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Dunaiski CM, Kock MM, Chan WY, Ismail A, Peters RPH. Molecular epidemiology and antimicrobial resistance of vaginal Candida glabrata isolates in Namibia. Med Mycol 2024; 62:myae009. [PMID: 38308518 DOI: 10.1093/mmy/myae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 02/01/2024] [Indexed: 02/04/2024] Open
Abstract
Candida glabrata is the most common non-albicans Candida species that causes vulvovaginal candidiasis (VVC). Given the intrinsically low susceptibility of C. glabrata to azole drugs, investigations into C. glabrata prevalence, fungal susceptibility profile, and molecular epidemiology are necessary to optimise the treatment of VVC. This molecular epidemiological study was conducted to determine antifungal drug profile, single nucleotide polymorphisms (SNPs) associated with phenotypic antifungal resistance and epidemic diversity of C. glabrata isolates from women with VVC in Namibia. Candida glabrata isolates were identified using phenotypic and molecular methods. Antifungal susceptibility of strains was determined for fluconazole, itraconazole, amphotericin B, and anidulafungin. Whole genome sequencing was used to determine SNPs in antifungal resistance genes and sequence type (ST) allocation. Among C. glabrata isolates, all (20/20; 100%) exhibited phenotypic resistance to the azole class antifungal drug, (fluconazole), and phenotypic susceptibility to the polyene class (amphotericin B), and the echinocandins (anidulafungin). Non-synonymous SNPs were identified in antifungal resistance genes of all fluconazole-resistant C. glabrata isolates including ERG6 (15%), ERG7 (15%), CgCDR1 (25%), CgPDR1 (60%), SNQ2 (10%), FKS1 (5.0%), FKS2 (5.0%), CgFPS1 (5.0%), and MSH2 (15%). ST15 (n = 8/20, 40%) was predominant. This study provides important insight into phenotypic and genotypic antifungal resistance across C. glabrata isolates from women with VVC in Namibia. In this study, azole resistance is determined by an extensive range of SNPs, while the observed polyene and echinocandin resistance-associated SNPs despite phenotypic susceptibility require further investigation.
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Affiliation(s)
- Cara M Dunaiski
- Namibia University of Sciences and Technology, Department of Health and Applied Sciences, Windhoek 10005, Namibia
- University of Pretoria, Department of Medical Microbiology, Pretoria 0001, South Africa
| | - Marleen M Kock
- University of Pretoria, Department of Medical Microbiology, Pretoria 0001, South Africa
- National Health Laboratory Service, Tshwane, Academic Division, Pretoria 3191, South Africa
| | - Wai Yin Chan
- Sequencing Core Facility, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0081, South Africa
- Right to care, Centurion 0157, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - Remco P H Peters
- University of Pretoria, Department of Medical Microbiology, Pretoria 0001, South Africa
- University of Cape Town, Division of Medical Microbiology, Cape Town 7701, South Africa
- Foundation for Professional Development, Research Unit, East London 5217, South Africa
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2
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Badrane H, Cheng S, Dupont CL, Hao B, Driscoll E, Morder K, Liu G, Newbrough A, Fleres G, Kaul D, Espinoza JL, Clancy CJ, Nguyen MH. Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures. Nat Commun 2023; 14:5918. [PMID: 37739935 PMCID: PMC10516878 DOI: 10.1038/s41467-023-41509-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
The longstanding model is that most bloodstream infections (BSIs) are caused by a single organism. We perform whole genome sequencing of five-to-ten strains from blood culture (BC) bottles in each of ten patients with Candida glabrata BSI. We demonstrate that BCs contain mixed populations of clonal but genetically diverse strains. Genetically distinct strains from two patients exhibit phenotypes that are potentially important during BSIs, including differences in susceptibility to antifungal agents and phagocytosis. In both patients, the clinical microbiology lab recovered a fluconazole-susceptible index strain, but we identify mixed fluconazole-susceptible and -resistant populations. Diversity in drug susceptibility is likely clinically relevant, as fluconazole-resistant strains were subsequently recovered by the clinical laboratory during persistent or relapsing infections. In one patient, unrecognized respiration-deficient small colony variants are fluconazole-resistant and significantly attenuated for virulence during murine candidiasis. Our data suggest a population-based model of C. glabrata genotypic and phenotypic diversity during BSIs.
