Development of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates

ABSTRACT Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of health care facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting; therefore, genotyping...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Theun de Groot, Ynze Puts, Indira Berrio, Anuradha Chowdhary, Jacques F. Meis
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Candida auris genotyping infection control short tandem repeats Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/bacacdd627fe49b383eedd9d8641efd1
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:bacacdd627fe49b383eedd9d8641efd1
record_format	dspace
spelling	oai:doaj.org-article:bacacdd627fe49b383eedd9d8641efd12021-11-15T15:56:58ZDevelopment of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates10.1128/mBio.02971-192150-7511https://doaj.org/article/bacacdd627fe49b383eedd9d8641efd12020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02971-19https://doaj.org/toc/2150-7511ABSTRACT Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of health care facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting; therefore, genotyping of C. auris is required. To enable fast and cost-effective genotyping, we developed a short tandem repeat (STR) typing assay for C. auris. STRs in C. auris were identified, and from an initial selection of 23 STRs, 12 were used to develop a STR typing assay. Having shown that the STR typing assay was reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis, we identified five major different C. auris clusters of South American, South Asian, African, East Asian, and Iranian origin. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the South Asian clade. Comparison with WGS demonstrated that isolates with <20 single nucleotide polymorphisms (SNPs) are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers. Altogether, a highly reproducible and specific STR typing assay for C. auris was developed; this assay distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing by >30 SNPs, as determined via WGS, are also separated. This new C. auris-specific genotyping technique is a rapid, reliable, and cost-effective alternative to WGS analysis to investigate outbreaks. IMPORTANCE Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and causes mainly hospital-associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole-genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. Whole-genome sequencing is costly and available only at a few centers, and AFLP is a complicated technique and hard to interpret. We describe a novel simple STR genotyping technique based on short tandem repeats in the C. auris genome. We also show that the performance of this STR-based genotyping technique has proven comparable to that of WGS. Overall, this work provides a novel, rapid, reliable, and cost-effective method of molecular outbreak investigations of C. auris.Theun de GrootYnze PutsIndira BerrioAnuradha ChowdharyJacques F. MeisAmerican Society for MicrobiologyarticleCandida aurisgenotypinginfection controlshort tandem repeatsMicrobiologyQR1-502ENmBio, Vol 11, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Candida auris genotyping infection control short tandem repeats Microbiology QR1-502
spellingShingle	Candida auris genotyping infection control short tandem repeats Microbiology QR1-502 Theun de Groot Ynze Puts Indira Berrio Anuradha Chowdhary Jacques F. Meis Development of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates
description	ABSTRACT Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of health care facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting; therefore, genotyping of C. auris is required. To enable fast and cost-effective genotyping, we developed a short tandem repeat (STR) typing assay for C. auris. STRs in C. auris were identified, and from an initial selection of 23 STRs, 12 were used to develop a STR typing assay. Having shown that the STR typing assay was reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis, we identified five major different C. auris clusters of South American, South Asian, African, East Asian, and Iranian origin. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the South Asian clade. Comparison with WGS demonstrated that isolates with <20 single nucleotide polymorphisms (SNPs) are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers. Altogether, a highly reproducible and specific STR typing assay for C. auris was developed; this assay distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing by >30 SNPs, as determined via WGS, are also separated. This new C. auris-specific genotyping technique is a rapid, reliable, and cost-effective alternative to WGS analysis to investigate outbreaks. IMPORTANCE Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and causes mainly hospital-associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole-genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. Whole-genome sequencing is costly and available only at a few centers, and AFLP is a complicated technique and hard to interpret. We describe a novel simple STR genotyping technique based on short tandem repeats in the C. auris genome. We also show that the performance of this STR-based genotyping technique has proven comparable to that of WGS. Overall, this work provides a novel, rapid, reliable, and cost-effective method of molecular outbreak investigations of C. auris.
format	article
author	Theun de Groot Ynze Puts Indira Berrio Anuradha Chowdhary Jacques F. Meis
author_facet	Theun de Groot Ynze Puts Indira Berrio Anuradha Chowdhary Jacques F. Meis
author_sort	Theun de Groot
title	Development of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates
title_short	Development of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates
title_full	Development of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates
title_fullStr	Development of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates
title_full_unstemmed	Development of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates
title_sort	development of <named-content content-type="genus-species">candida auris</named-content> short tandem repeat typing and its application to a global collection of isolates
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/bacacdd627fe49b383eedd9d8641efd1
work_keys_str_mv	AT theundegroot developmentofnamedcontentcontenttypegenusspeciescandidaaurisnamedcontentshorttandemrepeattypinganditsapplicationtoaglobalcollectionofisolates AT ynzeputs developmentofnamedcontentcontenttypegenusspeciescandidaaurisnamedcontentshorttandemrepeattypinganditsapplicationtoaglobalcollectionofisolates AT indiraberrio developmentofnamedcontentcontenttypegenusspeciescandidaaurisnamedcontentshorttandemrepeattypinganditsapplicationtoaglobalcollectionofisolates AT anuradhachowdhary developmentofnamedcontentcontenttypegenusspeciescandidaaurisnamedcontentshorttandemrepeattypinganditsapplicationtoaglobalcollectionofisolates AT jacquesfmeis developmentofnamedcontentcontenttypegenusspeciescandidaaurisnamedcontentshorttandemrepeattypinganditsapplicationtoaglobalcollectionofisolates
_version_	1718427115972460544

Development of <named-content content-type="genus-species">Candida auris</named-content> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates

Ejemplares similares