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OPATHY SIGNED

From Omics to Patient: Improving Diagnostics of Pathogenic Yeasts

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EC-Contrib. €

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Project "OPATHY" data sheet

The following table provides information about the project.

Coordinator
FUNDACIO CENTRE DE REGULACIO GENOMICA 

Organization address
address: CARRER DOCTOR AIGUADER 88
city: BARCELONA
postcode: 8003
website: www.crg.es

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Spain [ES]
 Project website http://www.opathy.eu
 Total cost 3˙319˙305 €
 EC max contribution 3˙319˙305 € (100%)
 Programme 1. H2020-EU.1.3.1. (Fostering new skills by means of excellent initial training of researchers)
 Code Call H2020-MSCA-ITN-2014
 Funding Scheme MSCA-ITN-ETN
 Starting year 2015
 Duration (year-month-day) from 2015-09-01   to  2019-08-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    FUNDACIO CENTRE DE REGULACIO GENOMICA ES (BARCELONA) coordinator 495˙745.00
2    UNIVERSITY COLLEGE DUBLIN, NATIONAL UNIVERSITY OF IRELAND, DUBLIN IE (DUBLIN) participant 531˙349.00
3    KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW NL (AMSTERDAM) participant 510˙748.00
4    THE UNIVERSITY COURT OF THE UNIVERSITY OF ABERDEEN UK (ABERDEEN) participant 273˙287.00
5    MEDIZINISCHE UNIVERSITAT INNSBRUCK AT (INNSBRUCK) participant 255˙934.00
6    QVQ HOLDING BV NL (UTRECHT) participant 255˙374.00
7    UNIVERSITEIT GENT BE (GENT) participant 250˙560.00
8    BRUKER DALTONIK GMBH DE (BREMEN) participant 249˙216.00
9    LEIBNIZ-INSTITUT FUR NATURSTOFF-FORSCHUNG UND INFEKTIONSBIOLOGIE EV HANS-KNOLL-ISTITUT DE (JENA) participant 249˙216.00
10    BIOTECH VANA SL ES (PATERNA (VALENCIA)) participant 247˙872.00

Map

 Project objective

OPATHY is an innovative translational research training network that will explore the potential of omics technologies, including genomics, transcriptomics and proteomics, to study the interactions of yeasts that cause disease to humans (e.g. Candida and Cryptococcus sp.) with their host, and to develop new diagnostic tools to monitor yeast infections in the clinic. Today, these infections are poorly understood, difficult to diagnose, and are becoming increasingly frequent and serious, affecting over 300 million people worldwide. OPATHY will exploit omics technologies to investigate host-pathogen interactions during yeast infection and colonization with a primary focus on their potential to develop innovative diagnostics tools to improve health care. For this proteomics, transcriptomics and genomics measurements of strains and infections will be integrated with state of the art computational analyses to identify novel biomarkers able to determine the infection stage, the infective pathogen, and the potential resistance traits. This knowledge will drive the development of diagnostic tools based on the detection of specific DNA sequences (by PCR) or antibodies (by Elisa or proteomics). These tools will be validated in a clinical study of key patient cohorts. The participation of two clinical centers and four companies is of paramount importance for the network to provide an integrative and transversal research and training environment. Importantly, the methodologies and approaches of OPATHY can be easily extended to the study and identification of other human, animal and plant microbial pathogens, or the tracing of relevant industrial organisms. Grounded on solid individual research projects, OPATHY will train Early Stage Researchers in several scientific technologies and fields and transferable skills, to boost their careers as innovative and creative researchers.

