1
|
Bergin S, Doorley LA, Rybak JM, Wolfe KH, Butler G, Cuomo CA, Rogers PD. Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes. Antimicrob Agents Chemother 2024:e0161923. [PMID: 38712935 DOI: 10.1128/aac.01619-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two persistent clinical lineages were identified. We identified copy number variation (CNV) of two genes, ERG11 and CDR1B, in resistant isolates. Two strains have a CNV at the ERG11 locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show that the annotated telomeric gene CDR1B is actually an artifactual in silico fusion of two highly similar neighboring CDR genes due to an assembly error in the C. parapsilosis CDC317 reference genome. We report highly variable copy numbers of the CDR1B region across the collection. Several strains have increased the expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the CDR gene family in the C. parapsilosis species complex, showing that it is a highly dynamic family.
Collapse
Affiliation(s)
- Sean Bergin
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Laura A Doorley
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kenneth H Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| |
Collapse
|
2
|
Rybak JM, Xie J, Martin-Vicente A, Guruceaga X, Thorn HI, Nywening AV, Ge W, Souza ACO, Shetty AC, McCracken C, Bruno VM, Parker JE, Kelly SL, Snell HM, Cuomo CA, Rogers PD, Fortwendel JR. A secondary mechanism of action for triazole antifungals in Aspergillus fumigatus mediated by hmg1. Nat Commun 2024; 15:3642. [PMID: 38684680 PMCID: PMC11059170 DOI: 10.1038/s41467-024-48029-2] [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: 06/27/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Triazole antifungals function as ergosterol biosynthesis inhibitors and are frontline therapy for invasive fungal infections, such as invasive aspergillosis. The primary mechanism of action of triazoles is through the specific inhibition of a cytochrome P450 14-α-sterol demethylase enzyme, Cyp51A/B, resulting in depletion of cellular ergosterol. Here, we uncover a clinically relevant secondary mechanism of action for triazoles within the ergosterol biosynthesis pathway. We provide evidence that triazole-mediated inhibition of Cyp51A/B activity generates sterol intermediate perturbations that are likely decoded by the sterol sensing functions of HMG-CoA reductase and Insulin-Induced Gene orthologs as increased pathway activity. This, in turn, results in negative feedback regulation of HMG-CoA reductase, the rate-limiting step of sterol biosynthesis. We also provide evidence that HMG-CoA reductase sterol sensing domain mutations previously identified as generating resistance in clinical isolates of Aspergillus fumigatus partially disrupt this triazole-induced feedback. Therefore, our data point to a secondary mechanism of action for the triazoles: induction of HMG-CoA reductase negative feedback for downregulation of ergosterol biosynthesis pathway activity. Abrogation of this feedback through acquired mutations in the HMG-CoA reductase sterol sensing domain diminishes triazole antifungal activity against fungal pathogens and underpins HMG-CoA reductase-mediated resistance.
Collapse
Affiliation(s)
- Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinhong Xie
- Graduate Program in Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Adela Martin-Vicente
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Xabier Guruceaga
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Harrison I Thorn
- Graduate Program in Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ashley V Nywening
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
- Integrated Program in Biomedical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Wenbo Ge
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ana C O Souza
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Amol C Shetty
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carrie McCracken
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Vincent M Bruno
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Josie E Parker
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Steven L Kelly
- Institute of Life Science, Swansea University Medical School, Swansea, Wales, UK
| | - Hannah M Snell
- Infectious Diseases and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina A Cuomo
- Infectious Diseases and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jarrod R Fortwendel
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA.
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA.
| |
Collapse
|
3
|
Coelho MA, David-Palma M, Shea T, Bowers K, McGinley-Smith S, Mohammad AW, Gnirke A, Yurkov AM, Nowrousian M, Sun S, Cuomo CA, Heitman J. Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion. bioRxiv 2024:2023.12.27.573464. [PMID: 38234769 PMCID: PMC10793447 DOI: 10.1101/2023.12.27.573464] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
Collapse
Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| |
Collapse
|
4
|
Bergin S, Doorley LA, Rybak JM, Wolfe KH, Butler G, Cuomo CA, Rogers PD. Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes. bioRxiv 2023:2023.12.13.571446. [PMID: 38168157 PMCID: PMC10760152 DOI: 10.1101/2023.12.13.571446] [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: 01/05/2024]
Abstract
We used whole-genome sequencing to analyse a collection of 35 fluconazole resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two probable outbreak groups were identified. We identified copy number variation of two genes, ERG11 and CDR1B, in resistant isolates. Two strains have a CNV at the ERG11 locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show the annotated telomeric gene CDR1B is actually an artefactual in silico fusion of two highly similar neighbouring CDR genes due to an assembly error in the C. parapsilosis CDC317 reference genome. We report highly variable copy numbers of the CDR1B region across the collection. Several strains have increased expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the CDR gene family in the C. parapsilosis species complex, showing that it is a highly dynamic family.
Collapse
Affiliation(s)
- Sean Bergin
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Laura A Doorley
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kenneth H Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
5
|
Schloss PD, Cuomo CA. More evidence of Impact Factor Mania. Microbiol Spectr 2023; 11:e0349623. [PMID: 37909768 PMCID: PMC10714965 DOI: 10.1128/spectrum.03496-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Affiliation(s)
- Patrick D. Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Christina A. Cuomo
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| |
Collapse
|
6
|
Sephton-Clark P, Temfack E, Tenor JL, Toffaletti DL, Loyse A, Molloy SF, Perfect JR, Bicanic T, Harrison TS, Lortholary O, Kouanfack C, Cuomo CA. Genetic diversity and microevolution in clinical Cryptococcus isolates from Cameroon. Med Mycol 2023; 61:myad116. [PMID: 37952096 PMCID: PMC10709296 DOI: 10.1093/mmy/myad116] [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: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
Cryptococcal meningitis is the second most common cause of death in people living with HIV/AIDS, yet we have a limited understanding of how cryptococcal isolates change over the course of infection. Cryptococcal infections are environmentally acquired, and the genetic diversity of these infecting isolates can also be geographically linked. Here, we employ whole genome sequences for 372 clinical Cryptococcus isolates from 341 patients with HIV-associated cryptococcal meningitis obtained via a large clinical trial, across both Malawi and Cameroon, to enable population genetic comparisons of isolates between countries. We see that isolates from Cameroon are highly clonal, when compared to those from Malawi, with differential rates of disruptive variants in genes with roles in DNA binding and energy use. For a subset of patients (22) from Cameroon, we leverage longitudinal sampling, with samples taken at days 7 and 14 post-enrollment, to interrogate the genetic changes that arise over the course of infection, and the genetic diversity of isolates within patients. We see disruptive variants arising over the course of infection in several genes, including the phagocytosis-regulating transcription factor GAT204. In addition, in 13% of patients sampled longitudinally, we see evidence for mixed infections. This approach identifies geographically linked genetic variation, signatures of microevolution, and evidence for mixed infections across a clinical cohort of patients affected by cryptococcal meningitis in Central Africa.
Collapse
Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Elvis Temfack
- Internal Medicine Unit, Douala General Hospital, Douala, Cameroon
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR 2000, Paris, France
| | - Jennifer L Tenor
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dena L Toffaletti
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Angela Loyse
- Institute of Infection and Immunity, St George's University of London, London, UK
- Clinical Academic Group in Infection, St George's University Hospital, London, UK
| | - Síle F Molloy
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - John R Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tihana Bicanic
- Institute of Infection and Immunity, St George's University of London, London, UK
- Clinical Academic Group in Infection, St George's University Hospital, London, UK
| | - Thomas S Harrison
- Institute of Infection and Immunity, St George's University of London, London, UK
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Olivier Lortholary
- Department of Infectious Diseases and Tropical Medicine, Paris Cité University, Necker-Enfants Malades Hospital, AP-HP, IHU Imagine, Paris, France
- Mycology Department and National Reference Center for Invasive Mycoses and Antifungals, Institut Pasteur, Paris, France
| | - Charles Kouanfack
- Department of Public Health, Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, Dschang, Cameroon
- Day Hospital, Hospital Central Yaoundé, Yaoundé, Cameroon
- Research Center for Emerging and Re-emerging Diseases, Cameroon Baptist Convention Health Services (CBCHS), Yaoundé, Cameroon
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
7
|
Sephton-Clark P, Nguyen T, Hoa NT, Ashton P, van Doorn HR, Ly VT, Le T, Cuomo CA. Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam. Genetics 2023; 224:iyad100. [PMID: 37226893 PMCID: PMC10411598 DOI: 10.1093/genetics/iyad100] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 03/29/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei, is difficult to treat and impacts those living in endemic regions of Southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome-wide association study approaches to a cohort of 336 T. marneffei isolates collected from patients who enrolled in the Itraconazole vs Amphotericin B for Talaromycosis trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multistrain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered during T. marneffei infection, providing an initial view of how pathogen genetics affects disease outcomes.
Collapse
Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thu Nguyen
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Oxford University, Ho Chi Minh City 749000, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX37LG, UK
- Microbiology department and Biological Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City 740500, Vietnam
| | - Philip Ashton
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool CH647TE, UK
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX37LG, UK
- Oxford University Clinical Research Unit, Oxford University, Hanoi 113000, Vietnam
| | - Vo Trieu Ly
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX37LG, UK
- Department of Medicine and Pharmacy, Hospital for Tropical Diseases, Ho Chi Minh City 749000, Vietnam
| | - Thuy Le
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC 27710, USA
- Tropical Medicine Research Center for Talaromycosis, Pham Ngoc Thach University of Medicine, Ho Chi Minh City 740500, Vietnam
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
8
|
Shea T, Mohabir JT, Kurbessoian T, Berdy B, Fontaine J, Gnirke A, Livny J, Stajich JE, Cuomo CA. Genome Sequence of Lichtheimia ornata, an Emerging Opportunistic Mucorales Pathogen. Microbiol Resour Announc 2023:e0033823. [PMID: 37289095 DOI: 10.1128/mra.00338-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Lichtheimia ornata is an emerging opportunistic Mucorales pathogen that is associated with fatal infections in immunocompromised individuals. While these environmentally acquired infections have rarely been reported to date, cases were noted in a recent analysis of coronavirus disease 2019 (COVID-19)-associated mucormycosis in India. Here, we report the annotated genome sequence of the environmental isolate CBS 291.66.
Collapse
Affiliation(s)
- Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jason T Mohabir
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Tania Kurbessoian
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Brittany Berdy
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - James Fontaine
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andreas Gnirke
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
9
|
Sephton-Clark P, Nguyen T, Hoa NT, Ashton P, van Doorn HR, Ly VT, Le T, Cuomo CA. Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam. bioRxiv 2023:2023.03.30.534926. [PMID: 37034632 PMCID: PMC10081260 DOI: 10.1101/2023.03.30.534926] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei , is difficult to treat and impacts those living in endemic regions of southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome wide association study approaches to a cohort of 336 T. marneffei isolates collected from patients who enrolled in the Itraconazole versus Amphotericin B for Talaromycosis (IVAP) trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multi-strain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered during T. marneffei infection, providing an initial view of how pathogen genetics affects disease outcomes.