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Affiliation(s)
| | | | | | - Binghua Hao
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Guojun Liu
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Drishti Kaul
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | | | - Cornelius J Clancy
- University of Pittsburgh, Pittsburgh, PA, USA
- VA Pittsburgh Healthcare System, Pittsburgh, PA, USA
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3
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Štefánek M, Garaiová M, Valček A, Jordao L, Bujdáková H. Comparative Analysis of Two Candida parapsilosis Isolates Originating from the Same Patient Harbouring the Y132F and R398I Mutations in the ERG11 Gene. Cells 2023; 12:1579. [PMID: 37371049 DOI: 10.3390/cells12121579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
This work presents a comparative analysis of two clinical isolates of C. parapsilosis, isolated from haemoculture (HC) and central venous catheter (CVC). Both strains harboured Y132F and R398I mutations in the gene ERG11 associated with resistance to fluconazole (FLC). Differences between the HC and CVC isolates were addressed in terms of virulence, resistance to FLC, and lipid distribution. Expression of the ERG6 and ERG9 genes, lipid analysis, fatty acid composition, and lipase activity were assessed via qPCR, thin-layer chromatography/high-performance liquid chromatography, gas chromatography, and spectrophotometry, respectively. Regulation of the ERG6 and ERG9 genes did not prove any impact on FLC resistance. Analysis of lipid metabolism showed a higher accumulation of lanosterol in both the isolates regardless of FLC presence. Additionally, a decreased level of triacylglycerols (TAG) with an impact on the composition of total fatty acids (FA) was observed for both isolates. The direct impact of the ERG11 mutations on lipid/FA analysis has not been confirmed. The higher lipase activity observed for C. parapsilosis HC isolate could be correlated with the significantly decreased level of TAG. The very close relatedness between both the isolates suggests that one isolate was derived from another after the initial infection of the host.
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Affiliation(s)
- Matúš Štefánek
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
| | - Martina Garaiová
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dúbravska Cesta 9, 840 05 Bratislava, Slovakia
| | - Adam Valček
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
| | - Luisa Jordao
- Research and Development Unit, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal
| | - Helena Bujdáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
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4
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Stefanini I, Stoakes E, Wu HHT, Xu-McCrae L, Hussain A, Moat J, Dowson CG, David MD, Constantinidou C. Genomic Assembly of Clinical Candida glabrata (Nakaseomyces glabrata) Isolates Reveals within-Species Structural Plasticity and Association with In Vitro Antifungal Susceptibility. Microbiol Spectr 2022; 10:e0182722. [PMID: 36354359 PMCID: PMC9769630 DOI: 10.1128/spectrum.01827-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/19/2022] [Indexed: 11/12/2022] Open
Abstract
The opportunistic human pathogen Candida glabrata has become an increasingly important threat to human health, with infections globally characterized by high mortality rates and multidrug resistance. To face this threat, more efficient diagnostic and therapeutic approaches are required, underpinning research to help define the intraspecies epidemiology, genetic variability, and therefore, diagnostic and therapeutic target stability. Previous comparative genetics studies conducted on limited numbers of strains only revealed partial resolution of chromosomal settings. In this study, by combining short- and long-read genome sequencing, phenotypic characterization, and comparative genomics over a large set of strains, we detected strict relationships between large chromosomal rearrangements and phylogenetic clades, genes subjected to different selective pressures, and new sets of genes associated with resistance to antifungals. Overall, these results not only provide a fundamental contribution to our knowledge of C. glabrata evolution and epidemiology but may also lay the foundations for the future development of tailored therapeutic approaches. IMPORTANCE The human pathogen Candida glabrata has become a global threat to human health, with infections characterized by high mortality and multidrug resistance. We have obtained nine fully assembled genomes from clinical isolates through a combination of short- and long-read sequencing approaches. The quality and completeness of such genomes and their subsequent comparison to the broadest set of genomes so far allowed us to pinpoint chromosomal rearrangements in several genomes and detect phylogenetic clades that were not associated with geographic location or isolation source. We identified a new set of genes associated with resistance to antifungals coding for adhesin or adhesin-like proteins, suggesting C. glabrata resists antifungals by forming aggregates or adhering to the host tissue. These results, which provide a fundamental contribution to our knowledge of C. glabrata evolution and epidemiology, may initiate the development of precision medicine interventions for patients with suspected or proven invasive fungal infections.
