4.5 Article

Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biology

Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy

Daniel R. Knight et al.

Summary: Research on over 12,000 C. difficile genomes revealed major taxonomic incoherence and clear species boundaries for the recently described cryptic clades CI-III. This discovery has significant implications for the global population structure of C. difficile and the Peptostreptococcaceae taxonomy as a whole. Additionally, the unique toxin gene architecture of these newly identified genomospecies may impact the diagnosis of CDI.
Article Genetics & Heredity

Generalizable characteristics of false- positive bacterial variant calls

Stephen J. Bush

Summary: Minimizing false positives is crucial in variant calling, and using Snippy is found to be the most direct way to achieve this. The study also highlights the issue of a disproportionate number of false calls near indels in variant calling pipelines.

MICROBIAL GENOMICS (2021)

Review Infectious Diseases

Clostridium difficile and One Health

S. C. Lim et al.

CLINICAL MICROBIOLOGY AND INFECTION (2020)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biotechnology & Applied Microbiology

Producing polished prokaryotic pangenomes with the Panaroo pipeline

Gerry Tonkin-Hill et al.

GENOME BIOLOGY (2020)

Article Genetics & Heredity

An in silico survey of Clostridioides difficile extrachromosomal elements

Bastian V. H. Hornung et al.

MICROBIAL GENOMICS (2019)

Article Medicine, General & Internal

Clostridium difficile infection and antibiotic-associated diarrhoea

Benjamin H. Mullish et al.

CLINICAL MEDICINE (2018)

Review Infectious Diseases

How to: diagnose infection caused by Clostridium difficile

C. Gateau et al.

CLINICAL MICROBIOLOGY AND INFECTION (2018)

Review Microbiology

Bacteriophages Contribute to Shaping Clostridioides (Clostridium) difficile Species

Louis-Charles Fortier

FRONTIERS IN MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Article Biochemical Research Methods

stringMLST: a fast k-mer based tool for multilocus sequence typing

Anuj Gupta et al.

BIOINFORMATICS (2017)

Article Biotechnology & Applied Microbiology

A Clostridioides difficile bacteriophage genome encodes functional binary toxin-associated genes

Thomas Riedel et al.

JOURNAL OF BIOTECHNOLOGY (2017)

Article Biochemistry & Molecular Biology

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Jaime Huerta-Cepas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Ryan R. Wick et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Review Chemistry, Analytical

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

Leighton Pritchard et al.

ANALYTICAL METHODS (2016)

Article Multidisciplinary Sciences

Highly Divergent Clostridium difficile Strains Isolated from the Environment

Sandra Janezic et al.

PLOS ONE (2016)

Article Medicine, General & Internal

Clostridium difficile infection

Wiep Klaas Smits et al.

NATURE REVIEWS DISEASE PRIMERS (2016)

Article Biotechnology & Applied Microbiology

Mash: fast genome and metagenome distance estimation using MinHash

Brian D. Ondov et al.

GENOME BIOLOGY (2016)

Review Medicine, General & Internal

Diagnosis and Treatment of Clostridium difficile in Adults A Systematic Review

Natasha Bagdasarian et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2015)

Article Multidisciplinary Sciences

Clostridium difficile: New Insights into the Evolution of the Pathogenicity Locus

Marc Monot et al.

SCIENTIFIC REPORTS (2015)

Article Microbiology

A New Type of Toxin A-Negative, Toxin B-Positive Clostridium difficile Strain Lacking a Complete tcdA Gene

Sandra Janezic et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Evolutionary Biology

Evolutionary History of the Clostridium difficile Pathogenicity Locus

Kate E. Dingle et al.

GENOME BIOLOGY AND EVOLUTION (2014)

Article Microbiology

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

Mincheol Kim et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2014)

Article Immunology

Importance of Toxin A, Toxin B, and CDT in Virulence of an Epidemic Clostridium difficile Strain

Sarah A. Kuehne et al.

JOURNAL OF INFECTIOUS DISEASES (2014)

Review Gastroenterology & Hepatology

Clostridium difficile binary toxin CDT Mechanism, epidemiology, and potential clinical importance

Dale N. Gerding et al.

GUT MICROBES (2014)

Article Microbiology

The Comprehensive Antibiotic Resistance Database

Andrew G. McArthur et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)

Article Biotechnology & Applied Microbiology

Phylomark, a Tool To Identify Conserved Phylogenetic Markers from Whole-Genome Alignments

Jason W. Sahl et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)

Article Medicine, General & Internal

The effect of hospital-acquired infection with Clostridium difficile on length of stay in hospital

Alan J. Forster et al.

CANADIAN MEDICAL ASSOCIATION JOURNAL (2012)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Genetics & Heredity

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Mark A. DePristo et al.

NATURE GENETICS (2011)

Article Multidisciplinary Sciences

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

J. Gregory Caporaso et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

genoPlotR: comparative gene and genome visualization in R

Lionel Guy et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Biotechnology & Applied Microbiology

Detection and Enumeration of Clostridium difficile Spores in Retail Beef and Pork

J. Scott Weese et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Review Infectious Diseases

Antimicrobial resistance in Clostridium difficile

Haihui Huang et al.

INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS (2009)

Article Public, Environmental & Occupational Health

Quantitative detection of Clostridium difficile in hospital environmental samples by real-time polymerase chain reaction

R. Mutters et al.

JOURNAL OF HOSPITAL INFECTION (2009)

Article Multidisciplinary Sciences

Toxin B is essential for virulence of Clostridium difficile

Dena Lyras et al.

NATURE (2009)

Review Biochemistry & Molecular Biology

The rpoB gene as a tool for clinical microbiologists

Toidi Adekambi et al.

TRENDS IN MICROBIOLOGY (2009)

Article Immunology

Clostridium difficile in retail ground meat, Canada

Alexander Rodriguez-Palacios et al.

EMERGING INFECTIOUS DISEASES (2007)

Article Biochemical Research Methods

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

Visualization of comparative genomic analyses by BLAST score ratio

DA Rasko et al.

BMC BIOINFORMATICS (2005)

Article Biotechnology & Applied Microbiology

Versatile and open software for comparing large genomes

S Kurtz et al.

GENOME BIOLOGY (2004)