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Daneshnia F, Floyd DJ, Ryan AP, Ghahfarokhy PM, Ebadati A, Jusuf S, Munoz J, Jeffries NE, Elizabeth Yvanovich E, Apostolopoulou A, Perry AM, Lass-Flörl C, Birinci A, Hilmioğlu-Polat S, Ilkit M, Butler G, Nobile CJ, Arastehfar A, Mansour MK. Evaluation of outbreak persistence caused by multidrug-resistant and echinocandin-resistant Candida parapsilosis using multidimensional experimental and epidemiological approaches. Emerg Microbes Infect 2024; 13:2322655. [PMID: 38380673 PMCID: PMC10916928 DOI: 10.1080/22221751.2024.2322655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Candida parapsilosis is known to cause severe and persistent outbreaks in clinical settings. Patients infected with multidrug-resistant C. parapsilosis (MDR Cp) isolates were identified in a large Turkish hospital from 2017-2020. We subsequently identified three additional patients infected with MDR Cp isolates in 2022 from the same hospital and two echinocandin-resistant (ECR) isolates from a single patient in another hospital. The increasing number of MDR and ECR isolates contradicts the general principle that the severe fitness cost associated with these phenotypes could prevent their dominance in clinical settings. Here, we employed a multidimensional approach to systematically assess the fitness costs of MDR and ECR C. parapsilosis isolates. Whole-genome sequencing revealed a novel MDR genotype infecting two patients in 2022. Despite severe in vitro defects, the levels and tolerances of the biofilms of our ECR and MDR isolates were generally comparable to those of susceptible wild-type isolates. Surprisingly, the MDR and ECR isolates showed major alterations in their cell wall components, and some of the MDR isolates consistently displayed increased tolerance to the fungicidal activities of primary human neutrophils and were more immunoevasive during exposure to primary human macrophages. Our systemic infection mouse model showed that MDR and ECR C. parapsilosis isolates had comparable fungal burden in most organs relative to susceptible isolates. Overall, we observed a notable increase in the genotypic diversity and frequency of MDR isolates and identified MDR and ECR isolates potentially capable of causing persistent outbreaks in the future.
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Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel J. Floyd
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam P. Ryan
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Pegah Mosharaf Ghahfarokhy
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California – Merced, Merced, CA, USA
| | - Arefeh Ebadati
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | - Sebastian Jusuf
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Julieta Munoz
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | | | | | - Anna Apostolopoulou
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin M. Perry
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | - Cornelia Lass-Flörl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Innsbruck, Austria
| | - Asuman Birinci
- Department of Medical Microbiology, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Türkiye
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Türkiye
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California – Merced, Merced, CA, USA
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael K. Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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2
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Arastehfar A, Daneshnia F, Floyd DJ, Jeffries NE, Salehi M, Perlin DS, Ilkit M, Lass-Flöerl C, Mansour MK. Echinocandin persistence directly impacts the evolution of resistance and survival of the pathogenic fungus Candida glabrata. mBio 2024; 15:e0007224. [PMID: 38501869 PMCID: PMC11005346 DOI: 10.1128/mbio.00072-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Recent epidemiological studies documented an alarming increase in the prevalence of echinocandin-resistant (ECR) Candida glabrata blood isolates. ECR isolates are known to arise from a minor subpopulation of a clonal population, termed echinocandin persisters. Although it is believed that isolates with a higher echinocandin persistence (ECP) are more likely to develop ECR, the implication of ECP needs to be better understood. Moreover, replacing laborious and time-consuming traditional approaches to determine ECP levels with rapid, convenient, and reliable tools is imperative to advance our understanding of this emerging concept in clinical practice. Herein, using extensive ex vivo and in vivo systemic infection models, we showed that high ECP isolates are less effectively cleared by micafungin treatment and exclusively give rise to ECR colonies. Additionally, we developed a flow cytometry-based tool that takes advantage of a SYTOX-based assay for the stratification of ECP levels. Once challenged with various collections of echinocandin-susceptible blood isolates, our assay reliably differentiated ECP levels in vitro and predicted ECP levels in real time under ex vivo and in vivo conditions when compared to traditional methods relying on colony-forming unit counting. Given the high and low ECP predictive values of 92.3% and 82.3%, respectively, our assay showed a high agreement with traditional approach. Collectively, our study supports the concept of ECP level determination in clinical settings and provides a robust tool scalable for high-throughput settings. Application of this tool facilitates the interrogation of mutant and drug libraries to further our understanding of persister biology and designing anti-persister therapeutics. IMPORTANCE Candida glabrata is a prevalent fungal pathogen able to replicate inside macrophages and rapidly develop resistance against frontline antifungal echinocandins. Multiple studies have shown that echinocandin resistance is fueled by the survival of a small subpopulation of susceptible cells surviving lethal concentrations of echinocandins. Importantly, bacterial pathogens that exhibit high antibiotic persistence also impose a high burden and generate more antibiotic-resistant colonies. Nonetheless, the implications of echinocandin persistence (ECP) among the clinical isolates of C. glabrata have not been defined. Additionally, ECP level determination relies on a laborious and time-consuming method, which is prone to high variation. By exploiting in vivo systemic infection and ex vivo models, we showed that C. glabrata isolates with a higher ECP are associated with a higher burden and more likely develop echinocandin resistance upon micafungin treatment. Additionally, we developed an assay that reliably determines ECP levels in real time. Therefore, our study identified C. glabrata isolates displaying high ECP levels as important entities and provided a reliable and convenient tool for measuring echinocandin persistence, which is extendable to other fungal and bacterial pathogens.
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Affiliation(s)
- Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel J. Floyd
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Mostafa Salehi
- Department Industrial Engineering Faculty of K.N., Toosi University of Technology, Tehran, Iran
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, District of Columbia, USA
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Türkiye
| | - Cornelia Lass-Flöerl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Innsbruck, Austria
| | - Michael K. Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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3
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Arastehfar A, Daneshnia F, Hovhannisyan H, Fuentes D, Cabrera N, Quinteros C, Ilkit M, Ünal N, Hilmioğlu-Polat S, Jabeen K, Zaka S, Desai JV, Lass-Flörl C, Shor E, Gabaldon T, Perlin DS. Overlooked Candida glabrata petites are echinocandin tolerant, induce host inflammatory responses, and display poor in vivo fitness. mBio 2023; 14:e0118023. [PMID: 37772846 PMCID: PMC10653939 DOI: 10.1128/mbio.01180-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/04/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Candida glabrata is a major fungal pathogen, which is able to lose mitochondria and form small and slow-growing colonies, called "petite." This attenuated growth rate has created controversies and questioned the clinical importance of petiteness. Herein, we have employed multiple omics technologies and in vivo mouse models to critically assess the clinical importance of petite phenotype. Our WGS identifies multiple genes potentially underpinning petite phenotype. Interestingly, petite C. glabrata cells engulfed by macrophages are dormant and, therefore, are not killed by the frontline antifungal drugs. Interestingly, macrophages infected with petite cells mount distinct transcriptomic responses. Consistent with our ex vivo observations, mitochondrial-proficient parental strains outcompete petites during systemic and gut colonization. Retrospective examination of C. glabrata isolates identified petite prevalence a rare entity, which can significantly vary from country to country. Collectively, our study overcomes the existing controversies and provides novel insights regarding the clinical relevance of petite C. glabrata isolates.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - Hrant Hovhannisyan
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diego Fuentes
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nathaly Cabrera
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Nevzat Ünal
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | | | - Kauser Jabeen
- Department of Pathology & Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sadaf Zaka
- Department of Pathology & Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Jigar V. Desai
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | | | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Toni Gabaldon
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA
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4
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Daneshnia F, Arastehfar A, Lombardi L, Binder U, Scheler J, Vahedi Shahandashti R, Hagen F, Lass-Flörl C, Mansour MK, Butler G, Perlin DS. Candida parapsilosis isolates carrying mutations outside FKS1 hotspot regions confer high echinocandin tolerance and facilitate the development of echinocandin resistance. Int J Antimicrob Agents 2023; 62:106831. [PMID: 37121442 DOI: 10.1016/j.ijantimicag.2023.106831] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/05/2023] [Accepted: 04/24/2023] [Indexed: 05/02/2023]
Abstract
Candida parapsilosis is a significant cause of candidemia worldwide. Echinocandin-resistant (ECR) and echinocandin-tolerant (ECT) C. parapsilosis isolates have been reported in various countries but are rare. Resistance and tolerance are predominantly caused by mutations related to the hotspot (HS) regions of the FKS1 gene. A relatively high proportion of clinical C. parapsilosis isolates carrying mutations outside the HS regions has been noted in some studies, but an association with echinocandin (EC) resistance or tolerance was not explored. Herein, CRISPR-Cas9 was used and the association between amino acid substitution in FKS1 outside HS 1/2 (V595I, S745L, M1328I, F1386S, and A1422G) with EC susceptibility profile was delineated. None of the mutations conferred EC resistance, but they resulted in a significantly higher level of EC tolerance than the parental isolate, ATCC 22019. When incubated on agar plates containing ECs, specifically caspofungin and micafungin, ECR colonies were exclusively observed among ECT isolates, particularly mutants carrying V595I, S745L, and F1386S. Additionally, mutants had significantly better growth rates in yeast extract peptone dextrose (YPD) and YPD containing agents inducing membrane and oxidative stresses. The mutants had a trivial fitness cost in the Galleria mellonella model relative to ATCC 22019. Collectively, this study supports epidemiological studies to catalog mutations occurring outside the HS regions of FKS1, even if they do not confer EC resistance. These mutations are important as they potentially confer a higher level of EC tolerance and a higher propensity to develop EC resistance, therefore unveiling a novel mechanism of EC tolerance in C. parapsilosis. The identification of EC tolerance in C. parapsilosis may have direct clinical benefit in patient management.
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Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA; Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, 1012 WX, The Netherlands
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Ulrike Binder
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Jakob Scheler
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Roya Vahedi Shahandashti
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Ferry Hagen
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, 1012 WX, The Netherlands; Westerdijk Fungal Biodiversity Institute, Utrecht, 3584CT, The Netherlands; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, 3584CX, The Netherlands
| | - Cornelia Lass-Flörl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Michael K Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA; Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, 1012 WX, The Netherlands
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA; Hackensack Meridian School of Medicine, Nutley, NJ 07710, USA; Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, 20057, USA.