Collapse
Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 02142
| | - Thu Nguyen
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, North Carolina, USA 27710
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom OX37LG
- Microbiology department and Biological Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Philip Ashton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK CH647TE
| | - H. Rogier van Doorn
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom OX37LG
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Vo Trieu Ly
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom OX37LG
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Thuy Le
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, North Carolina, USA 27710
- Tropical Medicine Research Center for Talaromycosis, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 02142
| |
Collapse
|
10
|
Li X, Muñoz JF, Gade L, Argimon S, Bougnoux ME, Bowers JR, Chow NA, Cuesta I, Farrer RA, Maufrais C, Monroy-Nieto J, Pradhan D, Uehling J, Vu D, Yeats CA, Aanensen DM, d’Enfert C, Engelthaler DM, Eyre DW, Fisher MC, Hagen F, Meyer W, Singh G, Alastruey-Izquierdo A, Litvintseva AP, Cuomo CA. Comparing genomic variant identification protocols for Candida auris. Microb Genom 2023; 9:mgen000979. [PMID: 37043380 PMCID: PMC10210944 DOI: 10.1099/mgen.0.000979] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/09/2023] [Indexed: 04/13/2023] Open
Abstract
Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of C. auris variant calling, a consensus VCF of genotypes discovered by 10 or more pipelines across these 35 diverse isolates and variants for 2 samples identified from whole-genome alignments. This study provides a foundation for evaluating SNP calling pipelines and developing best practices for future fungal genomic studies.
Collapse
Affiliation(s)
- Xiao Li
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - José F. Muñoz
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Silvia Argimon
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - Marie-Elisabeth Bougnoux
- Institut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
- Université Paris Cité, Hôpital Necker-Enfants-Malades, Unité de Parasitologie-Mycologie, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Jolene R. Bowers
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, AZ 86005, USA
| | - Nancy A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA, 30329, USA
| | - Isabel Cuesta
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Rhys A. Farrer
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, EX4 4PY, UK
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS USR 3756, Hub de Bioinformatique et Biostatistique, Paris, France
| | - Juan Monroy-Nieto
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, AZ 86005, USA
| | - Dibyabhaba Pradhan
- All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Jessie Uehling
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, Netherlands
| | - Corin A. Yeats
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - Christophe d’Enfert
- Institut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - David M. Engelthaler
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, AZ 86005, USA
| | - David W. Eyre
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Matthew C. Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Wieland Meyer
- Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
| | - Gagandeep Singh
- All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Anastasia P. Litvintseva
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA, 30329, USA
| | | |
Collapse
|
11
|
Yorki S, Shea T, Cuomo CA, Walker BJ, LaRocque RC, Manson AL, Earl AM, Worby CJ. Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes. Brief Bioinform 2023; 24:bbad050. [PMID: 36804804 PMCID: PMC10025444 DOI: 10.1093/bib/bbad050] [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: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (ARGs). For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even at low coverages, LR assemblies allowed for the placement of ARGs within longer, E. coli-specific contigs, thus pinpointing their taxonomic origin. HY assemblies identified resistance genes with high accuracy and had lower contiguity than LR assemblies. Each assembler type's strengths were maintained even when our isolate was spiked in with a competing strain, which fragmented and reduced the accuracy of all assemblies. For strain characterization and determining gene context, LR assembly is optimal, while for base-accurate gene identification, SR assemblers outperform other options. HY assembly offers contiguity and base accuracy, but requires generating data on multiple platforms, and may suffer high misassembly rates when strain diversity exists. Our results highlight the trade-offs associated with each approach for recovering low-abundance taxa, and that the optimal approach is goal-dependent.
Collapse
Affiliation(s)
- Sosie Yorki
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruce J Walker
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Applied Invention, LLC, Cambridge, MA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|
12
|
Chowdhary A, Gupta N, Wurster S, Kumar R, Mohabir JT, Tatavarthy S, Mittal V, Rani P, Barman P, Sachdeva N, Singh A, Sharma B, Jiang Y, Cuomo CA, Kontoyiannis DP. Multimodal analysis of the COVID-19-associated mucormycosis outbreak in Delhi, India indicates the convergence of clinical and environmental risk factors. Mycoses 2023; 66:515-526. [PMID: 36790120 DOI: 10.1111/myc.13578] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND The aetiology of the major outbreak of COVID-19-associated mucormycosis (CAM) in India in spring 2021 remains incompletely understood. Herein, we provide a multifaceted and multi-institutional analysis of clinical, pathogen-related, environmental and healthcare-related factors during CAM outbreak in the metropolitan New Delhi area. METHODS We reviewed medical records of all patients diagnosed with biopsy-proven CAM (n = 50) at 7 hospitals in the New Delhi, and NCR area in April-June 2021. Two multivariate logistic regression models were used to compare clinical characteristics of CAM cases with COVID-19-hospitalised contemporary patients as controls (n = 69). Additionally, meteorological parameters and mould spore concentrations in outdoor air were analysed. Selected hospital fomites were cultured. Mucorales isolates from CAM patients were analysed by ITS sequencing and whole-genome sequencing (WGS). RESULTS Independent risk factors for CAM identified by multivariate analysis were previously or newly diagnosed diabetes mellitus, active cancer and severe COVID-19 infection. Supplemental oxygen, remdesivir therapy and ICU admission for COVID-19 were associated with reduced CAM risk. The CAM incidence peak was preceded by an uptick in environmental spore concentrations in the preceding 3-4 weeks that correlated with increasing temperature, high evaporation and decreasing relative humidity. Rhizopus was the most common genus isolated, but we also identified two cases of the uncommon Mucorales, Lichtheimia ornata. WGS found no clonal population of patient isolates. No Mucorales were cultured from hospital fomites. CONCLUSIONS An intersection of host and environmental factors contributed to the emergence of CAM. Surrogates of access to advanced COVID-19 treatment were associated with lower CAM risk.
Collapse
Affiliation(s)
- Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India.,National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Nitesh Gupta
- Pulmonary Medicine, Safdarjung Hospital, Vardhman Mahavir Medical College, New Delhi, India
| | - Sebastian Wurster
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Raj Kumar
- Department of Pulmonary Medicine, National Centre of Respiratory Allergy Asthma and Immunology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Jason T Mohabir
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Vikas Mittal
- Pulmonary Medicine, Max Super Specialty Hospital, New Delhi, India
| | - Preeti Rani
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | | | - Neelam Sachdeva
- Department of Microbiology, Rajiv Gandhi Cancer Institute & Research Center, New Delhi, India
| | - Ashutosh Singh
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India.,National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Brijesh Sharma
- Department of Medicine, Ram Manohar Lohia Hospital & Postgraduate Institute of Medical Education and Research, New Delhi, India
| | - Ying Jiang
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dimitrios P Kontoyiannis
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
13
|
Abstract
Genomic approaches are widely applied to study the genetic basis of antifungal drug resistance in clinical isolates and experimental studies. Whole-genome sequencing of clinical isolates can comprehensively identify mutations associated with drug resistance and their frequency across fungal populations. In addition, genome comparison of serially collected isolates, such as from patient samples or in vitro drug selection experiments, will identify a small number of changes that can be evaluated for association with drug resistance. Here, we provide a detailed protocol for the computational analysis of genome sequences to identify variants associated with drug resistance.
Collapse
Affiliation(s)
- Aina Martinez-Zurita
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
14
|
Sephton-Clark P, Tenor JL, Toffaletti DL, Meyers N, Giamberardino C, Molloy SF, Palmucci JR, Chan A, Chikaonda T, Heyderman R, Hosseinipour M, Kalata N, Kanyama C, Kukacha C, Lupiya D, Mwandumba HC, Harrison T, Bicanic T, Perfect JR, Cuomo CA. Genomic Variation across a Clinical Cryptococcus Population Linked to Disease Outcome. mBio 2022; 13:e0262622. [PMID: 36354332 PMCID: PMC9765290 DOI: 10.1128/mbio.02626-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 09/16/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022] Open
Abstract
Cryptococcus neoformans is the causative agent of cryptococcosis, a disease with poor patient outcomes that accounts for approximately 180,000 deaths each year. Patient outcomes may be impacted by the underlying genetics of the infecting isolate; however, our current understanding of how genetic diversity contributes to clinical outcomes is limited. Here, we leverage clinical, in vitro growth and genomic data for 284 C. neoformans isolates to identify clinically relevant pathogen variants within a population of clinical isolates from patients with human immunodeficiency virus (HIV)-associated cryptococcosis in Malawi. Through a genome-wide association study (GWAS) approach, we identify variants associated with the fungal burden and the growth rate. We also find both small and large-scale variation, including aneuploidy, associated with alternate growth phenotypes, which may impact the course of infection. Genes impacted by these variants are involved in transcriptional regulation, signal transduction, glycosylation, sugar transport, and glycolysis. We show that growth within the central nervous system (CNS) is reliant upon glycolysis in an animal model and likely impacts patient mortality, as the CNS yeast burden likely modulates patient outcome. Additionally, we find that genes with roles in sugar transport are enriched in regions under selection in specific lineages of this clinical population. Further, we demonstrate that genomic variants in two genes identified by GWAS impact virulence in animal models. Our approach identifies links between the genetic variation in C. neoformans and clinically relevant phenotypes and animal model pathogenesis, thereby shedding light on specific survival mechanisms within the CNS and identifying the pathways involved in yeast persistence. IMPORTANCE Infection outcomes for cryptococcosis, most commonly caused by C. neoformans, are influenced by host immune responses as well as by host and pathogen genetics. Infecting yeast isolates are genetically diverse; however, we lack a deep understanding of how this diversity impacts patient outcomes. To better understand both clinical isolate diversity and how diversity contributes to infection outcomes, we utilize a large collection of clinical C. neoformans samples that were isolated from patients enrolled in a clinical trial across 3 hospitals in Malawi. By combining whole-genome sequence data, clinical data, and in vitro growth data, we utilize genome-wide association approaches to examine the genetic basis of virulence. Genes with significant associations display virulence attributes in both murine and rabbit models, demonstrating that our approach can identify potential links between genetic variants and patho-biologically significant phenotypes.
Collapse
Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jennifer L. Tenor
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dena L. Toffaletti
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nancy Meyers
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Charles Giamberardino
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Síle F. Molloy
- Centre for Global Health, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
- Clinical Academic Group in Infection, St George's University Hospital, London, United Kingdom
| | - Julia R. Palmucci
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Adrienne Chan
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Tarsizio Chikaonda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert Heyderman
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mina Hosseinipour
- UNC Project Malawi, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Newton Kalata
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Cecilia Kanyama
- UNC Project Malawi, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Christopher Kukacha
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Duncan Lupiya
- Tisungane Clinic, Zomba Central Hospital, Zomba, Malawi
| | - Henry C. Mwandumba
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Thomas Harrison
- Centre for Global Health, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
- Clinical Academic Group in Infection, St George's University Hospital, London, United Kingdom
| | - Tihana Bicanic
- Centre for Global Health, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
- Clinical Academic Group in Infection, St George's University Hospital, London, United Kingdom
| | - John R. Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
15
|
Rybak JM, Cuomo CA, Rogers PD. The molecular and genetic basis of antifungal resistance in the emerging fungal pathogen Candida auris. Curr Opin Microbiol 2022; 70:102208. [PMID: 36242897 PMCID: PMC10364995 DOI: 10.1016/j.mib.2022.102208] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 01/25/2023]
Abstract
Fungal infections are responsible for significant morbidity and mortality. Resistance to the limited number of agents in the antifungal armamentarium among pathogenic fungi represents a growing public health threat. Particularly concerning is the emerging fungal pathogen Candida auris that frequently exhibits resistance to the triazole class of antifungals and amphotericin B, and for which isolates resistant to all of the major antifungal classes have been reported. In this brief review, we provide an overview of what is currently known about the molecular and genetic basis for antifungal resistance in this fungal pathogen.
