart W, Shehab K, Viswanathan VK, Vedantam G. Prevalence of diagnostically-discrepant Clostridioides difficile clinical specimens: insights from longitudinal surveillance. Front Med (Lausanne) 2023; 10:1238159. [PMID: 37928470 PMCID: PMC10622765 DOI: 10.3389/fmed.2023.1238159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Background Clostridioides difficile Infection (CDI) is a healthcare-associated diarrheal disease prevalent worldwide. A common diagnostic algorithm relies on a two-step protocol that employs stool enzyme immunoassays (EIAs) to detect the pathogen, and its toxins, respectively. Active CDI is deemed less likely when the Toxin EIA result is negative, even if the pathogen-specific EIA is positive for C. difficile. We recently reported, however, that low-toxin-producing C. difficile strains recovered from Toxin-negative ('discrepant') clinical stool specimens can be fully pathogenic, and cause lethality in a rodent CDI model. To document frequency of discrepant CDI specimens, and evaluate C. difficile strain diversity, we performed longitudinal surveillance at a Southern Arizona tertiary-care hospital. Methods Diarrheic stool specimens from patients with clinical suspicion of CDI were obtained over an eight-year period (2015-2022) from all inpatient and outpatient Units of a > 600-bed Medical Center in Southern Arizona. Clinical laboratory EIA testing identified C. difficile-containing specimens, and classified them as Toxin-positive or Toxin-negative. C. difficile isolates recovered from the stool specimens were DNA fingerprinted using an international phylogenetic lineage assignment system ("ribotyping"). For select isolates, toxin abundance in stationary phase supernatants of pure cultures was quantified via EIA. Results Of 8,910 diarrheic specimens that underwent diagnostic testing, 1733 (19.4%) harbored C. difficile. Our major findings were that: (1) C. difficile prevalence and phylogenetic diversity was stable over the 8-year period; (2) toxigenic C. difficile was recovered from 69% of clinically Tox-neg ('discrepant') specimens; (3) the six most prevalent USA ribotypes were recovered in significant proportions (>60%) from Tox-neg specimens; and (4) toxin-producing C. difficile recovered from discrepant specimens produced less toxin than strains of the same ribotype isolated from non-discrepant specimens. Conclusion Our study highlights the dominance of Toxin EIA-negative CDI specimens in a clinical setting and the high frequency of known virulent ribotypes in these specimens. Therefore, a careful reevaluation of the clinical relevance of diagnostically-discrepant specimens particularly in the context of missed CDI diagnoses and C. difficile persistence, is warranted.
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Affiliation(s)
- Farhan Anwar
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Marielle Clark
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Jason Lindsey
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Rachel Claus-Walker
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Asad Mansoor
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Evy Nguyen
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Justin Billy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - William Lainhart
- Department of Pathology, Clinical Microbiology Laboratories, Banner University Medical Center, Tucson, AZ, United States
| | - Kareem Shehab
- Department of Pediatrics, College of Medicine, University of Arizona, Tucson, AZ, United States
| | - V. K. Viswanathan
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
- Bio5 Institute for Collaborative Research, University of Arizona, Tucson, AZ, United States
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
- Bio5 Institute for Collaborative Research, University of Arizona, Tucson, AZ, United States
- Southern Arizona VA Healthcare System, Tucson, AZ, United States
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4
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Jolivet S, Couturier J, Grohs P, Vilfaillot A, Zahar JR, Frange P, Casetta A, Moulin V, Lawrence C, Baune P, Bourgeois C, Bouffier A, Laussucq C, Sienzonit L, Picard S, Podglajen I, Kassis-Chikhani N, Barbut F. Prevalence and risk factors of toxigenic Clostridioides difficile asymptomatic carriage in 11 French hospitals. Front Med (Lausanne) 2023; 10:1221363. [PMID: 37547619 PMCID: PMC10402895 DOI: 10.3389/fmed.2023.1221363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
Clostridioides difficile infection (CDI) incidence has increased over the last 20 years. Studies suggest that asymptomatic carriers may be an important reservoir of C. difficile in healthcare settings. We conducted a point prevalence study to estimate the toxigenic C. difficile asymptomatic carriage rate and the associated risk factors in patients >3 years old. Between September 16, 2019 and January 15, 2020, all patients hospitalized in 11 healthcare facilities in the Paris urban area were included in the study. They were screened on the day of the survey for toxigenic C. difficile carriage by rectal swab and interviewed. Isolates were characterized by PCR ribotyping and multiplex PCR targeting toxin genes. A logistic regression model was used to determine the risk factors associated with toxigenic C. difficile asymptomatic carriage using uni- and multivariate analysis in the subpopulation of patients >3 years old. During the study period, 2,389 patients were included and screened. The median age was 62 years (interquartile range 35-78 years) and 1,153 were male (48.3%). Nineteen patients had a previous CDI (0.9%). Overall, 185/2389 patients were positive for C. difficile (7.7%), including 93 toxigenic strains (3.9%): 77 (82.8%) were asymptomatic (prevalence 3.2%) whereas 12 (12.9%) were diarrheic. Prevalences of toxigenic C. difficile were 3.5% in patients >3 years old and 7.0% in ≤3 years old subjects, respectively. Toxigenic strains mainly belonged to PCR ribotypes 106 (n = 14, 15.0%), 014 (n = 12, 12.9%), and 020 (n = 10, 10.8%). Among toxigenic strains, 6 (6.4%) produced the binary toxin. In multivariate analysis, two factors were positively associated with toxigenic C. difficile asymptomatic carriage in patients >3 years old: multidrug-resistant organisms co-carriage [adjusted Odd Ratio (aOR) 2.3, CI 95% 1.2-4.7, p = 0.02] and previous CDI (aOR 5.8, CI 95% 1.2-28.6, p = 0.03). Conversely, consumption of raw milk products were associated with reduced risk of toxigenic C. difficile colonization (aOR 0.5, CI 95% 0.2-0.9, p = 0.01). We showed that there was a low prevalence of asymptomatic toxigenic C. difficile carriage in hospitalized patients. Consumption of raw milk prevents toxigenic C. difficile colonization, probably due to the barrier effect of milk-associated bacteria.
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Affiliation(s)
- Sarah Jolivet
- Unité de prévention du risque infectieux, Hôpital Saint Antoine, Paris, France
| | - Jeanne Couturier
- Laboratoire de microbiologie de l’environnement, Hôpital Saint Antoine, Paris, France
- National Reference Laboratory for Clostridioides difficile, Paris, France
| | - Patrick Grohs
- Laboratoire de microbiologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Aurélie Vilfaillot
- Unité de Recherche Clinique, Hôpital Européen Georges Pompidou, Paris, France
- INSERM Centre d’Investigation Clinique 1418, Paris, France
| | - Jean-Ralph Zahar
- Unité de Prévention du Risque infectieux, Hôpitaux Avicenne, Bobigny/Jean Verdier, Bondy/René Muret, Sevran, France
| | - Pierre Frange
- Équipe de Prévention du Risque infectieux, Laboratoire de microbiologie clinique, Hôpital Necker – Enfants malades, Groupe hospitalier Assistance Publique – Hôpitaux de Paris (APHP) Centre – Université Paris Cité, Paris, France
| | - Anne Casetta
- Équipe de Prévention du Risque infectieux, Hôpital Cochin, Paris, France
| | - Véronique Moulin
- Équipe de Prévention du Risque infectieux, Hôpitaux Corentin Celton/Vaugirard, Issy-les-Moulineaux, France
| | - Christine Lawrence
- Équipe de Prévention du Risque infectieux, GHU Paris-Saclay site R. Poincaré, Garches, France
| | - Patricia Baune
- Équipe de Prévention du Risque infectieux, Hôpital Paul Brousse, Villejuif, France
| | - Cléo Bourgeois
- Unité de Recherche Clinique, Hôpital Européen Georges Pompidou, Paris, France
- INSERM Centre d’Investigation Clinique 1418, Paris, France
| | - Axel Bouffier
- Unité de Recherche Clinique, Hôpital Européen Georges Pompidou, Paris, France
- INSERM Centre d’Investigation Clinique 1418, Paris, France
| | - Claudine Laussucq
- Laboratoire de microbiologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Lydia Sienzonit
- Laboratoire de microbiologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Simon Picard
- Laboratoire de microbiologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Isabelle Podglajen
- Laboratoire de microbiologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Najiby Kassis-Chikhani
- Équipe de Prévention du Risque infectieux, Hôpital Européen Georges Pompidou, Paris, France
| | - Frédéric Barbut
- Unité de prévention du risque infectieux, Hôpital Saint Antoine, Paris, France
- Laboratoire de microbiologie de l’environnement, Hôpital Saint Antoine, Paris, France
- National Reference Laboratory for Clostridioides difficile, Paris, France
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Williamson CHD, Roe CC, Terriquez J, Hornstra H, Lucero S, Nunnally AE, Vazquez AJ, Vinocur J, Plude C, Nienstadt L, Stone NE, Celona KR, Wagner DM, Keim P, Sahl JW. A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment. Microb Genom 2023; 9. [PMID: 37347682 DOI: 10.1099/mgen.0.001046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. difficile infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled C. difficile from clinical, environmental, and canine reservoirs in Flagstaff, Arizona, USA, to understand the distribution and transmission of the pathogen in a One Health framework; Flagstaff is a medium-sized, geographically isolated city with a single hospital system, making it an ideal site to characterize genomic overlap between sequenced C. difficile isolates across reservoirs. An analysis of 562 genomes from Flagstaff isolates identified 65 sequence types (STs), with eight STs being found across all three reservoirs and another nine found across two reservoirs. A screen of toxin genes in the pathogenicity locus identified nine STs where all isolates lost the toxin genes needed for CDI manifestation (tcdB, tcdA), demonstrating the widespread distribution of non-toxigenic C. difficile (NTCD) isolates in all three reservoirs; 15 NTCD genomes were sequenced from symptomatic, clinical samples, including two from mixed infections that contained both tcdB+ and tcdB- isolates. A comparative single nucleotide polymorphism (SNP) analysis of clinically derived isolates identified 78 genomes falling within clusters separated by ≤2 SNPs, indicating that ~19 % of clinical isolates are associated with potential healthcare-associated transmission clusters; only symptomatic cases were sampled in this study, and we did not sample asymptomatic transmission. Using this same SNP threshold, we identified genomic overlap between canine and soil isolates, as well as putative transmission between environmental and human reservoirs. The core genome of isolates sequenced in this study plus a representative set of public C. difficile genomes (n=136), was 2690 coding region sequences, which constitutes ~70 % of an individual C. difficile genome; this number is significantly higher than has been published in some other studies, suggesting that genome data quality is important in understanding the minimal number of genes needed by C. difficile. This study demonstrates the close genomic overlap among isolates sampled across reservoirs, which was facilitated by maximizing the genomic search space used for comprehensive identification of potential transmission events. Understanding the distribution of toxigenic and non-toxigenic C. difficile across reservoirs has implications for surveillance sampling strategies, characterizing routes of infections, and implementing mitigation measures to limit human infection.