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5
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Arastehfar A, Daneshnia F, Hovhannisyan H, Fuentes D, Cabrera N, Quintin C, Ilkit M, Ünal N, Hilmioğlu-Polat S, Jabeen K, Zaka S, Desai JV, Lass-Flörl C, Shor E, Gabaldon T, Perlin DS. Overlooked Candida glabrata petites are echinocandin tolerant, induce host inflammatory responses, and display poor in vivo fitness. bioRxiv 2023:2023.06.15.545195. [PMID: 37398397 PMCID: PMC10312775 DOI: 10.1101/2023.06.15.545195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Small colony variants (SCVs) are relatively common among some bacterial species and are associated with poor prognosis and recalcitrant infections. Similarly, Candida glabrata - a major intracellular fungal pathogen - produces small and slow-growing respiratory-deficient colonies, termed "petite." Despite reports of clinical petite C . glabrata strains, our understanding of petite behavior in the host remains obscure. Moreover, controversies exist regarding in-host petite fitness and its clinical relevance. Herein, we employed whole-genome sequencing (WGS), dual-RNAseq, and extensive ex vivo and in vivo studies to fill this knowledge gap. WGS identified multiple petite-specific mutations in nuclear and mitochondrially-encoded genes. Consistent with dual-RNAseq data, petite C . glabrata cells did not replicate inside host macrophages and were outcompeted by their non-petite parents in macrophages and in gut colonization and systemic infection mouse models. The intracellular petites showed hallmarks of drug tolerance and were relatively insensitive to the fungicidal activity of echinocandin drugs. Petite-infected macrophages exhibited a pro-inflammatory and type I IFN-skewed transcriptional program. Interrogation of international C . glabrata blood isolates ( n =1000) showed that petite prevalence varies by country, albeit at an overall low prevalence (0-3.5%). Collectively, our study sheds new light on the genetic basis, drug susceptibility, clinical prevalence, and host-pathogen responses of a clinically overlooked phenotype in a major fungal pathogen. Importance Candida glabrata is a major fungal pathogen, which is able to lose mitochondria and form small and slow-growing colonies, called "petite". This attenuated growth rate has created controversies and questioned the clinical importance of petiteness. Herein, we have employed multiple omicstechnologies and in vivo mouse models to critically assess the clinical importance of petite phenotype. Our WGS identifies multiple genes potentially underpinning petite phenotype. Interestingly, petite C. glabrata cells engulfed by macrophages are dormant and therefore are not killed by the frontline antifungal drugs. Interestingly, macrophages infected with petite cells mount distinct transcriptomic responses. Consistent with our ex-vivo observations, mitochondrial-proficient parental strains outcompete petites during systemic and gut colonization. Retrospective examination of C. glabrata isolates identified petite prevalence a rare entity, can significantly vary from country to country. Collectively, our study overcomes the existing controversies and provides novel insights regarding the clinical relevance of petite C. glabrata isolates.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam1012 WX, The Netherlands
| | - Hrant Hovhannisyan
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diego Fuentes
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nathaly Cabrera
- Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Nevzat Ünal
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | | | - Kauser Jabeen
- Department of Pathology & Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sadaf Zaka
- Department of Pathology & Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Jigar V. Desai
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | | | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Department of Medical Sciences, Hackensack School of Medicine, Nutley, New Jersey, USA
| | - Toni Gabaldon
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Department of Medical Sciences, Hackensack School of Medicine, Nutley, New Jersey, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Washington DC 20057, USA
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6
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Daneshnia F, de Almeida Júnior JN, Ilkit M, Lombardi L, Perry AM, Gao M, Nobile CJ, Egger M, Perlin DS, Zhai B, Hohl TM, Gabaldón T, Colombo AL, Hoenigl M, Arastehfar A. Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap. Lancet Microbe 2023; 4:e470-e480. [PMID: 37121240 PMCID: PMC10634418 DOI: 10.1016/s2666-5247(23)00067-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 05/02/2023]
Abstract
Candida parapsilosis is one of the most commen causes of life-threatening candidaemia, particularly in premature neonates, individuals with cancer of the haematopoietic system, and recipients of organ transplants. Historically, drug-susceptible strains have been linked to clonal outbreaks. However, worldwide studies started since 2018 have reported severe outbreaks among adults caused by fluconazole-resistant strains. Outbreaks caused by fluconazole-resistant strains are associated with high mortality rates and can persist despite strict infection control strategies. The emergence of resistance threatens the efficacy of azoles, which is the most widely used class of antifungals and the only available oral treatment option for candidaemia. The fact that most patients infected with fluconazole-resistant strains are azole-naive underscores the high potential adaptability of fluconazole-resistant strains to diverse hosts, environmental niches, and reservoirs. Another concern is the multidrug-resistant and echinocandin-tolerant C parapsilosis isolates, which emerged in 2020. Raising awareness, establishing effective clinical interventions, and understanding the biology and pathogenesis of fluconazole-resistant C parapsilosis are urgently needed to improve treatment strategies and outcomes.
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Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - João N de Almeida Júnior
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil; Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Türkiye
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Austin M Perry
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA; Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
| | - Marilyn Gao
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA; Health Sciences Research Institute, University of California Merced, Merced, CA, USA
| | - Matthias Egger
- Division of Infectious Diseases, ECMM Excellence Center, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; Department of Medical Sciences, Hackensack School of Medicine, Nutley, NJ, USA; Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Bing Zhai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine and Human Oncology, and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Toni Gabaldón
- Life Sciences Programme, Supercomputing Center, Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Barcelona, Spain
| | - Arnaldo Lopes Colombo
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Martin Hoenigl
- Division of Infectious Diseases, ECMM Excellence Center, Department of Internal Medicine, Medical University of Graz, Graz, Austria; Bio TechMed, Graz, Austria; Translational Medical Mycology Research Group, Medical University of Graz, Graz, Austria.
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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7
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Daneshnia F, Hilmioğlu-Polat S, Ilkit M, Fuentes D, Lombardi L, Binder U, Scheler J, Hagen F, Mansour MK, Butler G, Lass-Flörl C, Gabaldon T, Arastehfar A. Whole-genome sequencing confirms a persistent candidaemia clonal outbreak due to multidrug-resistant Candida parapsilosis. J Antimicrob Chemother 2023:7143692. [PMID: 37100456 DOI: 10.1093/jac/dkad112] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/24/2023] [Indexed: 04/28/2023] Open
Abstract
OBJECTIVES Although perceived as a rare clinical entity, recent studies have noted the emergence of MDR C. parapsilosis (MDR-Cp) isolates from single patients (resistant to both azole and echinocandins). We previously reported a case series of MDR-Cp isolates carrying a novel FKS1R658G mutation. Herein, we identified an echinocandin-naive patient infected with MDR-Cp a few months after the previously described isolates. WGS and CRISPR-Cas9 editing were used to explore the origin of the new MDR-Cp isolates, and to determine if the novel mutation confers echinocandin resistance. METHODS WGS was applied to assess the clonality of these isolates and CRISPR-Cas9 editing and a Galleria mellonella model were used to examine whether FKS1R658G confers echinocandin resistance. RESULTS Fluconazole treatment failed, and the patient was successfully treated with liposomal amphotericin B (LAMB). WGS proved that all historical and novel MDR-Cp strains were clonal and distant from the fluconazole-resistant outbreak cluster in the same hospital. CRISPR-Cas9 editing and G. mellonella virulence assays confirmed that FKS1R658G confers echinocandin resistance in vitro and in vivo. Interestingly, the FKS1R658G mutant showed a very modest fitness cost compared with the parental WT strain, consistent with the persistence of the MDR-Cp cluster in our hospital. CONCLUSIONS Our study showcases the emergence of MDR-Cp isolates as a novel threat in clinical settings, which undermines the efficacy of the two most widely used antifungal drugs against candidiasis, leaving only LAMB as a last resort. Additionally, surveillance studies and WGS are warranted to effectively establish infection control and antifungal stewardship strategies.
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Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, 1012 WX, The Netherlands
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Diego Fuentes
- Comparative Genomics group, Life Sciences department, Barcelona Supercomputing Center (BSC-CNS), Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
- Comparative Genomics group, Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Carrer Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Ulrike Binder
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Jakob Scheler
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Ferry Hagen
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, 1012 WX, The Netherlands
- Westerdijk Fungal Biodiversity Institute, Utrecht, 3584CT, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, 3584CX, The Netherlands
| | - Michael K Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115USA
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Cornelia Lass-Flörl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Toni Gabaldon
- Comparative Genomics group, Life Sciences department, Barcelona Supercomputing Center (BSC-CNS), Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
- Comparative Genomics group, Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Carrer Baldiri Reixac 10, 08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115USA
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8
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Arastehfar A, Daneshnia F, Cabrera N, Penalva-Lopez S, Sarathy J, Zimmerman M, Shor E, Perlin DS. Macrophage internalization creates a multidrug-tolerant fungal persister reservoir and facilitates the emergence of drug resistance. Nat Commun 2023; 14:1183. [PMID: 36864040 PMCID: PMC9981703 DOI: 10.1038/s41467-023-36882-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/22/2023] [Indexed: 03/04/2023] Open
Abstract
Candida glabrata is a major fungal pathogen notable for causing recalcitrant infections, rapid emergence of drug-resistant strains, and its ability to survive and proliferate within macrophages. Resembling bacterial persisters, a subset of genetically drug-susceptible C. glabrata cells can survive lethal exposure to the fungicidal echinocandin drugs. Herein, we show that macrophage internalization induces cidal drug tolerance in C. glabrata, expanding the persister reservoir from which echinocandin-resistant mutants emerge. We show that this drug tolerance is associated with non-proliferation and is triggered by macrophage-induced oxidative stress, and that deletion of genes involved in reactive oxygen species detoxification significantly increases the emergence of echinocandin-resistant mutants. Finally, we show that the fungicidal drug amphotericin B can kill intracellular C. glabrata echinocandin persisters, reducing emergence of resistance. Our study supports the hypothesis that intra-macrophage C. glabrata is a reservoir of recalcitrant/drug-resistant infections, and that drug alternating strategies can be developed to eliminate this reservoir.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, 1012 WX, The Netherlands
| | - Nathaly Cabrera
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Suyapa Penalva-Lopez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Jansy Sarathy
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Matthew Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA.
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA.
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA.
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA.
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, 20057, USA.
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9
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Daneshnia F, de Almeida Júnior JN, Arastehfar A, Lombardi L, Shor E, Moreno L, Mendes AV, Barberino MG, Yamamoto DT, Butler G, Perlin DS, Colombo AL. Determinants of fluconazole resistance and echinocandin tolerance in C. parapsilosis isolates causing a large clonal candidemia outbreak among COVID-19 patients in a Brazilian ICU. Emerg Microbes Infect 2022; 11:2264-2274. [PMID: 36066554 PMCID: PMC9542950 DOI: 10.1080/22221751.2022.2117093] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Patients presenting with severe COVID-19 are predisposed to acquire secondary fungal infections such as COVID-19-associated candidemia (CAC), which are associated with poor clinical outcomes despite antifungal treatment. The extreme burden imposed on clinical facilities during the COVID-19 pandemic has provided a permissive environment for the emergence of clonal outbreaks of multiple Candida species, including C. auris and C. parapsilosis. Here we report the largest clonal CAC outbreak to date caused by fluconazole resistant (FLZR) and echinocandin tolerant (ECT) C. parapsilosis. Sixty C. parapsilosis strains were obtained from 57 patients at a tertiary care hospital in Brazil, 90% of them were FLZR and ECT. Although only 35.8% of FLZR isolates contained an ERG11 mutation, all of them contained the TAC1L518F mutation and significantly overexpressed CDR1. Introduction of TAC1L518F into a susceptible background increased the MIC of fluconazole and voriconazole 8-fold and resulted in significant basal overexpression of CDR1. Additionally, FLZR isolates exclusively harbored E1939G outside of Fks1 hotspot-2, which did not confer echinocandin resistance, but significantly increased ECT. Multilocus microsatellite typing showed that 51/60 (85%) of the FLZR isolates belonged to the same cluster, while the susceptible isolates each represented a distinct lineage. Finally, biofilm production in FLZR isolates was significantly lower than in susceptible counterparts Suggesting that it may not be an outbreak determinant. In summary, we show that TAC1L518F and FKS1E1393G confer FLZR and ECT, respectively, in CAC-associated C. parapsilosis. Our study underscores the importance of antifungal stewardship and effective infection control strategies to mitigate clonal C. parapsilosis outbreaks.