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Affiliation(s)
- Irene Stefanini
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Emily Stoakes
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Houdini H. T. Wu
- UK Health Security Agency Public Health Laboratory, Birmingham, United Kingdom
| | - Li Xu-McCrae
- UK Health Security Agency Public Health Laboratory, Birmingham, United Kingdom
| | - Abid Hussain
- UK Health Security Agency Public Health Laboratory, Birmingham, United Kingdom
| | - John Moat
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Miruna D. David
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
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Voropaev AD, Yekaterinchev DA, Urban YN, Zverev VV, Nesvizhsky YV, Voropaeva EA, Likhanskaya EI, Afanasiev MS, Afanasiev SS. <i>CDR1, CDR2, MDR1</i> and <i>ERG11</i> expression in azole resistant <i>Сandida albicans</i> isolated from HIV-infected patients in city of Moscow. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2022. [DOI: 10.15789/2220-7619-ccm-1931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Candida fungi are common opportunistic microorganisms capable of causing infections of various localization, as well as life-threatening conditions in immunocompromised patients, such as HIV-infected individuals, oncology patients, subjects undergoing HSCT, which number has been steadily increasing in recent years. In addition, resistance to anti-fungal drugs has been spreading as well. Naturally sensitive to azoles, C. albicans possess a variety of mechanisms of acquired resistance, including efflux transporters and target protein-encoding gene amplification. This study was conducted to assess a prevalence of such mechanisms in the isolates sample obtained from HIV-infected patients in the Moscow region of the Russian Federation, characterize a relationship between these mechanisms and patterns of developing drug resistance. 18 strains of C. albicans resistant to fluconazole and voriconazole were isolated from HIV-infected patients with recurrent oropharyngeal candidiasis in the Moscow region. The expression levels of the ERG11, MDR1, CDR1, CDR2 genes involved in the formation of acquired azole resistance were measured using quantitative PCR, the 2CT method with ACT and PMA genes as control genes and reference values of sensitive isolates. Expression levels exceeding the average values of sensitive isolates by more than 3 standard deviations were considered significantly elevated. In most of the isolates, elevated levels of CDR1 and CDR2 gene expression were found: 89% and 78%, respectively. The expression level of the MDR1 gene was increased only in 28% of cases. ERG11 expression levels were significantly elevated in 78% of the isolates. Expression levels of all resistance genes studied were significantly increased in 4 strains. In this sample of C. albicans isolates, acquired resistance is mainly associated with efflux vectors encoded by the CDR1 and CDR2 genes. Also, in most isolates, an increased expression level for the azole target protein gene ERG11 was detected. The expression level of the efflux transporter gene MDR1 was increased in the smallest number of samples. It is also impossible to exclude a potential role of other mechanisms in developing acquired resistance, such as mutations in the ERG11 gene. It can be assumed that the identified mechanisms of resistance result from long-term, widespread, and sometimes uncontrolled use of azoles, including those in treatment and prevention of candidiasis in HIV-infected patients.
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6
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Jiang S, Chen Y, Han S, Lv L, Li L. Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms 2022; 10:microorganisms10101882. [PMID: 36296159 PMCID: PMC9609632 DOI: 10.3390/microorganisms10101882] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Shengyi Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Correspondence: ; Tel.: +86-0571-8723-6458
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7
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Salazar SB, Pinheiro MJF, Sotti-Novais D, Soares AR, Lopes MM, Ferreira T, Rodrigues V, Fernandes F, Mira NP. Disclosing azole resistance mechanisms in resistant Candida glabrata strains encoding wild-type or gain-of-function CgPDR1 alleles through comparative genomics and transcriptomics. G3 (BETHESDA, MD.) 2022; 12:jkac110. [PMID: 35532173 PMCID: PMC9258547 DOI: 10.1093/g3journal/jkac110] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 04/25/2022] [Indexed: 12/03/2022]
Abstract
The pathogenic yeast Candida glabrata is intrinsically resilient to azoles and rapidly acquires resistance to these antifungals, in vitro and in vivo. In most cases azole-resistant C. glabrata clinical strains encode hyperactive CgPdr1 variants, however, resistant strains encoding wild-type CgPDR1 alleles have also been isolated, although remaining to be disclosed the underlying resistance mechanism. In this study, we scrutinized the mechanisms underlying resistance to azoles of 8 resistant clinical C. glabrata strains, identified along the course of epidemiological surveys undertaken in Portugal. Seven of the strains were found to encode CgPdr1 gain-of-function variants (I392M, E555K, G558C, and I803T) with the substitutions I392M and I803T being herein characterized as hyper-activating mutations for the first time. While cells expressing the wild-type CgPDR1 allele required the mediator subunit Gal11A to enhance tolerance to fluconazole, this was dispensable for cells expressing the I803T variant indicating that the CgPdr1 interactome is shaped by different gain-of-function substitutions. Genomic and transcriptomic profiling of the sole azole-resistant C. glabrata isolate encoding a wild-type CgPDR1 allele (ISTB218) revealed that under fluconazole stress this strain over-expresses various genes described to provide protection against this antifungal, while also showing reduced expression of genes described to increase sensitivity to these drugs. The overall role in driving the azole-resistance phenotype of the ISTB218 C. glabrata isolate played by these changes in the transcriptome and genome of the ISTB218 isolate are discussed shedding light into mechanisms of resistance that go beyond the CgPdr1-signalling pathway and that may alone, or in combination, pave the way for the acquisition of resistance to azoles in vivo.
