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Global genomic population structure of Clostridioides difficile

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1001/jamainternmed.2013.7056openalex-snapshot

Epidemiology of Community-AssociatedClostridium difficileInfection, 2009 Through 2011

inferredcites →https://doi.org/10.1001/jamainternmed.2016.0177openalex-snapshot

Effect of Detecting and Isolating Clostridium difficile Carriers at Hospital Admission on the Incidence of C difficile Infections

inferredcites →https://doi.org/10.1002/9780470515075openalex-snapshot

The R Book

inferredcites →https://doi.org/10.1007/978-3-319-72799-8_13openalex-snapshot

Non-human C. difficile Reservoirs and Sources: Animals, Food, Environment

inferredcites →https://doi.org/10.1016/0377-0427(87)90125-7openalex-snapshot

Silhouettes: A graphical aid to the interpretation and validation of cluster analysis

inferredcites →https://doi.org/10.1016/j.anaerobe.2016.06.008openalex-snapshot

Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O’Toole 1935) Prévot 1938

inferredcites →https://doi.org/10.1016/j.ijmm.2019.03.001openalex-snapshot

Hospital outbreak due to Clostridium difficile ribotype 018 (RT018) in Southern Germany

inferredcites →https://doi.org/10.1017/ice.2017.119openalex-snapshot

DistinguishingClostridium difficileRecurrence From Reinfection: Independent Validation of Current Recommendations

inferredcites →https://doi.org/10.1017/ice.2018.106openalex-snapshot

Transmission ofClostridium difficilefrom asymptomatically colonized or infected long-term care facility residents

inferredcites →https://doi.org/10.1038/ng.2478openalex-snapshot

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

inferredcites →https://doi.org/10.1038/nrgastro.2016.25openalex-snapshot

Clostridium difficile infection: epidemiology, diagnosis and understanding transmission

inferredcites →https://doi.org/10.1038/nrmicro2164openalex-snapshot

Clostridium difficile infection: new developments in epidemiology and pathogenesis

inferredcites →https://doi.org/10.1038/s41598-019-43464-4openalex-snapshot

Whole-genome sequencing reveals nosocomial Clostridioides difficile transmission and a previously unsuspected epidemic scenario

inferredcites →https://doi.org/10.1053/j.gastro.2016.12.035openalex-snapshot

Asymptomatic Carriers Contribute to Nosocomial Clostridium difficile Infection: A Cohort Study of 4508 Patients

inferredcites →https://doi.org/10.1056/nejmoa1216064openalex-snapshot

Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

inferredcites →https://doi.org/10.1093/cid/civ1037openalex-snapshot

Editorial Commentary: Whole-Genome Sequencing ofClostridium difficile: Exquisitely Sensitive but Not Yet Optimally Applied

inferredcites →https://doi.org/10.1093/cid/cix338openalex-snapshot

Comparison of Control of Clostridium difficile Infection in Six English Hospitals Using Whole-Genome Sequencing

inferredcites →https://doi.org/10.1093/cid/ciy149openalex-snapshot

Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA)

inferredcites →https://doi.org/10.1093/gbe/evt204openalex-snapshot

Evolutionary History of the Clostridium difficile Pathogenicity Locus

inferredcites →https://doi.org/10.1093/gigascience/giaa007openalex-snapshot

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

inferredcites →https://doi.org/10.1099/jmm.0.47714-0openalex-snapshot

Characterization of Clostridium difficile isolates using capillary gel electrophoresis-based PCR ribotyping

inferredcites →https://doi.org/10.1099/mic.0.000700openalex-snapshot

Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens

inferredcites →https://doi.org/10.1099/mic.0.055459-0openalex-snapshot

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

inferredcites →https://doi.org/10.1101/613554openalex-snapshot

The user’s guide to comparative genomics with EnteroBase, including case studies on transmissions of micro-clades of Salmonella , the phylogeny of ancient and modern Yersinia pestis genomes, and the core genomic diversity of all Escherichia

inferredcites →https://doi.org/10.1101/gr.232397.117openalex-snapshot

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

inferredcites →https://doi.org/10.1128/aac.00146-08openalex-snapshot

Clostridium difficileInfections in a Canadian Tertiary Care Hospital before and during a Regional Epidemic Associated with the BI/NAP1/027 Strain

inferredcites →https://doi.org/10.1128/aem.03032-14openalex-snapshot

Nationwide Surveillance Study of Clostridium difficile in Australian Neonatal Pigs Shows High Prevalence and Heterogeneity of PCR Ribotypes

inferredcites →https://doi.org/10.1128/jcm.01296-16openalex-snapshot

Comparative Genome Analysis and Global Phylogeny of the Toxin Variant Clostridium difficile PCR Ribotype 017 Reveals the Evolution of Two Independent Sublineages

inferredcites →https://doi.org/10.1128/jcm.01384-17openalex-snapshot

Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans

inferredcites →https://doi.org/10.1128/jcm.01440-13openalex-snapshot

Clostridium difficile Genotypes in Piglet Populations in Germany

inferredcites →https://doi.org/10.1128/jcm.01987-17openalex-snapshot

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile

inferredcites →https://doi.org/10.1128/jcm.02536-05openalex-snapshot

Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes

inferredcites →https://doi.org/10.1128/mbio.00446-19openalex-snapshot

Evolutionary and Genomic Insights into Clostridioides difficile Sequence Type 11: a Diverse Zoonotic and Antimicrobial-Resistant Lineage of Global One Health Importance

inferredcites →https://doi.org/10.1186/s12859-017-1907-2openalex-snapshot

BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness

inferredcites →https://doi.org/10.1186/s12864-016-2708-0openalex-snapshot

Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing

inferredcites →https://doi.org/10.1371/journal.pcbi.1004041openalex-snapshot

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

inferredcites →https://doi.org/10.1371/journal.pgen.1004874openalex-snapshot

Distinct Genealogies for Plasmids and Chromosome

inferredcites →https://doi.org/10.1371/journal.pgen.1007261openalex-snapshot

A genomic overview of the population structure of Salmonella

inferredcites →https://doi.org/10.1371/journal.pone.0104579openalex-snapshot

Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

inferredcites →https://doi.org/10.1371/journal.pone.0139811openalex-snapshot

Tracing the Spread of Clostridium difficile Ribotype 027 in Germany Based on Bacterial Genome Sequences

inferredcites →https://doi.org/10.2807/ese.13.41.19000-enopenalex-snapshot

Distribution and antimicrobial susceptibility patterns of Clostridium difficile PCR ribotypes in English hospitals, 2007-08

inferredcites →https://doi.org/10.3201/eid1604.090859openalex-snapshot

Fluoroquinolone Resistance andClostridium difficile, Germany

inferredcites →https://doi.org/10.3389/fmicb.2018.00901openalex-snapshot

Convergent Loss of ABC Transporter Genes From Clostridioides difficile Genomes Is Associated With Impaired Tyrosine Uptake and p-Cresol Production

inferredcites →https://doi.org/10.3389/fpubh.2019.00164openalex-snapshot

Genomic Delineation of Zoonotic Origins of Clostridium difficile

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1099/mgen.0.000428openalex-snapshot

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

inferred← citeshttps://doi.org/10.1099/mgen.0.000484openalex-snapshot

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

inferred← citeshttps://doi.org/10.1101/2020.01.03.894154openalex-snapshot

Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN

inferred← citeshttps://doi.org/10.1101/613554openalex-snapshot

inferred← citeshttps://doi.org/10.1101/gr.251678.119openalex-snapshot

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

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