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Affiliation(s)
| | - Chandler C Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Heidie Hornstra
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samantha Lucero
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Amalee E Nunnally
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam J Vazquez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | | | - Nathan E Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kimberly R Celona
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Kociolek LK, Gerding DN, Carrico R, Carling P, Donskey CJ, Dumyati G, Kuhar DT, Loo VG, Maragakis LL, Pogorzelska-Maziarz M, Sandora TJ, Weber DJ, Yokoe D, Dubberke ER. Strategies to prevent Clostridioides difficile infections in acute-care hospitals: 2022 Update. Infect Control Hosp Epidemiol 2023; 44:527-549. [PMID: 37042243 PMCID: PMC10917144 DOI: 10.1017/ice.2023.18] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Affiliation(s)
- Larry K. Kociolek
- Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States
| | - Dale N. Gerding
- Edward Hines Jr. Veterans’ Affairs (VA) Hospital, Hines, Illinois, United States
| | - Ruth Carrico
- Norton Healthcare, Louisville, Kentucky, United States
| | - Philip Carling
- Boston University School of Medicine, Boston, Massachusetts, United States
| | - Curtis J. Donskey
- Case Western Reserve University School of Medicine, Cleveland VA Medical Center, Cleveland, Ohio, United States
| | - Ghinwa Dumyati
- University of Rochester Medical Center, Rochester, New York, United States
| | - David T. Kuhar
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Vivian G. Loo
- McGill University, McGill University Health Centre, Montréal, Québec, Canada
| | - Lisa L. Maragakis
- Johns Hopkins University School of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, United States
| | | | - Thomas J. Sandora
- Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - David J. Weber
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Deborah Yokoe
- University of California San Francisco, UCSF Health-UCSF Medical Center, San Francisco, California, United States and
| | - Erik R. Dubberke
- Washington University School of Medicine, St. Louis, Missouri, United States
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7
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Anwar F, Roxas BAP, Shehab KW, Ampel N, Viswanathan VK, Vedantam G. Low-Toxin Clostridioides difficile RT027 Strains Exhibit Robust Virulence. Emerg Microbes Infect 2022; 11:1982-1993. [PMID: 35880487 PMCID: PMC9361768 DOI: 10.1080/22221751.2022.2105260] [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] [Indexed: 12/02/2022]
Abstract
Clostridioides difficile is a leading cause of healthcare-associated infections worldwide. Currently, there is a lack of consensus for an optimal diagnostic method for C. difficile infection (CDI). Multi-step diagnostic algorithms use enzyme immunosorbent analysis (EIA)-based detection of C. difficile toxins TcdA/TcdB in stool, premised on the rationale that EIA toxin-negative (Tox−) patients have less severe disease and shorter diarrhoea duration. The aim of this study was to characterize toxigenic (i.e. tcdA/tcdB-positive) C. difficile strains isolated from diarrheic patient stool with an EIA Tox− (i.e. “discrepant”) CDI diagnostic test result. Recovered strains were DNA fingerprinted (ribotyped), subjected to multiple toxin, genome and proteome evaluations, and assessed for virulence. Overall, of 1243 C. difficile-positive patient stool specimens from Southern Arizona hospitals, 31% were discrepant. For RT027 (the most prevalent ribotype)-containing specimens, 34% were discrepant; the corresponding RT027 isolates were cytotoxic to cultured fibroblasts, but their total toxin levels were comparable to, or lower than, the historic low-toxin-producing C. difficile strain CD630. Nevertheless, these low-toxin RT027 strains (LT-027) exhibited similar lethality to a clade-matched high-toxin RT027 strain in Golden Syrian hamsters, and heightened colonization and persistence in mice. Genomics and proteomics analyses of LT-027 strains identified unique genes and altered protein abundances, respectively, relative to high-toxin RT027 strains. Collectively, our data highlight the robust virulence of LT-027 C. difficile, provide a strong argument for reconsidering the clinical significance of a Tox− EIA result, and underscore the potential limitations of current diagnostic protocols.
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Affiliation(s)
- Farhan Anwar
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Bryan Angelo P Roxas
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Kareem W Shehab
- Department of Pediatrics, The University of Arizona College of Medicine, Tucson, AZ, USA
| | | | - V K Viswanathan
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA.,Department of Immunobiology, The University of Arizona College of Medicine, Tucson, AZ, USA.,BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, AZ, USA
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA.,Department of Immunobiology, The University of Arizona College of Medicine, Tucson, AZ, USA.,BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, AZ, USA.,Southern Arizona VA Healthcare System, Tucson, AZ, USA
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8
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Eyre DW. Infection prevention and control insights from a decade of pathogen whole-genome sequencing. J Hosp Infect 2022; 122:180-186. [PMID: 35157991 PMCID: PMC8837474 DOI: 10.1016/j.jhin.2022.01.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
Abstract
Pathogen whole-genome sequencing has become an important tool for understanding the transmission and epidemiology of infectious diseases. It has improved our understanding of sources of infection and transmission routes for important healthcare-associated pathogens, including Clostridioides difficile and Staphylococcus aureus. Transmission from known infected or colonized patients in hospitals may explain fewer cases than previously thought and multiple introductions of these pathogens from the community may play a greater a role. The findings have had important implications for infection prevention and control. Sequencing has identified heterogeneity within pathogen species, with some subtypes transmitting and persisting in hospitals better than others. It has identified sources of infection in healthcare-associated outbreaks of food-borne pathogens, Candida auris and Mycobacterium chimera, as well as individuals or groups involved in transmission and historical sources of infection. SARS-CoV-2 sequencing has been central to tracking variants during the COVID-19 pandemic and has helped understand transmission to and from patients and healthcare workers despite prevention efforts. Metagenomic sequencing is an emerging technology for culture-independent diagnosis of infection and antimicrobial resistance. In future, sequencing is likely to become more accessible and widely available. Real-time use in hospitals may allow infection prevention and control teams to identify transmission and to target interventions. It may also provide surveillance and infection control benchmarking. Attention to ethical and wellbeing issues arising from sequencing identifying individuals involved in transmission is important. Pathogen whole-genome sequencing has provided an incredible new lens to understand the epidemiology of healthcare-associated infection and to better control and prevent these infections.
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Affiliation(s)
- D W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK; National Institiute for Health Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK; Oxford University Hospitals, Oxford, UK.
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9
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Whole-Genome Sequencing Reveals the High Nosocomial Transmission and Antimicrobial Resistance of Clostridioides difficile in a Single Center in China, a Four-Year Retrospective Study. Microbiol Spectr 2022; 10:e0132221. [PMID: 35019676 PMCID: PMC8754133 DOI: 10.1128/spectrum.01322-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile, which causes life-threatening diarrheal disease, presents an urgent threat to health care systems. In this study, we present a retrospective genomic and epidemiological analysis of C. difficile in a large teaching hospital. First, we collected 894 nonduplicate fecal samples from patients during a whole year to elucidate the C. difficile molecular epidemiology. We then presented a detailed description of the population structure of C. difficile based on 270 isolates separated between 2015 and 2020 and clarified the genetic and phenotypic features by MIC and whole-genome sequencing. We observed a high carriage rate (19.4%, 173/894) of C. difficile among patients in this hospital. The population structure of C. difficile was diverse with a total of 36 distinct STs assigned. In total, 64.8% (175/270) of the isolates were toxigenic, including four CDT-positive (C. difficile transferase) isolates, and 50.4% (135/268) of the isolates were multidrug-resistant. Statistically, the rates of resistance to erythromycin, moxifloxacin, and rifaximin were higher for nontoxigenic isolates. Although no vancomycin-resistant isolates were detected, the MIC for vancomycin was higher for toxigenic isolates (P < 0.01). The in-hospital transmission was observed, with 43.8% (110/251) of isolates being genetically linked to a prior case. However, no strong correlation was detected between the genetic linkage and epidemiological linkage. Asymptomatic colonized patients play the same role in nosocomial transmission as infected patients, raising the issue of routine screening of C. difficile on admission. This work provides an in-depth description of C. difficile in a hospital setting and paves the way for better surveillance and effective prevention of related diseases in China. IMPORTANCEClostridioides difficile infections (CDI) are the leading cause of healthcare-associated diarrhea and are known to be resistant to multiple antibiotics. In the past decade, C. difficile has emerged rapidly and has spread globally, causing great concern among American and European countries. However, research on CDI remains limited in China. Here, we characterized the comprehensive spectrum of C. difficile by whole-genome sequencing (WGS) in a Chinese hospital, showing a high detection rate among patients, diverse genome characteristics, a high level of antibiotic resistance, and an unknown nosocomial transmission risk of C. difficile. During the study period, two C. difficile transferase (CDT)-positive isolates belonging to a new multilocus sequence type (ST820) were detected, which have caused serious clinical symptoms. This work describes C. difficile integrally and provides new insight into C. difficile surveillance based on WGS in China.