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Affiliation(s)
- Sara B Salazar
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Maria Joana F Pinheiro
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Danielle Sotti-Novais
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Ana R Soares
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro 3810, Portugal
| | - Maria M Lopes
- Departamento de Microbiologia e Imunologia, Faculdade de Farmácia da Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Teresa Ferreira
- Laboratório de Microbiologia, Hospital Dona Estefânia (Centro Hospitalar Universitário Lisboa Central), Lisboa 1169-045, Portugal
| | - Vitória Rodrigues
- Seção de Microbiologia, Laboratório SYNLAB—Lisboa, Grupo SYNLAB Portugal, Lisboa 1070-061, Portugal
| | - Fábio Fernandes
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Nuno P Mira
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
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Identification of Clinical Isolates of Candida albicans with Increased Fitness in Colonization of the Murine Gut. J Fungi (Basel) 2021; 7:jof7090695. [PMID: 34575733 PMCID: PMC8468482 DOI: 10.3390/jof7090695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/22/2022] Open
Abstract
The commensal and opportunistic pathogen Candida albicans is an important cause of fungal diseases in humans, with the gastrointestinal tract being an important reservoir for its infections. The study of the mechanisms promoting the C. albicans commensal state has attracted considerable attention over the last few years, and several studies have focused on the identification of the intestinal human mycobiota and the characterization of Candida genes involved in its establishment as a commensal. In this work, we have barcoded 114 clinical C. albicans isolates to identify strains with an enhanced fitness in a murine gastrointestinal commensalism model. The 114 barcoded clinical isolates were pooled in four groups of 28 to 30 strains that were inoculated by gavage in mice previously treated with antibacterial therapy. Eight strains that either exhibited higher colonization load and/or remained in the gut after antibiotic removal were selected. The phenotypic analysis of these strains compared to an RFP-tagged SC5314 wild type strain did not reveal any specific trait associated with its increased colonization; all strains were able to filament and six of the eight strains displayed invasive growth on Spider medium. Analysis of one of these strains, CaORAL3, revealed that although mice required previous bacterial microbiota reduction with antibiotics to be able to be colonized, removal of this procedure could take place the same day (or even before) Candida inoculation. This strain was able to colonize the intestine of mice already colonized with Candida without antibiotic treatment in co-housing experiments. CaORAL3 was also able to be established as a commensal in mice previously colonized by another (CaHG43) or the same (CaORAL3) C. albicans strain. Therefore, we have identified C. albicans isolates that display higher colonization load than the standard strain SC5314 which will surely facilitate the analysis of the factors that regulate fungal colonization.
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Hassan Y, Chew SY, Than LTL. Candida glabrata: Pathogenicity and Resistance Mechanisms for Adaptation and Survival. J Fungi (Basel) 2021; 7:jof7080667. [PMID: 34436206 PMCID: PMC8398317 DOI: 10.3390/jof7080667] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 02/06/2023] Open
Abstract
Candida glabrata is a yeast of increasing medical relevance, particularly in critically ill patients. It is the second most isolated Candida species associated with invasive candidiasis (IC) behind C. albicans. The attributed higher incidence is primarily due to an increase in the acquired immunodeficiency syndrome (AIDS) population, cancer, and diabetic patients. The elderly population and the frequent use of indwelling medical devices are also predisposing factors. This work aimed to review various virulence factors that facilitate the survival of pathogenic C. glabrata in IC. The available published research articles related to the pathogenicity of C. glabrata were retrieved and reviewed from four credible databases, mainly Google Scholar, ScienceDirect, PubMed, and Scopus. The articles highlighted many virulence factors associated with pathogenicity in C. glabrata, including adherence to susceptible host surfaces, evading host defences, replicative ageing, and producing hydrolytic enzymes (e.g., phospholipases, proteases, and haemolysins). The factors facilitate infection initiation. Other virulent factors include iron regulation and genetic mutations. Accordingly, biofilm production, tolerance to high-stress environments, resistance to neutrophil killings, and development of resistance to antifungal drugs, notably to fluconazole and other azole derivatives, were reported. The review provided evident pathogenic mechanisms and antifungal resistance associated with C. glabrata in ensuring its sustenance and survival.
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Affiliation(s)
- Yahaya Hassan
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Bayero University Kano, Kano 700241, Nigeria;
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Shu Yih Chew
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
- Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-39769-2373
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10
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Kidd SE, Crawford LC, Halliday CL. Antifungal Susceptibility Testing and Identification. Infect Dis Clin North Am 2021; 35:313-339. [PMID: 34016280 DOI: 10.1016/j.idc.2021.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The requirement for antifungal susceptibility testing is increasing given the availability of new drugs, increasing populations of individuals at risk for fungal infection, and emerging multiresistant fungi. Rapid and accurate fungal identification remains at the forefront of laboratory efforts to guide empiric therapy. Antifungal susceptibility testing methods have greatly improved, but are subject to variation in results between methods. Careful standardization, validation, and extensive training of users is essential to ensure susceptibility results are clinically useful and interpreted appropriately. Interpretive criteria for many drugs and species are still lacking, but this will continue to evolve.