Collapse
Affiliation(s)
- Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
16
|
Huang S, Tang YW, Cuomo CA, Wang H, Jia X. Editorial: New threats of antibiotic-resistant bacteria and fungi. Front Med (Lausanne) 2022; 9:1078940. [DOI: 10.3389/fmed.2022.1078940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/08/2022] [Indexed: 11/20/2022] Open
|
17
|
Alanio A, Snell HM, Cordier C, Desnos-Olivier M, Dellière S, Aissaoui N, Sturny-Leclère A, Da Silva E, Eblé C, Rouveau M, Thégat M, Zebiche W, Lafaurie M, Denis B, Touratier S, Benyamina M, Dudoignon E, Hamane S, Cuomo CA, Dépret F. First Patient-to-Patient Intrahospital Transmission of Clade I Candida auris in France Revealed after a Two-Month Incubation Period. Microbiol Spectr 2022; 10:e0183322. [PMID: 36094221 PMCID: PMC9604096 DOI: 10.1128/spectrum.01833-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/25/2022] [Indexed: 12/31/2022] Open
Abstract
Candida auris is a recently described emerging pathogen in hospital settings. Five genetic clades have been delineated, with each clade being isolated from specific geographic regions. We here describe the first transmission between 2 patients (P0 and P1) of a clade I C. auris strain imported into our burn intensive care unit from the Middle East. The strains have been investigated with whole-genome sequencing, which validated the high similarity of the genomes between isolates from P0 and P1. We repeatedly screened the two patients and contact patients (i.e., other patients present in the same hospital ward at the time of the first positive sample from P0 or P1; n = 49; 268 tests) with fungal culture and a C. auris-specific quantitative PCR assay to assess transmission patterns. We observed that P1 developed C. auris colonization between 41 and 61 days after potential exposure to P0 contamination, despite three negative screening tests as recommended by our national authorities. This study illustrates that transmission of C. auris between patients can lead to long-term incubation times before the detection of colonization. The recommended screening strategy may not be optimal and should be improved in the light of our findings. IMPORTANCE While large outbreaks of C. auris in hospital settings have been described, few clear cases of direct transmission have been documented. We here investigated the transmission of C. auris clade I between two patients with a 41- to 61-day delay between exposure and the development of colonization. This may lead to changes in the recommendations concerning treatment of C. auris cases, as an incubation period of this length is one of the first to be reported.
Collapse
Affiliation(s)
- Alexandre Alanio
- Institut Pasteur, Université Paris Cité, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, UMR2000, Paris, France
- Laboratoire de parasitologie-mycologie, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Paris, France
- Université Paris Cité, Paris, France
| | | | - Camille Cordier
- Laboratoire de parasitologie-mycologie, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Paris, France
| | - Marie Desnos-Olivier
- Institut Pasteur, Université Paris Cité, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, UMR2000, Paris, France
| | - Sarah Dellière
- Institut Pasteur, Université Paris Cité, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, UMR2000, Paris, France
- Laboratoire de parasitologie-mycologie, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Paris, France
- Université Paris Cité, Paris, France
| | - Nesrine Aissaoui
- Laboratoire de parasitologie-mycologie, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Paris, France
| | - Aude Sturny-Leclère
- Institut Pasteur, Université Paris Cité, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, UMR2000, Paris, France
| | - Elodie Da Silva
- Laboratoire de parasitologie-mycologie, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Paris, France
| | - Cyril Eblé
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Martine Rouveau
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Micheline Thégat
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Widad Zebiche
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Matthieu Lafaurie
- Equipe Opérationnelle d’Hygiène, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Blandine Denis
- Equipe Opérationnelle d’Hygiène, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sophie Touratier
- Service de maladies infectieuses et tropicales, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mourad Benyamina
- Pharmacie centrale, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Département d’anesthésie réanimation, réanimation chirurgicale et centre de traitement des brûlés, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Emmanuel Dudoignon
- Pharmacie centrale, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Département d’anesthésie réanimation, réanimation chirurgicale et centre de traitement des brûlés, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Samia Hamane
- Laboratoire de parasitologie-mycologie, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Paris, France
| | | | - François Dépret
- Université Paris Cité, Paris, France
- Pharmacie centrale, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Département d’anesthésie réanimation, réanimation chirurgicale et centre de traitement des brûlés, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- FHU PROMICE, Paris, France
- INSERM UMR-942, Paris, France
- Réseau INI-CRCT, Nancy, France
| |
Collapse
|
18
|
Carolus H, Sofras D, Sephton-Clark P, Goossens L, Chen A, Pierson S, Romero CL, Subotić A, Meis JF, Cuomo CA, Van Dijck P. S2.5d Exploring multidrug resistance, fitness compensation, and collateral sensitivity in Candida auris : Fight fire with fire? Med Mycol 2022. [PMCID: PMC9515916 DOI: 10.1093/mmy/myac072.s2.5d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
S2.5 Rare yeasts, September 21, 2022, 3:00 PM - 4:30 PM Candida auris (C. auris) is a recently emerged human fungal pathogen of growing concern due to its ability to acquire extensive multidrug resistance (MDR) to all four antifungal drug classes. The unprecedented extent of MDR in C. auris, suggests accelerated resistance evolution, novel mechanisms of resistance, and/or potential fitness compensation. Despite being the first fungus to be officially considered an urgent antimicrobial resistance threat by the CDC (US), insights into the resistance mechanisms and evolutionary dynamics of C. auris are still scarce. By using high-throughput in vitro experimental evolution with various antifungal drugs, we have obtained a library of resistant strains from four different clades. Through both genome and targeted sequencing, we have discovered novel mutations, especially for polyene resistance, which indicate new mechanisms of resistance and fitness compensation. For the validation of mutations, we have optimized a recyclable CRISPR/Cas9 tool for C. auris based on the C. albicans HIS-FLP system. By mapping drug susceptibility responses of evolved strains across a library of several antifungals and repurposed drugs, we have discovered trends of cross-resistance and collateral sensitivity. Both phenomena have been extensively studied in tumors and bacteria but remain unexplored in fungi. In the light of these observations, we explore novel treatment schemes that prevent antifungal drug resistance development in C. auris and other pathogenic fungi.
Collapse
Affiliation(s)
- Hans Carolus
- Laboratory of Molecular Cell Biology , Department of Biology, KU Leuven, Leuven , Belgium
| | - Dimitrios Sofras
- Laboratory of Molecular Cell Biology , Department of Biology, KU Leuven, Leuven , Belgium
| | | | - Louise Goossens
- Laboratory of Molecular Cell Biology , Department of Biology, KU Leuven, Leuven , Belgium
| | - Alicia Chen
- Laboratory of Molecular Cell Biology , Department of Biology, KU Leuven, Leuven , Belgium
| | - Siebe Pierson
- Laboratory of Molecular Cell Biology , Department of Biology, KU Leuven, Leuven , Belgium
| | - Celia Lobo Romero
- Laboratory of Molecular Cell Biology , Department of Biology, KU Leuven, Leuven , Belgium
| | - Ana Subotić
- Laboratory of Molecular Cell Biology , Department of Biology, KU Leuven, Leuven , Belgium
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases , Canisius-Wilhelmina Hospital, Nijmegen , The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ , Nijmegen , The Netherlands
| | | | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology , Department of Biology, KU Leuven, Leuven , Belgium
| |
Collapse
|
19
|
Gow NAR, Johnson C, Berman J, Coste AT, Cuomo CA, Perlin DS, Bicanic T, Harrison TS, Wiederhold N, Bromley M, Chiller T, Edgar K. The importance of antimicrobial resistance in medical mycology. Nat Commun 2022; 13:5352. [PMID: 36097014 PMCID: PMC9466305 DOI: 10.1038/s41467-022-32249-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/22/2022] [Indexed: 01/08/2023] Open
Abstract
Prior to the SARS-CoV-2 pandemic, antibiotic resistance was listed as the major global health care priority. Some analyses, including the O'Neill report, have predicted that deaths due to drug-resistant bacterial infections may eclipse the total number of cancer deaths by 2050. Although fungal infections remain in the shadow of public awareness, total attributable annual deaths are similar to, or exceeds, global mortalities due to malaria, tuberculosis or HIV. The impact of fungal infections has been exacerbated by the steady rise of antifungal drug resistant strains and species which reflects the widespread use of antifungals for prophylaxis and therapy, and in the case of azole resistance in Aspergillus, has been linked to the widespread agricultural use of antifungals. This review, based on a workshop hosted by the Medical Research Council and the University of Exeter, illuminates the problem of antifungal resistance and suggests how this growing threat might be mitigated.
Collapse
Affiliation(s)
- Neil A R Gow
- MRC Centre for Medical Mycology, School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Carolyn Johnson
- Medical Research Council, Polaris House, Swindon, SN2 1FL, UK.
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 418 Britannia Building, Ramat Aviv, 69978, Israel
| | - Alix T Coste
- Microbiology Institute, University Hospital Lausanne, rue du Bugnon 48, 1011, Lausanne, Switzerland
| | - Christina A Cuomo
- (CAC) Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian health, Nutley, NJ, 07110, USA
| | - Tihana Bicanic
- Institute of Infection and Immunity, St George's University of London, London, SW17 0RE, UK
- Clinical Academic Group in Infection, St George's University Hospitals NHS Foundation Trust, London, SW17 0QT, UK
| | - Thomas S Harrison
- MRC Centre for Medical Mycology, School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK
- Institute of Infection and Immunity, St George's University of London, London, SW17 0RE, UK
- Clinical Academic Group in Infection, St George's University Hospitals NHS Foundation Trust, London, SW17 0QT, UK
| | - Nathan Wiederhold
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Mike Bromley
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK
| | - Tom Chiller
- Center for Disease Control and Prevention Mycotic Disease Branch 1600 Clifton Rd, MSC-09, Atlanta, 30333, GA, USA
| | - Keegan Edgar
- Center for Disease Control and Prevention Mycotic Disease Branch 1600 Clifton Rd, MSC-09, Atlanta, 30333, GA, USA
| |
Collapse
|
20
|
Matzko ME, Sephton-Clark PCS, Young EL, Jhaveri TA, Martinsen MA, Mojica E, Boykin R, Pierce VM, Cuomo CA, Bhattacharyya RP. A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture. Med Mycol 2022; 60:6674770. [PMID: 36002024 PMCID: PMC9989835 DOI: 10.1093/mmy/myac065] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 01/24/2023] Open
Abstract
Invasive fungal infections are increasingly common and carry high morbidity and mortality, yet fungal diagnostics lag behind bacterial diagnostics in rapidly identifying the causal pathogen. We previously devised a fluorescent hybridization-based assay to identify bacteria within hours directly from blood culture bottles without subculture, called phylogeny-informed rRNA-based strain identification (Phirst-ID). Here, we adapt this approach to unambiguously identify 11 common pathogenic Candida species, including C. auris, with 100% accuracy from laboratory culture (33 of 33 strains in a reference panel, plus 33 of 33 additional isolates tested in a validation panel). In a pilot study on 62 consecutive positive clinical blood cultures from two hospitals that showed yeast on Gram stain, Candida Phirst-ID matched the clinical laboratory result for 58 of 59 specimens represented in the 11-species reference panel, without misclassifying the 3 off-panel species. It also detected mixed Candida species in 2 of these 62 specimens, including the one discordant classification, that were not identified by standard clinical microbiology workflows; in each case the presence of both species was validated by both clinical and experimental data. Finally, in three specimens that grew both bacteria and yeast, we paired our prior bacterial probeset with this new Candida probeset to detect both pathogen types using Phirst-ID. This simple, robust assay can provide accurate Candida identification within hours directly from blood culture bottles, and the conceptual approach holds promise for pan-microbial identification in a single workflow. LAY SUMMARY Candida bloodstream infections cause considerable morbidity and mortality, yet slow diagnostics delay recognition, worsening patient outcomes. We develop and validate a novel molecular approach to accurately identify Candida species directly from blood culture one day faster than standard workflows.
