Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains

Open Forum Infectious Diseases
Bradley T EndresKevin W Garey

Abstract

The epidemic Clostridioides difficile ribotype 027 strain resulted from the dissemination of 2 separate fluoroquinolone-resistant lineages: FQR1 and FQR2. Both lineages were reported to originate in North America; however, confirmatory large-scale investigations of C difficile ribotype 027 epidemiology using whole genome sequencing has not been undertaken in the United States. Whole genome sequencing and single-nucleotide polymorphism (SNP) analysis was performed on 76 clinical ribotype 027 isolates obtained from hospitalized patients in Texas with C difficile infection and compared with 32 previously sequenced worldwide strains. Maximum-likelihood phylogeny based on a set of core genome SNPs was used to construct phylogenetic trees investigating strain macro- and microevolution. Bayesian phylogenetic and phylogeographic analyses were used to incorporate temporal and geographic variables with the SNP strain analysis. Whole genome sequence analysis identified 2841 SNPs including 900 nonsynonymous mutations, 1404 synonymous substitutions, and 537 intergenic changes. Phylogenetic analysis separated the strains into 2 prominent groups, which grossly differed by 28 SNPs: the FQR1 and FQR2 lineages. Five isolates were identified as p...Continue Reading

References

Sep 28, 1998·Biochimica Et Biophysica Acta·D C Hooper
Feb 18, 2003·JAMA : the Journal of the American Medical Association·Melinda M NeuhauserJohn P Quinn
Apr 19, 2003·The Journal of Antimicrobial Chemotherapy·A M Emmerson, A M Jones
Oct 20, 2004·The Journal of Biological Chemistry·Hanna-Kirsti S LeirosSeán M McSweeney
Dec 3, 2005·The New England Journal of Medicine·L Clifford McDonaldDale N Gerding
Feb 6, 2008·FEMS Microbiology Reviews·André ZapunThierry Vernet
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Aug 15, 2009·Drugs·Xian-Zhi Li, Hiroshi Nikaido
Jan 1, 2009·Microbial Biotechnology·Anna FàbregaJordi Vila
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Sep 20, 2012·Proceedings of the National Academy of Sciences of the United States of America·Heewook LeePatricia L Foster
Oct 23, 2013·Antimicrobial Agents and Chemotherapy·Sushim Kumar GuptaJean-Marc Rolain
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Apr 12, 2014·PLoS Computational Biology·Remco BouckaertAlexei J Drummond
Nov 21, 2014·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·C W KnetschT D Lawley
Nov 26, 2014·Genome Medicine·Michael InouyeKathryn E Holt
Aug 21, 2015·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Samuel L AitkenKevin W Garey
Dec 20, 2015·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Nitin KumarTrevor D Lawley
May 18, 2016·Molecular Biology and Evolution·Filip BielejecPhilippe Lemey
May 10, 2017·Open Forum Infectious Diseases·M Jahangir AlamKevin W Garey
Jan 20, 2018·Environmental Microbiology·Kathryn L NawrockiShonna M McBride
Aug 3, 2018·Current Infectious Disease Reports·L W GoneauJ B Gubbay
Sep 27, 2018·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Bradley T EndresKevin W Garey

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Citations

Apr 30, 2019·Current Opinion in Clinical Nutrition and Metabolic Care·Yiming Zhang, Brian J DeBosch
Jun 10, 2020·Antimicrobial Agents and Chemotherapy·Khurshida BegumKevin W Garey
Jul 29, 2020·The Journal of Antimicrobial Chemotherapy·Eugénie BassèresKevin W Garey
Nov 20, 2020·Open Forum Infectious Diseases·Travis J CarlsonKevin W Garey

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Datasets Mentioned

BETA
FN545816

Methods Mentioned

BETA
protein folding

Software Mentioned

SAMtools
RedDog
Bowtie2
R
FigTree
BEAST2
BEAST
FastQC
Trimmomatic
SRST2 pipeline

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