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Affiliation(s)
- Sarah E Kidd
- National Mycology Reference Centre, Microbiology & Infectious Diseases, SA Pathology, SA Pathology (Frome Campus), PO Box 14, Rundle Mall, Adelaide, South Australia 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Lucy C Crawford
- Microbiology & Infectious Diseases, SA Pathology, PO Box 14, Rundle Mall, Adelaide, South Australia 5000, Australia; Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Catriona L Halliday
- Clinical Mycology Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, The University of Sydney, Level 3 ICPMR, Darcy Road, Westmead, New South Wales 2145, Australia
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11
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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] [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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12
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Cárdenas Parra LY, Perez Cárdenas JE. Mecanismos de resistencia a fluconazol expresados por Candida glabrata: una situación para considerar en la terapéutica. INVESTIGACIÓN EN ENFERMERÍA: IMAGEN Y DESARROLLO 2020. [DOI: 10.11144/javeriana.ie22.mrfe] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Introducción: Los esfuerzos terapéuticos orientados a atender las micosis por Candida spp. se han enfocado en el empleo de azoles; sin embargo, en la literatura científica se discute su beneficio, por los amplios y descritos mecanismos de resistencia. Objetivo: Describir los mecanismos de resistencia al fluconazol expresados por la especie Candida glabrata, con la intención de que sean considerados dentro de las variables de elegibilidad para la intervención. Método: Se realizó una revisión integrativa utilizando la pregunta orientadora: ¿cuáles son los mecanismos de resistencia al fluconazol expresados por la especie Candida glabrata? Veintinueve estudios obtenidos de la base de datos PubMed cumplieron los criterios del análisis crítico propuesto por el instrumento PRISMA, utilizado para la selección de los artículos incluidos para su revisión en este manuscrito. Las categorías bajo las cuales se organizaron los elementos de análisis fueron: sobrexpresión de bombas de eflujo y modificaciones en la enzima lanosterol 14-alfa-desmetilasa. Resultados: Los mecanismos de resistencia al fluconazol expresados por Candida glabrata están determinados principalmente por la regulación a la alza de bombas de adenosina-trifosfato Binding Cassette (ABC) y por la modificación del punto de unión con su blanco farmacológico: la enzima lanosterol 14-alfa-desmetilasa. Conclusión: Los mecanismos de resistencia expresados por Candida glabrata se asocian con la modificación estructural de la diana farmacológica y la sobreexpresión de bombas de eflujo de manera diferencial a otras especies. Se sugiere que Candida glabrata es intrínsecamente menos susceptible al fluconazol.
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13
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Kidd SE, Chen SCA, Meyer W, Halliday CL. A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready? Front Microbiol 2020; 10:2903. [PMID: 31993022 PMCID: PMC6971168 DOI: 10.3389/fmicb.2019.02903] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.
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Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, SA, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Research and Education Network, Westmead Hospital, Westmead, NSW, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
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14
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Tiew PY, Mac Aogain M, Ali NABM, Thng KX, Goh K, Lau KJX, Chotirmall SH. The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges. Mycopathologia 2020; 185:207-231. [PMID: 31894501 PMCID: PMC7223441 DOI: 10.1007/s11046-019-00413-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Micheál Mac Aogain
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | | | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Karlyn Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kenny J X Lau
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.
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15
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Antifungal Activity of Crude Extract from the Rhizome and Root of Smilacina japonica A. Gray. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 2019:5320203. [PMID: 31379963 PMCID: PMC6662278 DOI: 10.1155/2019/5320203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/01/2019] [Indexed: 11/18/2022]
Abstract
This study aimed to investigate the antifungal activity of hydroalcoholic extract from Smilacina japonica A. Gray (SJA) against different fungi. The minimum inhibitory concentration (MIC) for SJA was determined by the broth microdilution method. The antifungal effects of SJA against Candida albicans were further confirmed by cell growth test and time-kill curve test. The effects of SJA on the fungal morphology and ultrastructure were also evaluated. SJA has a broad-spectrum antifungal activity. The MICs of SJA against different fungi, including fluconazole-sensitive and -resistant Candida albicans, other Candida species, and Cryptococcus neoformans, ranged from 208 μg/ml to 1665 μg/ml. Furthermore, SJA displayed fungicidal activity against varied fungi and obviously inhibited the hyphal growth of fungi. The mechanism study revealed that the antifungal activity of SJA might be associated with its effect on the cell morphology and ultrastructure.
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16
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Carreté L, Ksiezopolska E, Gómez-Molero E, Angoulvant A, Bader O, Fairhead C, Gabaldón T. Genome Comparisons of Candida glabrata Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations. Front Microbiol 2019; 10:112. [PMID: 30809200 PMCID: PMC6379656 DOI: 10.3389/fmicb.2019.00112] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/18/2019] [Indexed: 11/13/2022] Open
Abstract
Candida glabrata is an opportunistic fungal pathogen that currently ranks as the second most common cause of candidiasis. Although the mechanisms underlying virulence and drug resistance in C. glabrata are now starting to be elucidated, we still lack a good understanding of how this yeast adapts during the course of an infection. Outstanding questions are whether the observed genomic plasticity of C. glabrata plays a role during infection, or what levels of genetic variation exist within an infecting clonal population. To shed light onto the genomic variation within infecting C. glabrata populations, we compared the genomes of 11 pairs and one trio of serial clinical isolates, each obtained from a single patient. Our results provide a catalog of genetic variations existing within clonal infecting isolates, and reveal an enrichment of non-synonymous changes in genes encoding cell-wall proteins. Genetic variation and the presence of non-synonymous mutations and copy number variations accumulated within the host, suggest that clonal populations entail a non-negligible level of genetic variation that may reflect selection processes that occur within the human body. As we show here, these genomic changes can underlie phenotypic differences in traits that are relevant for infection.