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Affiliation(s)
- Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - João N de Almeida Júnior
- Special Mycology Laboratory, Federal University of São Paulo, Brazil.,Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.,Hackensack Meridian School of Medicine, Nutley NJ 07710, USA
| | - Lis Moreno
- Hospital São Rafael, Salvador, Brazil.,Instituto D'OR de Pesquisa e Ensino (IDOR)
| | - Ana Verena Mendes
- Hospital São Rafael, Salvador, Brazil.,Instituto D'OR de Pesquisa e Ensino (IDOR)
| | | | | | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.,Hackensack Meridian School of Medicine, Nutley NJ 07710, USA.,Georgetown University Lombardi Comprehensive Cancer Center, Washington DC 20057, USA
| | - Arnaldo Lopes Colombo
- Special Mycology Laboratory, Federal University of São Paulo, Brazil.,Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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10
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Daneshnia F, Hilmioğlu Polat S, Ilkit M, Shor E, de Almeida Júnior JN, Favarello LM, Colombo AL, Arastehfar A, Perlin DS. Determinants of fluconazole resistance and the efficacy of fluconazole and milbemycin oxim combination against Candida parapsilosis clinical isolates from Brazil and Turkey. Front Fungal Biol 2022; 3:906681. [PMID: 37746198 PMCID: PMC10512262 DOI: 10.3389/ffunb.2022.906681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/11/2022] [Indexed: 09/26/2023]
Abstract
Fluconazole-resistant Candida parapsilosis (FLZR-CP) outbreaks are a growing public health concern and have been reported in numerous countries. Patients infected with FLZR-CP isolates show fluconazole therapeutic failure and have a significantly increased mortality rate. Because fluconazole is the most widely used antifungal agent in most regions with outbreaks, it is paramount to restore its antifungal activity. Milbemycin oxim (MOX), a well-known canine endectocide, is a potent efflux pump inhibitor that significantly potentiates the activity of fluconazole against FLZR C. glabrata and C. albicans. However, the FLZ-MOX combination has not been tested against FLZR-CP isolates, nor is it known whether MOX may also potentiate the activity of echinocandins, a different class of antifungal drugs. Furthermore, the extent of involvement of efflux pumps CDR1 and MDR1 and ergosterol biosynthesis enzyme ERG11 and their link with gain-of-function (GOF) mutations in their transcription regulators (TAC1, MRR1, and UPC2) are poorly characterized among FLZR-CP isolates. We analyzed 25 C. parapsilosis isolates collected from outbreaks in Turkey and Brazil by determining the expression levels of CDR1, MDR1, and ERG11, examining the presence of potential GOF mutations in their transcriptional regulators, and assessing the antifungal activity of FLZ-MOX and micafungin-MOX against FLZR and multidrug-resistant (MDR) C. parapsilosis isolates. ERG11 was found to be universally induced by fluconazole in all isolates, while expression of MDR1 was unchanged. Whereas mutations in MRR1 and UPC2 were not detected, CDR1 was overexpressed in three Brazilian FLZR-CP isolates, which also carried a novel TAC1L518F mutation. Of these three isolates, one showed increased basal expression of CDR1, while the other two overexpressed CDR1 only in the presence of fluconazole. Interestingly, MOX showed promising antifungal activity against FLZR isolates, reducing the FLZ MIC 8- to 32-fold. However, the MOX and micafungin combination did not exert activity against an MDR C. parapsilosis isolate. Collectively, our study documents that the mechanisms underpinning FLZR are region specific, where ERG11 mutations were the sole mechanism of FLZR in Turkish FLZR-CP isolates, while simultaneous overexpression of CDR1 was observed in some Brazilian counterparts. Moreover, MOX and fluconazole showed potent synergistic activity, while the MOX-micafungin combination showed no synergy.
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Affiliation(s)
- Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Turkey
| | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Hackensack Meridian School of Medicine, Nutley, NJ, United States
| | - João Nobrega de Almeida Júnior
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Central (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Larissa M. Favarello
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Arnaldo Lopes Colombo
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Hackensack Meridian School of Medicine, Nutley, NJ, United States
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, United States
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11
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Arastehfar A, Ünal N, Hoşbul T, Özarslan MA, Karakoyun AS, Polat F, Fuentes D, Gümral R, Turunç T, Daneshnia F, Perlin DS, Lass-Flörl C, Gabaldón T, Ilkit M, Nguyen MH. Candidemia among COVID-19 patients in Turkey admitted to ICUs: A retrospective multicenter study. Open Forum Infect Dis 2022; 9:ofac078. [PMID: 35345665 PMCID: PMC8903397 DOI: 10.1093/ofid/ofac078] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Background We evaluated the epidemiology of candidemia among coronavirus disease 2019 (COVID-19) patients admitted to intensive care units (ICUs). Methods We conducted a retrospective multicenter study in Turkey between April and December 2020. Results Twenty-eight of 148 enrolled patients developed candidemia, yielding an incidence of 19% and incidence rate of 14/1000 patient-days. The probability of acquiring candidemia at 10, 20, and 30 days of ICU admission was 6%, 26%, and 50%, respectively. More than 80% of patients received antibiotics, corticosteroid, and mechanical ventilation. Receipt of a carbapenem (odds ratio [OR] = 6.0, 95% confidence interval [CI] = 1.6–22.3, P = .008), central venous catheter (OR = 4.3, 95% CI = 1.3–14.2, P = .02), and bacteremia preceding candidemia (OR = 6.6, 95% CI = 2.1–20.1, P = .001) were independent risk factors for candidemia. The mortality rate did not differ between patients with and without candidemia. Age (OR = 1.05, 95% CI = 1.01–1.09, P = .02) and mechanical ventilation (OR = 61, 95% CI = 15.8–234.9, P < .0001) were independent risk factors for death. Candida albicans was the most prevalent species overall. In Izmir, Candida parapsilosis accounted for 50% (2 of 4) of candidemia. Both C parapsilosis isolates were fluconazole nonsusceptible, harbored Erg11-Y132F mutation, and were clonal based on whole-genome sequencing. The 2 infected patients resided in ICUs with ongoing outbreaks due to fluconazole-resistant C parapsilosis. Conclusions Physicians should be aware of the elevated risk for candidemia among patients with COVID-19 who require ICU care. Prolonged ICU exposure and ICU practices rendered to COVID-19 patients are important contributing factors to candidemia. Emphasis should be placed on (1) heightened infection control in the ICU and (2) developing antibiotic stewardship strategies to reduce irrational antimicrobial therapy.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Nevzat Ünal
- University of Health Sciences, Adana City Training and Research Hospital, Laboratory of Medical Microbiology, Adana, 01370, Turkey
| | - Tuğrul Hoşbul
- Department of Microbiology, Gulhane Training and Research Hospital, University of Health Sciences, Ankara, 06010, Turkey
| | | | - Ayşe Sultan Karakoyun
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, 01330, Turkey
| | - Furkan Polat
- Department of Microbiology, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Diego Fuentes
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Jordi Girona, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ramazan Gümral
- Department of Microbiology, Gulhane Training and Research Hospital, University of Health Sciences, Ankara, 06010, Turkey
| | - Tuba Turunç
- University of Health Sciences, Adana Faculty of Medicine, Adana City Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Adana, 01370, Turkey
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Toni Gabaldón
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Jordi Girona, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, 01330, Turkey
| | - M Hong Nguyen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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12
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Arastehfar A, Marcet-Houben M, Daneshnia F, Taj-Aldeen S, Batra D, Lockhart S, Shor E, Gabaldón T, Perlin D. Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy. Stud Mycol 2021; 100:100133. [PMID: 34909054 PMCID: PMC8640552 DOI: 10.1016/j.simyco.2021.100133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Candida glabrata is the second leading cause of candidemia in many countries and is one of the most concerning yeast species of nosocomial importance due to its increasing rate of antifungal drug resistance and emerging multidrug-resistant isolates. Application of multilocus sequence typing (MLST) to clinical C. glabrata isolates revealed an association of certain sequence types (STs) with drug resistance and mortality. The current C. glabrata MLST scheme is based on single nucleotide polymorphisms (SNPs) at six loci and is therefore relatively laborious and costly. Furthermore, only a few high-quality C. glabrata reference genomes are available, limiting rapid analysis of clinical isolates by whole genome sequencing. In this study we provide long-read based assemblies for seven additional clinical strains belonging to three different STs and use this information to simplify the C. glabrata MLST scheme. Specifically, a comparison of these genomes identified highly polymorphic loci (HPL) defined by frequent insertions and deletions (indels), two of which proved to be highly resolutive for ST. When challenged with 53 additional isolates, a combination of TRP1 (a component of the current MLST scheme) with either of the two HPL fully recapitulated ST identification. Therefore, our comparative genomic analysis identified a new typing approach combining SNPs and indels and based on only two loci, thus significantly simplifying ST identification in C. glabrata. Because typing tools are instrumental in addressing numerous clinical and biological questions, our new MLST scheme can be used for high throughput typing of C. glabrata in clinical and research settings.