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Haider A, Alavi F, Siddiqa A, Abbas H, Patel H. Fulminant Pseudomembranous Colitis Leading to Clostridium Paraputrificum Bacteremia. Cureus 2021; 13:e13763. [PMID: 33842139 PMCID: PMC8022762 DOI: 10.7759/cureus.13763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Clostridium species are spore-forming gram-positive anaerobic rod bacteria that cause a broad range of infections in humans, including intra-abdominal infections, myonecrosis, and bacteremia. Pseudomembranous colitis (PMC) is a severe form of infection caused by Clostridioides difficile. Clostridial bacteremia usually occurs in the settings of neutropenia, alcohol abuse, diabetes mellitus, sickle cell anemia, malignancy, hemodialysis, inflammatory bowel disease, and AIDS. We report a case of fulminant PMC leading to C. paraputrificum bacteremia in an otherwise immunocompetent patient. To our knowledge, this is the first case report of such an occurrence.
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Affiliation(s)
- Asim Haider
- Internal Medicine, BronxCare Health System, Bronx, USA
| | - Fareeha Alavi
- Internal Medicine, BronxCare Health System, Bronx, USA
| | | | - Hafsa Abbas
- Gastroenterology, BronxCare Health System, Bronx, USA
| | - Harish Patel
- Gastroenterology, BronxCare Health System, Bronx, USA
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11
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Perry MD, White PL, Morris TE. Impact of the introduction of nucleic acid amplification testing on Clostridioides difficile detection and ribotype distribution in Wales. Anaerobe 2020; 67:102313. [PMID: 33309680 DOI: 10.1016/j.anaerobe.2020.102313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To determine the impact of the 2018 introduction of nucleic acid amplification tests (NAATs) for C. difficile detection on the laboratory diagnosis of C. difficile infection (CDI), and the distribution of C. difficile ribotypes. METHODS A retrospective analysis of five years (2015-2019) of C. difficile diagnostic laboratory and PCR ribotyping test results. RESULTS A total of 255,104 diagnostic results, from 136,353 patients were analysed: 199,794 samples where glutamate dehydrogenase (GDH) was used as the primary screen; and 55,310 where NAATs were employed. An overall decrease in frontline positivity from 2015 to 2019 (10.3% [n = 5017] to 6% [n = 3190] - p < 0.0001) was observed, despite an increase in the number of samples tested (48,778 to 52,839). NAAT positivity was lower than GDH (p < 0.0001) for the two years where it was implemented. The variance was accounted for by increased overall C. difficile isolation and reduced toxin negative strain culture from NAAT positive samples (p < 0.0001). Ribotype distribution (6546 samples) remained stable with decreasing RT27 isolation in each year except 2017 (p < 0.0001). RT78 was associated with toxin A/B EIA positivity (p < 0.0001). CONCLUSIONS Use of NAAT for the detection of C. difficile, as part of a 2-step algorithm, has not led to an increase in CDI laboratory diagnostic test positivity. In spite of ribotype distribution being comparable for screening in toxin A/B positive samples, there is a significantly greater correlation between NAAT positivity and culture of toxigenic strains compared to GDH.
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Affiliation(s)
- Michael D Perry
- Public Health Wales Microbiology, University Hospital of Wales, Heath Park, Cardiff, UK.
| | - P Lewis White
- Public Health Wales Microbiology, University Hospital of Wales, Heath Park, Cardiff, UK
| | - Trefor E Morris
- Public Health Wales Microbiology, University Hospital of Wales, Heath Park, Cardiff, UK
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12
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Reduced Clostridioides difficile infection in a pragmatic stepped-wedge initiative using admission surveillance to detect colonization. PLoS One 2020; 15:e0230475. [PMID: 32191763 PMCID: PMC7082001 DOI: 10.1371/journal.pone.0230475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/29/2020] [Indexed: 12/12/2022] Open
Abstract
Background Clostridioides difficile Infection (CDI) is a persistent healthcare issue. In the US, CDI is the most common infectious cause of hospital-onset (HO) diarrhea. Objective Assess the impact of admission testing for toxigenic C. difficile colonization on the incidence of HO-CDI. Design Pragmatic stepped-wedge Infection Control initiative. Setting NorthShore University HealthSystem is a four-hospital system near Chicago, IL. Patients All patients admitted to the four hospitals during the initiative. Interventions From September 2017 through August 2018 we conducted a quality improvement program where admitted patients had a peri-rectal swab tested for toxigenic C. difficile. All colonized patients were placed into contact precautions. Measurements We tested admissions who: i) had been hospitalized within two months, ii) had a past C. difficile positive test, and/or iii) were in a long-term care facility within six months. We measured compliance with all other practices to reduce the incidence of HO-CDI. Results 30% of admissions were tested and 8.3% were positive. In the year prior to the initiative (Period 1) there were 63,057 admitted patients when HO-CDI incidence was 5.96 cases/10,000 patient days. During the 12-month initiative (Period 2) there were 62,760 admissions and the HO-CDI incidence was 4.23 cases/10,000 patient days (p = 0.02). There were no other practice or antibiotic use changes. Continuing admission surveillance provided a HO-CDI incidence of 2.9 cases/10,000 patient days during the final 9 months of 2018 (p<0.0001 compared to Period 1), equaling <1 case/1,000 admissions. Limitations This was not a randomized controlled trial, and multiple prevention practices were in place at the time of the admission surveillance initiative. Conclusion Admission C. difficile surveillance testing is an important tool for preventing hospital-onset C. difficile infection. Registration This quality improvement initiative is registered at ClinicalTrials.gov. The unique registration identifier number is NCT04014608.
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Waker E, Ambrozkiewicz F, Kulecka M, Paziewska A, Skubisz K, Cybula P, Targoński Ł, Mikula M, Walewski J, Ostrowski J. High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years. Front Microbiol 2020; 11:1618. [PMID: 32793147 PMCID: PMC7384382 DOI: 10.3389/fmicb.2020.01618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022] Open
Abstract
Aims: Clostridium difficile (C. difficile) infection (CDI) is the main cause of healthcare-associated infectious diarrhea. We used whole-genome sequencing (WGS) to measure the prevalence and genetic variability of C. difficile at a single hemato-oncology ward over a 10 year period. Methods: Between 2008 and 2018, 2077 stool samples were obtained from diarrheal patients hospitalized at the Department of Lymphoma; of these, 618 were positive for toxin A/B. 140 isolates were then subjected to WGS on Ion Torrent PGM sequencer. Results: 36 and 104 isolates were recovered from 36 to 46 patients with single and multiple CDIs, respectively. Of these, 131 strains were toxigenic. Toxin gene profiles tcdA(+);tcdB(+);cdtA/cdtB(+) and tcdA(+);tcdB(+);cdtA/cdtB(-) were identified in 122 and nine strains, respectively. No isolates showed reduced susceptibility to metronidazole and vancomycin. All tested strains were resistant to ciprofloxacin, and 72.9, 42.9, and 72.9% of strains were resistant to erythromycin, clindamycin, or moxifloxacin, respectively. Multi-locus sequence typing (MLST) identified 23 distinct sequence types (STs) and two unidentified strains. Strains ST1 and ST42 represented 31 and 30.1% of all strains tested, respectively. However, while ST1 was detected across nearly all years studied, ST42 was detected only from 2009 to 2011. Conclusion: The high proportion of infected patients in 2008-2011 may be explained by the predominance of more transmissible and virulent C. difficile strains. Although this retrospective study was not designed to define outbreaks of C. difficile, the finding that most isolates exhibited high levels of genetic relatedness suggests nosocomial acquisition.
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Affiliation(s)
- Edyta Waker
- Department of Clinical Microbiology, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Łukasz Targoński
- Department of Lymphoproliferative Diseases, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
- *Correspondence: Jerzy Ostrowski,
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Khodaparast S, Mohabati Mobarez A, Saberifiroozi M. A Two-Step Approach for Diagnosing Glutamate Dehydrogenase Genes by Conventional Polymerase Chain Reaction from Clostridium difficile Isolates. Middle East J Dig Dis 2019; 11:135-140. [PMID: 31687111 PMCID: PMC6819966 DOI: 10.15171/mejdd.2019.139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/10/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Clostridium difficile is the major causative agent of nosocomial antibiotic-associated colitis. The gold standard for C. difficile detection is stool culture followed by cytotoxic assay, although it is laborious and time-consuming. We developed a screening test based on a two-step conventional polymerase chain reaction (PCR) approach to detect gluD, the glutamate dehydrogenase (GDH) enzyme gene, which is a marker for screening of C. difficile. Targeting gluD comparing to the conserved stable genetic element of pathogenicity locus (PaLoc), with an accessory gene of Cdd3, was an effective method for the detection of this pathogen from patients with enterocolitis.
METHODS
Fresh fecal samples of the patients who were clinically suspicious for antibiotic-associated colitis were collected. Stool specimens were cultured on the cycloserine-cefoxitin fructose agar (CCFA) in an anaerobic condition, following alcohol shock treatment and enrichment in Clostridium difficile Brucella broth (CDBB). On confirmed colonies, PCR was carried out for detection of PaLoc subsidiary gene, Cdd3, and toxicogenic genes, tcdA and tcdB. The gluD that is GDH gene detection was performed by conventional PCR on the extracted DNA from 578 fresh stool samples.