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Affiliation(s)
- Laia Carreté
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ewa Ksiezopolska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Emilia Gómez-Molero
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Adela Angoulvant
- Génétique Quantitative et Évolution Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Orsay, France.,Parasitology and Mycology Department, Bicêtre University Hospital, Paris-Sud University, Le Kremlin-Bicêtre, France
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Cécile Fairhead
- Génétique Quantitative et Évolution Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Orsay, France
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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17
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Pais P, Galocha M, Viana R, Cavalheiro M, Pereira D, Teixeira MC. Microevolution of the pathogenic yeasts Candida albicans and Candida glabrata during antifungal therapy and host infection. MICROBIAL CELL 2019; 6:142-159. [PMID: 30854392 PMCID: PMC6402363 DOI: 10.15698/mic2019.03.670] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Infections by the pathogenic yeasts Candida albicans and Candida glabrata are among the most common fungal diseases. The success of these species as human pathogens is contingent on their ability to resist antifungal therapy and thrive within the human host. C. glabrata is especially resilient to azole antifungal treatment, while C. albicans is best known for its wide array of virulence features. The core mechanisms that underlie antifungal resistance and virulence in these pathogens has been continuously addressed, but the investigation on how such mechanisms evolve according to each environment is scarcer. This review aims to explore current knowledge on micro-evolution experiments to several treatment and host-associated conditions in C. albicans and C. glabrata. The analysis of adaptation strategies that evolve over time will allow to better understand the mechanisms by which Candida species are able to achieve stable phenotypes in real-life scenarios, which are the ones that should constitute the most interesting drug targets.
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Affiliation(s)
- Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Mónica Galocha
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Romeu Viana
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Mafalda Cavalheiro
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Diana Pereira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Miguel Cacho Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
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18
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Sanglard D. Finding the needle in a haystack: Mapping antifungal drug resistance in fungal pathogen by genomic approaches. PLoS Pathog 2019; 15:e1007478. [PMID: 30703166 PMCID: PMC6355021 DOI: 10.1371/journal.ppat.1007478] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Dominique Sanglard
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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19
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Biswas C, Marcelino VR, Van Hal S, Halliday C, Martinez E, Wang Q, Kidd S, Kennedy K, Marriott D, Morrissey CO, Arthur I, Weeks K, Slavin MA, Sorrell TC, Sintchenko V, Meyer W, Chen SCA. Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types. Front Microbiol 2018; 9:2946. [PMID: 30559734 PMCID: PMC6287553 DOI: 10.3389/fmicb.2018.02946] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/16/2018] [Indexed: 12/31/2022] Open
Abstract
Candida glabrata is a pathogen with reduced susceptibility to azoles and echinocandins. Analysis by traditional multilocus sequence typing (MLST) has recognized an increasing number of sequence types (STs), which vary with geography. Little is known about STs of C. glabrata in Australia. Here, we utilized whole genome sequencing (WGS) to study the genetic diversity of 51 Australian C. glabrata isolates and sought associations between STs over two time periods (2002-2004, 2010-2017), and with susceptibility to fluconazole by principal component analysis (PCA). Antifungal susceptibility was determined using Sensititre YeastOneTM Y010 methodology and WGS performed on the NextSeq 500 platform (Illumina) with in silico MLST STs inferred by WGS data. Single nucleotide polymorphisms (SNPs) in genes linked to echinocandin, azole and 5-fluorocytosine resistance were analyzed. Of 51 isolates, WGS identified 18 distinct STs including four novel STs (ST123, ST124, ST126, and ST127). Four STs accounted for 49% of isolates (ST3, 15.7%; ST83, 13.7%; ST7, 9.8%; ST26, 9.8%). Split-tree network analysis resolved isolates to terminal branches; many of these comprised multiple isolates from disparate geographic settings but four branches contained Australian isolates only. ST3 isolates were common in Europe, United States and now Australia, whilst ST8 and ST19, relatively frequent in the United States, were rare/absent amongst our isolates. There was no association between ST distribution (genomic similarity) and the two time periods or with fluconazole susceptibility. WGS identified mutations in the FKS1 (S629P) and FKS2 (S663P) genes in three, and one, echinocandin-resistant isolate(s), respectively. Both mutations confer phenotypic drug resistance. Twenty-five percent (13/51) of isolates were fluconazole-resistant (MIC ≥ 64 μg/ml) of which 9 (18%) had non wild-type MICs to voriconazole and posaconazole. Multiple SNPs were present in genes linked to azole resistance such as CgPDR1 and CgCDR1, as well as several in MSH2; however, SNPs occurred in both azole-susceptible and azole-resistant isolates. Although no particular SNP in these genes was definitively associated with resistance, azole-resistant/non-wild type isolates had a propensity to harbor SNPs resulting in amino acid substitutions in Pdr1 beyond the first 250 amino acid positions. The presence of SNPs may be markers of STs. Our study shows the value of WGS for high-resolution sequence typing of C. glabrata, discovery of novel STs and potential to monitor trends in genetic diversity. WGS assessment for echinocandin resistance augments phenotypic susceptibility testing.
