Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae : Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov

Frontiers in Microbiology
Florian TaginiGilbert Greub

Abstract

Corynebacterium diphtheriae is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic C. diphtheriae infections. Here, a C. diphtheriae strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel with PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of C. diphtheriae revealed that the strains CHUV2995, CCUG 5865 and CMCNS703 share a lower average nucleotide identity (ANI) (95.24 to 95.39%) with the C. diphtheriae NCTC 11397T reference genome than all other C. diphtheriae genomes (>98.15%). Core genome phylogeny confirmed the presence of two monophyletic clades. Based on these findings, we propose here two new C. diphtheriae subspecies to replace the lineage denomination used in previous multilocus sequence typing studies: C. diphtheriae su...Continue Reading

References

Aug 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·J BoydJ R Murphy
Jan 1, 1997·Clinical Microbiology Reviews·G FunkeK A Bernard
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Nov 25, 1998·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·J GublerM Altwegg
Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Feb 21, 2007·Bioinformatics·Jan KrumsiekThomas Rattei
Jun 1, 2007·Nucleic Acids Research·Ibtissem GrissaChristine Pourcel
Dec 23, 2008·Brazilian Journal of Medical and Biological Research = Revista Brasileira De Pesquisas Médicas E Biológicas·R HirataA L Mattos-Guaraldi
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Oct 22, 2010·Journal of Clinical Microbiology·Katia JatonGilbert Greub
Dec 15, 2010·BMC Bioinformatics·Keith A Jolley, Martin C J Maiden
Jan 8, 2011·Journal of Medical Microbiology·Becky EdwardsPaul A Hoskisson
May 25, 2011·Expert Review of Vaccines·Nicholas R E Kitchin
Oct 27, 2011·Molecular Microbiology·Thomas SpirigRobert T Clubb
Nov 19, 2011·FEMS Microbiology Reviews·Antony CroxattoGilbert Greub
Jan 17, 2013·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·E FarfourN Guiso
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Feb 26, 2013·BMC Bioinformatics·Jan P Meier-KolthoffMarkus Göker
Nov 10, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Vartul SangalPaul A Hoskisson
Nov 12, 2013·Emerging Infectious Diseases·Aleksandra A Zasada
Nov 30, 2013·Nucleic Acids Research·Robert D FinnMarco Punta
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
Feb 8, 2014·International Journal of Systematic and Evolutionary Microbiology·Mincheol KimJongsik Chun
Mar 20, 2014·Bioinformatics·Torsten Seemann
Jul 17, 2014·Journal of Infection and Public Health·Rosemarie Philippa FitzGeraldDona Nelun Perera
Nov 28, 2014·Nucleic Acids Research·Michael Y GalperinEugene V Koonin
Oct 2, 2015·Current Opinion in Microbiology·Andrés Vázquez-Torres, Andreas J Bäumler
Nov 21, 2015·Journal of Molecular Biology·Minoru KanehisaKanae Morishima
May 5, 2016·Nucleic Acids Research·David ArndtDavid S Wishart
Jun 15, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Vartul Sangal, Paul A Hoskisson
Oct 21, 2016·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·D M MeinelA Egli

❮ Previous
Next ❯

Citations

Jan 8, 2019·International Journal of Systematic and Evolutionary Microbiology·Aharon Oren, George M Garrity
Sep 10, 2019·Frontiers in Public Health·Helena M B Seth-Smith, Adrian Egli
Nov 29, 2020·Genome Medicine·Melanie HennartSylvain Brisse
Sep 16, 2021·Journal of Clinical Microbiology·Julien GuglielminiSylvain Brisse
Dec 31, 2021·Clinical Chemistry·Erik Munson

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJEB24256

Methods Mentioned

BETA
PCR
bronchoalveolar lavage
X-ray
biopsy
biopsies

Software Mentioned

OrthoFinder
NUCmer
Prokka
GhostKOALA
PubMLST
Qualimap
SAMtools
Mafft
tBLASTN
CRISPRfinder

Related Concepts

Related Feeds

CRISPR Ribonucleases Deactivation

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on mechanisms that underlie deactivation of CRISPR ribonucleases. Here is the latest research.

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.