RESULTS
57 (9.8%) strains of C. difficile were approved by conventional PCR for gluD and Cdd3 genes, in which 37 (6.4%) colonies had tcdA+/tcdB+ genotype, 2 (0.3%) tcdA+/tcdB-, 4 (0.7%) tcdA-/ tcdB+ and the remaining 14 (2.4%) colonies were tcdA and tcdB negative.
CONCLUSION
These results demonstrate that targeting gluD by PCR is quite promising for rapid detection of C. difficile from fresh fecal samples. Furthermore, the multiple-gene analysis for tcdA and tcdB assay proved a reliable approach for diagnosing of toxigenic strains among clinical samples.
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Affiliation(s)
- Sepideh Khodaparast
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University. Tehran, Iran
| | - Ashraf Mohabati Mobarez
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University. Tehran, Iran
| | - Mehdi Saberifiroozi
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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15
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Kociolek LK, Gerding DN, Espinosa RO, Patel SJ, Shulman ST, Ozer EA. Clostridium difficile Whole Genome Sequencing Reveals Limited Transmission Among Symptomatic Children: A Single-Center Analysis. Clin Infect Dis 2019; 67:229-234. [PMID: 29370348 DOI: 10.1093/cid/ciy060] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 01/20/2018] [Indexed: 01/05/2023] Open
Abstract
Background Although pediatric Clostridium difficile infections (CDIs) are increasing, C. difficile transmission patterns among children are poorly understood. Methods We performed whole genome sequencing (WGS) on C. difficile isolates collected from children diagnosed with CDI between December 2012 and December 2013 at a single academic medical center. Genome sequences of isolates from CDIs diagnosed ≥8 weeks after study initiation were compared to all study isolate genome sequences. Among patients with isogenic isolates (≤2-3 core genome single nucleotide variants [SNVs] identified by pairwise SNV analyses), common inpatient and/or outpatient healthcare exposures were investigated. Results Among 131 CDIs in 107 children, WGS identified 104 genetically distinct isolates. Of 84 incident CDIs occurring ≥8 weeks after study initiation, only 10 (11.9%) were caused by a strain isogenic to another cohort CDI isolate (putative transmission events). Proportions of each CDI class putatively associated with transmission were hospital-onset healthcare facility-associated (HCFA), 2/16 (12.5%); community-onset HCFA, 1/17 (5.9%); indeterminate, 1/11 (9.1%); community-associated (CA), 5/40 (12.5%); and recurrent, 1/21 (4.8%). Transmission events among CA and HCFA CDIs were similarly infrequent (5/40 [12.5%] vs 3/33 [9.1%]; P = .64). Shared healthcare facility exposures were only identified among 7/10 putative transmission events. Potential community transmission (same postal code) was not identified. Conclusions WGS identified a highly diverse group of C. difficile isolates among children with CDI, including those with HCFA CDI. Clostridium difficile transmission among symptomatic children was very uncommon. Among putatively transmitted cases, investigation of shared healthcare exposures often did not identify a potential transmission source.
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Affiliation(s)
- Larry K Kociolek
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago.,Division of Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago
| | - Dale N Gerding
- Department of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood.,Department of Medicine, Edward Hines, Jr. Veterans Administration Hospital, Hines
| | - Robyn O Espinosa
- Division of Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago
| | - Sameer J Patel
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago.,Division of Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago
| | - Stanford T Shulman
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago.,Division of Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago
| | - Egon A Ozer
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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16
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Eyre DW, Davies KA, Davis G, Fawley WN, Dingle KE, De Maio N, Karas A, Crook DW, Peto TEA, Walker AS, Wilcox MH. Two Distinct Patterns of Clostridium difficile Diversity Across Europe Indicating Contrasting Routes of Spread. Clin Infect Dis 2019; 67:1035-1044. [PMID: 29659747 PMCID: PMC6137122 DOI: 10.1093/cid/ciy252] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 04/05/2018] [Indexed: 01/05/2023] Open
Abstract
Background Rates of Clostridium difficile infection vary widely across Europe, as do prevalent ribotypes. The extent of Europe-wide diversity within each ribotype, however, is unknown. Methods Inpatient diarrheal fecal samples submitted on a single day in summer and winter (2012–2013) to laboratories in 482 European hospitals were cultured for C. difficile, and isolates the 10 most prevalent ribotypes were whole-genome sequenced. Within each ribotype, country-based sequence clustering was assessed using the ratio of the median number of single-nucleotide polymorphisms between isolates within versus across different countries, using permutation tests. Time-scaled Bayesian phylogenies were used to reconstruct the historical location of each lineage. Results Sequenced isolates (n = 624) were from 19 countries. Five ribotypes had within-country clustering: ribotype 356, only in Italy; ribotype 018, predominantly in Italy; ribotype 176, with distinct Czech and German clades; ribotype 001/072, including distinct German, Slovakian, and Spanish clades; and ribotype 027, with multiple predominantly country-specific clades including in Hungary, Italy, Germany, Romania, and Poland. By contrast, we found no within-country clustering for ribotypes 078, 015, 002, 014, and 020, consistent with a Europe-wide distribution. Fluoroquinolone resistance was significantly more common in within-country clustered ribotypes (P = .009). Fluoroquinolone-resistant isolates were also more tightly clustered geographically with a median (interquartile range) of 43 (0–213) miles between each isolate and the most closely genetically related isolate, versus 421 (204–680) miles in nonresistant pairs (P < .001). Conclusions Two distinct patterns of C. difficile ribotype spread were observed, consistent with either predominantly healthcare-associated acquisition or Europe-wide dissemination via other routes/sources, for example, the food chain.
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Affiliation(s)
- David W Eyre
- Nuffield Department of Medicine, University of Oxford
| | - Kerrie A Davies
- Healthcare Associated Infections Research Group, University of Leeds
| | - Georgina Davis
- Healthcare Associated Infections Research Group, University of Leeds
| | - Warren N Fawley
- Healthcare Associated Infections Research Group, University of Leeds.,Public Health England, Leeds
| | - Kate E Dingle
- Nuffield Department of Medicine, University of Oxford
| | | | | | | | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford
| | | | - Mark H Wilcox
- Healthcare Associated Infections Research Group, University of Leeds
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Janezic S, Rupnik M. Development and Implementation of Whole Genome Sequencing-Based Typing Schemes for Clostridioides difficile. Front Public Health 2019; 7:309. [PMID: 31709221 PMCID: PMC6821651 DOI: 10.3389/fpubh.2019.00309] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022] Open
Abstract
Clostridioides difficile is an important nosocomial pathogen increasingly observed in the community and in different non-human reservoirs. The epidemiology and transmissibility of C. difficile has been studied using a variety of typing methods, including more recently developed whole-genome sequence (WGS) analysis that is becoming used routinely for bacterial typing worldwide. Here we review the schemes for WGS-based typing methods available for C. difficile and their applications in the field of human C. difficile infection (CDI). The two main approaches to discover genomic variations are single nucleotide variant (SNV) analysis and methods based on gene-by-gene comparisons (frequently called core genome or whole genome MLST, cgMLST, or wgMLST). SNV analysis currently provides the ultimate resolution, however, typing nomenclature and standardized methodology are missing. On the other hand, gene-by-gene approaches allow portability and standardized nomenclature, and are therefore becoming increasingly popular in bacterial epidemiology and outbreak investigation. Two commercial software packages (BioNumerics and Ridom SeqSphere+) and an open source database (EnteroBase) for allele and sequence type determination for C. difficile are currently available. Proof-of-concept WGS studies have already enabled advances in the investigation of the population structure of C. difficile species, microevolution within the epidemic strains, intercontinental transmission over time and in tracking of transmission events. WGS of clinical C. difficile isolates demonstrated a considerable genetic diversity suggesting diverse reservoirs for CDI. WGS was also shown to aid in resolving relapses and reinfections in recurrent CDI and has potential for use as a tool for assessing hospital infection prevention and control performance.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.,Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.,Medical Faculty, University of Maribor, Maribor, Slovenia
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Krutova M, Briksi A, Tkadlec J, Zajac M, Matejkova J, Nyc O, Drevinek P. Evaluation of a Gastrointestinal Pathogen Panel Immunoassay in Stool Testing of Patients with Suspected Clostridioides ( Clostridium) difficile Infection. J Clin Microbiol 2019; 57:e00710-19. [PMID: 31391230 PMCID: PMC6760961 DOI: 10.1128/jcm.00710-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/05/2019] [Indexed: 02/04/2023] Open
Abstract
Clostridioides (Clostridium) difficile infection (CDI) is the most common causative pathogen of health care-associated gastrointestinal infections; however, due to the overlap of clinical symptoms with those of other causes of acute gastroenteritis, the selection of the most appropriate laboratory test is difficult. From April to October 2018, 640 stool samples requested for CDI testing were examined using the mariPOC CDI and Gastro test (ArcDia), which allows the detection of C. difficile glutamate dehydrogenase (GDH) and toxin A/B, norovirus genogroups GI and GII.4, rotavirus, adenovirus, and Campylobacter spp. In parallel, the C. Diff Quik Chek Complete test (Alere) was used as a routine diagnostic assay, and C. difficile toxigenic culture was used as a reference method. The sensitivity of the mariPOC CDI and Gastro test was comparable to that of C. Diff Quik Chek Complete for the detection of GDH (96.40% [95% confidence interval {CI}, 91.81% to 98.82%] versus 95.68% [95% CI, 90.84 to 98.40%]; P = 1.00) and was higher for the detection of toxin A/B (66.67% [95% CI, 57.36 to 75.11%] versus 55.56% [95% CI, 46.08 to 64.74%]; P = 0.00). The specificity of the mariPOC CDI and Gastro test was lower than that of C. Diff Quik Chek Complete for GDH detection (95.21% [95% CI, 92.96% to 96.91%] versus 97.60% [95% CI, 95.85% to 98.76%]; P = 0.04) and comparable to that of C. Diff Quik Chek Complete for toxin A/B detection (99.24 [95% CI, 98.05% to 99.79%] versus 99.81% [95% CI, 98.94% to 100.0%]; P = 0.37). In 29 cases (4.53%), other causative agents of diarrhea were detected (Campylobacter spp. [n = 17], rotavirus [n = 7], and norovirus genogroup GII.4 [n = 5]).
