From Omics to Patient: Improving Diagnostics of Pathogenic Yeasts

Deliverables

Full Map Transcriptomic/proteomics pipeline

Full Map Transcriptomicproteomics pipeline

Enrichment tool based on llama antibodies
Verification of gene expression data from in vitro, ex vivo and in vivo samples
Validated PCR assays for resistant Candida isolates
Comparative transcriptomics of all transcriptional data

Comparative transcriptomics of all transcriptional data; identification of Candida-specific, species-specific and stage specific fungal and host pattern and factors

OPATHY OMICS pipeline
Validated biomarkers candidiasis
Validated PCR assays for Candida pathogens
OPATHY final symposium and publication
Dissection of RNAseq samples from Candida-blood infections for diagnostic purposes

Dissection of RNAseq samples from Candida-blood infections for diagnostic purposes

In vitro, ex vivo and in vivo transcriptional profiles of all Candida species

In vitro ex vivo and in vivo transcriptional profiles of all Candida species

Analysis of the role of identified factors
In vitro, ex vivo Infection models established and characterized for all Candida species

In vitro ex vivo Infection models established and characterized for all Candida species

Improved proteomics-based diagnostics of pathogenic yeast species complexes

Validated biomarkers for resistant Candida isolates
Proteomics-based diagnostics of infected clinical materials
Proteomics-based diagnostics of resistant isolates

Publications

Proof of Concept for MBT ASTRA, a Rapid Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS)-Based Method To Detect Caspofungin Resistance in Candida albicans and Candida glabrata

Author(s): Mansoureh Vatanshenassan, Teun Boekhout, Cornelia Lass-Flörl, Michaela Lackner, Sören Schubert, Markus Kostrzewa, Katrin Sparbier
Published in: Journal of Clinical Microbiology, Issue 56/9, 2018, ISSN 0095-1137
Publisher: American Society for Microbiology
DOI: 10.1128/JCM.00420-18

Low-Cost Tetraplex PCR for the Global Spreading Multi-Drug Resistant Fungus, Candida auris and Its Phylogenetic Relatives

Author(s): Amir Arastehfar, Wenjie Fang, Hamid Badali, Afsane Vaezi, Weiwei Jiang, Wanqing Liao, Weihua Pan, Ferry Hagen, Teun Boekhout
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.01119

nextPARS: parallel probing of RNA structures in Illumina

Author(s): Ester Saus, Jesse R. Willis, Leszek P. Pryszcz, Ahmed Hafez, Carlos Llorens, Heinz Himmelbauer, Toni Gabaldón
Published in: RNA, Issue 24/4, 2018, Page(s) 609-619, ISSN 1355-8382
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.063073.117

Comparison of the efficiency of different cell lysis methods and different commercial methods for RNA extraction from Candida albicans stored in RNAlater

Author(s): Antonio Rodríguez, Mario Vaneechoutte
Published in: BMC Microbiology, Issue 19/1, 2019, ISSN 1471-2180
Publisher: BioMed Central
DOI: 10.1186/s12866-019-1473-z

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin

Author(s): Verónica Mixão, Antonio Perez Hansen, Ester Saus, Teun Boekhout, Cornelia Lass-Florl, Toni Gabaldón
Published in: Frontiers in Genetics, Issue 10, 2019, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2019.00383

Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications

Author(s): Aimilia A. Stavrou, Verónica Mixão, Teun Boekhout, Toni Gabaldón
Published in: Yeast, Issue 35/6, 2018, Page(s) 425-429, ISSN 0749-503X
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/yea.3303

Identification of an Exceptionally Long Intron in the HAC1 Gene of Candida parapsilosis

Author(s): Elise Iracane, Paul D. Donovan, Mihaela Ola, Geraldine Butler, Linda M. Holland
Published in: mSphere, Issue 3/6, 2018, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/msphere.00532-18

Candida auris Identification and Rapid Antifungal Susceptibility Testing Against Echinocandins by MALDI-TOF MS

Author(s): Mansoureh Vatanshenassan, Teun Boekhout, Jacques F. Meis, Judith Berman, Anuradha Chowdhary, Ronen Ben-Ami, Katrin Sparbier, Markus Kostrzewa
Published in: Frontiers in Cellular and Infection Microbiology, Issue 9, 2019, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2019.00020

Plasmid-Based CRISPR-Cas9 Gene Editing in Multiple Candida Species

Author(s): Lisa Lombardi, João Oliveira-Pacheco, Geraldine Butler
Published in: mSphere, Issue 4/2, 2019, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/msphere.00125-19

In vitro antifungal activity of amphotericin B and 11 comparators against Aspergillus terreus species complex