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Affiliation(s)
- Chayanika Biswas
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Vanessa R Marcelino
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Sebastiaan Van Hal
- Department of Infectious Diseases and Microbiology, New South Wales Health Pathology, Royal Prince Alfred Hospital, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Sarah Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, SA, Australia
| | - Karina Kennedy
- Department of Microbiology and Infectious Diseases, Canberra Hospital & Health Services, Australian National University Medical School, Canberra, ACT, Australia
| | - Deborah Marriott
- Department of Microbiology and Infectious Diseases, St Vincent's Hospital, Sydney, NSW, Australia
| | - C Orla Morrissey
- Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, VIC, Australia
| | - Ian Arthur
- Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Perth, WA, Australia
| | - Kerry Weeks
- Department of Microbiology and Infectious Diseases, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Monica A Slavin
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Tania C Sorrell
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW, Australia
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20
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Ksiezopolska E, Gabaldón T. Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens. Genes (Basel) 2018; 9:genes9090461. [PMID: 30235884 PMCID: PMC6162425 DOI: 10.3390/genes9090461] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023] Open
Abstract
Fungal infections, such as candidiasis caused by Candida, pose a problem of growing medical concern. In developed countries, the incidence of Candida infections is increasing due to the higher survival of susceptible populations, such as immunocompromised patients or the elderly. Existing treatment options are limited to few antifungal drug families with efficacies that vary depending on the infecting species. In this context, the emergence and spread of resistant Candida isolates are being increasingly reported. Understanding how resistance can evolve within naturally susceptible species is key to developing novel, more effective treatment strategies. However, in contrast to the situation of antibiotic resistance in bacteria, few studies have focused on the evolutionary mechanisms leading to drug resistance in fungal species. In this review, we will survey and discuss current knowledge on the genetic bases of resistance to antifungal drugs in Candida opportunistic pathogens. We will do so from an evolutionary genomics perspective, focusing on the possible evolutionary paths that may lead to the emergence and selection of the resistant phenotype. Finally, we will discuss the potential of future studies enabled by current developments in sequencing technologies, in vitro evolution approaches, and the analysis of serial clinical isolates.
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Affiliation(s)
- Ewa Ksiezopolska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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21
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Beardsley J, Halliday CL, Chen SCA, Sorrell TC. Responding to the emergence of antifungal drug resistance: perspectives from the bench and the bedside. Future Microbiol 2018; 13:1175-1191. [PMID: 30113223 PMCID: PMC6190174 DOI: 10.2217/fmb-2018-0059] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/01/2018] [Indexed: 12/15/2022] Open
Abstract
The incidence of serious fungal infections is increasing rapidly, and yet the rate of new drugs becoming available to treat them is slow. The limited therapeutic armamentarium is a challenge for clinicians, because the available drugs are often toxic, expensive, difficult to administer, ineffective or a combination of all four. Given this setting, the emergence of resistance is especially concerning, and a review of the topic is timely. Here we discuss antifungal drug resistance in Candida spp. and Aspergillus spp. with reference to the most commonly used first-line antifungal agents - azoles and echinocandins. We review the resistance mechanisms of the leading pathogens, how resistance can be identified in the diagnostic lab and the clinical implications of resistance once detected.
