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

2019 ◽  
Author(s):  
Theun de Groot ◽  
Ynze Puts ◽  
Indira Berrio ◽  
Anuradha Chowdhary ◽  
Jacques F. Meis
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Cost Effective ◽  
Whole Genome ◽  
Candida Auris ◽  
Str Typing ◽  
Pathogenic Yeast ◽  
Str Analysis ◽  
Microsatellite Typing

AbstractCandida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of healthcare 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 microsatellite typing assay for C. auris.Short tandem repeats (STRs) in C. auris were identified, and a novel STR typing assay for C. auris was developed using 4 panels of three multiplex PCRs. Having shown that the microsatellite typing assay was highly 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, namely, South-America, South-Asia, Africa, East-Asia and Iran. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the East Asian clade. Comparison with WGS demonstrated that isolates with <20 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 microsatellite typing assay for C. auris was developed, which distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing >20 SNPs, as determined via WGS, are also separated. This new C. auris specific genotyping technique is a rapid, reliable, cost-effective alternative to WGS analysis to speedily investigate outbreaks.ImportanceCandida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and mainly causes 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. While the former is costly and only available in few centers, AFLP is a complicated technique and standardization is not possible. We describe a novel simple microsatellite genotyping technique based on small tandem repeats in the C. auris genome. Further we show that this microsatellite based genotyping technique has been proven comparable to WGS. Overall, this work provides a novel, rapid, reliable and cost-effective method of molecular outbreaks investigations of C. auris.

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

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Theun de Groot ◽  
Ynze Puts ◽  
Indira Berrio ◽  
Anuradha Chowdhary ◽  
Jacques F. Meis
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
South Asian ◽  
Tandem Repeat ◽  
Cost Effective ◽  
Whole Genome ◽  
Candida Auris ◽  
Str Typing ◽  
Content Type ◽  
Short Tandem

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.

scholarly journals Colonisation and Transmission Dynamics of Candida auris among Chronic Respiratory Diseases Patients Hospitalised in a Chest Hospital, Delhi, India: A Comparative Analysis of Whole Genome Sequencing and Microsatellite Typing

2021 ◽  
Vol 7 (2) ◽  
pp. 81 ◽  
Author(s):  
Anamika Yadav ◽  
Anubhav Singh ◽  
Yue Wang ◽  
Merlijn HI van Haren ◽  
Ashutosh Singh ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Respiratory Diseases ◽  
Healthcare Setting ◽  
Whole Genome ◽  
Global Public Health ◽  
Microsatellite Genotyping ◽  
Candida Auris ◽  
Chronic Respiratory Diseases ◽  
Microsatellite Typing

Candida auris is a nosocomial pathogen responsible for an expanding global public health threat. This ascomycete yeast has been frequently isolated from hospital environments, representing a significant reservoir for transmission in healthcare settings. Here, we investigated the relationships among C. auris isolates from patients with chronic respiratory diseases admitted in a chest hospital and from their fomites, using whole-genome sequencing (WGS) and multilocus microsatellite genotyping. Overall, 37.5% (n = 12/32) patients developed colonisation by C. auris including 9.3% of the screened patients that were colonised at the time of admission and 75% remained colonised till discharge. Furthermore, 10% of fomite samples contained C. auris in rooms about 8.5 days after C. auris colonised patients were admitted. WGS and microsatellite typing revealed that multiple strains contaminated the fomites and colonised different body sites of patients. Notably, 37% of C. auris isolates were resistant to amphotericin B but with no amino acid substitution in ERG2, ERG3, ERG5, and ERG6 as compared to the reference strain B8441 in any of our strains. In addition, 55% of C. auris isolates likely had two copies of the MDR1 gene. Our results suggest significant genetic and ecological diversities of C. auris in healthcare setting. The WGS and microsatellite genotyping methods provided complementary results in genotype identification.

scholarly journals Rapid diagnosis of SCA36 in a three-generation family using short-read whole genome sequencing data

2019 ◽  
Author(s):  
Haloom Rafehi ◽  
David J. Szmulewicz ◽  
Kate Pope ◽  
Mathew Wallis ◽  
John Christodoulou ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Cost Effective ◽  
Repeat Expansion ◽  
Rapid Diagnosis ◽  
Whole Genome Sequencing Data ◽  
Molecular Testing ◽  
Whole Genome ◽  
Sequencing Data

AbstractBackgroundSpinocerebellar ataxias (SCA) are often caused by expansions of short tandem repeats (STRs). Recent methodological advances have made repeat expansion (RE) detection with whole genome sequencing (WGS) feasible.ObjectivesTo determine the genetic basis of ataxia in a multigenerational Australian pedigree, with autosomal dominant inheritance.Methods and ResultsWGS was performed on three affected relatives. The sequence data was screened for known pathogenic REs using two repeat expansion detection tools: exSTRa and ExpansionHunter. This screen provided a clear and rapid diagnosis (<five days from receiving the sequencing data) of SCA36, a rare form of ataxia caused by an intronic GGCCTG RE in NOP56.Conclusionsthe that diagnosis of rare ataxias caused by REs is highly feasible and cost effective with WGS. We propose that WGS be implemented as the frontline, cost effective methodology for molecular testing of individuals with a clinical diagnosis of ataxia.