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Affiliation(s)
- A. Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - M. Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - F. Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | | | - D. Batra
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - S.R. Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - E. Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
- Hackensack Meridian Health School of Medicine, Nutley, NJ, 07710, USA
| | - T. Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - D.S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
- Hackensack Meridian Health School of Medicine, Nutley, NJ, 07710, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Department of Microbiology and Immunology, Washington, DC, 20057, USA
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13
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Hafez A, Futami R, Arastehfar A, Daneshnia F, Miguel A, Roig FJ, Soriano B, Perez-Sánchez J, Boekhout T, Gabaldón T, Llorens C. SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files. Bioinformatics 2021; 37:1610-1612. [PMID: 33079985 DOI: 10.1093/bioinformatics/btaa903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/07/2020] [Accepted: 10/07/2020] [Indexed: 12/27/2022] Open
Abstract
MOTIVATION Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user's expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences' analysis. RESULT SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets. AVAILABILITYAND IMPLEMENTATION SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ahmed Hafez
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Faculty of Computers and Information, Minia University, Minia, Egypt
| | - Ricardo Futami
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | - Amir Arastehfar
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Farnaz Daneshnia
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana Miguel
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | - Francisco J Roig
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain.,Facultad de Ciencias de la Salud, Universidad San Jorge, Zaragoza, Spain
| | - Beatriz Soriano
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | | | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Toni Gabaldón
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carlos Llorens
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
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14
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Arastehfar A, Daneshnia F, Hilmioglu-Polat S, Ilkit M, Yasar M, Polat F, Metin DY, Dokumcu ÜZ, Pan W, Hagen F, Boekhout T, Perlin DS, Lass-Flörl C. Genetically related micafungin-resistant Candida parapsilosis blood isolates harbouring novel mutation R658G in hotspot 1 of Fks1p: a new challenge? J Antimicrob Chemother 2021; 76:418-422. [PMID: 33175162 DOI: 10.1093/jac/dkaa419] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Echinocandin resistance rarely occurs in clinical Candida parapsilosis isolates and the underlying mechanism is unknown. OBJECTIVES To determine the prevalence of echinocandin resistance and the underlying mechanism for a large collection of C. parapsilosis blood isolates and to determine whether the echinocandin-resistant isolates were clonally related. METHODS C. parapsilosis blood isolates (n = 213) were subjected to antifungal susceptibility testing (CLSI M27), for micafungin, anidulafungin, amphotericin B and, if appropriate, caspofungin. Hotspot (HS) 1 and HS2 of FKS1 were sequenced for all isolates (n = 213) and microsatellite typing was performed for echinocandin-resistant isolates. RESULTS All isolates were susceptible to amphotericin B and two isolates were intermediate to anidulafungin (MIC = 4 mg/L), while micafungin resistance was noted in four isolates (MIC >8 mg/L); three of which were also fluconazole resistant and therefore were MDR. Interestingly, micafungin-resistant isolates, but not those intermediate to anidulafungin, carried novel mutation R658G in HS1 of Fks1p; three of which also harboured Y132F+K143R in Erg11. The first isolate (MICR1) was recovered in November 2017 from a patient admitted to paediatric gastroenterology who showed therapeutic failure under caspofungin treatment. MICR2-MICR4 were collected during 2018-19 and were recovered from three echinocandin-naive paediatric-surgery patients; the isolates shared the same genotype. CONCLUSIONS Herein, for the first time (to the best of our knowledge), we identified micafungin-resistant C. parapsilosis blood isolates harbouring a novel mutation in HS1 of FKS1, which was likely attributable to in vitro micafungin resistance and in vivo caspofungin therapeutic failure. The acquisition of micafungin-resistant C. parapsilosis isolates in echinocandin-naive patients likely implicates clonal expansion, as supported by the close genetic relatedness of MICR2-MICR4.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | | | - Macit Ilkit
- Divison of Mycology, University of Çukurova, Adana, Turkey
| | - Melike Yasar
- Division of Mycology, University of Ege, Izmir, Turkey
| | - Furkan Polat
- Division of Mycology, University of Ege, Izmir, Turkey
| | | | - Ülküm Zafer Dokumcu
- Department of Paediatric Surgery, Faculty of Medicine, University of Ege, Izmir, Turkey
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,University Medical Center Utrecht, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Paediatric Surgery, Faculty of Medicine, University of Ege, Izmir, Turkey.,Institute of Biodiversity and Ecosystems Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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15
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Arastehfar A, Daneshnia F, Hafez A, Khodavaisy S, Najafzadeh MJ, Charsizadeh A, Zarrinfar H, Salehi M, Shahrabadi ZZ, Sasani E, Zomorodian K, Pan W, Hagen F, Ilkit M, Kostrzewa M, Boekhout T. Antifungal susceptibility, genotyping, resistance mechanism, and clinical profile of Candida tropicalis blood isolates. Med Mycol 2021; 58:766-773. [PMID: 31828316 PMCID: PMC7398758 DOI: 10.1093/mmy/myz124] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Candida tropicalis is one of the major candidaemia agents, associated with the highest mortality rates among Candida species, and developing resistance to azoles. Little is known about the molecular mechanisms of azole resistance, genotypic diversity, and the clinical background of C. tropicalis infections. Consequently, this study was designed to address those questions. Sixty-four C. tropicalis bloodstream isolates from 62 patients from three cities in Iran (2014–2019) were analyzed. Strain identification, antifungal susceptibility testing, and genotypic diversity analysis were performed by MALDI-TOF MS, CLSI-M27 A3/S4 protocol, and amplified fragment length polymorphism (AFLP) fingerprinting, respectively. Genes related to drug resistance (ERG11, MRR1, TAC1, UPC2, and FKS1 hotspot9s) were sequenced. The overall mortality rate was 59.6% (37/62). Strains were resistant to micafungin [minimum inhibitory concentration (MIC) ≥1 μg/ml, 2/64], itraconazole (MIC > 0.5 μg/ml, 2/64), fluconazole (FLZ; MIC ≥ 8 μg/ml, 4/64), and voriconazole (MIC ≥ 1 μg/ml, 7/64). Pan-azole and FLZ + VRZ resistance were observed in one and two isolates, respectively, while none of the patients were exposed to azoles. MRR1 (T255P, 647S), TAC1 (N164I, R47Q), and UPC2 (T241A, Q340H, T381S) mutations were exclusively identified in FLZ-resistant isolates. AFLP fingerprinting revealed five major and seven minor genotypes; genotype G4 was predominant in all centers. The increasing number of FLZ-R C. tropicalis blood isolates and acquiring FLZ-R in FLZ-naive patients limit the efficiency of FLZ, especially in developing countries. The high mortality rate warrants reaching a consensus regarding the nosocomial mode of C. tropicalis transmission.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | | | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arezoo Charsizadeh
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammadreza Salehi
- Department of infectious diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Zare Shahrabadi
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elahe Sasani
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Weihua Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | | | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam1012 WX, The Netherlands
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16
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Arastehfar A, Kargar ML, Mohammadi SR, Roudbary M, Ghods N, Haghighi L, Daneshnia F, Tavakoli M, Jafarzadeh J, Hedayati MT, Wang H, Fang W, Carvalho A, Ilkit M, Perlin DS, Lass-Flörl C. A High Rate of Recurrent Vulvovaginal Candidiasis and Therapeutic Failure of Azole Derivatives Among Iranian Women. Front Microbiol 2021; 12:655069. [PMID: 33995315 PMCID: PMC8113757 DOI: 10.3389/fmicb.2021.655069] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Recurrent vulvovaginal candidiasis (RVVC) is one of the most prevalent fungal infections in humans, especially in developing countries; however, it is underestimated and regarded as an easy-to-treat condition. RVVC may be caused by dysbiosis of the microbiome and other host-, pathogen-, and antifungal drug-related factors. Although multiple studies on host-related factors affecting the outcome have been conducted, such studies on Candida-derived factors and their association with RVVC are lacking. Thus, fluconazole-tolerant (FLZT) isolates may cause fluconazole therapeutic failure (FTF), but this concept has not been assessed in the context of Candida-associated vaginitis. Iran is among the countries with the highest burden of RVVC; however, comprehensive studies detailing the clinical and microbiological features of this complication are scarce. Therefore, we conducted a 1-year prospective study with the aim to determine the RVVC burden among women referred to a gynecology hospital in Tehran, the association of the previous exposure to clotrimazole and fluconazole with the emergence of FLZT and fluconazole-resistant (FLZR) Candida isolates, and the relevance of these phenotypes to FTF. The results indicated that about 53% of the patients (43/81) experienced RVVC. Candida albicans and C. glabrata constituted approximately 90% of the yeast isolates (72 patients). Except for one FLZT C. tropicalis isolate, FLZR and FLZT phenotypes were detected exclusively in patients with RVVC; among them, 27.9% (12/43) harbored FLZR strains. C. albicans constituted 81.2% of FLZR (13/16) and 100% of the FLZT (13/13) isolates, respectively, and both phenotypes were likely responsible for FTF, which was also observed among patients with RVVC infected with fluconazole-susceptible isolates. Thus, FTF could be due to host-, drug-, and pathogen-related characteristics. Our study indicates that FLZT and FLZR isolates may arise following the exposure to over-the-counter (OTC) topical azole (clotrimazole) and that both phenotypes can cause FTF. Therefore, the widespread use of OTC azoles can influence fluconazole therapeutic success, highlighting the necessity of controlling the use of weak topical antifungals among Iranian women.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Melika Laal Kargar
- Department of Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | | | - Maryam Roudbary
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nayereh Ghods
- Department of Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Ladan Haghighi
- Department of Obstetrics and Gynecology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Mahin Tavakoli
- Department of Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Jalal Jafarzadeh
- Department of Medical Mycology and Parasitology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Taghi Hedayati
- Invasive Fungi Research Center, Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Huiwei Wang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Macit Ilkit
- Division of Mycology, University of Çukurova, Adana, Turkey
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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17
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Arastehfar A, Hilmioğlu-Polat S, Daneshnia F, Pan W, Hafez A, Fang W, Liao W, Şahbudak-Bal Z, Metin DY, Júnior JNDA, Ilkit M, Perlin DS, Lass-Flörl C. Clonal Candidemia Outbreak by Candida parapsilosis Carrying Y132F in Turkey: Evolution of a Persisting Challenge. Front Cell Infect Microbiol 2021; 11:676177. [PMID: 33968809 PMCID: PMC8101544 DOI: 10.3389/fcimb.2021.676177] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
As the second leading etiological agent of candidemia in Turkey and the cause of severe fluconazole-non-susceptible (FNS) clonal outbreaks, Candida parapsilosis emerged as a major health threat at Ege University Hospital (EUH). Evaluation of microbiological and pertinent clinical profiles of candidemia patients due to C. parapsilosis in EUH in 2019–2020. Candida parapsilosis isolates were collected from blood samples and identified by sequencing internal transcribed spacer ribosomal DNA. Antifungal susceptibility testing was performed in accordance with CLSI M60 protocol and ERG11 and HS1/HS2-FKS1 were sequenced to explore the fluconazole and echinocandin resistance, respectively. Isolates were typed using a multilocus microsatellite typing assay. Relevant clinical data were obtained for patients recruited in the current study. FNS C. parapsilosis isolates were recovered from 53% of the patients admitted to EUH in 2019–2020. Y132F was the most frequent mutation in Erg11. All patients infected with C. parapsilosis isolates carrying Y132F, who received fluconazole showed therapeutic failure and significantly had a higher mortality than those infected with other FNS and susceptible isolates (50% vs. 16.1%). All isolates carrying Y132F grouped into one major cluster and mainly recovered from patients admitted to chest diseases and pediatric surgery wards. The unprecedented increase in the number of Y132F C. parapsilosis, which corresponded with increased rates of fluconazole therapeutic failure and mortality, is worrisome and highlights the urgency for strict infection control strategies, antifungal stewardship, and environmental screening in EUH.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Suleyha Hilmioğlu-Polat
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Ege, Izmir, Turkey
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Dilek Yeşim Metin
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Ege, Izmir, Turkey
| | - João N de Almeida Júnior
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil.,Laboratório Central (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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18
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Arastehfar A, Khanjari S, Zareshahrabadi Z, Fang W, Pan W, Asadpour E, Daneshnia F, Ilkit M, Boekhout T, Perlin DS, Zand F, Zomorodian K. Clinical and microbiological features of candiduria in critically ill adult patients in Shiraz, Iran (2016-2018): deviations from international guidelines and fluconazole therapeutic failure. Med Mycol 2020; 59:myaa092. [PMID: 33305331 DOI: 10.1093/mmy/myaa092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Abstract
Candiduria is common among patients admitted to intensive care units (ICUs); however, clinical and microbiological data are limited, which accounts for non-compliance with international guidelines, including over treatment of asymptomatic candiduria that promotes antifungal resistance. This prospective study included adult patients admitted to ICUs of five referral hospitals in Shiraz, Iran, during 2016-2018. Species were identified by MALDI-TOF MS, and antifungal susceptibility was assessed according to CLSI M27-A3/S4. Among 2086 patients, 162 and 293 developed candiduria and bacteriuria, respectively. In total, 174 yeast isolates were collected; 88.5% were Candida albicans (91/174; 52.2%), C. glabrata (38/174; 21.8%), and C. tropicalis (25/174; 14.3%). Antifungal resistance was rare; only two isolates (one C. tropicalis and one C. krusei) were fluconazole resistant. Symptomatic candiduria was noted in 31.4% of patients (51/162); only 37% (19/51) of them were treated and 36.82% (7/19) showed fluconazole therapeutic failure. Two symptomatic patients developed candidemia shortly after candiduria. Among asymptomatic patients, 31.5% (35/111) were overtreated with fluconazole. The mortality rate was 25.3% (41/162); it did not differ between symptomatic and asymptomatic patients. Our results indicate that deviation from standard-of-care treatment for candiduria is a matter of concern given the high rate of fluconazole therapeutic failure among patients with symptomatic candiduria. LAY SUMMARY Candiduria is an underestimated clinical presentation among critically ill patients and detailed data are scarce in this regard. Given the high rate of fluconazole therapeutic failure and development of candidemia in some cases, the mistreatment of candiduria should not be overlooked by clinicians.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Sara Khanjari
