Correction for Cairns et al., “Comparative Genome Analysis and Global Phylogeny of the Toxin Variant Clostridium difficile PCR Ribotype 017 Reveals the Evolution of Two Independent Sublineages”

Cairns, M. D.; Preston, Mark D.; Hall, Christopher D.; Gerding, Dale N.; Hawkey, Peter M.; Katô, Hirofumi; Kim, H.; Kuijper, Ed J.; Lawley, Trevor D.; Pituch, Hanna; Reid, Sharon J.; Kullin, Brian; Riley, Thomas V.; Solomon, Katie; Tsai, Pei-Jane; Weese, J. Scott; Stabler, Richard A.; Wren, Brendan W.

doi:10.1128/jcm.00487-17

Cited by 3 publications

(2 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This could be due to non-specificity of our assay; however, C. difficile strains with presence of binary toxin B but not binary toxin A gene have been described (24,25). Also, we detected both toxin A and B gene peaks in RT017 samples, while this ribotype is known to produce only toxin B (26)(27)(28). This was observed previously by Persson et al: some strains that lack toxin A expression can still harbor parts of toxin A gene which can be detected by PCR (17).…”

Section: Application Of Direct Ribotyping During An Outbreak With C supporting

confidence: 85%

Simultaneous detection and ribotyping of Clostridioides difficile, and toxin gene detection directly on fecal samples

Rossen

Prehn

Koek

et al. 2021

Preprint

View full text Add to dashboard Cite

Background: Clostridioides difficile is the most common cause of nosocomial diarrhea. Ribotyping of cultured strains by a PCR-based test is used to study potential transmission between patients. We aimed to develop a rapid test that can be applied directly on fecal samples for simultaneous detection and ribotyping of C. difficile, as well as detection of toxin genes.Methods: We developed a highly specific and sensitive primer set for simultaneous detection and ribotyping of C. difficile directly on total fecal DNA. Toxin genes were detected with primers adapted from Persson et al. (CMI, 2008). Our study set comprised 130 fecal samples: 65 samples with positive qPCR for C. difficile toxin A/B genes and 65 C. difficile qPCR negative samples. PCR products were analyzed by capillary gel electrophoresis. Results: Ribosomal DNA fragment peak profiles and toxin genes were detected in all 65 C. difficile positive fecal samples and in none of the 65 C. difficile negative samples. The 65 samples were assigned to 27 ribotypes by the Dutch reference laboratory. Our peak profiles corresponded to these ribotypes, except for two samples. During a C. difficile outbreak, patients were correctly allocated to the outbreak-cluster based on the results of direct fecal ribotyping, before C. difficile isolates were cultured and conventionally typed.Conclusion: C. difficile ribotyping directly on fecal DNA is feasible, with sensitivity and specificity comparable to that of diagnostic toxin gene qPCR and with ribotype assignment similar to that obtained by conventional typing on DNA from cultured isolates. This supports simultaneous diagnosis and typing to recognize an outbreak.

show abstract

Section: Application Of Direct Ribotyping During An Outbreak With C supporting

confidence: 85%

Simultaneous detection and ribotyping of Clostridioides difficile, and toxin gene detection directly on fecal samples

Rossen

Prehn

Koek

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…For C. difficile , SNV-based typing has been used to study the microevolution of CDI in the hospital setting (154) and to investigate localized transmission and international dissemination of major clinically important lineages such as RTs 027 (16) and 017 (159). But as outlined below, this approach has also been used to delineate cryptic transmission pathways of C. difficile between animals, humans, and their shared environment.…”