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Affiliation(s)
- Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Ales Briksi
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Jan Tkadlec
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Miroslav Zajac
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Jana Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Otakar Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
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19
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Clostridioides difficile Whole-Genome Sequencing Reveals Limited Within-Host Genetic Diversity in a Pediatric Cohort. J Clin Microbiol 2019; 57:JCM.00559-19. [PMID: 31315950 DOI: 10.1128/jcm.00559-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/04/2019] [Indexed: 02/04/2023] Open
Abstract
Whole-genome sequencing (WGS) is a highly sensitive method for identifying genetic relatedness and transmission of Clostridioides difficile strains. Previous studies suggest that as few as 3 core genome single-nucleotide variants (SNVs) discriminate between genetically distinct isolates. Because a single C. difficile colony is selected from culture for WGS, significant within-host genetic diversity could preclude identification of transmission events. To evaluate the likelihood of missed transmission events using WGS of single colonies from culture, we examined within-host genetic diversity among C. difficile isolates collected from children. We performed WGS using an Illumina MiSeq instrument on 8 C. difficile colonies randomly selected from each culture performed on stool collected from 10 children (8 children diagnosed with C. difficile infection and 2 children with asymptomatic carriage); 77/80 (96%) isolate sequences were successfully assembled. Among 8/10 (80%) children, all isolates were the same sequence type (ST). The other 2 children each had mixed infection with two STs, although one ST predominated. Among 9/10 (90%) children, isotypic isolates differed by ≤2 SNVs; an isotypic isolate in the remaining child differed by 3 to SNVs relative to the other isolates from that child. Overall, among the 77 isolates collected from 10 stool cultures, 74/77 (96%) were clonal (i.e., same ST and ≤2 core genome SNVs) to other isolates in stool culture. In summary, we identified rare C. difficile within-host genetic diversity in children, suggesting that WGS of a single colony from stool is likely to appropriately characterize isolate clonality and putative transmission events in the majority of cases.
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Correlation between tcdB gene PCR cycle threshold and severe Clostridium difficile disease. Anaerobe 2019; 59:141-144. [PMID: 31254653 DOI: 10.1016/j.anaerobe.2019.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/12/2019] [Accepted: 06/26/2019] [Indexed: 01/05/2023]
Abstract
A retrospective study, including all samples tested for Clostridium difficile from 2015 to 2018, was conducted. 222 and 199 patients were respectively classified as having a mild/moderate or severe disease. A CT ≤ 26 was significantly associated with severe disease. Furthermore, low CT values were significantly associated to older patients and leukocytosis.
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Biggs M, Iqbal T, Holden E, Clewer V, Garvey M. Effect of using fidaxomicin on recurrent Clostridium difficile infection. J Hosp Infect 2019; 102:165-167. [DOI: 10.1016/j.jhin.2018.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 10/27/2022]
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How do we define recurrence in Clostridium difficile infection? J Hosp Infect 2019; 102:171-173. [DOI: 10.1016/j.jhin.2018.07.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 11/22/2022]
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Mileto S, Das A, Lyras D. Enterotoxic Clostridia: Clostridioides difficile Infections. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0015-2018. [PMID: 31124432 PMCID: PMC11026080 DOI: 10.1128/microbiolspec.gpp3-0015-2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile is a Gram-positive, anaerobic, spore forming pathogen of both humans and animals and is the most common identifiable infectious agent of nosocomial antibiotic-associated diarrhea. Infection can occur following the ingestion and germination of spores, often concurrently with a disruption to the gastrointestinal microbiota, with the resulting disease presenting as a spectrum, ranging from mild and self-limiting diarrhea to severe diarrhea that may progress to life-threating syndromes that include toxic megacolon and pseudomembranous colitis. Disease is induced through the activity of the C. difficile toxins TcdA and TcdB, both of which disrupt the Rho family of GTPases in host cells, causing cell rounding and death and leading to fluid loss and diarrhea. These toxins, despite their functional and structural similarity, do not contribute to disease equally. C. difficile infection (CDI) is made more complex by a high level of strain diversity and the emergence of epidemic strains, including ribotype 027-strains which induce more severe disease in patients. With the changing epidemiology of CDI, our understanding of C. difficile disease, diagnosis, and pathogenesis continues to evolve. This article provides an overview of the current diagnostic tests available for CDI, strain typing, the major toxins C. difficile produces and their mode of action, the host immune response to each toxin and during infection, animal models of disease, and the current treatment and prevention strategies for CDI.
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Affiliation(s)
- S Mileto
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia, 3800
| | - A Das
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia, 3800
| | - D Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia, 3800
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Eyre DW, Didelot X, Buckley AM, Freeman J, Moura IB, Crook DW, Peto TEA, Walker AS, Wilcox MH, Dingle KE. Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage. EBioMedicine 2019; 43:347-355. [PMID: 31036529 PMCID: PMC6558026 DOI: 10.1016/j.ebiom.2019.04.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Clostridium difficile ribotype-027, ribotype-078, and ribotype-017 are virulent and epidemic lineages. Trehalose metabolism variants in these ribotypes, combined with increased human trehalose consumption, have been hypothesised to have contributed to their emergence and virulence. METHODS 5232 previously whole-genome sequenced C. difficile isolates were analysed. Clinical isolates were used to investigate the impact of trehalose metabolism variants on mortality. Import data were used to estimate changes in dietary trehalose. Ribotype-027 virulence was investigated in a clinically reflective gut model. FINDINGS Trehalose metabolism variants found in ribotype-027 and ribotype-017 were widely distributed throughout C. difficile clade-2 and clade-4 in 24/29 (83%) and 10/11 (91%) of sequence types (STs), respectively. The four-gene trehalose metabolism cluster described in ribotype-078 was common in genomes from all five clinically-important C. difficile clades (40/167 [24%] STs). The four-gene cluster was variably present in 208 ribotype-015 infections (98 [47%]); 27/208 (13%) of these patients died within 30-days of diagnosis. Adjusting for age, sex, and infecting ST, there was no association between 30-day all-cause mortality and the four-gene cluster (OR 0.36 [95%CI 0.09-1.34, p = 0.13]). Synthetic trehalose imports in the USA, UK, Germany and the EU were < 1 g/capita/year during 2000-2006, and < 9 g/capita/year 2007-2012, compared with dietary trehalose from natural sources of ~100 g/capita/year. Trehalose supplementation did not increase ribotype-027 virulence in a clinically-validated gut model. INTERPRETATION Trehalose metabolism variants are common in C. difficile. Increases in total dietary trehalose during the early-mid 2000s C. difficile epidemic were likely relatively minimal. Alternative explanations are required to explain why ribotype-027, ribotype-078 and ribotype-017 have been successful. FUNDING National Institute for Health Research. Gut model experiments only: Hayashibara Co. Ltd.
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Affiliation(s)
- David W Eyre
- Big Data Institute, University of Oxford, UK; Nuffield Department of Medicine, University of Oxford, UK.
| | - Xavier Didelot
- School of Life Sciences, Department of Statistics, University of Warwick, UK
| | - Anthony M Buckley
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Jane Freeman
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Ines B Moura
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Kate E Dingle
- Nuffield Department of Medicine, University of Oxford, UK
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Eyre DW, Shaw R, Adams H, Cooper T, Crook DW, Griffin RM, Mannion P, Morgan M, Morris T, Perry M, Jones S, Peto TEA, Sutton J, Walker AS, Williams D, Craine N. WGS to determine the extent of Clostridioides difficile transmission in a high incidence setting in North Wales in 2015. J Antimicrob Chemother 2019; 74:1092-1100. [PMID: 30561656 DOI: 10.1093/jac/dky523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/06/2018] [Accepted: 11/16/2018] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Rates of Clostridioides (Clostridium) difficile infection (CDI) are higher in North Wales than elsewhere in the UK. We used WGS to investigate if this is due to increased healthcare-associated transmission from other cases. METHODS Healthcare and community C. difficile isolates from patients across North Wales (February-July 2015) from glutamate dehydrogenase (GDH)-positive faecal samples underwent WGS. Data from patient records, hospital management systems and national antimicrobial use surveillance were used. RESULTS Of the 499 GDH-positive samples, 338 (68%) were sequenced and 299 distinct infections/colonizations were identified, 229/299 (77%) with toxin genes. Only 39/229 (17%) toxigenic isolates were related within ≤2 SNPs to ≥1 infections/colonizations from a previously sampled patient, i.e. demonstrated evidence of possible transmission. Independent predictors of possible transmission included healthcare exposure in the last 12 weeks (P = 0.002, with rates varying by hospital), infection with MLST types ST-1 (ribotype 027) and ST-11 (predominantly ribotype 078) compared with all other toxigenic STs (P < 0.001), and cephalosporin exposure in the potential transmission recipient (P = 0.02). Adjusting for all these factors, there was no additional effect of ward workload (P = 0.54) or failure to meet cleaning targets (P = 0.25). Use of antimicrobials is higher in North Wales compared with England and the rest of Wales. CONCLUSIONS Levels of transmission detected by WGS were comparable to previously described rates in endemic settings; other explanations, such as variations in antimicrobial use, are required to explain the high levels of CDI. Cephalosporins are a risk factor for infection with C. difficile from another infected or colonized case.