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Zareshahrabadi
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Wenjie Fang
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Elham Asadpour
- Shiraz Anesthesiology and Critical Care Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Teun Boekhout
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystems Dynamics (IBED, University of Amsterdam, Amsterdam, The Netherlands
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Farid Zand
- Shiraz Anesthesiology and Critical Care Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Anesthesia and Critical Care Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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19
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Arastehfar A, Hilmioğlu-Polat S, Daneshnia F, Hafez A, Salehi M, Polat F, Yaşar M, Arslan N, Hoşbul T, Ünal N, Metin DY, Gürcan Ş, Birinci A, Koç AN, Pan W, Ilkit M, Perlin DS, Lass-Flörl C. Recent Increase in the Prevalence of Fluconazole-Non-susceptible Candida tropicalis Blood Isolates in Turkey: Clinical Implication of Azole-Non-susceptible and Fluconazole Tolerant Phenotypes and Genotyping. Front Microbiol 2020; 11:587278. [PMID: 33123116 PMCID: PMC7573116 DOI: 10.3389/fmicb.2020.587278] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022] Open
Abstract
Candida tropicalis is the fourth leading cause of candidemia in Turkey. Although C. tropicalis isolates from 1997 to 2017 were characterized as fully susceptible to antifungals, the increasing global prevalence of azole-non-susceptible (ANS) C. tropicalis and the association between high fluconazole tolerance (HFT) and fluconazole therapeutic failure (FTF) prompted us to re-evaluate azole susceptibility of C. tropicalis in Turkey. In this study, 161 C. tropicalis blood isolates from seven clinical centers were identified by ITS rDNA sequencing, genotyped by multilocus microsatellite typing, and tested for susceptibility to five azoles, two echinocandins, and amphotericin B (AMB); antifungal resistance mechanisms were assessed by sequencing of ERG11 and FKS1 genes. The results indicated that C. tropicalis isolates, which belonged to 125 genotypes grouped into 11 clusters, were fully susceptible to echinocandins and AMB; however, 18.6% of them had the ANS phenotype but only two carried the ANS-conferring mutation (Y132F). HFT was recorded in 52 isolates, 10 of which were also ANS. Large proportions of patients infected with ANS and HFT isolates (89 and 40.7%, respectively) showed FTF. Patients infected with azole-susceptible or ANS isolates did not differ in mortality, which, however, was significantly lower for those infected with HFT isolates (P = 0.007). There were significant differences in mortality (P = 0.02), ANS (P = 0.012), and HFT (P = 0.007) among genotype clusters. The alarming increase in the prevalence of C. tropicalis blood isolates with ANS and HFT in Turkey and the notable FTF rate should be a matter of public health concern.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | | | | | | | - Mohammadreza Salehi
- Department of Infectious Diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Furkan Polat
- Department of Microbiology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Melike Yaşar
- Department of Microbiology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Nazlı Arslan
- Department of Microbiology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Tuğrul Hoşbul
- Department of Microbiology, Gulhane Training and Research Hospital, University of Health Sciences, Ankara, Turkey
| | - Nevzat Ünal
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Turkey.,Department of Microbiology, Adana City Hospital, University of Health Sciences, Adana, Turkey
| | - Dilek Yeşim Metin
- Department of Microbiology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Şaban Gürcan
- Department of Microbiology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Asuman Birinci
- Department of Microbiology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Ayşe Nedret Koç
- Department of Microbiology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Turkey
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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20
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Arastehfar A, Lass-Flörl C, Garcia-Rubio R, Daneshnia F, Ilkit M, Boekhout T, Gabaldon T, Perlin DS. The Quiet and Underappreciated Rise of Drug-Resistant Invasive Fungal Pathogens. J Fungi (Basel) 2020; 6:E138. [PMID: 32824785 PMCID: PMC7557958 DOI: 10.3390/jof6030138] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/22/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Human fungal pathogens are attributable to a significant economic burden and mortality worldwide. Antifungal treatments, although limited in number, play a pivotal role in decreasing mortality and morbidities posed by invasive fungal infections (IFIs). However, the recent emergence of multidrug-resistant Candida auris and Candida glabrata and acquiring invasive infections due to azole-resistant C. parapsilosis, C. tropicalis, and Aspergillus spp. in azole-naïve patients pose a serious health threat considering the limited number of systemic antifungals available to treat IFIs. Although advancing for major fungal pathogens, the understanding of fungal attributes contributing to antifungal resistance is just emerging for several clinically important MDR fungal pathogens. Further complicating the matter are the distinct differences in antifungal resistance mechanisms among various fungal species in which one or more mechanisms may contribute to the resistance phenotype. In this review, we attempt to summarize the burden of antifungal resistance for selected non-albicansCandida and clinically important Aspergillus species together with their phylogenetic placement on the tree of life. Moreover, we highlight the different molecular mechanisms between antifungal tolerance and resistance, and comprehensively discuss the molecular mechanisms of antifungal resistance in a species level.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA;
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Rocio Garcia-Rubio
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA;
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (F.D.); (T.B.)
| | - Macit Ilkit
- Division of Mycology, University of Çukurova, 01330 Adana, Turkey;
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (F.D.); (T.B.)
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Toni Gabaldon
- Life Sciences Programme, Barcelona, Supercomputing Center (BSC-CNS), Jordi Girona, 08034 Barcelona, Spain;
- Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), 08024 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA;
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21
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Arastehfar A, Daneshnia F, Salehi M, Yaşar M, Hoşbul T, Ilkit M, Pan W, Hagen F, Arslan N, Türk-Dağı H, Hilmioğlu-Polat S, Perlin DS, Lass-Flörl C. Low level of antifungal resistance of Candida glabrata blood isolates in Turkey: Fluconazole minimum inhibitory concentration and FKS mutations can predict therapeutic failure. Mycoses 2020; 63:911-920. [PMID: 32413170 PMCID: PMC7497236 DOI: 10.1111/myc.13104] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/25/2020] [Accepted: 05/02/2020] [Indexed: 12/26/2022]
Abstract
Background Candida glabrata is the third leading cause of candidaemia in Turkey; however, the data regarding antifungal resistance mechanisms and genotypic diversity in association with their clinical implication are limited. Objectives To assess genotypic diversity, antifungal susceptibility and mechanisms of drug resistance of Cglabrata blood isolates and their association with patients' outcome in a retrospective multicentre study. Patients/Methods Isolates from 107 patients were identified by ITS sequencing and analysed by multilocus microsatellite typing, antifungal susceptibility testing, and sequencing of PDR1 and FKS1/2 hotspots (HSs). Results Candida glabrata prevalence in Ege University Hospital was twofold higher in 2014‐2019 than in 2005‐2014. Six of the analysed isolates had fluconazole MICs ≥ 32 µg/mL; of them, five harboured unique PDR1 mutations. Although echinocandin resistance was not detected, three isolates had mutations in HS1‐Fks1 (S629T, n = 1) and HS1‐Fks2 (S663P, n = 2); one of the latter was also fluconazole‐resistant. All patients infected with isolates carrying HS‐FKS mutations and/or demonstrating fluconazole MIC ≥ 32 µg/mL (except one without clinical data) showed therapeutic failure (TF) with echinocandin and fluconazole; seven such isolates were collected in Ege (n = 4) and Gulhane (n = 3) hospitals and six detected recently. Among 34 identified genotypes, none were associated with mortality or enriched for fluconazole‐resistant isolates. Conclusion Antifungal susceptibility testing should be supplemented with HS‐FKS sequencing to predict TF for echinocandins, whereas fluconazole MIC ≥ 32 µg/mL may predict TF. Recent emergence of C glabrata isolates associated with antifungal TF warrants future comprehensive prospective studies in Turkey.
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Affiliation(s)
- Amir Arastehfar
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Farnaz Daneshnia
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Mohammadreza Salehi
- Department of Infectious Diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Melike Yaşar
- Department of Medical Microbiology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Tuğrul Hoşbul
- Department of Medical Microbiology, Gulhane Training and Research Hospital, University of Health Sciences, Ankara, Turkey
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Turkey
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,University Medical Center Utrecht, Utrecht, The Netherlands.,People's Hospital, Jining, China
| | - Nazlı Arslan
- Department of Medical Microbiology, Dokuz Eylül University Faculty of Medicine, Izmir, Turkey
| | - Hatice Türk-Dağı
- Department of Microbiology, Faculty of Medicine, Selcuk University, Konya, Turkey
| | | | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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22
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Arastehfar A, Yazdanpanah S, Bakhtiari M, Fang W, Pan W, Mahmoudi S, Pakshir K, Daneshnia F, Boekhout T, Ilkit M, Perlin DS, Zomorodian K, Zand F. Epidemiology of candidemia in Shiraz, southern Iran: A prospective multicenter study (2016-2018). Med Mycol 2020; 59:422-430. [PMID: 32692816 DOI: 10.1093/mmy/myaa059] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/21/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Systematic candidemia studies, especially in southern Iran, are scarce. In the current prospective study, we investigated candidemia in three major healthcare centers of Shiraz, the largest city in southern Iran. Yeast isolates from blood and other sterile body fluids were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and subjected to antifungal susceptibility testing (AFST) using the broth microdilution method. Clinical data were retrieved from patients' medical records. In total, 113 yeast isolates were recovered from 109 patients, over 60% of whom received fluconazole. Antifungal drugs were prescribed without considering species identification or AFST. The all-cause mortality rate was 28%. Almost 30% of the patients were from intensive care units (ICUs). Candida albicans (56/113; 49.5%) was the most prevalent species followed by C. glabrata (26/113; 23%), C. parapsilosis (13/113; 11.5%), C. tropicalis (7/113; 6.2%), and C. dubliniensis (5/113; 4.4%). Only five isolates showed antifungal resistance or decreased susceptibility to fluconazole: one C. orthopsilosis isolate from an azole-naïve patient and two C. glabrata, one C. albicans, and one C. dubliniensis isolates from patients treated with azoles, who developed therapeutic failure against azoles later. Our results revealed a low level of antifungal resistance but a notable rate of azole therapeutic failure among patients with candidemia due to non-albicans Candida species, which threaten the efficacy of fluconazole, the most widely used antifungal in southern regions of Iran. Candidemia studies should not be confined to ICUs and treatment should be administered based on species identification and AFST results.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Samira Yazdanpanah
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mina Bakhtiari
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Wenjie Fang
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Shahram Mahmoudi
- Department of Medical Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Keyvan Pakshir
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China.,Institute of Biodiversity and Ecosystems Dynamics (IBED, University of Amsterdam, Amsterdam, The Netherlands
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farid Zand
- Department of Anesthesia and Critical Care Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,Shiraz Anesthesiology and Critical Care Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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23
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Jiang M, Pan W, Arasthfer A, Fang W, Ling L, Fang H, Daneshnia F, Yu J, Liao W, Pei H, Li X, Lass-Flörl C. Development and Validation of a Rapid, Single-Step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) System Potentially to Be Used for Reliable and High-Throughput Screening of COVID-19. Front Cell Infect Microbiol 2020; 10:331. [PMID: 32626666 PMCID: PMC7313420 DOI: 10.3389/fcimb.2020.00331] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/29/2020] [Indexed: 11/13/2022] Open
Abstract
Objectives: Development and validation of a single-step and accurate reverse transcriptase loop-mediated isothermal amplification technique (RT-LAMP) for rapid identification of SARS-CoV-2 relative to commercial quantitative reverse transcriptase real-time PCR (qRT-PCR) assays to allow prompt initiation of proper medical care and containment of virus spread. Methods: Primers showing optimal in-silico features were subjected to analytical sensitivity and specificity to assess the limit of detection (LOD) and cross-reaction with closely- and distantly-related viral species, and clinically prominent bacterial and fungal species. In order to evaluate the clinical utility, our RT-LAMP was subjected to a large number of clinical samples, including 213 negative and 47 positive patients, relative to two commercial quantitative RT-PCR assays. Results: The analytical specificity and sensitivity of our assay was 100% and 500 copies/ml when serial dilution was performed in both water and sputum. Subjecting our RT-LAMP assay to clinical samples showed a high degree of specificity (99.5%), sensitivity (91.4%), positive predictive value (97.7%), and negative predictive value (98.1%) when used relative to qRT-PCR. Our RT-LAMP assay was two times faster than qRT-PCR and is storable at room temperature. A suspected case that later became positive tested positive using both our RT-LAMP and the two qRT-PCR assays, which shows the capability of our assay for screening purposes. Conclusions: We present a rapid RT-LAMP assay that could extend the capacity of laboratories to process two times more clinical samples relative to qRT-PCR and potentially could be used for high-throughput screening purposes when demand is increasing at critical situations.