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Affiliation(s)
- Justin Beardsley
- Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney & Westmead Institute for Medical Research, Westmead, NSW, Australia
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Catriona L Halliday
- The Center for Infectious Diseases & Microbiology Laboratory Services, ICPMR Pathology West, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Sharon C-A Chen
- Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney & Westmead Institute for Medical Research, Westmead, NSW, Australia
- The Center for Infectious Diseases & Microbiology Laboratory Services, ICPMR Pathology West, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney & Westmead Institute for Medical Research, Westmead, NSW, Australia
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22
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Biswas C, Chen SCA, Halliday C, Martinez E, Rockett RJ, Wang Q, Timms VJ, Dhakal R, Sadsad R, Kennedy KJ, Playford G, Marriott DJ, Slavin MA, Sorrell TC, Sintchenko V. Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance. J Vis Exp 2017. [PMID: 29364212 DOI: 10.3791/56714] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Candida glabrata can rapidly acquire mutations that result in drug resistance, especially to azoles and echinocandins. Identification of genetic mutations is essential, as resistance detected in vitro can often be correlated with clinical failure. We examined the feasibility of using whole genome sequencing (WGS) for genome-wide analysis of antifungal drug resistance in C. glabrata. The aim was torecognize enablers and barriers in the implementation WGS and measure its effectiveness. This paper outlines the key quality control checkpoints and essential components of WGS methodology to investigate genetic markers associated with reduced susceptibility to antifungal agents. It also estimates the accuracy of data analysis and turn-around-time of testing. Phenotypic susceptibility of 12 clinical, and one ATCC strain of C. glabrata was determined through antifungal susceptibility testing. These included three isolate pairs, from three patients, that developed rise in drug minimum inhibitory concentrations. In two pairs, the second isolate of each pair developed resistance to echinocandins. The second isolate of the third pair developed resistance to 5-flucytosine. The remaining comprised of susceptible and azole resistant isolates. Single nucleotide polymorphisms (SNPs) in genes linked to echinocandin, azole and 5-flucytosine resistance were confirmed in resistant isolates through WGS using the next generation sequencing. Non-synonymous SNPs in antifungal resistance genes such as FKS1, FKS2, CgPDR1, CgCDR1 and FCY2 were identified. Overall, an average of 98% of the WGS reads of C. glabrata isolates mapped to the reference genome with about 75-fold read depth coverage. The turnaround time and cost were comparable to Sanger sequencing. In conclusion, WGS of C. glabrata was feasible in revealing clinically significant gene mutations involved in resistance to different antifungal drug classes without the need for multiple PCR/DNA sequencing reactions. This represents a positive step towards establishing WGS capability in the clinical laboratory for simultaneous detection of antifungal resistance conferring substitutions.
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Affiliation(s)
- Chayanika Biswas
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital;
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rebecca J Rockett
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Verlaine J Timms
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rajat Dhakal
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rosemarie Sadsad
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Karina J Kennedy
- Department of Microbiology and Infectious Diseases, Canberra Hospital and Health Services, Australian National University Medical School
| | - Geoffrey Playford
- Department of Microbiology and Infectious Diseases, Canberra Hospital and Health Services, Australian National University Medical School; Infection Management Services, Australian National University Medical School
| | - Deborah J Marriott
- Department of Microbiology and Infectious Diseases, St. Vincent's Hospital
| | - Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
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23
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Carreté L, Ksiezopolska E, Pegueroles C, Gómez-Molero E, Saus E, Iraola-Guzmán S, Loska D, Bader O, Fairhead C, Gabaldón T. Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans. Curr Biol 2017; 28:15-27.e7. [PMID: 29249661 PMCID: PMC5772174 DOI: 10.1016/j.cub.2017.11.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/13/2017] [Accepted: 11/09/2017] [Indexed: 12/30/2022]
Abstract
Candida glabrata is an opportunistic fungal pathogen that ranks as the second most common cause of systemic candidiasis. Despite its genus name, this yeast is more closely related to the model yeast Saccharomyces cerevisiae than to other Candida pathogens, and hence its ability to infect humans is thought to have emerged independently. Moreover, C. glabrata has all the necessary genes to undergo a sexual cycle but is considered an asexual organism due to the lack of direct evidence of sexual reproduction. To reconstruct the recent evolution of this pathogen and find footprints of sexual reproduction, we assessed genomic and phenotypic variation across 33 globally distributed C. glabrata isolates. We cataloged extensive copy-number variation, which particularly affects genes encoding cell-wall-associated proteins, including adhesins. The observed level of genetic variation in C. glabrata is significantly higher than that found in Candida albicans. This variation is structured into seven deeply divergent clades, which show recent geographical dispersion and large within-clade genomic and phenotypic differences. We show compelling evidence of recent admixture between differentiated lineages and of purifying selection on mating genes, which provides the first evidence for the existence of an active sexual cycle in this yeast. Altogether, our data point to a recent global spread of previously genetically isolated populations and suggest that humans are only a secondary niche for this yeast. Candida glabrata strains can be clustered into highly genetically divergent clades Genetic structure suggests a recent global spread of previously isolated populations The existence of sex in C. glabrata is supported by genomic footprints of selection Mating-type switching occurs in C. glabrata natural populations but is error prone
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Affiliation(s)
- Laia Carreté
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Ewa Ksiezopolska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Cinta Pegueroles
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Emilia Gómez-Molero
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, Göttingen 37075, Germany
| | - Ester Saus
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Susana Iraola-Guzmán
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Damian Loska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, Göttingen 37075, Germany
| | - Cecile Fairhead
- GQE-Le Moulon, INRA-Université Paris-Sud-CNRS-AgroParisTech, 91400 Orsay, France
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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24
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Antifungal Susceptibility Testing of Candida and Cryptococcus Species and Mechanisms of Resistance: Implications for Clinical Laboratories. CURRENT FUNGAL INFECTION REPORTS 2017. [DOI: 10.1007/s12281-017-0282-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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