Collapse
Affiliation(s)
- Michelle E Matzko
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Poppy C S Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Eleanor L Young
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Tulip A Jhaveri
- Microbiology Laboratory, Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Melanie A Martinsen
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Evan Mojica
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rich Boykin
- NanoString Technologies, Inc., Seattle, WA 98109, USA
| | - Virginia M Pierce
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Roby P Bhattacharyya
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| |
Collapse
|
21
|
Helmstetter N, Chybowska AD, Delaney C, Da Silva Dantas A, Gifford H, Wacker T, Munro C, Warris A, Jones B, Cuomo CA, Wilson D, Ramage G, Farrer RA. Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets. Genetics 2022; 221:iyac031. [PMID: 35199143 PMCID: PMC9071574 DOI: 10.1093/genetics/iyac031] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
Candida glabrata is the second most common etiological cause of worldwide systemic candidiasis in adult patients. Genome analysis of 68 isolates from 8 hospitals across Scotland, together with 83 global isolates, revealed insights into the population genetics and evolution of C. glabrata. Clinical isolates of C. glabrata from across Scotland are highly genetically diverse, including at least 19 separate sequence types that have been recovered previously in globally diverse locations, and 1 newly discovered sequence type. Several sequence types had evidence for ancestral recombination, suggesting transmission between distinct geographical regions has coincided with genetic exchange arising in new clades. Three isolates were missing MATα1, potentially representing a second mating type. Signatures of positive selection were identified in every sequence type including enrichment for epithelial adhesins thought to facilitate fungal adhesin to human epithelial cells. In patent microevolution was identified from 7 sets of recurrent cases of candidiasis, revealing an enrichment for nonsynonymous and frameshift indels in cell surface proteins. Microevolution within patients also affected epithelial adhesins genes, and several genes involved in drug resistance including the ergosterol synthesis gene ERG4 and the echinocandin target FKS1/2, the latter coinciding with a marked drop in fluconazole minimum inhibitory concentration. In addition to nuclear genome diversity, the C. glabrata mitochondrial genome was particularly diverse, with reduced conserved sequence and conserved protein-encoding genes in all nonreference ST15 isolates. Together, this study highlights the genetic diversity within the C. glabrata population that may impact virulence and drug resistance, and 2 major mechanisms generating this diversity: microevolution and genetic exchange/recombination.
Collapse
Affiliation(s)
- Nicolas Helmstetter
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | | | - Christopher Delaney
- School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Hugh Gifford
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Theresa Wacker
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Carol Munro
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Adilia Warris
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Brian Jones
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | | | - Duncan Wilson
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Gordon Ramage
- School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rhys A Farrer
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
22
|
Salamzade R, Manson AL, Walker BJ, Brennan-Krohn T, Worby CJ, Ma P, He LL, Shea TP, Qu J, Chapman SB, Howe W, Young SK, Wurster JI, Delaney ML, Kanjilal S, Onderdonk AB, Bittencourt CE, Gussin GM, Kim D, Peterson EM, Ferraro MJ, Hooper DC, Shenoy ES, Cuomo CA, Cosimi LA, Huang SS, Kirby JE, Pierce VM, Bhattacharyya RP, Earl AM. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance. Genome Med 2022; 14:37. [PMID: 35379360 PMCID: PMC8981930 DOI: 10.1186/s13073-022-01040-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 07/22/2021] [Accepted: 03/22/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. METHODS To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years. RESULTS Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. CONCLUSIONS Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.
Collapse
Affiliation(s)
- Rauf Salamzade
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.14003.360000 0001 2167 3675Present Address: Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Abigail L. Manson
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Bruce J. Walker
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,Applied Invention, Cambridge, MA 02139 USA
| | - Thea Brennan-Krohn
- grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Colin J. Worby
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Peijun Ma
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Lorrie L. He
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Terrance P. Shea
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - James Qu
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sinéad B. Chapman
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Whitney Howe
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sarah K. Young
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Jenna I. Wurster
- grid.38142.3c000000041936754XDepartment of Ophthalmology, Department of Microbiology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, 240 Charles St., Boston, MA 02114 USA
| | - Mary L. Delaney
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Sanjat Kanjilal
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, MA 02215 USA
| | - Andrew B. Onderdonk
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Cassiana E. Bittencourt
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA 92868 USA
| | - Gabrielle M. Gussin
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - Diane Kim
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - Ellena M. Peterson
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA 92868 USA
| | - Mary Jane Ferraro
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - David C. Hooper
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Erica S. Shenoy
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Christina A. Cuomo
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Lisa A. Cosimi
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Susan S. Huang
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - James E. Kirby
- grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Virginia M. Pierce
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Roby P. Bhattacharyya
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Ashlee M. Earl
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| |
Collapse
|
23
|
Passer AR, Clancey SA, Shea T, David-Palma M, Averette AF, Boekhout T, Porcel BM, Nowrousian M, Cuomo CA, Sun S, Heitman J, Coelho MA. Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex. eLife 2022; 11:79114. [PMID: 35713948 PMCID: PMC9296135 DOI: 10.7554/elife.79114] [Citation(s) in RCA: 4] [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: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
<title>eLife digest</title>. Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved a variety of strategies to reproduce. Normally, fungi reproduce in one of two ways: either they reproduce asexually, with one individual producing a new individual identical to itself, or they reproduce sexually, with two individuals of different 'mating types' contributing to produce a new individual. However, individuals of some species exhibit 'homothallism' or self-fertility: these individuals can produce reproductive cells that are universally compatible, and therefore can reproduce sexually with themselves or with any other cell in the population. Homothallism has evolved multiple times throughout the fungal kingdom, suggesting it confers advantage when population numbers are low or mates are hard to find. Yet some homothallic fungi been overlooked compared to heterothallic species, whose mating types have been well characterised. Understanding the genetic basis of homothallism and how it evolved in different species can provide insights into pathogenic species that cause fungal disease. With that in mind, Passer, Clancey et al. explored the genetic basis of homothallism in Cryptococcus depauperatus, a close relative of C. neoformans, a species that causes fungal infections in humans. A combination of genetic sequencing techniques and experiments were applied to analyse, compare, and manipulate C. depauperatus' genome to see how this species evolved self-fertility. Passer, Clancey et al. showed that C. depauperatus evolved the ability to reproduce sexually by itself via a unique evolutionary pathway. The result is a form of homothallism never reported in fungi before. C. depauperatus lost some of the genes that control mating in other species of fungi, and acquired genes from the opposing mating types of a heterothallic ancestor to become self-fertile. Passer, Clancey et al. also found that, unlike other Cryptococcus species that switch between asexual and sexual reproduction, C. depauperatus grows only as long, branching filaments called hyphae, a sexual form. The species reproduces sexually with itself throughout its life cycle and is unable to produce a yeast (asexual) form, in contrast to other closely related species. This work offers new insights into how different modes of sexual reproduction have evolved in fungi. It also provides another interesting case of how genome plasticity and evolutionary pressures can produce similar outcomes, homothallism, via different evolutionary paths. Lastly, assembling the complete genome of C. depauperatus will foster comparative studies between pathogenic and non-pathogenic Cryptococcus species.
Collapse
Affiliation(s)
- Andrew Ryan Passer
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Terrance Shea
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity InstituteUtrechtNetherlands,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of AmsterdamAmsterdamNetherlands
| | - Betina M Porcel
- Génomique Métabolique, CNRS, University Evry, Université Paris-SaclayEvryFrance
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität BochumBochumGermany
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| |
Collapse
|
24
|
Bagal UR, Phan J, Welsh RM, Misas E, Wagner D, Gade L, Litvintseva AP, Cuomo CA, Chow NA. MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris. Methods Mol Biol 2022; 2517:215-228. [PMID: 35674957 DOI: 10.1007/978-1-0716-2417-3_17] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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] [Indexed: 06/15/2023]
Abstract
Candida auris is an urgent public health threat characterized by high drug-resistant rates and rapid spread in healthcare settings worldwide. As part of the C. auris response, molecular surveillance has helped public health officials track the global spread and investigate local outbreaks. Here, we describe whole-genome sequencing analysis methods used for routine C. auris molecular surveillance in the United States; methods include reference selection, reference preparation, quality assessment and control of sequencing reads, read alignment, and single-nucleotide polymorphism calling and filtration. We also describe the newly developed pipeline MycoSNP, a portable workflow for performing whole-genome sequencing analysis of fungal organisms including C. auris.
Collapse
Affiliation(s)
- Ujwal R Bagal
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John Phan
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rory M Welsh
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Elizabeth Misas
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nancy A Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| |
Collapse
|
25
|
Shea TP, Cuomo CA. Generating Complete Genome Assemblies of Candida auris. Methods Mol Biol 2022; 2517:205-214. [PMID: 35674956 DOI: 10.1007/978-1-0716-2417-3_16] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genomic studies of Candida auris are underpinned by the generation of high-quality genome assemblies. These reference genomes have been essential for investigations of the evolution and epidemiology of this emerging fungal pathogen. In addition to genomic epidemiology studies of local outbreaks and analysis of the global emergence of this species, comparisons of genomes of isolates from the five major clades have revealed differences in gene content and genomic structure. Here, we provide a detailed protocol for generating complete genome assemblies for C. auris.
Collapse
Affiliation(s)
- Terrance P Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
26
|
Carolus H, Pierson S, Mun?oz JF, Subotić A, Cruz RB, Cuomo CA, Van Dijck P. Genome-wide analysis of experimentally evolved Candida auris reveals multiple novel mechanisms of multidrug-resistance. Access Microbiol 2021. [DOI: 10.1099/acmi.cc2021.po0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Candida auris is globally recognized as an opportunistic fungal pathogen of high concern, due to its extensive multidrug-resistance (MDR). Still, molecular mechanisms of MDR are largely unexplored. This is the first account of genome wide evolution of MDR in C. auris obtained through serial in vitro exposure to azoles, polyenes and echinocandins. We show the stepwise accumulation of multiple novel mutations in genes known and unknown in antifungal drug resistance, albeit almost all new for C. auris. Echinocandin resistance was accompanied by a codon deletion in FKS1hot spot 1 and a substitution in FKS1 ‘novel’ hot spot 3. Mutations in ERG3 and CIS2 further increased the echinocandin MIC. Decreased azole susceptibility was linked to a mutation in transcription factor TAC1b and overexpression of the drug efflux pump Cdr1; a segmental duplication of chromosome 1 containing ERG11; and a whole chromosome 5 duplication, which contains TAC1b. The latter was associated with increased expression of ERG11, TAC1band CDR2, but not CDR1. The simultaneous emergence of nonsense mutations in ERG3 and ERG11 was shown to decrease amphotericin B susceptibility, accompanied with fluconazole cross resistance. A mutation in MEC3, a gene mainly known for its role in DNA damage homeostasis, further increased the polyene MIC. Overall, this study shows the alarming potential and diversity for MDR development in C. auris, even in a clade until now not associated with MDR (clade II),hereby stressing its clinical importance and the urge for future research.
Collapse
Affiliation(s)
- Hans Carolus
- VIB Center for Microbiology, Belgium
- KU Leuven, Belgium
| | | | | | - Ana Subotić
- VIB Center for Microbiology, Belgium
- KU Leuven, Belgium
| | | | | | | |
Collapse
|
27
|
Romsdahl J, Schultzhaus Z, Cuomo CA, Dong H, Abeyratne-Perera H, Hervey WJ, Wang Z. Phenotypic Characterization and Comparative Genomics of the Melanin-Producing Yeast Exophiala lecanii-corni Reveals a Distinct Stress Tolerance Profile and Reduced Ribosomal Genetic Content. J Fungi (Basel) 2021; 7:1078. [PMID: 34947060 PMCID: PMC8709033 DOI: 10.3390/jof7121078] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
The black yeast Exophiala lecanii-corni of the order Chaetothyriales is notable for its ability to produce abundant quantities of DHN-melanin. While many other Exophiala species are frequent causal agents of human infection, E. lecanii-corni CBS 102400 lacks the thermotolerance requirements that enable pathogenicity, making it appealing for use in targeted functional studies and biotechnological applications. Here, we report the stress tolerance characteristics of E. lecanii-corni, with an emphasis on the influence of melanin on its resistance to various forms of stress. We find that E. lecanii-corni has a distinct stress tolerance profile that includes variation in resistance to temperature, osmotic, and oxidative stress relative to the extremophilic and pathogenic black yeast Exophiala dermatitidis. Notably, the presence of melanin substantially impacts stress resistance in E. lecanii-corni, while this was not found to be the case in E. dermatitidis. The cellular context, therefore, influences the role of melanin in stress protection. In addition, we present a detailed analysis of the E. lecanii-corni genome, revealing key differences in functional genetic content relative to other ascomycetous species, including a significant decrease in abundance of genes encoding ribosomal proteins. In all, this study provides insight into how genetics and physiology may underlie stress tolerance and enhances understanding of the genetic diversity of black yeasts.