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Affiliation(s)
- Minghua Jiang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Amir Arasthfer
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liyan Ling
- Department of Laboratory Medicine, Pinghu Second People's Hospital, Jiaxing, China
| | - Hua Fang
- Department of Laboratory Medicine, Pudong New Area People's Hospital, Shanghai, China
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hao Pei
- Department of Laboratory Medicine, Wuxi No. 5 People's Hospital, Wuxi, China
| | - Xiaojing Li
- Department of Dermatology, Affiliated Hospital of Hebei University of Engineering, Handan, China
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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24
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Arastehfar A, Daneshnia F, Najafzadeh MJ, Hagen F, Mahmoudi S, Salehi M, Zarrinfar H, Namvar Z, Zareshahrabadi Z, Khodavaisy S, Zomorodian K, Pan W, Theelen B, Kostrzewa M, Boekhout T, Lass-Flörl C. Evaluation of Molecular Epidemiology, Clinical Characteristics, Antifungal Susceptibility Profiles, and Molecular Mechanisms of Antifungal Resistance of Iranian Candida parapsilosis Species Complex Blood Isolates. Front Cell Infect Microbiol 2020; 10:206. [PMID: 32509592 PMCID: PMC7253641 DOI: 10.3389/fcimb.2020.00206] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/16/2020] [Indexed: 11/13/2022] Open
Abstract
Clonal expansion of fluconazole resistant (FLZ-R) Candida parapsilosis isolates is increasingly being identified in many countries, while there is no study exploring the antifungal susceptibility pattern, genetic diversity, and clinical information for Iranian C. parapsilosis blood isolates. Candida parapsilosis species complex blood isolates (n = 98) were recovered from nine hospitals located in three major cities, identified by MALDI-TOF MS, and their genetic relatedness was examined by AFLP fingerprinting. Antifungal susceptibility testing followed CLSI-M27-A3 and ERG11, MRR1 and hotspots 1/2 (HS1/2) of FKS1 were sequenced to assess the azole and echinocandin resistance mechanisms, respectively. Ninety-four C. parapsilosis and four Candida orthopsilosis isolates were identified from 90 patients. Only 43 patients received systemic antifungal drugs with fluconazole as the main antifungal used. The overall mortality rate was 46.6% (42/90) and death mostly occurred for those receiving systemic antifungals (25/43) relative to those not treated (17/47). Although, antifungal-resistance was rare, one isolate was multidrug-resistant (FLZ = 16 μg/ml and micafungin = 8 μg/ml) and the infected patient showed therapeutic failure to FLZ prophylaxis. Mutations causing azole and echinocandin resistance were not found in the genes studied. AFLP revealed five genotypes (G) and G1 was the main one (59/94; 62.7%). Clinical outcome was significantly associated with city (P = 0.02, α <0.05) and Mashhad was significantly associated with mortality (P = 0.03, α <0.05). Overall, we found a low level of antifungal resistance for Iranian C. parapsilosis blood isolates, but the noted MDR strain can potentially become the source of future infections and challenge the antifungal therapy in antifungal-naïve patients. AFLP typing results warrants confirmation using other resolutive typing methods.
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Affiliation(s)
- Amir Arastehfar
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ferry Hagen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Shahram Mahmoudi
- Department of Medical Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Salehi
- Department of Infectious Diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Namvar
- Department of Microbiology, School of Biological Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Zareshahrabadi
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Weihua Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Bart Theelen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | | | - Teun Boekhout
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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25
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Megri Y, Arastehfar A, Boekhout T, Daneshnia F, Hörtnagl C, Sartori B, Hafez A, Pan W, Lass-Flörl C, Hamrioui B. Candida tropicalis is the most prevalent yeast species causing candidemia in Algeria: the urgent need for antifungal stewardship and infection control measures. Antimicrob Resist Infect Control 2020; 9:50. [PMID: 32264966 PMCID: PMC7140370 DOI: 10.1186/s13756-020-00710-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/24/2020] [Indexed: 12/29/2022] Open
Abstract
Background Despite being associated with a high mortality and economic burden, data regarding candidemia are scant in Algeria. The aim of this study was to unveil the epidemiology of candidemia in Algeria, evaluate the antifungal susceptibility pattern of causative agents and understand the molecular mechanisms of antifungal resistance where applicable. Furthermore, by performing environmental screening and microsatellite typing we sought to identify the source of infection. Methods We performed a retrospective epidemiological-based surveillance study and collected available blood yeast isolates recovered from the seven hospitals in Algiers. To identify the source of infection, we performed environmental screening from the hands of healthcare workers (HCWs) and high touch areas. Species identification was performed by API Auxa-Color and MALDI-TOF MS and ITS sequencing was performed for species not reliably identified by MALDI-TOF MS. Antifungal susceptibility testing followed CLSI M27-A3/S4 and included all blood and environmental yeast isolates. ERG11 sequencing was performed for azole-resistant Candida isolates. Microsatellite typing was performed for blood and environmental Candida species, where applicable. Results Candida tropicalis (19/66) was the main cause of candidemia in these seven hospitals, followed by Candida parapsilosis (18/66), Candida albicans (18/66), and Candida glabrata (7/66). The overall mortality rate was 68.6% (35/51) and was 81.2% for C. tropicalis-infected patients (13/16). Fluconazole was the main antifungal drug used (12/51); 41% of the patients (21/51) did not receive any systemic treatment. Candida parapsilosis was isolated mainly from the hands of HCWs (7/28), and various yeasts were collected from high-touch areas (11/47), including Naganishia albida, C. parapsilosis and C. glabrata. Typing data revealed interhospital transmission on two occasions for C. parapsilosis and C. glabrata, and the same clone of C. parapsilosis infected two patients within the same hospital. Resistance was only noted for C. tropicalis against azoles (6/19) and fluconazole-resistant C. tropicalis isolates (≥8 μg/ml) (6/19) contained a novel P56S (5/6) amino acid substitution and a previously reported one (V234F; 1/6) in Erg11p. Conclusions Collectively, our data suggest an urgent need for antifungal stewardship and infection control strategies to improve the clinical outcome of Algerian patients with candidemia. The high prevalence of C. tropicalis joined by fluconazole-resistance may hamper the therapeutic efficacy of fluconazole, the frontline antifungal drug used in Algeria.
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Affiliation(s)
- Youcef Megri
- Parasitology and Mycology Department, Mustapha University Hospital, 16000, Algiers, Algeria
| | - Amir Arastehfar
- Yeast Department, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands. .,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands.
| | - Teun Boekhout
- Yeast Department, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Farnaz Daneshnia
- Yeast Department, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Caroline Hörtnagl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Sartori
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ahmed Hafez
- Biotechvana, 46980, Paterna, Valencia, Spain
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, 200003, China.
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Boussad Hamrioui
- Parasitology and Mycology Department, Mustapha University Hospital, 16000, Algiers, Algeria
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26
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Arastehfar A, Fang W, Al-Hatmi AMS, Afsarian MH, Daneshnia F, Bakhtiari M, Sadati SK, Badali H, Khodavaisy S, Hagen F, Liao W, Pan W, Zomorodian K, Boekhout T. Unequivocal identification of an underestimated opportunistic yeast species, Cyberlindnera fabianii, and its close relatives using a dual-function PCR and literature review of published cases. Med Mycol 2020; 57:833-840. [PMID: 30649481 PMCID: PMC6739237 DOI: 10.1093/mmy/myy148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 11/12/2018] [Accepted: 12/02/2018] [Indexed: 12/26/2022] Open
Abstract
Although Cyberlindnera fabinaii is a rare opportunist yeast species, its ability to cause septicemia, produce biofilm, and rapid acquisition of resistance to fluconazole and voriconazole, reinforced the urge for its identification from its closely related species. Widely used biochemical assays mainly identify Cyberlindnera fabinaii as Cyberlindnera jadinii and Wickerhamomyces anomalus, resulting in underestimation of this yeast in clinical settings. Moreover, the urge for a reliable molecular means of identification remains unsolved for 28 years. In order to unequivocally differentiate Cy. fabianii, Cy. mississipiensis, Cy. jadinii, and W. anomalus, we designed a dual-function multiplex polymerase chain reaction (PCR) assay. Challenging our dual-function multiplex PCR assay with 30 most clinically important yeast species, proved its specificity. Although conventional PCR could differentiate four target species, the real-time PCR counterpart due to Tm overlap misidentified Cy. mississipiensis as Cy. jadinii. Alongside of presenting a comprehensive literature review of published cases of Cy. fabianii from 1990 to 2018, we collected various clinical isolates from Tehran, Shiraz, and Fasa (July 1, 2017, to December 31, 2017) to find a passive relative distribution of these closely-related species in Iran. Subjecting our Iranian collection of yeast isolates to matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) MS and LSU and ITS rDNA sequencing revealed six isolates of Cy. fabianii (central venous catheter n = 2 and vaginal swabs n = 4) and one isolate of Cy. jadinii (vaginal swabs). Due to the use of biochemical assays in global ARTEMIS study, we encourage reidentification of clinical isolates of Cy. jadinii and Cy. jadinii using MALDI-TOF or Sanger sequencing that might lead to correcting the distribution of this fungus.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Wenjie Fang
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Abdullah M S Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands.,Ministry of Health, Directorate General of Health Services, Ibri, Oman
| | | | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Mina Bakhtiari
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Khanjari Sadati
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Badali
- Department of Medical Mycology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Wanqing Liao
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Weihua Pan
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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27
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Arastehfar A, Lim W, Daneshnia F, van de Sande WWJ, Fahal AH, Desnos-Ollivier M, de Hoog GS, Boekhout T, Ahmed SA. Madurella real-time PCR, a novel approach for eumycetoma diagnosis. PLoS Negl Trop Dis 2020; 14:e0007845. [PMID: 31940343 PMCID: PMC6986762 DOI: 10.1371/journal.pntd.0007845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 01/28/2020] [Accepted: 10/14/2019] [Indexed: 11/20/2022] Open
Abstract
The genus Madurella comprising four species, M. fahalii, M. mycetomatis, M. pseudomycetomatis, and M. tropicana, represents the prevalent cause of eumycetoma worldwide. The four species are phenotypically similar and cause an invariable clinical picture, but differ markedly in their susceptibility to antifungal drugs, and epidemiological pattern. Therefore, specific identification is required for optimal management of Madurella infection and to reveal proper epidemiology of the species. In this study, a novel multiplex real-time PCR targeting the four Madurella species was developed and standardized. Evaluation of the assay using reference strains of the target and non-target species resulted in 100% specificity, high analytical reproducibility (R2 values >0.99) and a lowest detection limit of 3 pg target DNA. The accuracy of the real-time PCR was further assessed using biopsies from eumycetoma suspected patients. Unlike culture and DNA sequencing as gold standard diagnostic methods, the real-time PCR yielded accurate diagnosis with specific identification of the causative species in three hours compared to one or two weeks required for culture. The novel method reduces turnaround time as well as labor intensity and high costs associated with current reference methods. Mycetoma, a progressive and disfiguring disease, is one of the neglected tropical diseases, caused by both bacteria and fungi. Eumycetoma is the fungal type and mainly caused by species of the genus Madurella. Madurella mycetomatis is the most prevalent species worldwide. However, other species such as M. fahalii, M. pseudomycetomatis, and M. tropicana can also cause mycetoma and have a different susceptibility towards the drug used for treating mycetoma patients. Currently, we lack a rapid and non-culture-based technique that can readily identify these four species from clinical samples. Due to its sensitivity, and specificity, real-time PCR is re-recognized by European Organization for Research and Treatment of Cancer (EORTC) to directly identify fungal agents from clinical samples. We developed and validated a multiplex real-time PCR-based technique using the least expensive chemistry to identify Madurella species within 3–4 hours. Development of such a technique will allow rapid diagnosis of eumycetoma and timely initiation of appropriate antifungal therapy.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Wilson Lim
- Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Wendy W. J. van de Sande
- Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands
| | - Ahmed H. Fahal
- Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan
| | - Marie Desnos-Ollivier