 Deliverables

List of deliverables.
Dissection of RNAseq samples from Candida-blood infections for diagnostic purposes Websites, patent fillings, videos etc. 2020-02-21 17:57:55
OPATHY final symposium and publication Websites, patent fillings, videos etc. 2020-02-21 17:57:56
Validated biomarkers for resistant Candida isolates Websites, patent fillings, videos etc. 2020-02-21 17:57:55
Proteomics-based diagnostics of resistant isolates Websites, patent fillings, videos etc. 2020-02-21 17:57:55
Validated PCR assays for Candida pathogens Websites, patent fillings, videos etc. 2020-02-21 17:57:55
Verification of gene expression data from in vitro, ex vivo and in vivo samples Websites, patent fillings, videos etc. 2020-02-21 17:57:55
Validated biomarkers candidiasis Websites, patent fillings, videos etc. 2020-02-21 17:57:55
Analysis of the role of identified factors Websites, patent fillings, videos etc. 2020-02-21 17:57:55
Validated PCR assays for resistant Candida isolates Websites, patent fillings, videos etc. 2020-02-21 17:57:55
Enrichment tool based on llama antibodies Websites, patent fillings, videos etc. 2020-02-21 17:57:56
Comparative transcriptomics of all transcriptional data Websites, patent fillings, videos etc. 2020-02-21 17:57:55
OPATHY OMICS pipeline Websites, patent fillings, videos etc. 2020-02-21 17:57:54
Improved proteomics-based diagnostics of pathogenic yeast species complexes Websites, patent fillings, videos etc. 2020-02-21 17:57:54
Proteomics-based diagnostics of infected clinical materials Websites, patent fillings, videos etc. 2020-02-21 17:57:54
In vitro, ex vivo Infection models established and characterized for all Candida species Websites, patent fillings, videos etc. 2020-02-21 17:57:53
In vitro, ex vivo and in vivo transcriptional profiles of all Candida species Websites, patent fillings, videos etc. 2020-02-21 17:57:53
Full Map Transcriptomic/proteomics pipeline Websites, patent fillings, videos etc. 2020-02-21 17:57:53

Take a look to the deliverables list in detail:  detailed list of OPATHY deliverables.

