<i>Candida auris</i> otomycosis in Iran and review of recent literature

Abastabar, Mahdi; Haghani, Iman; Ahangarkani, Fatemeh; Rezai, Mohammad Sadegh; Armaki, Mojtaba Taghizadeh; Roodgari, Somayeh; Kiakojuri, Keyvan; Al‐Hatmi, Abdullah M. S.; Meis, Jacques F.; Badali, Hamid

doi:10.1111/myc.12886

Cited by 88 publications

(98 citation statements)

References 31 publications

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“…For the STR analysis 444 C. auris isolates from Austria(27), Belgium(28), Colombia (hospitals in Barranquilla, Bogota, Cartagena, Medellin, Popayan and Santa Maria), India(29), Iran(30), Japan(29), Korea(29), Kuwait(31), Oman(32), Pakistan(17), Russia(33), South-Africa(29), Spain(26), The Netherlands(34), United Kingdom(35) and Venezuela(6) were used. For a complete overview of isolates see Supplementary Table S2 .…”

Section: Methodsmentioning

confidence: 99%

Development of Candida auris microsatellite typing and its application on a global collection of isolates

Groot

Puts

Berrío

et al. 2019

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22Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections 23 most often occur in intensive care units of healthcare facilities. It is crucial to trace the source and 24 prevent further spread of C. auris during an outbreak setting, therefore, genotyping of C. auris is 25 required. To enable fast and cost-effective genotyping, we developed a microsatellite typing assay 26 for C. auris. 27 Short tandem repeats (STRs) in C. auris were identified, and a novel STR typing assay for C. auris was 28 developed using 4 panels of three multiplex PCRs. Having shown that the microsatellite typing assay 29 was highly reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify 30 genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis we identified five 31 major different C. auris clusters, namely, South-America, South-Asia, Africa, East-Asia and Iran. 32Overall, a total of 40 distinct genotypes were identified, with the largest variety in the East Asian 33clade. Comparison with WGS demonstrated that isolates with <20 SNPs are mostly not differentiated 34 by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR 35 markers. 36Altogether, a highly reproducible and specific microsatellite typing assay for C. auris was developed, 37 which distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates 38 differing >20 SNPs, as determined via WGS, are also separated. This new C. auris specific genotyping 39 technique is a rapid, reliable, cost-effective alternative to WGS analysis to speedily investigate 40 outbreaks. 41 Importance 42Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The 43 pathogen has spread worldwide and mainly causes hospital associated outbreaks. To track and trace 44 outbreaks and to relate them to new introductions from elsewhere, whole genome sequencing and 45 amplified fragment length polymorphism (AFLP) have been used for molecular typing. While the 46 former is costly and only available in few centers, AFLP is a complicated technique and 47 standardization is not possible. We describe a novel simple microsatellite genotyping technique 48 based on small tandem repeats in the C. auris genome. Further we show that this microsatellite 49 based genotyping technique has been proven comparable to WGS. Overall, this work provides a 50 novel, rapid, reliable and cost-effective method of molecular outbreaks investigations of C. auris. 51

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Section: Methodsmentioning

confidence: 99%

Development of Candida auris microsatellite typing and its application on a global collection of isolates

Groot

Puts

Berrío

et al. 2019

Preprint

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“…Interestingly, C. sequences. Recently, a fifth clade of C. auris was identified from a patient in Iran who never travelled outside that country (17). The WGS revealed that the Iran C. auris isolate was >200,000 SNPs apart from the other four clades (18).…”

Section: Downloaded Frommentioning

confidence: 99%

“…These populations were grouped into South Asian (I), East Asian (II), African (III), and South American (IV) clades. Recently, a fifth clade of C. auris was identified from a patient in Iran who never travelled outside that country (17). The WGS revealed that the Iran C. auris isolate was genetically distinct and separated by >200, 000 single nucleotide polymorphisms (SNPs) from the other four known C. auris clades (18).…”