- Institut Pasteur, Molecular Mycology Unit, National Reference Center for Invasive Mycoses and Antifungals, CNRS UMR2000, Paris, France
| | - Gerrit S. de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Center of Expertise in Mycology of Radboudumc / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Sarah. A. Ahmed
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
- * E-mail:
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Jiang M, Pan W, Arasthfer A, Fang W, Ling L, Fang H, Daneshnia F, Yu J, Liao W, Pei H, Li X, Lass-Flörl C. Development and Validation of a Rapid, Single-Step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) System Potentially to Be Used for Reliable and High-Throughput Screening of COVID-19. Front Cell Infect Microbiol 2020; 10:331. [PMID: 32626666 DOI: 10.1101/2020.03.15.20036376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/29/2020] [Indexed: 05/18/2023] Open
Abstract
Objectives: Development and validation of a single-step and accurate reverse transcriptase loop-mediated isothermal amplification technique (RT-LAMP) for rapid identification of SARS-CoV-2 relative to commercial quantitative reverse transcriptase real-time PCR (qRT-PCR) assays to allow prompt initiation of proper medical care and containment of virus spread. Methods: Primers showing optimal in-silico features were subjected to analytical sensitivity and specificity to assess the limit of detection (LOD) and cross-reaction with closely- and distantly-related viral species, and clinically prominent bacterial and fungal species. In order to evaluate the clinical utility, our RT-LAMP was subjected to a large number of clinical samples, including 213 negative and 47 positive patients, relative to two commercial quantitative RT-PCR assays. Results: The analytical specificity and sensitivity of our assay was 100% and 500 copies/ml when serial dilution was performed in both water and sputum. Subjecting our RT-LAMP assay to clinical samples showed a high degree of specificity (99.5%), sensitivity (91.4%), positive predictive value (97.7%), and negative predictive value (98.1%) when used relative to qRT-PCR. Our RT-LAMP assay was two times faster than qRT-PCR and is storable at room temperature. A suspected case that later became positive tested positive using both our RT-LAMP and the two qRT-PCR assays, which shows the capability of our assay for screening purposes. Conclusions: We present a rapid RT-LAMP assay that could extend the capacity of laboratories to process two times more clinical samples relative to qRT-PCR and potentially could be used for high-throughput screening purposes when demand is increasing at critical situations.
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Affiliation(s)
- Minghua Jiang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Amir Arasthfer
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liyan Ling
- Department of Laboratory Medicine, Pinghu Second People's Hospital, Jiaxing, China
| | - Hua Fang
- Department of Laboratory Medicine, Pudong New Area People's Hospital, Shanghai, China
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hao Pei
- Department of Laboratory Medicine, Wuxi No. 5 People's Hospital, Wuxi, China
| | - Xiaojing Li
- Department of Dermatology, Affiliated Hospital of Hebei University of Engineering, Handan, China
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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29
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Arastehfar A, Daneshnia F, Salehi MR, Zarrinfar H, Khodavaisy S, Haas PJ, Roudbary M, Najafzadeh MJ, Zomorodian K, Charsizadeh A, Brouwer C, Pan W, Hagen F, Boekhout T. Corrigendum: Molecular characterization and antifungal susceptibility testing of Candida nivariensis from blood samples - an Iranian multicentre study and a review of the literature. J Med Microbiol 2019; 68:1695. [PMID: 31685093 DOI: 10.1099/jmm.0.001075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Mohammad-Reza Salehi
- Department of Infectious Diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pieter-Jan Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Javad Najafzadeh
- Department of Medical Mycology and Parasitology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arezoo Charsizadeh
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Carlo Brouwer
- CBMR Scientific Inc, Edmonton, Canada.,BioAware Life Sciences Data Management Software, Belgium.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Teun Boekhout
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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30
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Arastehfar A, Wickes BL, Ilkit M, Pincus DH, Daneshnia F, Pan W, Fang W, Boekhout T. Identification of Mycoses in Developing Countries. J Fungi (Basel) 2019; 5:E90. [PMID: 31569472 PMCID: PMC6958481 DOI: 10.3390/jof5040090] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/22/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Brian L Wickes
- The Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana 01330, Turkey.
| | | | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX Amsterdam, The Netherlands.
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31
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Arastehfar A, Khodavaisy S, Daneshnia F, Najafzadeh MJ, Mahmoudi S, Charsizadeh A, Salehi MR, Zarrinfar H, Raeisabadi A, Dolatabadi S, Zare Shahrabadi Z, Zomorodian K, Pan W, Hagen F, Boekhout T. 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). Front Cell Infect Microbiol 2019; 9:264. [PMID: 31417877 PMCID: PMC6682699 DOI: 10.3389/fcimb.2019.00264] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/08/2019] [Indexed: 01/05/2023] Open
Abstract
Despite the increasing occurrence of Candida orthopsilosis and Candida metapsilosis in clinical settings, little is known about their microbiological and clinical properties. Herein, we conducted a national retrospective study (2014–2019) from multiple centers in Iran. Among the 1,770 Candida isolates collected, we identified 600 Candida parapsilosis species complex isolates. Isolate identification was performed by 9-plex PCR, matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS), and rDNA sequencing, and antifungal susceptibility testing (AFST) followed CLSI M27-A3/S4; genotyping was performed by amplified fragment length polymorphism (AFLP) analysis; and clinical information was mined. Thirty-one isolates of C. orthopsilosis from various clinical sources, one mixed sample (blood) concurrently containing C. orthopsilosis and C. parapsilosis and one isolate of C. metapsilosis from a nail sample were identified. Although both 9-plex PCR and MALDI-TOF successfully identified all isolates, only 9-plex PCR could identify the agents in a mixed sample. For the C. orthopsilosis isolates, resistance (non-wild type) was noted only for itraconazole (n = 4; 12.5%). Anidulafungin and fluconazole showed the highest and voriconazole had the lowest geometric mean values. AFLP analysis showed three main and four minor genotypes. Interestingly, 90% of nail isolates clustered with 80% of the blood isolates within two clusters, and four blood isolates recovered from four patients admitted to a hospital clustered into two genotypes and showed a high degree of similarity (>99.2%), which suggests that C. orthopsilosis disseminates horizontally. Supported by our data and published case studies, C. orthopsilosis and C. metapsilosis can be linked to challenging clinical failures, and successful outcomes are not always mirrored by in vitro susceptibility. Accordingly, conducting nationwide studies may provide more comprehensive data, which is required for a better prognosis and clinical management of patients.
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Affiliation(s)
- Amir Arastehfar
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Sadegh Khodavaisy
- Zoonoses Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran.,Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farnaz Daneshnia
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Mohammad-Javad Najafzadeh
- Department of Medical Mycology and Parasitology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shahram Mahmoudi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Arezoo Charsizadeh
- Immunology, Asthma, and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Reza Salehi
- Department of Infectious Diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Raeisabadi
- Department of Medical Mycology and Parasitology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Somayeh Dolatabadi
- Faculty of Engineering, Sabzevar University of New Technology, Sabzevar, Iran
| | - Zahra Zare Shahrabadi
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Weihua Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Teun Boekhout
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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32
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Zhang Q, Li H, Zhang K, Arastehfar A, Daneshnia F, Fang W, He P, Kuang W, Jiang G, Chen M, Boekhout T, Li S, Jiang W, Liao W, Pan W. Lumbar drainage for the treatment of refractory intracranial hypertension in HIV-negative cryptococcal meningitis. Future Microbiol 2019; 14:859-866. [PMID: 31165635 DOI: 10.2217/fmb-2019-0084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Aim: This study aims to evaluate lumbar drainage (LD) for controlling refractory intracranial hypertension among non-HIV cryptococcal meningitis patients. Patients & methods: A case–control study was designed to compare LD (case) with repeated lumbar puncture (control). Results: Both LD and repeated lumbar puncture can efficiently control refractory intracranial hypertension. LD group showed better clinical symptom remission, such as lower rate of headache, vision disorders, signs of meningeal irritation and conscious disturbance, than control group. LD group was reported with higher intracranial pressure reduction (173.75 ± 17.72 mmH2O) than those among control group (113.50 ± 14.94 mmH2O; p < 0.05). Conclusion: LD is an effective and safe alternative to control refractory intracranial hypertension in HIV-negative cryptococcal meningitis patients.
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Affiliation(s)
- Qilong Zhang
- Department of Internal Neurology, Jiangxi Chest Hospital, Jiangxi 330000, PR China
| | - Hang Li
- Department of Internal Neurology, Jiangxi Chest Hospital, Jiangxi 330000, PR China
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Keming Zhang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Peijuan He
- Department of Internal Neurology, Jiangxi Chest Hospital, Jiangxi 330000, PR China
| | - Weifeng Kuang
- Department of Internal Neurology, Jiangxi Chest Hospital, Jiangxi 330000, PR China
| | - Guoqiang Jiang
- Department of Internal Neurology, Jiangxi Chest Hospital, Jiangxi 330000, PR China
| | - Min Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Teun Boekhout
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam 1012 WX, The Netherlands
| | - Shuai Li
- Department of Clinical Laboratory, Yan'an People’s Hospital, Shanxi 716000, PR China
| | - Weiwei Jiang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
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33
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Arastehfar A, Daneshnia F, Kord M, Roudbary M, Zarrinfar H, Fang W, Hashemi SJ, Najafzadeh MJ, Khodavaisy S, Pan W, Liao W, Badali H, Rezaie S, Zomorodian K, Hagen F, Boekhout T. Corrigendum: 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. Front Cell Infect Microbiol 2019; 9:176. [PMID: 31192165 PMCID: PMC6546970 DOI: 10.3389/fcimb.2019.00176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 05/08/2019] [Indexed: 11/26/2022] Open
Affiliation(s)
- Amir Arastehfar
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Mohammad Kord
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Sayed Jamal Hashemi
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Zoonoses Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hamid Badali
- Department of Medical Mycology, Invasive Fungi Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sassan Rezaie
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Department of Medical Mycology and Parasitology, Basic Sciences in Infectious Diseases Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ferry Hagen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Teun Boekhout
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Yeast Biodiversity Department, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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34
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Arastehfar A, Daneshnia F, Farahyar S, Fang W, Salimi M, Salehi M, Hagen F, Weihua P, Roudbary M, Boekhout T. Incidence and spectrum of yeast species isolated from the oral cavity of Iranian patients suffering from hematological malignancies. J Oral Microbiol 2019; 11:1601061. [PMID: 31044032 PMCID: PMC6484487 DOI: 10.1080/20002297.2019.1601061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 03/22/2019] [Indexed: 01/05/2023] Open
Abstract
Background: Oral candidiasis (OC) has a profound effect on the life quality of immunocompromised patients, such as those undergoing chemotherapy. Objective: Systematic investigation of clinical outcome and microbiological features of yeast isolates recovered from the oral cavity of 150 Iranian patients with hematological malignancies. Design: MALDI-TOF MS, 21-plex PCR, and rDNA sequencing were used for identification. Antifungal susceptibility testing (broth microdilution, CLSI M27-A3/S4) and genotypic diversity of yeast isolates (amplified fragment length polymorphism) were assessed. Results: Nystatin treatment resulted in 70% therapeutic failure and administration of 150 mg fluconazole (FLZ) + nystatin for patients with OC relapse showed 70% clinical failure. Previous history of OC was significantly correlated with FLZ treatment requirement and nystatin failure (P = 0.005, α < 0.05). Candida albicans (80.3%) and Kluyveromyces marxianus (C. kefyr) (12.7%) were the two most prevalent yeast species isolated. FLZ and AMB exhibited the highest geometric mean values. 21-PCR showed 98.9% agreement with MALDI-TOF MS. K. marxianus isolates had the same genotype, while C. albicans isolates grouped in 15 genotypes. Conclusions: Marked rate of therapeutic failure of nystatin necessitated OC treatment with systemic antifungals. K. marxianus was the second most prevalent yeast and 21-plex PCR could be considered as an inexpensive identification tool.