 Publications

year authors and title journal last update
List of publications.
2019 Kontxi Martinez de San Vicente, Markus S. Schröder, Lisa Lombardi, Elise Iracane, Geraldine Butler
Correlating Genotype and Phenotype in the Asexual Yeast Candida orthopsilosis Implicates ZCF29 in Sensitivity to Caffeine
published pages: g3.400348.2019, ISSN: 2160-1836, DOI: 10.1534/g3.119.400348
\"G3: Genes|Genomes|Genetics\" 2020-02-21
2019 Antonio Pérez-Hansen, Cornelia Lass-Flörl, Michaela Lackner, M Aigner, A Alastruey-Izquierdo, S Arikan-Akdagli, O Bader, K Becker, T Boekhout, W Buzina, O A Cornely, P Hamal, S E Kidd, O Kurzai, K Lagrou, A Lopes Colombo, M Mares, H Masoud, J F Meis, S Oliveri, A C Rodloff, D Orth-Höller, I Guerrero-Lozano, M Sanguinetti, E Segal, S J Taj-Aldeen, A M Tortorano, L Trovato, G Walther, B Willinger
Antifungal susceptibility profiles of rare ascomycetous yeasts
published pages: , ISSN: 0305-7453, DOI: 10.1093/jac/dkz231
Journal of Antimicrobial Chemotherapy 2020-02-21
2019 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
First fungemia case due to environmental yeast Wickerhamomyces myanmarensis : detection by multiplex qPCR and antifungal susceptibility
published pages: 267-274, ISSN: 1746-0913, DOI: 10.2217/fmb-2018-0253
Future Microbiology 14/4 2020-02-21
2019 Amir Arastehfar, Farnaz Daneshnia, Shirin Farahyar, Wenjie Fang, Maryam Salimi, Mohammadreza Salehi, Ferry Hagen, Pan Weihua, Maryam Roudbary, Teun Boekhout
Incidence and spectrum of yeast species isolated from the oral cavity of Iranian patients suffering from hematological malignancies
published pages: 1601061, ISSN: 2000-2297, DOI: 10.1080/20002297.2019.1601061
Journal of Oral Microbiology 11/1 2020-02-21
2019 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
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)
published pages: , ISSN: 2235-2988, DOI: 10.3389/fcimb.2019.00264
Frontiers in Cellular and Infection Microbiology 9 2020-02-21
2019 Mansoureh Vatanshenassan, Amir Arastehfar, Teun Boekhout, Judith Berman, Cornelia Lass-Flörl, Katrin Sparbier, Markus Kostrzewa
Anidulafungin Susceptibility Testing of Candida glabrata Isolates from Blood Cultures by the MALDI Biotyper Antibiotic (Antifungal) Susceptibility Test Rapid Assay
published pages: , ISSN: 0066-4804, DOI: 10.1128/aac.00554-19
Antimicrobial Agents and Chemotherapy 63/9 2020-02-21
2019 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
Molecular characterization and antifungal susceptibility testing of Candida nivariensis from blood samples – an Iranian multicentre study and a review of the literature
published pages: 770-777, ISSN: 0022-2615, DOI: 10.1099/jmm.0.000963
Journal of Medical Microbiology 68/5 2020-02-21
2019 H Hovhannisyan, A Hafez, C Llorens, T Gabaldón
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
published pages: , ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btz626
Bioinformatics 2020-02-21
2019 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
Recent trends in molecular diagnostics of yeast infections: from PCR to NGS
published pages: , ISSN: 0168-6445, DOI: 10.1093/femsre/fuz015
FEMS Microbiology Reviews 2020-02-21
2019 Aimilia A Stavrou, Michaela Lackner, Cornelia Lass-Flörl, Teun Boekhout
The changing spectrum of Saccharomycotina yeasts causing candidemia: phylogeny mirrors antifungal susceptibility patterns for azole drugs and amphothericin B
published pages: , ISSN: 1567-1356, DOI: 10.1093/femsyr/foz037
FEMS Yeast Research 2020-02-21
2019 Verónica Mixão, Antonio Perez Hansen, Ester Saus, Teun Boekhout, Cornelia Lass-Florl, Toni Gabaldón
Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin
published pages: , ISSN: 1664-8021, DOI: 10.3389/fgene.2019.00383
Frontiers in Genetics 10 2020-02-21
2019 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
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
published pages: , ISSN: 0066-4804, DOI: 10.1128/aac.02503-18
Antimicrobial Agents and Chemotherapy 2020-02-21
2019 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
Novel multiplex real-time quantitative PCR detecting system approach for direct detection of Candida auris and its relatives in spiked serum samples
published pages: 33-45, ISSN: 1746-0913, DOI: 10.2217/fmb-2018-0227
Future Microbiology 14/1 2020-02-21
2019 Antonio Rodríguez, Mario Vaneechoutte
Comparison of the efficiency of different cell lysis methods and different commercial methods for RNA extraction from Candida albicans stored in RNAlater
published pages: , ISSN: 1471-2180, DOI: 10.1186/s12866-019-1473-z
