Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Emerging Microbes & Infections
Johanna L RhodesSilke Schelenz

Abstract

Candida auris was first described in 2009, and it has since caused nosocomial outbreaks, invasive infections, and fungaemia across at least 19 countries on five continents. An outbreak of C. auris occurred in a specialized cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak in the UK, involving a total of 72 patients. To understand the genetic epidemiology of C. auris infection both within this hospital and within a global context, we sequenced the outbreak isolate genomes using Oxford Nanopore Technologies and Illumina platforms to detect antifungal resistance alleles and reannotate the C. auris genome. Phylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin; the outbreak showed similar genetic diversity to that of the entire clade, and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the gene FKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the gene FUR1. These mutations add to a growing body of research on multiple antifungal...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 11, 1999·Nucleic Acids Research·A Bairoch, R Apweiler
Jan 10, 2003·Nucleic Acids Research·Daniel H HaftOwen White
May 25, 2004·Antimicrobial Agents and Chemotherapy·Andrew R DodgsonDavid R Soll
Apr 25, 2007·Nucleic Acids Research·Karin LagesenDavid W Ussery
Feb 13, 2009·Nature·Gianni LitiEdward J Louis
May 26, 2009·Nature·Geraldine ButlerChristina A Cuomo
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Feb 5, 2011·Emerging Infectious Diseases·David M EngelthalerS Arunmozhi Balajee
May 20, 2011·Nucleic Acids Research·Robert D FinnSean R Eddy
Jul 1, 2011·Journal of Clinical Microbiology·Wee Gyo LeeHee-Chang Jang
Jul 28, 2011·The Journal of Infectious Diseases·Ronen Ben-AmiDimitrios P Kontoyiannis
Mar 20, 2013·Indian Journal of Medical Microbiology·S SarmaA Rattan
Sep 21, 2013·Emerging Infectious Diseases·Anuradha ChowdharyJacques F Meis
Nov 30, 2013·Nucleic Acids Research·Robert D FinnMarco Punta
Dec 21, 2013·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·A ChowdharyJ F Meis
Jan 1, 2014·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·M Cuenca-Estrella
Jun 22, 2014·Journal of Clinical Microbiology·Anastasia P LitvintsevaDavid M Engelthaler
Jun 26, 2014·Emerging Infectious Diseases·Rindidzani E MagoboNelesh P Govender
Feb 11, 2015·Nature Genetics·Daniel C JeffaresJürg Bähler
Sep 9, 2015·BMC Genomics·Sharanya ChatterjeeUtpal S Tatu
Nov 10, 2015·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·Anupam PrakashAnuradha Chowdhary
Nov 28, 2015·Nucleic Acids Research·Robert HubleyTravis J Wheeler
Feb 4, 2016·Nature·Joshua QuickMiles W Carroll
Jul 28, 2016·The Journal of Infection·Belinda CalvoArnaldo Lopes Colombo
Oct 26, 2016·Antimicrobial Resistance and Infection Control·Silke SchelenzMatthew C Fisher
Dec 19, 2016·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Shawn R LockhartAnastasia P Litvintseva
Jan 19, 2017·Emerging Infectious Diseases·Ronen Ben-AmiTalya Finn
Jan 28, 2017·Frontiers in Microbiology·Sarah G WhaleyP David Rogers
Jan 31, 2017·Revista iberoamericana de micología·Alba Cecilia Ruiz GaitánJavier Pemán
Jul 8, 2017·Mycoses·Jalila MohsinAbdullah M S Al-Hatmi
Sep 16, 2017·The Journal of Infectious Diseases·Maiken Cavling Arendrup, Thomas F Patterson