Section: Genomic Insights Into the Evolution And Transmission Of C Dmentioning

confidence: 99%

Genomic Delineation of Zoonotic Origins of Clostridium difficile

Knight

Riley

2019

Front. Public Health

View full text Add to dashboard Cite

Clostridium difficile is toxin-producing antimicrobial resistant (AMR) enteropathogen historically associated with diarrhea and pseudomembranous colitis in hospitalized patients. In recent years, there have been dramatic increases in the incidence and severity of C. difficile infection (CDI), and associated morbidity and mortality, in both healthcare and community settings. C. difficile is an ancient and diverse species that displays a sympatric lifestyle, establishing itself in a range of ecological niches external to the healthcare system. These sources/reservoirs include food, water, soil, and over a dozen animal species, in particular, livestock such as pigs and cattle. In a manner analogous to human infection, excessive antimicrobial exposure, particularly to cephalosporins, is driving the expansion of C. difficile in livestock populations worldwide. Subsequent spore contamination of meat, vegetables grown in soil containing animal feces, agricultural by-products such as compost and manure, and the environment in general (households, lawns, and public spaces) is contributing to a persistent community source/reservoir of C. difficile and the insidious rise of CDI in the community. The whole-genome sequencing era continues to redefine our view of this complex pathogen. The application of high-resolution microbial genomics in a One Health framework (encompassing clinical, veterinary, and environment derived datasets) is the optimal paradigm for advancing our understanding of CDI in humans and animals. This approach has begun to yield critical insights into the genetic diversity, evolution, AMR, and zoonotic potential of C. difficile . In Europe, North America, and Australia, microevolutionary analysis of the C. difficile core genome shows strains common to humans and animals (livestock or companion animals) do not form distinct populations but share a recent evolutionary history. Moreover, for C. difficile sequence type 11 and PCR ribotypes 078 and 014, major lineages of One Health importance, this approach has substantiated inter-species clonal transmission between animals and humans. These findings indicate either a zoonosis or anthroponosis. Moreover, they challenge the existing paradigm and the long-held misconception that CDI is primarily a healthcare-associated infection. In this article, evolutionary, and zoonotic aspects of CDI are discussed, including the anthropomorphic factors that contribute to the spread of C. difficile from the farm to the community.

show abstract

The Epidemiology of Clostridium difficile Infection in Japan: A Systematic Review

Riley

Kimura

2018

Infect Dis Ther

View full text Add to dashboard Cite

To increase understanding of the epidemiology, risks, consequences and resource utilization of Clostridium difficile infection (CDI) in Japan, a systematic literature review was undertaken of relevant publications from January 2006 to November 2017. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and methods, 55 articles met the criteria for full review. The majority (58%) of studies were from a single site, with the most recent data from 2015. The incidence, reported prevalence and recurrence rate of CDI in Japan were 0.8–4.71/10,000 patient-days, 0.3–5.5/1000 patients and 3.3–27.3%, respectively, and varied according to setting, population, CDI definition and detection method. Most C. difficile isolates associated with CDI in Japan were toxin A+B+, with a low level of C. difficile binary toxin-positive (CDT+) strains (0–6.8% reported across studies). The most common C. difficile PCR ribotypes associated with infection in Japan were smz/018, 002, 052 and 369. Data regarding the impact of CDI on length of hospital stay were limited. Reported all-cause mortality in patients with CDI ranged from 3.4 to 15.1% between 2007 and 2013. Two studies assessed risk factors for CDI recurrence, identifying malignant disease, intensive care unit hospitalization and use of proton pump inhibitors as factors increasing the risk of initial and/or recurrent CDI. No study analyzed initial CDI treatment in relation to recurrence. More comprehensive surveillance and coordinated studies are needed to map trends, understand risk factors, and recognize the extent and impact of CDI in Japanese patients.FundingAstellas Pharma, Inc.Plain Language SummaryPlain language summary available for this article.Electronic supplementary materialThe online version of this article (10.1007/s40121-018-0186-1) contains supplementary material, which is available to authorized users.

show abstract

Correction for Cairns et al., “Comparative Genome Analysis and Global Phylogeny of the Toxin Variant Clostridium difficile PCR Ribotype 017 Reveals the Evolution of Two Independent Sublineages”

Cited by 3 publications

References 0 publications

Simultaneous detection and ribotyping of Clostridioides difficile, and toxin gene detection directly on fecal samples

Simultaneous detection and ribotyping of Clostridioides difficile, and toxin gene detection directly on fecal samples

Genomic Delineation of Zoonotic Origins of Clostridium difficile

The Epidemiology of Clostridium difficile Infection in Japan: A Systematic Review

Contact Info

Product

Resources

About