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Affiliation(s)
- David W Eyre
- Big Data Institute, University of Oxford, England, UK.,Nuffield Department of Medicine, University of Oxford, England, UK
| | - Robert Shaw
- Nuffield Department of Medicine, University of Oxford, England, UK
| | - Helen Adams
- Betsi Cadwaladr University Health Board, Ysbyty Gwynedd, Bangor, Wales, UK
| | - Tracey Cooper
- Betsi Cadwaladr University Health Board, Ysbyty Glan Clwyd, Bangor, Wales, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, England, UK
| | | | - Phil Mannion
- Public Health Wales, Microbiology, Ysbyty Glan Clwyd, Rhyl, Wales, UK
| | - Mari Morgan
- Public Health Wales, Health Protection, Capital Quarter, Cardiff, Wales, UK
| | - Trefor Morris
- Public Health Wales, Microbiology, Heath Hospital, Cardiff, Wales, UK
| | - Michael Perry
- Public Health Wales, Microbiology, Heath Hospital, Cardiff, Wales, UK
| | - Sophie Jones
- Public Health Wales, Microbiology, Heath Hospital, Cardiff, Wales, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, England, UK
| | - Jonathan Sutton
- Betsi Cadwaladr University Health Board, Ysbyty Gwynedd, Bangor, Wales, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, England, UK
| | - Dafydd Williams
- Betsi Cadwaladr University Health Board, Ysbyty Gwynedd, Bangor, Wales, UK
| | - Noel Craine
- Public Health Wales, Health Protection, Ysbyty Gwynedd, Bangor, Wales, UK
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Ashraf Z, Rahmati E, Bender JM, Nanda N, She RC. GDH and toxin immunoassay for the diagnosis of Clostridioides (Clostridium) difficile infection is not a 'one size fit all' screening test. Diagn Microbiol Infect Dis 2018; 94:109-112. [PMID: 30696609 DOI: 10.1016/j.diagmicrobio.2018.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/22/2018] [Accepted: 12/22/2018] [Indexed: 01/01/2023]
Abstract
Diagnosing Clostridioides (Clostridium) difficile infection is challenged by lack of a clear gold standard. We sought to determine if the two-step algorithm (screening GDH and toxin lateral flow assay followed by tcdB PCR) would have adequate clinical performance at a tertiary care center. Of 486 patients, 310 (63.8%) were immunocompromised. Of 150 PCR-positive specimens, 52 (34.7%) were toxin-positive and 126 (84.0%) were GDH positive. Positive GDH or toxin results corresponded to lower PCR cycle threshold values (P < 0.01). PCR-positive patients had more frequently documented antibiotic usage (78.4% vs 66.9%, P = 0.05) and diarrhea (91.0% vs. 79.4%, P < 0.01) and less frequent alternate etiologies of diarrhea (27.3% vs. 41.1%, P = 0.004) or laxative use (24.6% vs 36.1%, P = 0.02). Toxin positivity was associated with antibiotic use (P < 0.01), but not with neutropenia, diarrhea, malignancy, or chemotherapy (P > 0.05). The application of the 2-step algorithm should be thoroughly evaluated in immunocompromised patient populations before implementation.
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Affiliation(s)
- Zuhha Ashraf
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Elham Rahmati
- Department of Medicine, Division of Infectious Diseases, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Jeffrey M Bender
- Department of Pediatrics, Division of Infectious Diseases, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Neha Nanda
- Department of Medicine, Division of Infectious Diseases, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Rosemary C She
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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Kutty PK, McDonald LC. Diagnosing an Infection Control Risk. Clin Infect Dis 2018; 64:1171-1173. [PMID: 28158635 DOI: 10.1093/cid/cix085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 01/26/2017] [Indexed: 12/17/2022] Open
Affiliation(s)
- Preeta K Kutty
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L Clifford McDonald
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Clostridium difficile in England: can we stop washing our hands? - Authors' reply. THE LANCET. INFECTIOUS DISEASES 2018; 17:478-479. [PMID: 28447949 DOI: 10.1016/s1473-3099(17)30185-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 11/20/2022]
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Krehelova M, Nyč O, Sinajová E, Krutova M. The predominance and clustering of Clostridioides (Clostridium) difficile PCR ribotype 001 isolates in three hospitals in Eastern Slovakia, 2017. Folia Microbiol (Praha) 2018; 64:49-54. [PMID: 29971567 DOI: 10.1007/s12223-018-0629-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/27/2018] [Indexed: 12/20/2022]
Abstract
This study aimed to implement a toxigenic culture as an optional third diagnostic step for glutamate dehydrogenase (GDH)-positive and toxin A/B-negative diarrheal stool samples into a diagnostic algorithm for Clostridioides (Clostridium) difficile infection (CDI), and to characterise C. difficile isolates for epidemiological purposes. During the 5-month study, 481 diarrhoeal stool samples from three Slovak hospitals were investigated and 66 non-duplicated GDH-positive stool samples were found. Of them, 36 were also toxin A/B-positive. Twenty-three GDH-positive and toxin A/B-negative stool samples were shown subsequently to be positive following toxigenic culture (TC). Molecular characterisation of C. difficile isolates showed the predominance of PCR ribotype (RT) 001 (n = 37, 56.1%) and the occurrence of RT 176 (n = 3, 4.5%). C. difficile RT 001 isolates clustered to eight clonal complexes (CCs) using multiple-locus variable-number tandem repeats analysis (MLVA). Interestingly, one third of RT 001 isolates clustering in these CCs were cultured from toxin A/B-negative stool samples. Our observations highlight the need of use multiple step diagnostic algorithm in CDI diagnosis in order to detect all CDI cases and to avoid the spread of C. difficile in healthcare settings.
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Affiliation(s)
| | - Otakar Nyč
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic
| | - Eva Sinajová
- Department of Microbiology, Medirex Group, Kosice, Slovakia
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic.
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Eyre DW, Fawley WN, Rajgopal A, Settle C, Mortimer K, Goldenberg SD, Dawson S, Crook DW, Peto TEA, Walker AS, Wilcox MH. Comparison of Control of Clostridium difficile Infection in Six English Hospitals Using Whole-Genome Sequencing. Clin Infect Dis 2018; 65:433-441. [PMID: 28575285 PMCID: PMC5850028 DOI: 10.1093/cid/cix338] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/07/2017] [Indexed: 12/31/2022] Open
Abstract
Background. Variation in Clostridium difficile infection (CDI) rates between healthcare institutions suggests overall incidence could be reduced if the lowest rates could be achieved more widely. Methods. We used whole-genome sequencing (WGS) of consecutive C. difficile isolates from 6 English hospitals over 1 year (2013–14) to compare infection control performance. Fecal samples with a positive initial screen for C. difficile were sequenced. Within each hospital, we estimated the proportion of cases plausibly acquired from previous cases. Results. Overall, 851/971 (87.6%) sequenced samples contained toxin genes, and 451 (46.4%) were fecal-toxin-positive. Of 652 potentially toxigenic isolates >90-days after the study started, 128 (20%, 95% confidence interval [CI] 17–23%) were genetically linked (within ≤2 single nucleotide polymorphisms) to a prior patient’s isolate from the previous 90 days. Hospital 2 had the fewest linked isolates, 7/105 (7%, 3–13%), hospital 1, 9/70 (13%, 6–23%), and hospitals 3–6 had similar proportions of linked isolates (22–26%) (P ≤ .002 comparing hospital-2 vs 3–6). Results were similar adjusting for locally circulating ribotypes. Adjusting for hospital, ribotype-027 had the highest proportion of linked isolates (57%, 95% CI 29–81%). Fecal-toxin-positive and toxin-negative patients were similarly likely to be a potential transmission donor, OR = 1.01 (0.68–1.49). There was no association between the estimated proportion of linked cases and testing rates. Conclusions. WGS can be used as a novel surveillance tool to identify varying rates of C. difficile transmission between institutions and therefore to allow targeted efforts to reduce CDI incidence.
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Affiliation(s)
- David W Eyre
- Nuffield Department of Medicine, University of Oxford
| | - Warren N Fawley
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust
| | - Anu Rajgopal
- Calderdale and Huddersfield NHS Foundation Trust
| | | | - Kalani Mortimer
- St. Helens and Knowsley Teaching Hospitals NHS Trust, Merseyside
| | | | - Susan Dawson
- Great Western Hospitals NHS Foundation Trust, Swindon, United Kingdom
| | | | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford
| | | | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust
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31
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Petrosillo N, Granata G, Cataldo MA. Novel Antimicrobials for the Treatment of Clostridium difficile Infection. Front Med (Lausanne) 2018; 5:96. [PMID: 29713630 PMCID: PMC5911476 DOI: 10.3389/fmed.2018.00096] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
The current picture of Clostridium difficile infection (CDI) is alarming with a mortality rate ranging between 3% and 15% and a CDI recurrence rate ranging from 12% to 40%. Despite the great efforts made over the past 10 years to face the CDI burden, there are still gray areas in our knowledge on CDI management. The traditional anti-CDI antimicrobials are not always adequate in addressing the current needs in CDI management. The aim of our review is to give an update on novel antimicrobials for the treatment of CDI, considering the currently available evidences on their efficacy, safety, molecular mechanism of action, and their probability to be successfully introduced into the clinical practice in the near future. We identified, through a PubMed search, 16 novel antimicrobial molecules under study for CDI treatment: cadazolid, surotomycin, ridinilazole, LFF571, ramoplanin, CRS3123, fusidic acid, nitazoxanide, rifampin, rifaximin, tigecycline, auranofin, NVB302, thuricin CD, lacticin 3147, and acyldepsipeptide antimicrobials. In comparison with the traditional anti-CDI antimicrobial treatment, some of the novel antimicrobials reviewed in this study offer several advantages, i.e., the favorable pharmacokinetic and pharmacodynamic profile, the narrow-spectrum activity against CD that implicates a low impact on the gut microbiota composition, the inhibitory activity on CD sporulation and toxins production. Among these novel antimicrobials, the most active compounds in reducing spore production are cadazolid, ridinilazole, CRS3123, ramoplanin and, potentially, the acyldepsipeptide antimicrobials. These antimicrobials may potentially reduce CD environment spread and persistence, thus reducing CDI healthcare-associated acquisition. However, some of them, i.e., surotomycin, fusidic acid, etc., will not be available due to lack of superiority versus standard of treatment. The most CD narrow-spectrum novel antimicrobials that allow to preserve microbiota integrity are cadazolid, ridinilazole, auranofin, and thuricin CD. In conclusion, the novel antimicrobial molecules under development for CDI have promising key features and advancements in comparison to the traditional anti-CDI antimicrobials. In the near future, some of these new molecules might be effective alternatives to fight CDI.