Collapse
Affiliation(s)
- Jillian Romsdahl
- National Research Council Postdoctoral Research Associate, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - Zachary Schultzhaus
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;
| | - Hong Dong
- Biotechnology Branch, CCDC Army Research Laboratory, Adelphi, MD 20783, USA;
| | - Hashanthi Abeyratne-Perera
- American Society for Engineering Education Postdoctoral Research Associate, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - W. Judson Hervey
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
| | - Zheng Wang
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
| |
Collapse
|
28
|
Rybak JM, Barker KS, Muñoz JF, Parker JE, Ahmad S, Mokaddas E, Abdullah A, Elhagracy RS, Kelly SL, Cuomo CA, Rogers PD. In vivo emergence of high-level resistance during treatment reveals the first identified mechanism of amphotericin B resistance in Candida auris. Clin Microbiol Infect 2021; 28:838-843. [PMID: 34915074 DOI: 10.1016/j.cmi.2021.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/08/2021] [Revised: 11/16/2021] [Accepted: 11/27/2021] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Candida auris has emerged as a healthcare-associated and multidrug-resistant fungal pathogen of great clinical concern. While as many as 50% of C. auris clinical isolates are reported to be resistant to amphotericin B, to date, no mechanisms contributing to this resistance have been identified. Here we describe the clinical case in which high-level amphotericin B resistance was acquired in vivo during therapy and undertake molecular and genetic studies to identify and characterize the genetic determinant of resistance. METHODS Whole genome sequencing was performed on four C. auris isolates obtained from a single patient case. Cas9-mediated genetic manipulations were then used to generate mutant strains harboring mutations of interest, and these strains were subsequently subjected to amphotericin B susceptibility testing, and comprehensive sterol profiling. RESULTS A novel mutation in C. auris sterol-methyltransferase gene, ERG6, was found to be associated with amphotericin B resistance, and this mutation alone conferred a >32-fold increase in amphotericin B resistance. Comprehensive sterol profiling revealed an abrogation of ergosterol biosynthesis and a corresponding accumulation of cholesta-type sterols in isolates and strains harboring the clinically-derived ERG6 mutation. CONCLUSIONS Together these findings definitively demonstrate mutations in C. auris ERG6 as the first identified mechanism of clinical amphotericin B resistance in C. auris and represent a significant step forward in the understanding of antifungal resistance in this emerging public health threat.
Collapse
Affiliation(s)
- Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Katherine S Barker
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - José F Muñoz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Josie E Parker
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea, UK
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait; Department of Microbiology, Ibn Sina Hospital, Shuwaikh, Kuwait
| | - Aneesa Abdullah
- Department of Microbiology, Ibn Sina Hospital, Shuwaikh, Kuwait
| | - Rehab S Elhagracy
- Department of Haematology, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Steve L Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea, UK
| | | | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
29
|
Kelly M, Pasmans F, Muñoz JF, Shea TP, Carranza S, Cuomo CA, Martel A. Diversity, multifaceted evolution, and facultative saprotrophism in the European Batrachochytrium salamandrivorans epidemic. Nat Commun 2021; 12:6688. [PMID: 34795258 PMCID: PMC8602665 DOI: 10.1038/s41467-021-27005-0] [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: 04/06/2021] [Accepted: 10/28/2021] [Indexed: 01/06/2023] Open
Abstract
While emerging fungi threaten global biodiversity, the paucity of fungal genome assemblies impedes thoroughly characterizing epidemics and developing effective mitigation strategies. Here, we generate de novo genomic assemblies for six outbreaks of the emerging pathogen Batrachochytrium salamandrivorans (Bsal). We reveal the European epidemic currently damaging amphibian populations to comprise multiple, highly divergent lineages demonstrating isolate-specific adaptations and metabolic capacities. In particular, we show extensive gene family expansions and acquisitions, through a variety of evolutionary mechanisms, and an isolate-specific saprotrophic lifecycle. This finding both explains the chytrid's ability to divorce transmission from host density, producing Bsal's enigmatic host population declines, and is a key consideration in developing successful mitigation measures.
Collapse
Affiliation(s)
- Moira Kelly
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium.
| | - Frank Pasmans
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Jose F. Muñoz
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, 02142 MA USA
| | - Terrance P. Shea
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, 02142 MA USA
| | - Salvador Carranza
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Christina A. Cuomo
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, 02142 MA USA
| | - An Martel
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium.
| |
Collapse
|
30
|
Schwartz IS, Muñoz JF, Kenyon CR, Govender NP, McTaggart L, Maphanga TG, Richardson S, Becker P, Cuomo CA, McEwen JG, Sigler L. Blastomycosis in Africa and the Middle East: A Comprehensive Review of Reported Cases and Reanalysis of Historical Isolates Based on Molecular Data. Clin Infect Dis 2021; 73:e1560-e1569. [PMID: 32766820 PMCID: PMC8492124 DOI: 10.1093/cid/ciaa1100] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Blastomycosis has been reported from countries in Africa and the Middle East, but a decades-long debate has persisted regarding whether this is the same disease known in North America and caused by Blastomyces dermatitidis and Blastomyces gilchristii. METHODS We reviewed published cases of human and veterinary blastomycosis from Africa and the Middle East. We abstracted epidemiological and clinical features of cases, including sites of disease, diagnosis, management, outcomes, and, where available, genetic and antigenic typing of case isolates. In addition, we sequenced nucleic acids from 9 clinical isolates from Africa deposited in global collections as B. dermatitidis; for 5, we sequenced the internal transcribed spacer regions, and for the other 4 we sequenced the whole genomes. RESULTS We identified 172 unique human patients with blastomycosis, including 159 patients from 25 African countries and 12 patients from 5 Middle Eastern countries, and also identified 7 reports of veterinary blastomycosis. In humans, cutaneous disease predominated (n = 100/137, 73%), followed by pulmonary (n = 73/129, 57%) and osteoarticular involvement (n = 61/128, 48%). Unusual direct microscopy/histopathological presentations included short hyphal fragments in tissues (n = 23/129, 18%). There were 34 genotyped case isolates that comprised 4 species: Blastomyces percursus (n = 22, 65%), from 8 countries throughout all regions; Blastomyces emzantsi (n = 9, 26%), from South Africa; B. dermatitidis (n = 1, 3%), from the Democratic Republic of Congo; and B. gilchristii (n = 2, 6%), from South Africa and Zimbabwe. CONCLUSIONS Blastomycosis occurs throughout Africa and the Middle East and is caused predominantly by B. percursus and, at least in South Africa, B. emzantsi, resulting in distinct clinical and pathological patterns of disease.
Collapse
Affiliation(s)
- Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jose F Muñoz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chris R Kenyon
- Clinical Sciences Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Nelesh P Govender
- National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Tsidiso G Maphanga
- National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Susan Richardson
- Division of Microbiology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pierre Becker
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Juan G McEwen
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Lynne Sigler
- Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Alberta, Canada
- UAMH Centre for Global Microfungal Diversity, University of Toronto, Ontario, Canada
| |
Collapse
|
31
|
Carolus H, Jacobs S, Lobo Romero C, Deparis Q, Cuomo CA, Meis JF, Van Dijck P. Diagnostic Allele-Specific PCR for the Identification of Candida auris Clades. J Fungi (Basel) 2021; 7:754. [PMID: 34575792 PMCID: PMC8471779 DOI: 10.3390/jof7090754] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/19/2022] Open
Abstract
Candida auris is an opportunistic pathogenic yeast that emerged worldwide during the past decade. This fungal pathogen poses a significant public health threat due to common multidrug resistance (MDR), alarming hospital outbreaks, and frequent misidentification. Genomic analyses have identified five distinct clades that are linked to five geographic areas of origin and characterized by differences in several phenotypic traits such as virulence and drug resistance. Typing of C. auris strains and the identification of clades can be a powerful tool in molecular epidemiology and might be of clinical importance by estimating outbreak and MDR potential. As C. auris has caused global outbreaks, including in low-income countries, typing C. auris strains quickly and inexpensively is highly valuable. We report five allele-specific polymerase chain reaction (AS-PCR) assays for the identification of C. auris and each of the five described clades of C. auris based on conserved mutations in the internal transcribed spacer (ITS) rDNA region and a clade-specific gene cluster. This PCR method provides a fast, cheap, sequencing-free diagnostic tool for the identification of C. auris, C. auris clades, and potentially, the discovery of new clades.
Collapse
Affiliation(s)
- Hans Carolus
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium; (H.C.); (S.J.); (C.L.R.)
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium;
| | - Stef Jacobs
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium; (H.C.); (S.J.); (C.L.R.)
| | - Celia Lobo Romero
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium; (H.C.); (S.J.); (C.L.R.)
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium;
| | - Quinten Deparis
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium;
- Laboratory for Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | | | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 Nijmegen, The Netherlands;
- Centre of Expertise in Mycology Radboudumc/CWZ, 6532 Nijmegen, The Netherlands
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium; (H.C.); (S.J.); (C.L.R.)
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium;
| |
Collapse
|
32
|
Fellers JP, Sakthikumar S, He F, McRell K, Bakkeren G, Cuomo CA, Kolmer JA. Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations. G3 (Bethesda) 2021; 11:jkab219. [PMID: 34544127 PMCID: PMC8496273 DOI: 10.1093/g3journal/jkab219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/01/2021] [Indexed: 11/14/2022]
Abstract
The wheat leaf rust fungus, Puccinia triticina Erikss., is a worldwide pathogen of tetraploid durum and hexaploid wheat. Many races of P. triticina differ for virulence to specific leaf rust resistance genes and are found in most wheat-growing regions of the world. Wheat cultivars with effective leaf rust resistance exert selection pressure on P. triticina populations for virulent race types. The objectives of this study were to examine whole-genome sequence data of 121 P. triticina isolates and to gain insight into race evolution. The collection included isolates comprising of many different race phenotypes collected worldwide from common and durum wheat. One isolate from wild wheat relative Aegilops speltoides and two from Ae. cylindrica were also included for comparison. Based on 121,907 informative variants identified relative to the reference Race 1-1 genome, isolates were clustered into 11 major lineages with 100% bootstrap support. The isolates were also grouped based on variation in 1311 predicted secreted protein genes. In gene-coding regions, all groups had high ratios of nonsynonymous to synonymous mutations and nonsense to readthrough mutations. Grouping of isolates based on two main variation principle components for either genome-wide variation or variation just within the secreted protein genes, indicated similar groupings. Variants were distributed across the entire genome, not just within the secreted protein genes. Our results suggest that recurrent mutation and selection play a major role in differentiation within the clonal lineages.
