First case of <i>Candida auris</i> infection in Belgium in a surgical patient from Kuwait

Dewaele, Klaas; Frans, Johan; Smismans, Annick; Ho, Erwin; Tollens, Tim; Lagrou, Katrien

doi:10.1080/17843286.2018.1555114

Cited by 18 publications

(15 citation statements)

References 38 publications

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“…Isolates. For the short tandem repeat (STR) analysis, 444 C. auris isolates from Austria (28), Belgium (29), Colombia (hospitals in Barranquilla, Bogota, Cartagena, Medellin, Popayan, and Santa Maria), India (30), Iran (31), Japan (30), South Korea (30), Kuwait (24), Oman (32), Pakistan (17), Russia (33), South Africa (30), Spain (27), The Netherlands (34), United Kingdom (35), and Venezuela (6) were used. For a complete overview of isolates, see Table S2 in the supplemental material.…”

Section: Methodsmentioning

confidence: 99%

Development of Candida auris Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates

Groot

Puts

Berrío

et al. 2020

mBio

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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.

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Section: Methodsmentioning

confidence: 99%

Development of Candida auris Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates

Groot

Puts

Berrío

et al. 2020

mBio

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“…A set of 96 C. auris isolates was obtained from the Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands ( n = 37), the Centers for Disease Control and Prevention (CDC, Atlanta, GA, USA; n = 10), and individual researchers ( n = 49). The majority of isolates came from India ( n = 38) [ 2 , 9 , 10 ], followed by 58 isolates from other geographical areas, namely Austria (from a Turkish patient) ( n = 1) [ 40 ], Belgium (from a Kuwaiti patient) ( n = 2) [ 41 ], Japan ( n = 3) [ 42 ], Israel ( n = 9) [ 43 , 44 ], Korea ( n = 3) [ 8 ], Malaysia ( n = 3) [ 45 ], Oman ( n = 13) [ 46 , 47 ], Pakistan ( n = 2), Saudi Arabia ( n = 2) [ 48 ], Spain ( n = 13) [ 49 ], South Africa ( n = 4), Switzerland ( n = 1) [ 50 ], and Venezuela ( n = 2) [ 13 ] ( Supplementary Table S1 ). The isolates were identified by MALDI-TOF MS (Bruker Daltonik) using routine settings [ 27 , 51 ], and the Bruker MBT Compass Library, Revision E (7854 reference entries).…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris

Vatanshenassan

Boekhout

Mauder

et al. 2020

JoF

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Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks.

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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

Preprint

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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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First case of Candida auris infection in Belgium in a surgical patient from Kuwait

Cited by 18 publications

References 38 publications

Development of Candida auris Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates

Development of Candida auris Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates

Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris

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

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