Comparative Genomics of Clostridium difficile

Janežič, Sandra; Garneau, Julian R.; Monot, Marc

doi:10.1007/978-3-319-72799-8_5

Cited by 11 publications

(7 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…More tellingly, non-toxigenic strains of clade 4, which lack the selective mechanisms of disease-causing strains, are almost without exception reported in Asia. Interestingly, toxinotype XXI (A + B + ) which is apparently the parent strain of RT 017, and the first of clade 4 to undergo recombination, is still in existence (Janezic et al, 2015a), but has been nowhere as successful as its progeny.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology

Elliott

Androga

Knight

et al. 2017

Infection, Genetics and Evolution

View full text Add to dashboard Cite

Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era.

show abstract

Section: Accepted Manuscriptmentioning

confidence: 99%

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology

Elliott

Androga

Knight

et al. 2017

Infection, Genetics and Evolution

View full text Add to dashboard Cite

show abstract

“…However, Hu25 was negative for all the toxin genes tested (tcdA, tcdB, cdtA and cdtB). The clade in which ST200 is located is still unclear but it has been proposed as a member of clade 6, based on the comparison of its core genome by whole genome sequencing (WGS) (33). On the other hand, ST122 has been proposed to belong to clades 6 and 1 based on MLST and WGS studies, respectively (34,35).…”

Section: Discussionmentioning

confidence: 99%

Incidence and characterization of Clostridium difficile in a secondary care hospital in Spain

Lasheras¹,

Burriel²,

Aspíroz³

et al. 2018

Rev Esp Enferm Dig

View full text Add to dashboard Cite

Introduction: Clostridium difficile (C. difficile) is a major nosocomial infectious agent in hospitals. Previous studies have addressed the high proportion of infection episodes that are overlooked in health care facilities. Objective: the main aim of this study was to characterize C. difficile clinical cases that occurred in a secondary care hospital during a five-month period. Material and methods: for this purpose, a total of 137 stool samples from the same number of patients with diarrhea were analyzed for the presence of C. difficile by culture techniques. An enzyme immunoassay (EIA) test for the detection of C. difficile and its toxins was also used in 50 cases (36.5%) for diagnostic purposes. Results: a total of 14 (10.2%) C. difficile isolates were obtained, of which nine (64.3%) were toxigenic. A mean incidence of 3.2 episodes of C. difficile infections (CDI) per 10,000 patients-days was estimated for the study period. Around 56% of the CDI cases were determined as hospitalacquired, whereas 44% originated in the community. Among these, only two episodes (22.2%) were detected in the hospital by the EIA test, which indicated that the hospital CDI detection protocol needed to be revised. One unusual C. difficile isolate was negative for all toxin genes examined and also for the non-toxigenic strain assay, which highlights the need to perform genome sequencing to study its pathogenicity locus insertion site organization. A stable metronidazole-resistant C. difficile strain and three strains showing multidrug resistance were detected in this study, suggesting that C. difficile antimicrobial susceptibility surveillance programs should be established in this health-care facility.

show abstract

“…In the case of C. difficile , a human pathogenic bacterium causing antibiotic-associated nosocomial infections, comparative analysis of the whole genome, including CRISPR-Cas systems has yielded insights into the diversity of strains and their virulence [ 41 ]. Type I-B CRISPR-Cas systems were identified in a large data set of 217 genomes, with each system carrying more than one CRISPR array, containing polymorphisms within the spacer content, enabling strain genotyping, as well as determining their phylogenetic relationships [ 18 ].…”

Section: Investigating Host-phage Interactions Within Select Body mentioning

confidence: 99%

Insights into the Human Virome Using CRISPR Spacers from Microbiomes

Hidalgo-Cantabrana

Sanozky-Dawes

Barrangou

2018

Viruses

View full text Add to dashboard Cite

Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.

show abstract

Comparative Genomics of Clostridium difficile

Cited by 11 publications

References 80 publications

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology

Incidence and characterization of Clostridium difficile in a secondary care hospital in Spain

Insights into the Human Virome Using CRISPR Spacers from Microbiomes

Contact Info

Product

Resources

About