❮ Previous
Next ❯

Citations

Aug 8, 2018·Antimicrobial Agents and Chemotherapy·Kelley R HealeyDavid S Perlin
Sep 21, 2018·Journal of Clinical Microbiology·D Joseph SextonAnastasia P Litvintseva
Apr 9, 2019·PLoS Pathogens·Jeniel E Nett
Jul 22, 2019·The Journal of Antimicrobial Chemotherapy·Shivaprakash M RudramurthyArunaloke Chakrabarti
Jul 5, 2019·Mycoses·Philipp KoehlerUNKNOWN European Confederation of Medical Mycology (ECMM)
Jul 17, 2019·Emerging Infectious Diseases·Nancy A ChowJacques F Meis
Jun 7, 2019·Archives of Pathology & Laboratory Medicine·D Jane HataUNKNOWN College of American Pathologists Microbiology Committee
Jul 11, 2019·Medical Mycology·Ivan M PchelinNatalya V Vasilyeva
Apr 17, 2020·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·Amira ElBaradei
Apr 3, 2020·Expert Review of Anti-infective Therapy·Arunaloke Chakrabarti, Shreya Singh
Jul 10, 2020·Pathogens and Disease·Taissa VilaMary Ann Jabra-Rizk
May 3, 2019·Current Infectious Disease Reports·Graham M Snyder, Sharon B Wright
Aug 23, 2019·Journal of Fungi·Milena Kordalewska, David S Perlin
Sep 27, 2018·Frontiers in Genetics·Pria N GhoshKieran A Bates
Nov 7, 2018·Journal of Intensive Care·Andrea CortegianiAnuradha Chowdhary
Apr 26, 2019·Current Genetics·Gustavo Bravo RuizAlexander Lorenz
May 1, 2020·Frontiers in Genetics·Aleksandra D ChybowskaRhys A Farrer
Aug 23, 2018·MBio·Chad J JohnsonJeniel E Nett
Mar 28, 2020·Emerging Infectious Diseases·Courtney R LaneDeborah A Williamson
Oct 9, 2019·Antimicrobial Agents and Chemotherapy·Milena KordalewskaDavid S Perlin
Jun 13, 2020·American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons·Nicole M TheodoropoulosStuart M Levitz
Sep 6, 2020·Antibiotics·María Guadalupe Frías-De-LeónErick Martínez-Herrera
Jul 24, 2020·Current Fungal Infection Reports·Alison R NovakScott W Mueller
Mar 12, 2020·MBio·Christina A Cuomo, Alexandre Alanio
Sep 5, 2019·Frontiers in Microbiology·Milena Kordalewska, David S Perlin
Aug 23, 2020·Journal of Fungi·Amir ArastehfarDavid S Perlin
Nov 17, 2020·Frontiers in Microbiology·Elizabeth MisasOliver K Clay
Nov 26, 2020·Journal of Fungi·Wadha AlfouzanMohammad R Al-Rashidi

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJEB20230
PRJNA392455

Methods Mentioned

BETA
Illumina sequencing
2500 sequencing

Software Mentioned

Burrows Aligner ( BWA )
Metrichor
GenemarkS
Picard
HMMER
GATK
ONT
MicrobesNG
MinKNOW
FastQC

Related Concepts

Related Feeds

Antimicrobial Resistance (ASM)

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Antimicrobial Resistance

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Candidiasis

Candidiasis is a common fungal infection caused by Candida and it can affect many parts for the body including mucosal membranes as well as the gastrointestinal, urinary, and respiratory tracts. Here is the latest research.

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Candidiasis (ASM)

Candidiasis is a common fungal infection caused by Candida and it can affect many parts for the body including mucosal membranes as well as the gastrointestinal, urinary, and respiratory tracts. Here is the latest research.

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Candida albicans

Candida albicans is an opportunistic, fungal pathogen of humans that frequently causes superficial infections of oral and vaginal mucosal surfaces of debilitated and susceptible individuals. Discover the latest research on Candida albicans here.

Related Papers

Clinical Microbiology Reviews
Anna Jeffery-SmithColin S Brown
Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America
Shawn R LockhartAnastasia P Litvintseva
Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America
Marwan M AzarVirginia M Pierce
American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons
Snigdha VallabhaneniTom M Chiller
© 2021 Meta ULC. All rights reserved