scholarly journals Using molecular testing and whole-genome sequencing for tuberculosis diagnosis in a low-burden setting: a cost-effectiveness analysis using transmission-dynamic modelling

Thorax ◽  
2021 ◽  
Vol 76 (3) ◽  
pp. 281-291 ◽  
Author(s):  
Tendai Mugwagwa ◽  
Ibrahim Abubakar ◽  
Peter J White
Keyword(s):  
Cost Effectiveness ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Drug Sensitivity ◽  
Cost Effective ◽  
Molecular Testing ◽  
Whole Genome ◽  
Transmission Dynamic ◽  
Sensitivity Testing ◽  
Combined Use

BackgroundDespite progress in TB control in low-burden countries like England and Wales, there are still diagnostic delays. Molecular testing and/or whole-genome sequencing (WGS) provide more rapid diagnosis but their cost-effectiveness is relatively unexplored in low-burden settings.MethodsAn integrated transmission-dynamic health economic model is used to assess the cost-effectiveness of using WGS to replace culture-based drug-sensitivity testing, versus using molecular testing versus combined use of WGS and molecular testing, for routine TB diagnosis. The model accounts for the effects of faster appropriate treatment in reducing transmission, benefiting health and reducing future treatment costs. Cost-effectiveness is assessed using incremental net benefit (INB) over a 10-year horizon with a quality-adjusted life-year valued at £20 000, and discounting at 3.5% per year.ResultsWGS shortens the time to drug sensitivity testing and treatment modification where necessary, reducing treatment and hospitalisation costs, with an INB of £7.1 million. Molecular testing shortens the time to TB diagnosis and treatment. Initially, this causes an increase in annual costs of treatment, but averting transmissions and future active TB disease subsequently, resulting in cost savings and health benefits to achieve an INB of £8.6 million (GeneXpert MTB/RIF) or £11.1 million (Xpert-Ultra). Combined use of Xpert-Ultra and WGS is the optimal strategy we consider, with an INB of £16.5 million.ConclusionRoutine use of WGS or molecular testing is cost-effective in a low-burden setting, and combined use is the most cost-effective option. Adoption of these technologies can help low-burden countries meet the WHO End TB Strategy milestones, particularly the UK, which still has relatively high TB rates.

scholarly journals Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting

2020 ◽  
Vol 148 ◽  
Author(s):  
J. L. Guthrie ◽  
L. Strudwick ◽  
B. Roberts ◽  
M. Allen ◽  
J. McFadzen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Variable Number ◽  
Yukon Territory ◽  
Contact Tracing ◽  
Whole Genome ◽  
Attitudes And Practices ◽  
Genomic Epidemiology ◽  
Recent Transmission

Abstract Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005–2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.

scholarly journals Whole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden

2019 ◽  
Vol 7 (10) ◽  
pp. 398 ◽  
Author(s):  
Sacchini ◽  
Wahab ◽  
Di Giannatale ◽  
Zilli ◽  
Abass ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Brucella Melitensis ◽  
Geographic Origin ◽  
Variable Number ◽  
Human Brucellosis ◽  
Whole Genome ◽  
Multiple Loci ◽  
Imported Cases

Human infections with Brucella melitensis are occasionally reported in Sweden, despite the fact that the national flocks of sheep and goats are officially free from brucellosis. The aim of our study was to analyze 103 isolates of B. melitensis collected from patients in Sweden between 1994 and 2016 and determine their putative geographic origin using whole genome sequencing (WGS)-based tools. The majority of the strains were assigned to East Mediterranean and African lineages. Both in silico Multiple Loci VNTR (Variable Number of Tandem Repeats) Analysis (MLVA) and core genome Multilocus Sequence Typing (cgMLST) analyses identified countries of the Middle East as the most probable source of origin of the majority of the strains. Isolates collected from patients with travel history to Iraq or Syria were often associated with genotypes from Turkey, as the cgMLST profiles from these countries clustered together. Sixty strains were located within a distance of 20 core genes to related genotypes from the publicly available database, and for eighteen isolates, the closest genotype was different by more than 50 loci. Our study showed that WGS based tools are effective in tracing back the geographic origin of infection of patients with unknown travel status, provided that public sequences from the location of the source are available.

scholarly journals Diagnosis of D-Bifunctional Protein Deficiency through Whole-Genome Sequencing: Implications for Cost-Effective Care

2015 ◽  
Vol 6 (3) ◽  
pp. 141-146 ◽  
Author(s):  
Alina Khromykh ◽  
Benjamin D. Solomon ◽  
Dale L. Bodian ◽  
Eyby L. Leon ◽  
Ramaswamy K. Iyer ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Cost Effective ◽  
Protein Deficiency ◽  
Whole Genome ◽  
Bifunctional Protein ◽  
Effective Care

scholarly journals Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population

Heliyon ◽  
2018 ◽  
Vol 4 (5) ◽  
pp. e00625
Author(s):  
Satoshi Hirata ◽  
Kaname Kojima ◽  
Kazuharu Misawa ◽  
Olivier Gervais ◽  
Yosuke Kawai ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Japanese Population ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Whole Genome ◽  
Population Scale ◽  
Short Tandem
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