Section: Introductionmentioning

confidence: 99%

Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018: Impact and Lessons Learned

et al. 2020

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Candida auris is a multidrug-resistant yeast which has emerged in health care facilities worldwide; however, little is known about identification methods, patient colonization, environmental survival, spread, and drug resistance. Colonization on both biotic (patients) and abiotic (health care objects) surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C. auris outbreak in New York (NY) from August 2016 through 2018. A total of 540 clinical isolates, 11,035 patient surveillance specimens, and 3,672 environmental surveillance samples were analyzed. Laboratory methods included matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for yeast isolate identification, real-time PCR for rapid surveillance sample screening, culture on selective/nonselective media for recovery of C. auris and other yeasts from surveillance samples, antifungal susceptibility testing to determine the C. auris resistance profile, and Sanger sequencing of the internal transcribed spacer (ITS) and D1/D2 regions of the ribosomal gene for C. auris genotyping. Results included (a) identification and confirmation of C. auris in 413 clinical isolates and 931 patient surveillance isolates as well as identification of 277 clinical cases and 350 colonized cases from 151 health care facilities, including 59 hospitals, 92 nursing homes, 1 long-term acute care hospital (LTACH), and 2 hospices, (b) successful utilization of an in-house developed C. auris real-time PCR assay for the rapid screening of patient and environmental surveillance samples, (c) demonstration of relatively heavier colonization of C. auris in nares than in the axilla/groin, and (d) predominance of the South Asia clade I with intrinsic resistance to fluconazole and elevated MIC to voriconazole (81%), amphotericin B (61%), flucytosine (5FC) (3%), and echinocandins (1%). These findings reflect greater regional prevalence and incidence of C. auris and the deployment of better detection tools in an unprecedented outbreak.

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“…The Korean collection used in the present study showed that since the first three reported cases of C. auris fungemia (1), only one patient isolate from blood cultures was obtained in 2017. The isolation of this organism from ear cultures has been observed continually from several hospitals in Korea (11,24). To date, no genotyping of the blood isolates of C. auris from the first three cases of fungemia in Korea has been reported.…”

Section: Figmentioning

confidence: 99%

Candida auris Clinical Isolates from South Korea: Identification, Antifungal Susceptibility, and Genotyping

et al. 2019

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Candida auris is an emerging worldwide fungal pathogen. Over the past 20 years, 61 patient isolates of C. auris (4 blood and 57 ear) have been obtained from 13 hospitals in Korea. Here, we reanalyzed those molecularly identified isolates using two matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) systems, including Biotyper and Vitek MS, followed by antifungal susceptibility testing, sequencing of the ERG11 gene, and genotyping. With a research-use-only (RUO) library, 83.6% and 93.4% of the isolates were correctly identified by Biotyper and Vitek MS, respectively. Using an in vitro diagnostic (IVD) library of Vitek MS, 96.7% of the isolates were correctly identified. Fluconazole-resistant isolates made up 62.3% of the isolates, while echinocandin- or multidrug-resistant isolates were not found. Excellent essential (within two dilutions, 96.7%) and categorical agreements (93.4%) between the Clinical and Laboratory Standards Institute (CLSI) and Vitek 2 (AST-YS07 card) methods were observed for fluconazole. Sequencing ERG11 for all 61 isolates revealed that only 3 fluconazole-resistant isolates showed the Erg11p amino acid substitution K143R. All 61 isolates showed identical multilocus sequence typing (MLST). Pulsed-field gel electrophoresis (PFGE) analyses revealed that both blood and ear isolates had the same or similar patterns. These results show that MALDI-TOF MS and Vitek 2 antifungal susceptibility systems can be reliable diagnostic tools for testing C. auris isolates from Korean hospitals. The Erg11p mutation was seldom found among Korean isolates of C. auris, and multidrug resistance was not found. Both MLST and PFGE analyses suggest that these isolates are genetically similar.

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Candida auris otomycosis in Iran and review of recent literature

Cited by 88 publications

References 31 publications

Development of Candida auris microsatellite typing and its application on a global collection of isolates

Development of Candida auris microsatellite typing and its application on a global collection of isolates

Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018: Impact and Lessons Learned

Candida auris Clinical Isolates from South Korea: Identification, Antifungal Susceptibility, and Genotyping

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