Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress 2023 EHA Congress 2023 ASCO Annual Meeting
Clinical Collections
Advances in Alzheimer’s

At a glance: The ONWARDS insulin icodec trials

A round-up of the ONWARDS phase 3 clinical trials evaluating the novel weekly insulin icodec in people with diabetes.
ADVANCED SEARCH
Log in
Top
Current Fungal Infection Reports
Published in: Current Fungal Infection Reports 2/2016

Open Access 01-06-2016 | Clinical Mycology Lab Issues (K Lagrou, Section Editor)

Next-Generation Sequencing in the Mycology Lab

Authors: Jan Zoll, Eveline Snelders, Paul E. Verweij, Willem J. G. Melchers

Published in: Current Fungal Infection Reports | Issue 2/2016

Login to get access

Abstract

New state-of-the-art techniques in sequencing offer valuable tools in both detection of mycobiota and in understanding of the molecular mechanisms of resistance against antifungal compounds and virulence. Introduction of new sequencing platform with enhanced capacity and a reduction in costs for sequence analysis provides a potential powerful tool in mycological diagnosis and research. In this review, we summarize the applications of next-generation sequencing techniques in mycology.
Literature
1.
The NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. The NIH human microbiome project. Genome Res. 2009;19:2317–23.CrossRefPubMedCentral
2.
Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.CrossRef
3.
Orgiazzi A, Bianciotto V, Bonfante P, Daghino S, Ghignone S, Lazzari A, et al. 454 Pyrosequencing analysis of fungal assemblages from geographically distant, disparate soils reveals spatial patterning and a core mycobiome. Diversity. 2013;5:73–98.CrossRef
4.
Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, et al. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science. 2012;336:1314–7.CrossRefPubMedPubMedCentral
5.
6.
7.•
Nguyen LDN, Viscogliosi E, Delhaes L. The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol. 2015;6(99):1–9. This review paper gives a clear overview of the relationship between various biomes in different body parts.
8.••
Mukherjee PK, Sendid B, Hoareau G, Colombel J, Poulain D, Ghannoum MA. Mycobiota in gastrointestinal diseases. Gastroenterol Hepatol. 2015;12:77–87. This review paper describes the connections between the mycobiome and the host in health and disease.
9.
Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010;6(1), e1000713.CrossRefPubMedPubMedCentral
10.
Lu Q, van den Ende AH, de Hoog GS, Li R, Accoceberry J, Durand-Joly I, et al. Reverse line blot hybridisation screening of Pseudallescheria/Scedosporium species in patients with cystic fibrosis: RLBof Scedosporium spp.in cystic fibrosis. Mycoses. 2011;54:5–11.CrossRefPubMed
11.
Dupuy AK, David MS, Li L, Heider TN, Peterson JD, Montano EA, et al. Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal. PLoS ONE. 2014;9(3), e90899.CrossRefPubMedPubMedCentral
12.
Willger SD, Grim SL, Dolben EL, Shipunova A, Hampton TH, Morrison HG, et al. Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis. Microbiome. 2014;2:40.CrossRefPubMedPubMedCentral
13.
Rodríguez MM, Pérez D, Chaves FJ, Esteve E, Marin-Garcia P, Xifra G, et al. Obesity changes the human gut mycobiome. Sci Rep. 2015;5:14600.CrossRef
14.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.CrossRefPubMedPubMedCentral
15.
16.
Caboche S, Audebert C, Hot D. High-throughput sequencing, a versatile weapon to support genome-based diagnosis in infectious diseases: applications to clinical bacteriology. Pathogens. 2014;3:258–79.CrossRefPubMedPubMedCentral
17.
Zoll J, Rahamat-Langendoen J, Ahout I, de Jonge MI, Jans J, Huijnen MA, et al. Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information. J Clin Virol. 2015;66:6–11.CrossRefPubMed
18.
Bavelaar HH, Rahamat-Langendoen J, Niesters HG, Zoll J, Melchers WJ. Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus. J Clin Virol. 2015;72:122–5.CrossRefPubMed
19.
Gouba N, Drancourt M. Digestive tract mycobiota: a source of infection. Med Mal Infect. 2015;45:9–16.CrossRefPubMed
20.•
Mukherjee PK, Chandra J, Retuerto M, Sikaroodi M, Brown RE, Jurevic R, et al. Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi. PLoS Pathog. 2014;10(3), e1003996. This paper describes the correlation of the oral mycobiome constitution in health and disease.CrossRefPubMedPubMedCentral
21.
22.
Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, et al. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am J Respir Crit Care Med. 2012;186:536–45.CrossRefPubMedPubMedCentral
23.••
Bittinger K, Charlson ES, Loy E, Shirley DJ, Haas AR, Laughlin A, et al. Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome Biol. 2014;15:487. This paper describes the interaction of the mycobiome with other microbiota.CrossRefPubMedPubMedCentral
24.••
Seed PC. The human mycobiome. Cold Spring Harbor Perspectives in Medicine. 2015;5:a019810. This review paper gives a clear overview of the human mycobiome.CrossRef
25.
Norman JM, Handley SA, Virgin HW. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology. 2014;146:1459–69.CrossRefPubMedPubMedCentral
26.
Underwood AP, Dallman T, Thomson NR, Williams M, Harker K, Perry N, et al. Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak. J Clin Microbiol. 2013;51:232–7.CrossRefPubMedPubMedCentral
27.
Araujo R. Towards the genotyping of fungi: methods, benefits and challenges. Curr Fungal Infect Rep. 2014;8:203–10.CrossRef
28.
Dannemiller KC, Reeves D, Bibby K, Yamamoto N, Peccia J. Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS). J Basic Microbiol. 2014;54:315–21.CrossRefPubMed
29.
Bueid A, Howard SJ, Moore CB, Richardson MD, Harrison E, et al. Azole antifungal resistance in Aspergillus fumigatus: 2008 and 2009. J Antimicrob Chemother. 2010;65:2116–8.CrossRefPubMed
30.
Lockhart SR, Frade JP, Etienne KA, Pfaller MA, Diekema DJ, et al. Azole resistance in Aspergillus fumigatus isolates from the ARTEMIS global surveillance is primarily due to the TR/L98H mutation in the cyp51A gene. Antimicrob Agents Chemother. 2011;55:4465–8.CrossRefPubMedPubMedCentral
31.
Snelders E, van der Lee HA, Kuijpers J, Rijs AJ, Varga J, et al. Emergence of azole resistance in Aspergillus fumigatus and spread of a single resistance mechanism. PLoS Med. 2008;5, e219.CrossRefPubMedPubMedCentral
32.
Verweij PE, Howard SJ, Melchers WJ, Denning DW. Azole-resistance in Aspergillus: proposed nomenclature and breakpoints. Drug Resist Updat. 2009;12:141–7.CrossRefPubMed
33.
Howard SJ, Cerar D, Anderson MJ, Albarrag A, Fisher MC, et al. Frequency and evolution of azole resistance in Aspergillus fumigatus associated with treatment failure. Emerg Infect Dis. 2009;15:1068–76.CrossRefPubMedPubMedCentral
34.
Garnaud C, Botterel F, Sertour N, Bougnoux M, Dannaoui E, Larrat S, et al. Next-generation sequencing offers new insights into the resistance of Candida spp. to echinocandins and azoles. J Antimicrob Chemother. 2015;70:2556–65.CrossRefPubMed
35.
Kanafani ZA, Perfect JR. Resistance to antifungal agents: mechanisms and clinical impact. Clin Infect Dis. 2008;46:120–8.CrossRefPubMed
36.
Ianiri G, Idnurm A. Essential gene discovery in the basidiomycete Cryptococcus neoformans for antifungal drug target prioritization. mBio. 2015;6, e02334-14.CrossRefPubMedPubMedCentral
37.
38.
Verweij PE, Snelders E, Kema GH, Mellado E, Melchers WJ. Azole resistance in Aspergillus fumigatus: a side-effect of environmental fungicide use? Lancet Infect Dis. 2009;9:789–95.CrossRefPubMed
39.
Snelders E, Huis In 't Veld RA, Rijs AJ, Kema GH, Melchers WJ, Verweij PE. Possible environmental origin of resistance of Aspergillus fumigatus to medical triazoles. Appl Environ Microbiol. 2009;75(12):4053–7.CrossRefPubMedPubMedCentral
40.
Camps SMT, Dutilh BE, Arendrup MC, Rijs AJMM, Snelders E, Huynen MA, et al. Discovery of a HapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing. PLoS ONE. 2012;7, e50034.CrossRefPubMedPubMedCentral
41.
Fraczek MG, Bromley M, Buied A, Moore CB, Rajendran R, Rautemaa R, et al. The cdr1B efflux transporter is associated with non-cyp51a-mediated itraconazole resistance in Aspergillus fumigatus. J Antimicrob Chemother. 2013;68:1486–96.CrossRefPubMed
42.
Hagiwara D, Takahashi H, Watanabe A, Takahashi-Nakaguchi A, Kawamoto S, Kamei K, et al. Whole-genome comparison of Aspergillus fumigatus strains serially isolated from patients with Aspergillosis. J Clin Microbiol. 2014;52:4202–9.CrossRefPubMedPubMedCentral
Metadata
Title
Next-Generation Sequencing in the Mycology Lab
Authors
Jan Zoll
Eveline Snelders
Paul E. Verweij
Willem J. G. Melchers
Publication date
01-06-2016
Publisher
Springer US
Published in
Current Fungal Infection Reports / Issue 2/2016
Print ISSN: 1936-3761
Electronic ISSN: 1936-377X
DOI
https://doi.org/10.1007/s12281-016-0253-6