Collapse
Affiliation(s)
- John P Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | | | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Katie McRell
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Guus Bakkeren
- Agriculture and Agri Food Canada, Summerland, BC V0H1Z0, USA
| | | | - James A Kolmer
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN 55108, USA
| |
Collapse
|
33
|
Gröhs Ferrareze PA, Maufrais C, Silva Araujo Streit R, Priest SJ, Cuomo CA, Heitman J, Staats CC, Janbon G. Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss. G3 (Bethesda) 2021; 11:6080769. [PMID: 33585873 PMCID: PMC8022950 DOI: 10.1093/g3journal/jkaa070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/24/2020] [Indexed: 12/15/2022]
Abstract
Evaluating the quality of a de novo annotation of a complex fungal genome based on RNA-seq data remains a challenge. In this study, we sequentially optimized a Cufflinks-CodingQuary-based bioinformatics pipeline fed with RNA-seq data using the manually annotated model pathogenic yeasts Cryptococcus neoformans and Cryptococcus deneoformans as test cases. Our results show that the quality of the annotation is sensitive to the quantity of RNA-seq data used and that the best quality is obtained with 5–10 million reads per RNA-seq replicate. We also showed that the number of introns predicted is an excellent a priori indicator of the quality of the final de novo annotation. We then used this pipeline to annotate the genome of the RNAi-deficient species Cryptococcus deuterogattii strain R265 using RNA-seq data. Dynamic transcriptome analysis revealed that intron retention is more prominent in C. deuterogattii than in the other RNAi-proficient species C. neoformans and C. deneoformans. In contrast, we observed that antisense transcription was not higher in C. deuterogattii than in the two other Cryptococcus species. Comparative gene content analysis identified 21 clusters enriched in transcription factors and transporters that have been lost. Interestingly, analysis of the subtelomeric regions in these three annotated species identified a similar gene enrichment, reminiscent of the structure of primary metabolic clusters. Our data suggest that there is active exchange between subtelomeric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential.
Collapse
Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Département de Mycologie, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, F-75015 Paris, France.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 15005, Brazil
| | - Corinne Maufrais
- Département de Mycologie, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, F-75015 Paris, France.,Département Biologie Computationnelle, Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Rodrigo Silva Araujo Streit
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 15005, Brazil
| | - Shelby J Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Charley Christian Staats
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 15005, Brazil
| | - Guilhem Janbon
- Département de Mycologie, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, F-75015 Paris, France
| |
Collapse
|
34
|
Geiser DM, Al-Hatmi AMS, Aoki T, Arie T, Balmas V, Barnes I, Bergstrom GC, Bhattacharyya MK, Blomquist CL, Bowden RL, Brankovics B, Brown DW, Burgess LW, Bushley K, Busman M, Cano-Lira JF, Carrillo JD, Chang HX, Chen CY, Chen W, Chilvers M, Chulze S, Coleman JJ, Cuomo CA, de Beer ZW, de Hoog GS, Del Castillo-Múnera J, Del Ponte EM, Diéguez-Uribeondo J, Di Pietro A, Edel-Hermann V, Elmer WH, Epstein L, Eskalen A, Esposto MC, Everts KL, Fernández-Pavía SP, da Silva GF, Foroud NA, Fourie G, Frandsen RJN, Freeman S, Freitag M, Frenkel O, Fuller KK, Gagkaeva T, Gardiner DM, Glenn AE, Gold SE, Gordon TR, Gregory NF, Gryzenhout M, Guarro J, Gugino BK, Gutierrez S, Hammond-Kosack KE, Harris LJ, Homa M, Hong CF, Hornok L, Huang JW, Ilkit M, Jacobs A, Jacobs K, Jiang C, Jiménez-Gasco MDM, Kang S, Kasson MT, Kazan K, Kennell JC, Kim HS, Kistler HC, Kuldau GA, Kulik T, Kurzai O, Laraba I, Laurence MH, Lee T, Lee YW, Lee YH, Leslie JF, Liew ECY, Lofton LW, Logrieco AF, López-Berges MS, Luque AG, Lysøe E, Ma LJ, Marra RE, Martin FN, May SR, McCormick SP, McGee C, Meis JF, Migheli Q, Mohamed Nor NMI, Monod M, Moretti A, Mostert D, Mulè G, Munaut F, Munkvold GP, Nicholson P, Nucci M, O'Donnell K, Pasquali M, Pfenning LH, Prigitano A, Proctor RH, Ranque S, Rehner SA, Rep M, Rodríguez-Alvarado G, Rose LJ, Roth MG, Ruiz-Roldán C, Saleh AA, Salleh B, Sang H, Scandiani MM, Scauflaire J, Schmale DG, Short DPG, Šišić A, Smith JA, Smyth CW, Son H, Spahr E, Stajich JE, Steenkamp E, Steinberg C, Subramaniam R, Suga H, Summerell BA, Susca A, Swett CL, Toomajian C, Torres-Cruz TJ, Tortorano AM, Urban M, Vaillancourt LJ, Vallad GE, van der Lee TAJ, Vanderpool D, van Diepeningen AD, Vaughan MM, Venter E, Vermeulen M, Verweij PE, Viljoen A, Waalwijk C, Wallace EC, Walther G, Wang J, Ward TJ, Wickes BL, Wiederhold NP, Wingfield MJ, Wood AKM, Xu JR, Yang XB, Yli-Mattila T, Yun SH, Zakaria L, Zhang H, Zhang N, Zhang SX, Zhang X. Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex. Phytopathology 2021; 111:1064-1079. [PMID: 33200960 DOI: 10.1094/phyto-08-20-0330-le] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.
Collapse
Affiliation(s)
- David M Geiser
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | | | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Tsutomu Arie
- Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Virgilio Balmas
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Gary C Bergstrom
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
| | | | - Cheryl L Blomquist
- Plant Pest Diagnostics Branch, California Department of Food and Agriculture, Sacramento, CA 95832, U.S.A
| | - Robert L Bowden
- Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), Manhattan, KS 66506, U.S.A
| | - Balázs Brankovics
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Daren W Brown
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Lester W Burgess
- Sydney Institute of Agriculture, Faculty of Science, University of Sydney, Sydney, Australia
| | - Kathryn Bushley
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Mark Busman
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - José F Cano-Lira
- Mycology Unit and IISPV, Universitat Rovira i Virgili Medical School, Reus, Spain
| | - Joseph D Carrillo
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chi-Yu Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, People's Republic of China
| | - Martin Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Sofia Chulze
- Research Institute on Mycology and Mycotoxicology, National Scientific and Technical Research Council, National University of Rio Cuarto, Rio Cuarto, Córdoba, Argentina
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | | | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - G Sybren de Hoog
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | | | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | | | - Wade H Elmer
- Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Akif Eskalen
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | | | - Kathryne L Everts
- Wye Research and Education Center, University of Maryland, Queenstown, MD 21658, U.S.A
| | - Sylvia P Fernández-Pavía
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | | | - Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - Gerda Fourie
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rasmus J N Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Stanley Freeman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Kevin K Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, U.S.A
| | - Tatiana Gagkaeva
- Laboratory of Mycology and Phytopathology, All-Russian Institute of Plant Protection, St. Petersburg-Pushkin, Russia
| | | | - Anthony E Glenn
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Scott E Gold
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Thomas R Gordon
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Nancy F Gregory
- Department of Plant and Soil Sciences, University of Delaware, DE 19716, U.S.A
| | - Marieka Gryzenhout
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Josep Guarro
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Universitat Rovira i Virgili, Reus, Spain
| | - Beth K Gugino
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | | | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Linda J Harris
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Mónika Homa
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences, University of Szeged, Szeged, Hungary
| | - Cheng-Fang Hong
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - László Hornok
- Institute of Plant Protection, Szent István University, Gödöllő, Hungary
| | - Jenn-Wen Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Sarıçam, Adana, Turkey
| | - Adriaana Jacobs
- Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - Karin Jacobs
- Department of Microbiology, Stellenbosch University, Matieland, South Africa
| | - Cong Jiang
- College of Plant Protection, Northwest Agriculture and Forestry University, Xianyang, People's Republic of China
| | - María Del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Matthew T Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, U.S.A
| | - Kemal Kazan
- CSIRO Agriculture and Food, St. Lucia, Australia
| | - John C Kennell
- Biology Department, St. Louis University, St. Louis, MO 63101, U.S.A
| | - Hye-Seon Kim
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - H Corby Kistler
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Gretchen A Kuldau
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Oliver Kurzai
- German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Imane Laraba
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Matthew H Laurence
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Theresa Lee
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - John F Leslie
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Edward C Y Liew
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Lily W Lofton
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Antonio F Logrieco
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Manuel S López-Berges
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Alicia G Luque
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Referencia de Micología, Universidad Nacional de Rosario, Rosario, Argentina
| | - Erik Lysøe
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Høgskoleveien, Ås, Norway
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Robert E Marra
- Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
| | - Frank N Martin
- Crop Improvement and Protection Research Unit, ARS-USDA, Salinas, CA 93905, U.S.A
| | - Sara R May
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Susan P McCormick
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Chyanna McGee
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Jacques F Meis
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Quirico Migheli
- Dipartimento di Agraria and Nucleo Ricerca Desertificazione, Università degli Studi di Sassari, Sassari, Italy
| | - N M I Mohamed Nor
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Michel Monod
- Laboratoire de Mycologie, Service de Dermatologie, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Antonio Moretti
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Diane Mostert
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Giuseppina Mulè
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | | | - Gary P Munkvold
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Marcio Nucci
- Hospital Universitário, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Milan, Italy
| | - Ludwig H Pfenning
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais State, Brazil
| | - Anna Prigitano
- Department of Biomedical Sciences for Health, University of Milano, Milan, Italy
| | - Robert H Proctor
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Stéphane Ranque
- Institut Hospitalier Universitaire Méditerranée Infection, Aix Marseille University, Marseille, France
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A
| | - Martijn Rep
- Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerardo Rodríguez-Alvarado
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Lindy Joy Rose
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Mitchell G Roth
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, U.S.A
| | - Carmen Ruiz-Roldán
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Amgad A Saleh
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Baharuddin Salleh
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - María Mercedes Scandiani
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Referencia de Micología, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jonathan Scauflaire
- Centre de Recherche et de Formation Agronomie, Haute Ecole Louvain en Hainaut, Montignies-sur-Sambre, Belgium
| | - David G Schmale
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, U.S.A
| | | | - Adnan Šišić
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Jason A Smith
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, U.S.A
| | - Christopher W Smyth
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902, U.S.A
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Ellie Spahr
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, U.S.A
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Emma Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Christian Steinberg
- Agroécologie, AgroSup Dijon, INRAE, University of Bourgogne Franche-Comté, Dijon, France
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, Japan
| | - Brett A Summerell
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Antonella Susca
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Cassandra L Swett
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | | | - Terry J Torres-Cruz
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Anna M Tortorano
- Department of Biomedical Sciences for Health, University of Milano, Milan, Italy
| | - Martin Urban
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Lisa J Vaillancourt
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Gary E Vallad
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | - Theo A J van der Lee
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Dan Vanderpool
- Department of Biology, Indiana University, Bloomington, IN 47405, U.S.A
| | - Anne D van Diepeningen
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Martha M Vaughan
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Eduard Venter
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, South Africa
| | - Marcele Vermeulen
- Department of Microbial Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Paul E Verweij
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Altus Viljoen
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Cees Waalwijk
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Emma C Wallace
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Grit Walther
- German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Jie Wang
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94702
| | - Todd J Ward
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Brian L Wickes
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Nathan P Wiederhold
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Ana K M Wood
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Jin-Rong Xu
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Xiao-Bing Yang
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Sung-Hwan Yun
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Republic of Korea
| | - Latiffah Zakaria
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, People's Republic of China
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, U.S.A
| | - Sean X Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, U.S.A
| | - Xue Zhang
- College of Plant Protection, Northwest Agriculture and Forestry University, Xianyang, People's Republic of China
| |
Collapse
|
35
|
Muñoz JF, Welsh RM, Shea T, Batra D, Gade L, Howard D, Rowe LA, Meis JF, Litvintseva AP, Cuomo CA. Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris. Genetics 2021; 218:iyab029. [PMID: 33769478 PMCID: PMC8128392 DOI: 10.1093/genetics/iyab029] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
Candida auris is an emerging fungal pathogen of rising concern due to global spread, the ability to cause healthcare-associated outbreaks, and antifungal resistance. Genomic analyses revealed that early contemporaneously detected cases of C. auris were geographically stratified into four major clades. While Clades I, III, and IV are responsible for ongoing outbreaks of invasive and multidrug-resistant infections, Clade II, also termed the East Asian clade, consists primarily of cases of ear infection, is often susceptible to all antifungal drugs, and has not been associated with outbreaks. Here, we generate chromosome-level assemblies of twelve isolates representing the phylogenetic breadth of these four clades and the only isolate described to date from Clade V. This Clade V genome is highly syntenic with those of Clades I, III, and IV, although the sequence is highly divergent from the other clades. Clade II genomes appear highly rearranged, with translocations occurring near GC-poor regions, and large subtelomeric deletions in most chromosomes, resulting in a substantially different karyotype. Rearrangements and deletion lengths vary across Clade II isolates, including two from a single patient, supporting ongoing genome instability. Deleted subtelomeric regions are enriched in Hyr/Iff-like cell-surface proteins, novel candidate cell wall proteins, and an ALS-like adhesin. Cell wall proteins from these families and other drug-related genes show clade-specific signatures of selection in Clades I, III, and IV. Subtelomeric dynamics and the conservation of cell surface proteins in the clades responsible for global outbreaks causing invasive infections suggest an explanation for the different phenotypes observed between clades.