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Affiliation(s)
- Nicola Petrosillo
- Clinical and Research Department for Infectious Diseases, Unit Systemic and Immunedepression-Associated Infections, National Institute for Infectious Diseases L. Spallanzani, Rome, Italy
| | - Guido Granata
- Clinical and Research Department for Infectious Diseases, Unit Systemic and Immunedepression-Associated Infections, National Institute for Infectious Diseases L. Spallanzani, Rome, Italy
| | - Maria Adriana Cataldo
- Clinical and Research Department for Infectious Diseases, Unit Systemic and Immunedepression-Associated Infections, National Institute for Infectious Diseases L. Spallanzani, Rome, Italy
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Validation of Active Surveillance Testing for Clostridium difficile Colonization Using the cobas Cdiff Test. J Clin Microbiol 2018; 56:JCM.01553-17. [PMID: 29367295 DOI: 10.1128/jcm.01553-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Clostridium difficile infection (CDI) is not declining in the United States. Nucleic acid amplification tests (NAAT) are used as part of active surveillance testing programs to prevent health care-associated infection. The objective of this study was to validate the cobas Cdiff Test on the cobas 4800 System (cobas) within a four-hospital system using prospectively collected perirectal swabs from asymptomatic patients at admission and during monthly intensive care unit (ICU) screening in an infection control CDI reduction program. Performance of the cobas was compared to that of toxigenic culture. Each positive cobas sample and the next following negative patient swab were cultured. The study design gave 273 samples processed by both cobas (137 positive and 136 negative) and culture (one negative swab was not cultured). Discrepant analysis was performed using a second NAAT, the Xpert C. difficile Epi test (Xpert). This strategy was compared to a medical record review for antibiotic receipt that would inhibit growth of C. difficile in colonic stool. None of the cobas-negative samples were culture positive. The cobas positive predictive value was 75.2% (95% confidence interval [CI], 66.9% to 82%) and positive percent agreement was 100% (95% CI, 96.0% to 100%). Overall agreement between cobas and direct toxigenic culture was 87.6% (95% CI, 83.1% to 91%). For the cobas-positive/culture-negative (discrepant) samples, 7 Xpert-positive samples were from patients receiving inhibitory antimicrobials; only 4 of 23 Xpert-negative samples received these agents (P = 0.00006). Our results support use of the cobas as a reliable assay for an active surveillance testing program to detect asymptomatic carriers of toxigenic C. difficile.
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Casari E, De Luca C, Calabrò M, Scuderi C, Daleno C, Ferrario A. Reducing rates of Clostridium difficile infection by switching to a stand-alone NAAT with clear sampling criteria. Antimicrob Resist Infect Control 2018; 7:40. [PMID: 29564088 PMCID: PMC5848539 DOI: 10.1186/s13756-018-0332-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/06/2018] [Indexed: 01/05/2023] Open
Abstract
Background Clostridium difficile infection is an important cause of morbidity and mortality but the optimal method of diagnosis for both patient management and infection prevention remains controversial. Methods Our hospital made a decision to switch from the use of toxin immunoassay to a stand-alone nucleic acid test. This change was accompanied by the provision of clear sampling guidance and rejection criteria and this study aimed to assess the impact of that change. We analysed sample numbers, numbers of positive results, and the proportion of cases assessed as healthcare acquired over a 6-year period during which the testing method was changed from a toxin A/B immunoassay to a stand-alone commercial nucleic acid test after the first two years. Results Sample numbers and numbers of cases assessed as healthcare acquired fell following the introduction of the nucleic acid test and sampling guidance, while infection rates in other hospitals in the same region remained relatively stable. Conclusions It is our opinion that the use of a highly sensitive assay together with clear sampling guidance offers the optimal approach to patient management and best use of isolation facilities.
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Affiliation(s)
- E Casari
- Microbiology Unit, Analysis Laboratory, Humanitas Research Hospital, via Manzoni, 56 20089 Rozzano, Milan, Italy
| | - C De Luca
- Microbiology Unit, Analysis Laboratory, Humanitas Research Hospital, via Manzoni, 56 20089 Rozzano, Milan, Italy
| | - M Calabrò
- Microbiology Unit, Analysis Laboratory, Humanitas Research Hospital, via Manzoni, 56 20089 Rozzano, Milan, Italy
| | - C Scuderi
- Microbiology Unit, Analysis Laboratory, Humanitas Research Hospital, via Manzoni, 56 20089 Rozzano, Milan, Italy
| | - C Daleno
- Microbiology Unit, Analysis Laboratory, Humanitas Research Hospital, via Manzoni, 56 20089 Rozzano, Milan, Italy
| | - A Ferrario
- Microbiology Unit, Analysis Laboratory, Humanitas Research Hospital, via Manzoni, 56 20089 Rozzano, Milan, Italy
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Moradigaravand D, Gouliouris T, Ludden C, Reuter S, Jamrozy D, Blane B, Naydenova P, Judge K, H. Aliyu S, F. Hadjirin N, A. Holmes M, Török E, M. Brown N, Parkhill J, Peacock S. Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages. Microb Genom 2018; 4:e000162. [PMID: 29498619 PMCID: PMC5885014 DOI: 10.1099/mgen.0.000162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/09/2018] [Indexed: 01/03/2023] Open
Abstract
There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C. difficile from 65 patients were highly diverse and that most cases were not linked to other active cases in the hospital. In total, 186 C. difficile isolates were isolated from effluent water obtained from 18 municipal treatment plants at the point of release into the environment. Whole genome comparisons of clinical and environmental isolates demonstrated highly related populations, and confirmed extensive release of toxigenic C. difficile into surface waters. An analysis based on multilocus sequence types (STs) identified 19 distinct STs in the clinical collection and 38 STs in the wastewater collection, with 13 of 44 STs common to both clinical and wastewater collections. Furthermore, we identified five pairs of highly similar isolates (≤2 SNPs different in the core genome) in clinical and wastewater collections. Strategies to control community acquisition should consider the need for bacterial control of treated wastewater.
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Affiliation(s)
| | | | | | - Sandra Reuter
- University of Freiburg, Freiburg im Breisgau, Germany
| | | | | | | | - Kim Judge
- Wellcome Trust Sanger Institute, Hinxton, UK
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Epidemiological aspects of healthcare-associated infections and microbial genomics. Eur J Clin Microbiol Infect Dis 2018; 37:823-831. [PMID: 29340898 DOI: 10.1007/s10096-017-3170-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 12/19/2017] [Indexed: 12/27/2022]
Abstract
Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO). Many microbial typing technologies have been developed and put to some level of executive practice, but it seems that the continued evolution in methodology has currently reached an apex: there is likely to be scientific and practical consensus on the ultimate typing potential of bacterial whole-genome sequencing (WGS). The possibility to perform pan-genomic nucleotide-to-nucleotide comparisons between strains belonging to a single species and to detect even minute changes in nucleotide order will identify closely related organisms, while upon accumulation of such mutations, independent descend can be assumed. Calibration of difference levels [i.e. number of single nucleotide polymorphisms (SNPs)] into categories of inter-strain relatedness needs to be performed in order to generate robust, portable typing schemes. Here, we will briefly discuss the state of affairs regarding bacterial epidemiology based upon WGS, its relatedness with the nomenclature of former typing approaches and the continuing need for a global typing language.
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Comparative Genomics of Clostridium difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1050:59-75. [PMID: 29383664 DOI: 10.1007/978-3-319-72799-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clostridium difficile, a gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of nosocomial diarrhoea in hospitals. The availability of genome sequences in large numbers, mainly due to the use of next-generation sequencing methods, have undoubtedly shown their immense advantages in the determination of the C. difficile population structure. The implementation of fine-scale comparative genomic approaches have paved the way to global transmission and recurrence studies, but also more targeted studies such as the PaLoc or the CRISPR/Cas systems. In this chapter, we provide an overview of the recent and significant findings on C. difficile using comparative genomics studies with implication for the epidemiology, infection control and understanding of the evolution of C. difficile.