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Affiliation(s)
- Amir Arastehfar
- Department of Yeasts , Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Department of Yeasts , Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Shirin Farahyar
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Center (MBiRC), Iran University of Medical Sciences, Tehran, Iran
| | - Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Maryam Salimi
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Salehi
- Department of infectious diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ferry Hagen
- Department of Yeasts , Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Pan Weihua
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Teun Boekhout
- Department of Yeasts , Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, Netherlands
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Arastehfar A, Daneshnia F, Salehi MR, Zarrinfar H, Khodavaisy S, Haas PJ, Roudbary M, Najafzadeh MJ, Zomorodian K, Charsizadeh A, Brouwer C, Pan W, Hagen F, Boekhout T. Molecular characterization and antifungal susceptibility testing of Candida nivariensis from blood samples - an Iranian multicentre study and a review of the literature. J Med Microbiol 2019; 68:770-777. [PMID: 30924763 DOI: 10.1099/jmm.0.000963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Identification of the emerging yeast species Candida nivariensis among presumptively identified Iranian Candida glabrata isolates. METHODOLOGY Clinical C. glabrata species complex isolates from blood (n=71; 33.3 %), urine (n=100; 46.9 %), vaginal swabs (n=20;9.4 %), BAL (n=10; 4.7 %), and sputum (n=12; 5.6 %) from Iran were investigated. Isolates were characterized by CHROMagar, multiplex PCRs, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), amplified fragment length polymorphism (AFLP) fingerprinting, internal transcribed spacer (ITS)/large subunit (LSU) rDNA and FKS1/FKS2 sequencing, and the European Committee on Antimicrobial Susceptibility Testing broth microdilution method. A comprehensive literature review was conducted and all the relevant clinical and microbiological data were collected. RESULTS Four C. nivariensis isolates were recovered from blood samples of three subjects and were all consistently identified by nine-plex PCR, Bruker MALDI-TOF MS, and LSU and ITS rDNA sequencing. AFLP genotyping clustered the isolates into two groups. Sequencing of the FKS1 and FKS2 hotspots showed no accountable amino acid substitutions. All isolates were susceptible to amphotericin B, fluconazole, itraconazole, posaconazole, voriconazole, anidulafungin and micafungin. CONCLUSION In total, 4 out of 213 clinical C. glabrata species complex candidemia isolates were C. nivariensis. Improvement of the BioMerieux Vitek MS database is required to accurately identify C. nivariensis and it is advised to alternatively use CHROMagar and/or PCR-based techniques. As other species within the Nakaseomyces clade may cause infection and showed high MIC values for antifungals, inclusion of their spectra into the MALDI-TOF MS database seems relevant. Due to developing resistance to fluconazole and insufficient efficacy of caspofungin, the combination of catheter removal plus treatment with caspofungin, or voriconazole, or micafungin might be effective for patients.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Mohammad-Reza Salehi
- Department of Infectious Diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Khodavaisy
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Pieter-Jan Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Javad Najafzadeh
- Department of Medical Mycology and Parasitology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arezoo Charsizadeh
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Carlo Brouwer
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,BioAware Life Sciences Data Management Software, Belgium.,CBMR Scientific Inc, Edmonton, Canada
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - Ferry Hagen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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Arastehfar A, Bakhtiari M, Daneshnia F, Fang W, Sadati SK, Al-Hatmi AM, Groenewald M, Sharifi-Mehr H, Liao W, Pan W, Zomorodian K, Hagen F, Boekhout T. First fungemia case due to environmental yeast Wickerhamomyces myanmarensis: detection by multiplex qPCR and antifungal susceptibility. Future Microbiol 2019; 14:267-274. [PMID: 30859860 PMCID: PMC6482385 DOI: 10.2217/fmb-2018-0253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Presenting the first clinical case of Wickerhamomyces myanmarensis. PATIENTS & METHODS Yeast cells were isolated from blood and central venous catheter of a 5.5-year-old male subject. API 20C AUX, MALDI-TOF MS, ITS and LSU rDNA sequencing, and our qPCR assay were used for identification and the MIC values were determined by CLSI M27-A3. RESULTS ITS and LSU rDNA sequencing identified both isolates as W. myanmarensis, while API 20C AUX and MALDI-TOF MS did not identify them correctly. Our qPCR specifically distinguished W. myanmarensis from W. anomalus. Isolate obtained from blood showed a higher MIC value for fluconazole, voriconazole and posaconazole. CONCLUSION Utilization of reliable identification tools might reveal the genuine spectrum of opportunistic yeast species.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Mina Bakhtiari
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Wenjie Fang
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Sara Khanjari Sadati
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdullah Ms Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Ministry of Health, Directorate General of Health Services, Ibri, Oman
| | | | - Hamid Sharifi-Mehr
- Biology Department, Faculty of Science, Sahid Bahonar University of Kerman, Kerman, Iran
| | - Wanqing Liao
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Weihua Pan
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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37
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Arastehfar A, Fang W, Al-Hatmi AMS, Afsarian MH, Daneshnia F, Bakhtiari M, Sadati SK, Badali H, Khodavaisy S, Hagen F, Liao W, Pan W, Zomorodian K, Boekhout T. Corrigendum: Unequivocal identification of an underestimated opportunistic yeast species, Cyberlindnera fabianii, and its close relatives using a dual-function PCR and literature review of published cases. Med Mycol 2019; 57:e12. [PMID: 30828712 DOI: 10.1093/mmy/myz025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Wenjie Fang
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Abdullah M S Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Ministry of Health, Directorate General of Health Services, Ibri, Oman
| | | | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Mina Bakhtiari
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Khanjari Sadati
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Badali
- Department of Medical Mycology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Wanqing Liao
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Weihua Pan
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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38
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Arastehfar A, Daneshnia F, Kord M, Roudbary M, Zarrinfar H, Fang W, Hashemi SJ, Najafzadeh MJ, Khodavaisy S, Pan W, Liao W, Badali H, Rezaie S, Zomorodian K, Hagen F, Boekhout T. 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. Front Cell Infect Microbiol 2019; 9:21. [PMID: 30828570 PMCID: PMC6385604 DOI: 10.3389/fcimb.2019.00021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/22/2019] [Indexed: 12/31/2022] Open
Abstract
Occurrence of non-Candida albicans Candida (NCAC) species that are associated with elevated MIC values and therapeutic failures are increasing. As a result, timely and accurate means of identification to the species level is becoming an essential part of diagnostic practices in clinical settings. In this study, 301 clinically isolated yeast strains recovered from various anatomical sites [Blood (n = 145), other sites (n = 156)] were used to assess the accuracy and practicality of API 20C AUX and 21-plex PCR compared to MALDI-TOF MS and large subunit rDNA (LSU rDNA). MALDI-TOF MS correctly identified 98.33% of yeast isolates, 100% of top five Candida species, 95.7% of rare yeast species, while 1.3% of isolates were misidentified. API 20C AUX correctly identified 83.7% of yeast isolates, 97.2% of top five Candida species, 61.8% of rare yeast species, while 16.2% of yeast isolates were misidentified. The 21-plex PCR, accurately identified 87.3% of yeast isolates, 100% of top five Candida species, 72% of rare yeast species, but it misidentified 1.3% of rare yeast species while 9.9% of whole yeast isolates were not identified. The combination of rapidity of 21-plex PCR and comprehensiveness of API 20C AUX, led to correct identification of 92% of included yeast isolates. Due to expensiveness of MALDI-TOF MS and sequencing, this combination strategy could be the most accurate and inexpensive alternative identification strategy for developing countries. Moreover, by the advent and development of cost-effective, reliable, and rapid PCR machines that cost 130 US dollars, 21-plex could be integrated in routine laboratories of developing and resource-limited countries to specifically identify 95% causative agents of yeast-related infections in human. Databases of MALDI-TOF MS, API 20C AUX, and the number of target species identified by 21-plex require further improvement to keep up with the diverse spectrum of yeast species.
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Affiliation(s)
- Amir Arastehfar
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Mohammad Kord
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Sayed Jamal Hashemi
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Zoonoses Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hamid Badali
- Department of Medical Mycology, Invasive Fungi Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sassan Rezaie
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Department of Medical Mycology and Parasitology, Basic Sciences in Infectious Diseases Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ferry Hagen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Teun Boekhout
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Yeast Biodiversity Department, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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Arastehfar A, Fang W, Daneshnia F, Al-Hatmi AM, Liao W, Pan W, Khan Z, Ahmad S, Rosam K, Lackner M, Lass-Flörl C, Hagen F, Boekhout T. Novel multiplex real-time quantitative PCR detecting system approach for direct detection of Candida auris and its relatives in spiked serum samples. Future Microbiol 2018; 14:33-45. [PMID: 30539665 DOI: 10.2217/fmb-2018-0227] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The multidrug-resistant opportunistic yeast species of Candida auris, Candida haemulonii, Candida duobushaemulonii and Candida pseudohaemulonii continue to endanger the healthcare settings around the globe. Due to the lack of a specific qPCR assay for detection of these species from clinical samples, we developed a multiplex qPCR assay. Analytical specificity and sensitivity showed 100% specificity and the sensitivity of up to ten genomes of target species with a high value of reproducibility (R2 >0.99). Subsequently, from spiked serum samples, our qPCR specifically could detect up to ten genomes of C. auris and one genome of C. haemulonii, C. duobushaemulonii and C. pseudohaemulonii (R2 >0.98). Lack of cross reaction with the human DNA, a high degree of specificity and sensitivity, showed the potential of our multiplex PCR for direct detection of C. auris and closely related species from serum samples of suspected patients. Future studies are warranted to assure its applicability in clinical settings.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands
| | - Wenjie Fang
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands
| | - Abdullah Ms Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands.,Center of Expertise in Mycology Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen 6500HB, The Netherlands.,Ministry of Health, Directorate General of Health Services, PO Box 393, 100 Muscat, Oman
| | - Wanqing Liao
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Weihua Pan
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Katharina Rosam
- Division of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Michaela Lackner
- Division of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China.,Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam 1012 WX, The Netherlands
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