Collapse
Affiliation(s)
- José F Muñoz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rory M Welsh
- Mycotic Diseases Branch, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Dakota Howard
- Division of Scientific Resources, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Lori A Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | | | | |
Collapse
|
36
|
Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC. Best practices on the differential expression analysis of multi-species RNA-seq. Genome Biol 2021; 22:121. [PMID: 33926528 PMCID: PMC8082843 DOI: 10.1186/s13059-021-02337-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 10/21/2020] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.
Collapse
Affiliation(s)
- Matthew Chung
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vincent M Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - José F Muñoz
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Greenebaum Cancer Center, University of Maryland, Baltimore, MD, 21201, USA.
| |
Collapse
|
37
|
Fu MS, Liporagi-Lopes LC, Dos Santos SR, Tenor JL, Perfect JR, Cuomo CA, Casadevall A. Amoeba Predation of Cryptococcus neoformans Results in Pleiotropic Changes to Traits Associated with Virulence. mBio 2021; 12:e00567-21. [PMID: 33906924 PMCID: PMC8092252 DOI: 10.1128/mbio.00567-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/30/2021] [Indexed: 11/20/2022] Open
Abstract
Amoeboid predators, such as amoebae, are proposed to select for survival traits in soil microbes such as Cryptococcus neoformans; these traits can also function in animal virulence by defeating phagocytic immune cells, such as macrophages. Consistent with this notion, incubation of various fungal species with amoebae enhanced their virulence, but the mechanisms involved are unknown. In this study, we exposed three strains of C. neoformans (1 clinical and 2 environmental) to predation by Acanthamoeba castellanii for prolonged times and then analyzed surviving colonies phenotypically and genetically. Surviving colonies comprised cells that expressed either pseudohyphal or yeast phenotypes, which demonstrated variable expression of traits associated with virulence, such as capsule size, urease production, and melanization. Phenotypic changes were associated with aneuploidy and DNA sequence mutations in some amoeba-passaged isolates, but not in others. Mutations in the gene encoding the oligopeptide transporter (CNAG_03013; OPT1) were observed among amoeba-passaged isolates from each of the three strains. Isolates derived from environmental strains gained the capacity for enhanced macrophage toxicity after amoeba selection and carried mutations on the CNAG_00570 gene encoding Pkr1 (AMP-dependent protein kinase regulator) but manifested reduced virulence in mice because they elicited more effective fungal-clearing immune responses. Our results indicate that C. neoformans survival under constant amoeba predation involves the generation of strains expressing pleiotropic phenotypic and genetic changes. Given the myriad potential predators in soils, the diversity observed among amoeba-selected strains suggests a bet-hedging strategy whereby variant diversity increases the likelihood that some will survive predation.IMPORTANCECryptococcus neoformans is a ubiquitous environmental fungus that is also a leading cause of fatal fungal infection in humans, especially among immunocompromised patients. A major question in the field is how an environmental yeast such as C. neoformans becomes a human pathogen when it has no need for an animal host in its life cycle. Previous studies showed that C. neoformans increases its pathogenicity after interacting with its environmental predator amoebae. Amoebae, like macrophages, are phagocytic cells that are considered an environmental training ground for pathogens to resist macrophages, but the mechanism by which C. neoformans changes its virulence through interactions with protozoa is unknown. Our study indicates that fungal survival in the face of amoeba predation is associated with the emergence of pleiotropic phenotypic and genomic changes that increase the chance of fungal survival, with this diversity suggesting a bet-hedging strategy to ensure that some forms survive.
Collapse
Affiliation(s)
- Man Shun Fu
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Livia C Liporagi-Lopes
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Samuel R Dos Santos
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Jennifer L Tenor
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - John R Perfect
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| |
Collapse
|
38
|
Carolus H, Pierson S, Muñoz JF, Subotić A, Cruz RB, Cuomo CA, Van Dijck P. Genome-Wide Analysis of Experimentally Evolved Candida auris Reveals Multiple Novel Mechanisms of Multidrug Resistance. mBio 2021; 12:e03333-20. [PMID: 33820824 PMCID: PMC8092288 DOI: 10.1128/mbio.03333-20] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
Candida auris is globally recognized as an opportunistic fungal pathogen of high concern, due to its extensive multidrug resistance (MDR). Still, molecular mechanisms of MDR are largely unexplored. This is the first account of genome-wide evolution of MDR in C. auris obtained through serial in vitro exposure to azoles, polyenes, and echinocandins. We show the stepwise accumulation of copy number variations and novel mutations in genes both known and unknown in antifungal drug resistance. Echinocandin resistance was accompanied by a codon deletion in FKS1 hot spot 1 and a substitution in FKS1 "novel" hot spot 3. Mutations in ERG3 and CIS2 further increased the echinocandin MIC. Decreased azole susceptibility was linked to a mutation in transcription factor TAC1b and overexpression of the drug efflux pump Cdr1, a segmental duplication of chromosome 1 containing ERG11, and a whole chromosome 5 duplication, which contains TAC1b The latter was associated with increased expression of ERG11, TAC1b, and CDR2 but not CDR1 The simultaneous emergence of nonsense mutations in ERG3 and ERG11 was shown to decrease amphotericin B susceptibility, accompanied with fluconazole cross-resistance. A mutation in MEC3, a gene mainly known for its role in DNA damage homeostasis, further increased the polyene MIC. Overall, this study shows the alarming potential for and diversity of MDR development in C. auris, even in a clade until now not associated with MDR (clade II), stressing its clinical importance and the urge for future research.IMPORTANCECandida auris is a recently discovered human fungal pathogen and has shown an alarming potential for developing multi- and pan-resistance toward all classes of antifungals most commonly used in the clinic. Currently, C. auris has been globally recognized as a nosocomial pathogen of high concern due to this evolutionary potential. So far, this is the first study in which the stepwise progression of multidrug resistance (MDR) in C. auris is monitored in vitro Multiple novel mutations in known resistance genes and genes previously not or vaguely associated with drug resistance reveal rapid MDR evolution in a C. auris clade II isolate. Additionally, this study shows that in vitro experimental evolution can be a powerful tool to discover new drug resistance mechanisms, although it has its limitations.
Collapse
Affiliation(s)
- Hans Carolus
- VIB Center for Microbiology, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - José F Muñoz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ana Subotić
- VIB Center for Microbiology, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Rita B Cruz
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Patrick Van Dijck
- VIB Center for Microbiology, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| |
Collapse
|
39
|
Barker BM, Cuomo CA, Govender NP. Editorial: Genomic Characterization of Emerging Human Fungal Pathogens. Front Genet 2021; 12:674765. [PMID: 33841515 PMCID: PMC8027301 DOI: 10.3389/fgene.2021.674765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/01/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | | | - Nelesh P Govender
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
40
|
Cissé OH, Ma L, Dekker JP, Khil PP, Youn JH, Brenchley JM, Blair R, Pahar B, Chabé M, Van Rompay KKA, Keesler R, Sukura A, Hirsch V, Kutty G, Liu Y, Peng L, Chen J, Song J, Weissenbacher-Lang C, Xu J, Upham NS, Stajich JE, Cuomo CA, Cushion MT, Kovacs JA. Genomic insights into the host specific adaptation of the Pneumocystis genus. Commun Biol 2021; 4:305. [PMID: 33686174 PMCID: PMC7940399 DOI: 10.1038/s42003-021-01799-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 11/21/2022] Open
Abstract
Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans. Cissé, Ma et al. utilize genomic data from Pneumocystis species infecting macaques, rabbit, dogs and rats to investigate the molecular basis of host specificity in Pneumocystis. Their analyses provide insight to the specific adaptations enabling the infection of humans by P. jirovecii.
Collapse
Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Jung-Ho Youn
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Robert Blair
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Rebekah Keesler
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Antti Sukura
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Li Peng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nathan S Upham
- Arizona State University, School of Life Sciences, Tempe, ARI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside-California, Riverside, CA, USA
| | - Christina A Cuomo
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melanie T Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| |
Collapse
|
41
|
Farrer RA, Borman AM, Inkster T, Fisher MC, Johnson EM, Cuomo CA. Genomic epidemiology of a Cryptococcus neoformans case cluster in Glasgow, Scotland, 2018. Microb Genom 2021; 7:mgen000537. [PMID: 33620303 PMCID: PMC8190611 DOI: 10.1099/mgen.0.000537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
In 2018, a cluster of two cases of cryptococcosis occurred at the Queen Elizabeth University Hospital (QEUH) in Glasgow, Scotland (UK). It was postulated that these cases may have been linked to pigeon droppings found on the hospital site, given there have been previous reports of Cryptococcus neoformans associated with pigeon guano. Although some samples of pigeon guano taken from the site yielded culturable yeast from genera related to Cryptococcus, they have since been classified as Naganishia or Papiliotrema spp., and no isolates of C. neoformans were recovered from either the guano or subsequent widespread air sampling. In an attempt to further elucidate any possible shared source of the clinical isolates, we used whole-genome sequencing and phylogenetic analysis to examine the relationship of the two Cryptococcus isolates from the QEUH cases, along with two isolates from sporadic cases treated at a different Glasgow hospital earlier in 2018. Our work demonstrated that these four clinical isolates were not clonally related; while all isolates were from the VNI global lineage and of the same mating type (MATα), the genotypes of the two QEUH isolates were separated by 1885 base changes and belonged to different sub-lineages, recently described as the intercontinental sub-clades VNIa-93 and VNIa-5. In contrast, one of the two sporadic 2018 clinical isolates was determined to belong to the VNIb sub-lineage and the other classified as a VNIV/VNI hybrid. Our work demonstrated that the two 2018 QEUH isolates and the two prior C. neoformans clinical isolates were all genetically distinct. It was not possible to determine whether the QEUH genotypes stemmed from independent sources or from the same source, i.e. pigeons carrying different genotypes, but it should be noted that whilst members of allied genera within the Tremellomycetes were isolated from the hospital environment, there were no environmental isolations of C. neoformans.