Author(s): Afsane Vaezi, Hamed Fakhim, Amir Arastehfar, Tahereh Shokohi, Mohammad T. Hedayati, Sadegh Khodavaisy, Ali Rezaei-Matehkolaei, Parisa Badiee, Ferry Hagen, Cornelia Lass-Flörl, Eric Dannaoui, Jacques F. Meis, Hamid Badali
Published in: Mycoses, Issue 61/2, 2018, Page(s) 134-142, ISSN 0933-7407
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/myc.12716

Comparison of 21-Plex PCR and API 20C AUX, MALDI-TOF MS, and rDNA Sequencing for a Wide Range of Clinically Isolated Yeast Species: Improved Identification by Combining 21-Plex PCR and API 20C AUX as an Alternative Strategy for Developing Countries

Author(s): Amir Arastehfar, Farnaz Daneshnia, Mohammad Kord, Maryam Roudbary, Hossein Zarrinfar, Wenjie Fang, Sayed Jamal Hashemi, Mohammad Javad Najafzadeh, Sadegh Khodavaisy, Weihua Pan, Wanqing Liao, Hamid Badali, Sassan Rezaie, Kamiar Zomorodian, Ferry Hagen, Teun Boekhout
Published in: Frontiers in Cellular and Infection Microbiology, Issue 9, 2019, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2019.00021

YEAST PANEL multiplex PCR for identification of clinically important yeast species: stepwise diagnostic strategy, useful for developing countries

Author(s): Amir Arastehfar, Wenjie Fang, Weihua Pan, Michaela Lackner, Wanqing Liao, Parisa Badiee, Kamiar Zomorodian, Hamid Badali, Ferry Hagen, Cornelia Lass-Flörl, Teun Boekhout
Published in: Diagnostic Microbiology and Infectious Disease, Issue 93/2, 2019, Page(s) 112-119, ISSN 0732-8893
Publisher: Elsevier BV
DOI: 10.1016/j.diagmicrobio.2018.09.007

Identification of nine cryptic species of Candida albicans, C. glabrata, and C. parapsilosis complexes using one-step multiplex PCR

Author(s): Amir Arastehfar, Wenjie Fang, Weihua Pan, Wanqing Liao, Liang Yan, Teun Boekhout
Published in: BMC Infectious Diseases, Issue 18/1, 2018, ISSN 1471-2334
Publisher: BioMed Central
DOI: 10.1186/s12879-018-3381-5

Novel multiplex real-time quantitative PCR detecting system approach for direct detection of Candida auris and its relatives in spiked serum samples

Author(s): Amir Arastehfar, Wenjie Fang, Farnaz Daneshnia, Abdullah MS Al-Hatmi, Wanqing Liao, Weihua Pan, Ziauddin Khan, Suhail Ahmad, Katharina Rosam, Michaela Lackner, Cornelia Lass-Flörl, Ferry Hagen, Teun Boekhout
Published in: Future Microbiology, Issue 14/1, 2019, Page(s) 33-45, ISSN 1746-0913
Publisher: Future Medicine Ltd.
DOI: 10.2217/fmb-2018-0227

Low level of antifungal resistance in Iranian isolates of Candida glabrata recovered from blood samples from multicenter (2015-2018): Potential prognostic values of genotyping and sequencing of PDR1

Author(s): Amir Arastehfar, Farnaz Daneshnia, Kamiar Zomorodian, Mohammad-Javad Najafzadeh, Sadegh Khodavaisy, Hossein Zarrinfar, Ferry Hagen, Zahra Zare Shahrabadi, Michaela Lackner, Hossein Mirhendi, Mohammadreza Salehi, Maryam Roudbary, Weihua Pan, Markus Kostrzewa, Teun Boekhout
Published in: Antimicrobial Agents and Chemotherapy, 2019, ISSN 0066-4804
Publisher: American Society for Microbiology
DOI: 10.1128/aac.02503-18

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

Author(s): A Arastehfar, T Boekhout, G Butler, G Buda De Cesare, E Dolk, T Gabaldóln, A Hafez, B Hube, F Hagen, H Hovhannisyan, E Iracane, M Kostrzewa, M Lackner, C Lass-Flörl, C Llorens, V Mixão, C Munro, J Oliveira-Pacheco, M Pekmezovic, A Pérez-Hansen, A Rodriguez Sanchez, F M Sauer, K Sparbier, A A Stavrou, M Vaneechoutte, M Vatanshenassan, Toni Gabaldón
Published in: FEMS Microbiology Reviews, 2019, ISSN 0168-6445
Publisher: Blackwell
DOI: 10.1093/femsre/fuz015

CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies

Author(s): H Hovhannisyan, A Hafez, C Llorens, T Gabaldón
Published in: Bioinformatics, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz626

Correlating Genotype and Phenotype in the Asexual Yeast Candida orthopsilosis Implicates ZCF29 in Sensitivity to Caffeine

Author(s): Kontxi Martinez de San Vicente, Markus S. Schröder, Lisa Lombardi, Elise Iracane, Geraldine Butler
Published in: "G3&#58; Genes|Genomes|Genetics", 2019, Page(s) g3.400348.2019, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1534/g3.119.400348

Molecular characterization and antifungal susceptibility testing of Candida nivariensis from blood samples – an Iranian multicentre study and a review of the literature

Author(s): Amir Arastehfar, Farnaz Daneshnia, Mohammad-Reza Salehi, Hossein Zarrinfar, Sadegh Khodavaisy, Pieter-Jan Haas, Maryam Roudbary, Mohammad-Javad Najafzadeh, Kamiar Zomorodian, Arezoo Charsizadeh, Carlo Brouwer, Weihua Pan, Ferry Hagen, Teun Boekhout
Published in: Journal of Medical Microbiology, Issue 68/5, 2019, Page(s) 770-777, ISSN 0022-2615
Publisher: Society for General Microbiology
DOI: 10.1099/jmm.0.000963

Incidence and spectrum of yeast species isolated from the oral cavity of Iranian patients suffering from hematological malignancies

Author(s): Amir Arastehfar, Farnaz Daneshnia, Shirin Farahyar, Wenjie Fang, Maryam Salimi, Mohammadreza Salehi, Ferry Hagen, Pan Weihua, Maryam Roudbary, Teun Boekhout
Published in: Journal of Oral Microbiology, Issue 11/1, 2019, Page(s) 1601061, ISSN 2000-2297
Publisher: Co-Action Publishing
DOI: 10.1080/20002297.2019.1601061

First fungemia case due to environmental yeast Wickerhamomyces myanmarensis : detection by multiplex qPCR and antifungal susceptibility

Author(s): Amir Arastehfar, Mina Bakhtiari, Farnaz Daneshnia, Wenjie Fang, Sara Khanjari Sadati, Abdullah MS Al-Hatmi, Marizeth Groenewald, Hamid Sharifi-Mehr, Wanqing Liao, Weihua Pan, Kamiar Zomorodian, Ferry Hagen, Teun Boekhout
Published in: Future Microbiology, Issue 14/4, 2019, Page(s) 267-274, ISSN 1746-0913
Publisher: Future Medicine Ltd.
DOI: 10.2217/fmb-2018-0253

Molecular Identification, Genotypic Diversity, Antifungal Susceptibility, and Clinical Outcomes of Infections Caused by Clinically Underrated Yeasts, Candida orthopsilosis, and Candida metapsilosis: An Iranian Multicenter Study (2014–2019)

Author(s): Amir Arastehfar, Sadegh Khodavaisy, Farnaz Daneshnia, Mohammad-Javad Najafzadeh, Shahram Mahmoudi, Arezoo Charsizadeh, Mohammad-Reza Salehi, Hossein Zarrinfar, Abbas Raeisabadi, Somayeh Dolatabadi, Zahra Zare Shahrabadi, Kamiar Zomorodian, Weihua Pan, Ferry Hagen, Teun Boekhout
Published in: Frontiers in Cellular and Infection Microbiology, Issue 9, 2019, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2019.00264

Nucleic acids enrichment of fungal pathogens to study host-pathogen interactions

Author(s): Antonio Rodríguez, Brecht Guillemyn, Paul Coucke, Mario Vaneechoutte
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-54608-x

Effects of the glucocorticoid betamethasone on the interaction of Candida albicans with human epithelial cells

Author(s): Ágnes Jakab, Selene Mogavero, Toni M. Förster, Marina Pekmezovic, Nadja Jablonowski, Viktor Dombrádi, István Pócsi, Bernhard Hube
Published in: Microbiology, Issue 162/12, 2016, Page(s) 2116-2125, ISSN 1350-0872
Publisher: Society for General Microbiology
DOI: 10.1099/mic.0.000383

Hybridization and emergence of virulence in opportunistic human yeast pathogens

Author(s): Verónica Mixão, Toni Gabaldón
Published in: Yeast, 2017, ISSN 0749-503X
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/yea.3242

Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens

Author(s): Hrant Hovhannisyan, Toni Gabaldón
Published in: Current Topics in Microbiology and Immunology, 2018
Publisher: Springer Berlin Heidelberg
DOI: 10.1007/82_2018_122

Deliverables

Publications

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