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Garvey MI, Bradley CW, Wilkinson MAC, Holden E. Can a toxin gene NAAT be used to predict toxin EIA and the severity of Clostridium difficile infection? Antimicrob Resist Infect Control 2017; 6:127. [PMID: 29270290 PMCID: PMC5735516 DOI: 10.1186/s13756-017-0283-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/23/2017] [Indexed: 12/17/2022] Open
Abstract
Background Diagnosis of C. difficile infection (CDI) is controversial because of the many laboratory methods available and their lack of ability to distinguish between carriage, mild or severe disease. Here we describe whether a low C. difficile toxin B nucleic acid amplification test (NAAT) cycle threshold (CT) can predict toxin EIA, CDI severity and mortality. Methods A three-stage algorithm was employed for CDI testing, comprising a screening test for glutamate dehydrogenase (GDH), followed by a NAAT, then a toxin enzyme immunoassay (EIA). All diarrhoeal samples positive for GDH and NAAT between 2012 and 2016 were analysed. The performance of the NAAT CT value as a classifier of toxin EIA outcome was analysed using a ROC curve; patient mortality was compared to CTs and toxin EIA via linear regression models. Results A CT value ≤26 was associated with ≥72% toxin EIA positivity; applying a logistic regression model we demonstrated an association between low CT values and toxin EIA positivity. A CT value of ≤26 was significantly associated (p = 0.0262) with increased one month mortality, severe cases of CDI or failure of first line treatment. The ROC curve probabilities demonstrated a CT cut off value of 26.6. Discussions Here we demonstrate that a CT ≤26 indicates more severe CDI and is associated with higher mortality. Samples with a low CT value are often toxin EIA positive, questioning the need for this additional EIA test. Conclusions A CT ≤26 could be used to assess the potential for severity of CDI and guide patient treatment.
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Affiliation(s)
- Mark I Garvey
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, B15 2WB, Edgbaston, Birmingham, UK.,Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham, UK
| | - Craig W Bradley
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, B15 2WB, Edgbaston, Birmingham, UK
| | - Martyn A C Wilkinson
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, B15 2WB, Edgbaston, Birmingham, UK
| | - Elisabeth Holden
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, B15 2WB, Edgbaston, Birmingham, UK
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Screening, prophylaxis and counselling before the start of biological therapies: A practical approach focused on IBD patients. Dig Liver Dis 2017; 49:1289-1297. [PMID: 28986117 DOI: 10.1016/j.dld.2017.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/03/2017] [Accepted: 09/04/2017] [Indexed: 02/07/2023]
Abstract
UNLABELLED The standard of care in the management of immune-mediated inflammatory conditions relies on immunomodulators, glucocorticoids, and biologicals (including anti-tumour necrosis factor -α and other monoclonal antibodies). These agents have an overall favourable benefit/risk ratio; however, they modulate the immune response as part of their mechanisms of action, and therefore they may increase the risk of developing infections, particularly in older patients or in patients with concomitant corticosteroids. Some of these infections may be preventable by immunization, chemoprophylaxis or counselling. AIM screening for and monitoring infections throughout these therapies is so mandatory to ensure patients' safety. Still, standardized guidelines focused on these procedures have yet to be established. This review aims to fill such a gap. The authors searched for articles published in English from 2009 until 2017 using PUBMED, with the terms "immunomodulators", "biological drugs", "anti-TNF α", "inflammatory bowel diseases", "immunomediated inflammatory diseases", "risk of infection", "infection prevention", "screening", "immunization", "tuberculosis", "latent tuberculosis", "listeriosis", "endemic mycosis", "Pneumocystis jiroveci pneumonia", "granulomatous infection", "varicella", "herpes virus", "hepatitis B", "hepatitis A", "hepatitis C" and identified the journal articles. Based on the literature and in their own experience the authors established recommendations and a practical guide for infections' screening, monitoring and prevention before and during immunomodulatory and biological therapies.
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Peterson LR, Young SA, Davis TE, Wang ZX, Duncan J, Noutsios C, Liesenfeld O, Osiecki JC, Lewinski MA. Evaluation of the cobas Cdiff Test for Detection of Toxigenic Clostridium difficile in Stool Samples. J Clin Microbiol 2017; 55:3426-3436. [PMID: 28954901 PMCID: PMC5703809 DOI: 10.1128/jcm.01135-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/22/2017] [Indexed: 12/18/2022] Open
Abstract
Nucleic acid amplification tests (NAATs) are reliable tools for the detection of toxigenic Clostridium difficile from unformed (liquid or soft) stool samples. The objective of this study was to evaluate performance of the cobas Cdiff test on the cobas 4800 system using prospectively collected stool specimens from patients suspected of having C. difficile infection (CDI). The performance of the cobas Cdiff test was compared to the results of combined direct and broth-enriched toxigenic culture methods in a large, multicenter clinical trial. Additional discrepancy analysis was performed by using the Xpert C. difficile Epi test. Sample storage was evaluated by using contrived and fresh samples before and after storage at -20°C. Testing was performed on samples from 683 subjects (306 males and 377 females); 113 (16.5%) of 683 subjects were positive for toxigenic C. difficile by direct toxigenic culture, and 141 of 682 subjects were positive by using the combined direct and enriched toxigenic culture method (reference method), for a prevalence rate of 20.7%. The sensitivity and specificity of the cobas Cdiff test compared to the combined direct and enriched culture method were 92.9% (131/141; 95% confidence interval [CI], 87.4% to 96.1%) and 98.7% (534/541; 95% CI, 97.4% to 99.4%), respectively. Discrepancy analysis using results for retested samples from a second NAAT (Xpert C. difficile/Epi test; Cepheid, Sunnyvale, CA) found no false-negative and 4 false-positive cobas Cdiff test results. There was no difference in positive and negative results in comparisons of fresh and stored samples. These results support the use of the cobas Cdiff test as a robust aid in the diagnosis of CDI.
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Affiliation(s)
- Lance R Peterson
- Department of Laboratory Medicine and Pathology, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Stephen A Young
- Department of Pathology, University of New Mexico HSC, Albuquerque, New Mexico, USA
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Thomas E Davis
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Zi-Xuam Wang
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - John Duncan
- Medical and Scientific Affairs, Roche Molecular Diagnostics, Pleasanton, California, USA
| | - Christopher Noutsios
- Medical and Scientific Affairs, Roche Molecular Diagnostics, Pleasanton, California, USA
| | - Oliver Liesenfeld
- Medical and Scientific Affairs, Roche Molecular Diagnostics, Pleasanton, California, USA
| | - John C Osiecki
- Medical and Scientific Affairs, Roche Molecular Diagnostics, Pleasanton, California, USA
| | - Michael A Lewinski
- Medical and Scientific Affairs, Roche Molecular Diagnostics, Pleasanton, California, USA
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40
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Behar L, Chadwick D, Dunne A, Jones CI, Proctor C, Rajkumar C, Sharratt P, Stanley P, Whiley A, Wilks M, Llewelyn MJ. Toxigenic Clostridium difficile colonization among hospitalised adults; risk factors and impact on survival. J Infect 2017; 75:20-25. [PMID: 28435086 PMCID: PMC5464213 DOI: 10.1016/j.jinf.2017.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 01/05/2023]
Abstract
OBJECTIVES To establish risk factors for Clostridium difficile colonization among hospitalized patients in England. METHODS Patients admitted to elderly medicine wards at three acute hospitals in England were recruited to a prospective observational study. Participants were asked to provide a stool sample as soon as possible after enrolment and then weekly during their hospital stay. Samples were cultured for C. difficile before ribotyping and toxin detection by PCR. A multivariable logistic regression model of risk factors for C. difficile colonization was fitted from univariable risk factors significant at the p < 0.05 level. RESULTS 410/727 participants submitted ≥1 stool sample and 40 (9.8%) carried toxigenic C. difficile in the first sample taken. Ribotype 106 was identified three times and seven other ribotypes twice. No ribotype 027 strains were identified. Independent predictors of colonization were previous C. difficile infection (OR 4.53 (95% C.I. 1.33-15.48) and malnutrition (MUST score ≥2) (OR 3.29 (95% C.I. 1.47-7.35)). Although C. difficile colonised patients experienced higher 90-day mortality, colonization was not an independent risk for death. CONCLUSIONS In a non-epidemic setting patients who have previously had CDI and have a MUST score of ≥2 are at increased risk of C. difficile colonization and could be targeted for active surveillance to prevent C. difficile transmission.
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Affiliation(s)
- Laura Behar
- Brighton and Sussex University Hospitals NHS Trust, Eastern Road, Brighton, East Sussex, BN2 5BE, United Kingdom
| | - David Chadwick
- The James Cook University Hospital, Marton Road, Middlesbrough, TS4 3BW, United Kingdom
| | - Angela Dunne
- Brighton and Sussex University Hospitals NHS Trust, Eastern Road, Brighton, East Sussex, BN2 5BE, United Kingdom
| | - Christopher I Jones
- Brighton and Sussex Medical School, University of Sussex, Falmer, East Sussex, BN1 9PS, United Kingdom
| | - Claire Proctor
- The James Cook University Hospital, Marton Road, Middlesbrough, TS4 3BW, United Kingdom
| | - Chakravarthi Rajkumar
- Brighton and Sussex University Hospitals NHS Trust, Eastern Road, Brighton, East Sussex, BN2 5BE, United Kingdom; Brighton and Sussex Medical School, University of Sussex, Falmer, East Sussex, BN1 9PS, United Kingdom
| | - Paula Sharratt
- Bradford Teaching Hospitals NHS Foundation Trust, Duckworth Lane, Bradford, BD9 6RJ, United Kingdom
| | - Philip Stanley
- Bradford Teaching Hospitals NHS Foundation Trust, Duckworth Lane, Bradford, BD9 6RJ, United Kingdom
| | - Angela Whiley
- Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, 4, Newark Street, London, E1 2AT, United Kingdom
| | - Mark Wilks
- Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, 4, Newark Street, London, E1 2AT, United Kingdom; Department of Infection, Barts Health NHS Trust, Pathology and Pharmacy, 80, Newark St, London, E1 2ES, United Kingdom
| | - Martin J Llewelyn
- Brighton and Sussex University Hospitals NHS Trust, Eastern Road, Brighton, East Sussex, BN2 5BE, United Kingdom; Brighton and Sussex Medical School, University of Sussex, Falmer, East Sussex, BN1 9PS, United Kingdom.
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