BMC Microbiology 19/1 2020-02-21
2019 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
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
published pages: , ISSN: 2235-2988, DOI: 10.3389/fcimb.2019.00021
Frontiers in Cellular and Infection Microbiology 9 2020-02-21
2018 Elise Iracane, Paul D. Donovan, Mihaela Ola, Geraldine Butler, Linda M. Holland
Identification of an Exceptionally Long Intron in the HAC1 Gene of Candida parapsilosis
published pages: , ISSN: 2379-5042, DOI: 10.1128/msphere.00532-18
mSphere 3/6 2020-02-21
2019 Amir Arastehfar, Wenjie Fang, Weihua Pan, Michaela Lackner, Wanqing Liao, Parisa Badiee, Kamiar Zomorodian, Hamid Badali, Ferry Hagen, Cornelia Lass-Flörl, Teun Boekhout
YEAST PANEL multiplex PCR for identification of clinically important yeast species: stepwise diagnostic strategy, useful for developing countries
published pages: 112-119, ISSN: 0732-8893, DOI: 10.1016/j.diagmicrobio.2018.09.007
Diagnostic Microbiology and Infectious Disease 93/2 2020-02-21
2018 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
In vitro antifungal activity of amphotericin B and 11 comparators against Aspergillus terreus species complex
published pages: 134-142, ISSN: 0933-7407, DOI: 10.1111/myc.12716
Mycoses 61/2 2020-02-21
2018 Aimilia A. Stavrou, Verónica Mixão, Teun Boekhout, Toni Gabaldón
Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications
published pages: 425-429, ISSN: 0749-503X, DOI: 10.1002/yea.3303
Yeast 35/6 2020-02-21
2018 Amir Arastehfar, Wenjie Fang, Weihua Pan, Wanqing Liao, Liang Yan, Teun Boekhout
Identification of nine cryptic species of Candida albicans, C. glabrata, and C. parapsilosis complexes using one-step multiplex PCR
published pages: , ISSN: 1471-2334, DOI: 10.1186/s12879-018-3381-5
BMC Infectious Diseases 18/1 2020-02-21
2018 Jelena Lazić, Vladimir Ajdačić, Sandra Vojnovic, Mario Zlatović, Marina Pekmezovic, Selene Mogavero, Igor Opsenica, Jasmina Nikodinovic-Runic
Bis-guanylhydrazones as efficient anti-Candida compounds through DNA interaction
published pages: 1889-1901, ISSN: 0175-7598, DOI: 10.1007/s00253-018-8749-3
Applied Microbiology and Biotechnology 102/4 2020-02-21
2019 Lisa Lombardi, João Oliveira-Pacheco, Geraldine Butler
Plasmid-Based CRISPR-Cas9 Gene Editing in Multiple Candida Species
published pages: , ISSN: 2379-5042, DOI: 10.1128/msphere.00125-19
mSphere 4/2 2020-02-21
2018 Amir Arastehfar, Wenjie Fang, Hamid Badali, Afsane Vaezi, Weiwei Jiang, Wanqing Liao, Weihua Pan, Ferry Hagen, Teun Boekhout
Low-Cost Tetraplex PCR for the Global Spreading Multi-Drug Resistant Fungus, Candida auris and Its Phylogenetic Relatives
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2018.01119
Frontiers in Microbiology 9 2020-02-21
2016 Ágnes Jakab, Selene Mogavero, Toni M. Förster​, Marina Pekmezovic​, Nadja Jablonowski​, Viktor Dombrádi​, István Pócsi​, Bernhard Hube
Effects of the glucocorticoid betamethasone on the interaction of Candida albicans with human epithelial cells
published pages: 2116-2125, ISSN: 1350-0872, DOI: 10.1099/mic.0.000383
Microbiology 162/12 2020-02-21
2018 Hrant Hovhannisyan, Toni Gabaldón
Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens
published pages: , ISSN: , DOI: 10.1007/82_2018_122
Current Topics in Microbiology and Immunology 2020-02-21
2018 Ester Saus, Jesse R. Willis, Leszek P. Pryszcz, Ahmed Hafez, Carlos Llorens, Heinz Himmelbauer, Toni Gabaldón
nextPARS: parallel probing of RNA structures in Illumina
published pages: 609-619, ISSN: 1355-8382, DOI: 10.1261/rna.063073.117
RNA 24/4 2020-02-21
2017 Verónica Mixão, Toni Gabaldón
Hybridization and emergence of virulence in opportunistic human yeast pathogens
published pages: , ISSN: 0749-503X, DOI: 10.1002/yea.3242
Yeast 2020-02-21
2018 Mansoureh Vatanshenassan, Teun Boekhout, Cornelia Lass-Flörl, Michaela Lackner, Sören Schubert, Markus Kostrzewa, Katrin Sparbier
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
published pages: , ISSN: 0095-1137, DOI: 10.1128/JCM.00420-18
Journal of Clinical Microbiology 56/9 2020-02-21
2018 Nada D. Savić, Sandra Vojnovic, Biljana Đ. Glišić, Aurélien Crochet, Aleksandar Pavic, Goran V. Janjić, Marina Pekmezović, Igor M. Opsenica, Katharina M. Fromm, Jasmina Nikodinovic-Runic, Miloš I. Djuran
Mononuclear silver(I) complexes with 1,7-phenanthroline as potent inhibitors of Candida growth
published pages: 760-773, ISSN: 0223-5234, DOI: 10.1016/j.ejmech.2018.07.049
European Journal of Medicinal Chemistry 156 2020-02-21

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