Other articles of this Issue 2/2016

Current Fungal Infection Reports 2/2016 Go to the issue

Clinical Mycology Lab Issues (K Lagrou, Section Editor)

Evolution of Cryptococcal Antigen Testing: What Is New?

Clinical Mycology Lab Issues (K Lagrou, Section Editor)

Therapeutic Drug Monitoring of Posaconazole: an Update

Current Management of Fungal Infections (RE Lewis, Section Editor)

Improved Radiographic Imaging of Invasive Fungal Disease: The Cornerstone to Antifungal Stewardship in the Hematology Units?

Current Management of Fungal Infections (RE Lewis, Section Editor)

Impact of New Diagnostic Approaches for Invasive Candidiasis on Antifungal Stewardship

Clinical Mycology Lab Issues (K Lagrou, Section Editor)

Point of Care Testing for the Diagnosis of Fungal Infections: Are We There Yet?

ACC 2024 Congress Coverage

Heart Failure Video

Year in Review: Heart failure and cardiomyopathies

Watch now

Watch this official video from ACC.24. Dr. Biykem Bozkurt discuss last year's major advances in heart failure and cardiomyopathies.

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

16-04-2024 Type 2 Diabetes News

Incentivised to exercise

11-04-2024 Lifestyle Modifications News

New intervention for STEMI-related cardiogenic shock

10-04-2024 Myocardial Infarction News

» View more highlights on the ACC 2024 congress hub page

Image Credits