Collapse
Affiliation(s)
- Rhys A. Farrer
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK
| | - Andrew M. Borman
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK
- Public Health England National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | - Teresa Inkster
- Department of Microbiology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Matthew C. Fisher
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Elizabeth M. Johnson
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK
- Public Health England National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | | |
Collapse
|
42
|
Beekman CN, Cuomo CA, Bennett RJ, Ene IV. Comparative genomics of white and opaque cell states supports an epigenetic mechanism of phenotypic switching in Candida albicans. G3 (Bethesda) 2021; 11:6108101. [PMID: 33585874 PMCID: PMC8366294 DOI: 10.1093/g3journal/jkab001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/28/2020] [Indexed: 01/08/2023]
Abstract
Several Candida species can undergo a heritable and reversible transition from a 'white' state to a mating proficient 'opaque' state. This ability relies on highly interconnected transcriptional networks that control cell-type-specific gene expression programs over multiple generations. Candida albicans, the most prominent pathogenic Candida species, provides a well-studied paradigm for the white-opaque transition. In this species, a network of at least eight transcriptional regulators controls the balance between white and opaque states that have distinct morphologies, transcriptional profiles, and physiological properties. Given the reversible nature and the high frequency of white-opaque transitions, it is widely assumed that this switch is governed by epigenetic mechanisms that occur independently of any changes in DNA sequence. However, a direct genomic comparison between white and opaque cells has yet to be performed. Here, we present a whole-genome comparative analysis of C. albicans white and opaque cells. This analysis revealed rare genetic changes between cell states, none of which are linked to white-opaque switching. This result is consistent with epigenetic mechanisms controlling cell state differentiation in C. albicans and provides direct evidence against a role for genetic variation in mediating the switch.
Collapse
Affiliation(s)
- Chapman N Beekman
- Department of Molecular Microbiology and Immunology,
Brown University, Providence, RI 02912, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad
Institute, Cambridge, MA 02142, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology,
Brown University, Providence, RI 02912, USA
| | - Iuliana V Ene
- Department of Molecular Microbiology and Immunology,
Brown University, Providence, RI 02912, USA
- Corresponding author:
| |
Collapse
|
43
|
Yu CH, Chen Y, Desjardins CA, Tenor JL, Toffaletti DL, Giamberardino C, Litvintseva A, Perfect JR, Cuomo CA. Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses. Microb Genom 2020; 6. [PMID: 31860441 PMCID: PMC7067042 DOI: 10.1099/mgen.0.000319] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 12/14/2022] Open
Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen that at its peak epidemic levels caused an estimated million cases of cryptococcal meningitis per year worldwide. This species can grow in diverse environmental (trees, soil and bird excreta) and host niches (intracellular microenvironments of phagocytes and free-living in host tissues). The genetic basic for adaptation to these different conditions is not well characterized, as most experimental work has relied on a single reference strain of C. neoformans. To identify genes important for yeast infection and disease progression, we profiled the gene expression of seven C. neoformans isolates grown in five representative in vitro environmental and in vivo conditions. We characterized gene expression differences using RNA-Seq (RNA sequencing), comparing clinical and environmental isolates from two of the major lineages of this species, VNI and VNBI. These comparisons highlighted genes showing lineage-specific expression that are enriched in subtelomeric regions and in lineage-specific gene clusters. By contrast, we find few expression differences between clinical and environmental isolates from the same lineage. Gene expression specific to in vivo stages reflects available nutrients and stresses, with an increase in fungal metabolism within macrophages, and an induction of ribosomal and heat-shock gene expression within the subarachnoid space. This study provides the widest view to date of the transcriptome variation of C. neoformans across natural isolates, and provides insights into genes important for in vitro and in vivo growth stages.
Collapse
Affiliation(s)
- Chen-Hsin Yu
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yuan Chen
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Jennifer L Tenor
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dena L Toffaletti
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Charles Giamberardino
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anastasia Litvintseva
- Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - John R Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | | |
Collapse
|
44
|
Teixeira MDM, Cattana ME, Matute DR, Muñoz JF, Arechavala A, Isbell K, Schipper R, Santiso G, Tracogna F, Sosa MDLÁ, Cech N, Alvarado P, Barreto L, Chacón Y, Ortellado J, Lima CMD, Chang MR, Niño-Vega G, Yasuda MAS, Felipe MSS, Negroni R, Cuomo CA, Barker B, Giusiano G. Genomic diversity of the human pathogen Paracoccidioides across the South American continent. Fungal Genet Biol 2020; 140:103395. [PMID: 32325168 PMCID: PMC7385733 DOI: 10.1016/j.fgb.2020.103395] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 12/15/2019] [Revised: 02/27/2020] [Accepted: 04/16/2020] [Indexed: 12/30/2022]
Abstract
Paracoccidioidomycosis (PCM) is a life-threatening systemic mycosis widely reported in the Gran Chaco ecosystem. The disease is caused by different species from the genus Paracoccidioides, which are all endemic to South and Central America. Here, we sequenced and analyzed 31 isolates of Paracoccidioides across South America, with particular focus on isolates from Argentina and Paraguay. The de novo sequenced isolates were compared with publicly available genomes. Phylogenetics and population genomics revealed that PCM in Argentina and Paraguay is caused by three distinct Paracoccidioides genotypes, P. brasiliensis (S1a and S1b) and P. restrepiensis (PS3). P. brasiliensis S1a isolates from Argentina are frequently associated with chronic forms of the disease. Our results suggest the existence of extensive molecular polymorphism among Paracoccidioides species, and provide a framework to begin to dissect the connection between genotypic differences in the pathogen and the clinical outcomes of the disease.
Collapse
Affiliation(s)
- Marcus de Melo Teixeira
- Northern Arizona University, Flagstaff, AZ, USA; Universidade de Brasília, Brasilia, Brazil.
| | - Maria Emilia Cattana
- Northern Arizona University, Flagstaff, AZ, USA; Hospital Dr. Julio C. Perrando, Resistencia, Chaco, Argentina
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - José F Muñoz
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Kristin Isbell
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | | | | | - Primavera Alvarado
- Servicio Autónomo Instituto de Biomedicina Dr. Jacinto Convit, Caracas, Venezuela
| | - Laura Barreto
- Instituto Superior de Formación Docente Salome Ureña, Santo Domingo, Dominican Republic
| | - Yone Chacón
- Hospital Señor del Milagro, Salta, Argentina
| | | | | | | | | | | | | | | | | | | | - Gustavo Giusiano
- Universidad Nacional del Nordeste, Resistencia, Chaco, Argentina.
| |
Collapse
|
45
|
Gade L, Muñoz JF, Sheth M, Wagner D, Berkow EL, Forsberg K, Jackson BR, Ramos-Castro R, Escandón P, Dolande M, Ben-Ami R, Espinosa-Bode A, Caceres DH, Lockhart SR, Cuomo CA, Litvintseva AP. Understanding the Emergence of Multidrug-Resistant Candida: Using Whole-Genome Sequencing to Describe the Population Structure of Candida haemulonii Species Complex. Front Genet 2020; 11:554. [PMID: 32587603 PMCID: PMC7298116 DOI: 10.3389/fgene.2020.00554] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 02/28/2020] [Accepted: 05/07/2020] [Indexed: 11/16/2022] Open
Abstract
The recent emergence of a multidrug-resistant yeast, Candida auris, has drawn attention to the closely related species from the Candida haemulonii complex that include C. haemulonii, Candida duobushaemulonii, Candida pseudohaemulonii, and the recently identified Candida vulturna. Here, we used antifungal susceptibility testing and whole-genome sequencing (WGS) to investigate drug resistance and genetic diversity among isolates of C. haemulonii complex from different geographic areas in order to assess population structure and the extent of clonality among strains. Although most isolates of all four species were genetically distinct, we detected evidence of the in-hospital transmission of C. haemulonii and C. duobushaemulonii in one hospital in Panama, indicating that these species are also capable of causing outbreaks in healthcare settings. We also detected evidence of the rising azole resistance among isolates of C. haemulonii and C. duobushaemulonii in Colombia, Panama, and Venezuela linked to substitutions in ERG11 gene as well as amplification of this gene in C. haemulonii in isolates in Colombia suggesting the presence of evolutionary pressure for developing azole resistance in this region. Our results demonstrate that these species need to be monitored as possible causes of outbreaks of invasive infection.
Collapse
Affiliation(s)
- Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jose F Muñoz
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, United States
| | - Mili Sheth
- Biotechnology Core Facility Branch, DSR/NCEZID - Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Darlene Wagner
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States.,IHRC, Inc., Atlanta, GA, United States
| | - Elizabeth L Berkow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Kaitlin Forsberg
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Brendan R Jackson
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Ruben Ramos-Castro
- Department of Clinical and Molecular Microbiology, Instituto Conmemorativo Gorgas de Estudios de La Salud, Panama City, Panama
| | - Patricia Escandón
- Grupo de Microbiologia, Instituto Nacional de Salud, Bogotá, Colombia
| | - Maribel Dolande
- Departamento de Micología, Instituto Nacional de Higiene Rafael Rangel, Caracas, Venezuela
| | - Ronen Ben-Ami
- Tel Aviv Sourasky Medical Center, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Andrés Espinosa-Bode
- DGHP (Division of Global Health Protection), Central America Region Office, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Diego H Caceres
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, Netherlands
| | - Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, United States
| | - Anastasia P Litvintseva
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| |
Collapse
|
46
|
Fisher MC, Gurr SJ, Cuomo CA, Blehert DS, Jin H, Stukenbrock EH, Stajich JE, Kahmann R, Boone C, Denning DW, Gow NAR, Klein BS, Kronstad JW, Sheppard DC, Taylor JW, Wright GD, Heitman J, Casadevall A, Cowen LE. Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture. mBio 2020; 11:e00449-20. [PMID: 32371596 PMCID: PMC7403777 DOI: 10.1128/mbio.00449-20] [Citation(s) in RCA: 194] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The fungal kingdom includes at least 6 million eukaryotic species and is remarkable with respect to its profound impact on global health, biodiversity, ecology, agriculture, manufacturing, and biomedical research. Approximately 625 fungal species have been reported to infect vertebrates, 200 of which can be human associated, either as commensals and members of our microbiome or as pathogens that cause infectious diseases. These organisms pose a growing threat to human health with the global increase in the incidence of invasive fungal infections, prevalence of fungal allergy, and the evolution of fungal pathogens resistant to some or all current classes of antifungals. More broadly, there has been an unprecedented and worldwide emergence of fungal pathogens affecting animal and plant biodiversity. Approximately 8,000 species of fungi and Oomycetes are associated with plant disease. Indeed, across agriculture, such fungal diseases of plants include new devastating epidemics of trees and jeopardize food security worldwide by causing epidemics in staple and commodity crops that feed billions. Further, ingestion of mycotoxins contributes to ill health and causes cancer. Coordinated international research efforts, enhanced technology translation, and greater policy outreach by scientists are needed to more fully understand the biology and drivers that underlie the emergence of fungal diseases and to mitigate against their impacts. Here, we focus on poignant examples of emerging fungal threats in each of three areas: human health, wildlife biodiversity, and food security.
Collapse
Affiliation(s)
- Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, United Kingdom
| | - Sarah J Gurr
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - David S Blehert
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, USA
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Eva H Stukenbrock
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - David W Denning
- The National Aspergillosis Centre, Wythenshawe Hospital, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Neil A R Gow
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Bruce S Klein
- Department of Pediatrics, Department of Internal Medicine, and Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Donald C Sheppard
- McGill Interdisciplinary Initiative in Infection and Immunology, Departments of Medicine, Microbiology & Immunology, McGill University, Montreal, Canada
| | - John W Taylor
- University of California-Berkeley, Department of Plant and Microbial Biology, Berkeley, California, USA
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
47
|
Chow NA, Muñoz JF, Gade L, Berkow EL, Li X, Welsh RM, Forsberg K, Lockhart SR, Adam R, Alanio A, Alastruey-Izquierdo A, Althawadi S, Araúz AB, Ben-Ami R, Bharat A, Calvo B, Desnos-Ollivier M, Escandón P, Gardam D, Gunturu R, Heath CH, Kurzai O, Martin R, Litvintseva AP, Cuomo CA. Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses. mBio 2020; 11:e03364-19. [PMID: 32345637 PMCID: PMC7188998 DOI: 10.1128/mbio.03364-19] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/01/2020] [Indexed: 01/26/2023] Open
Abstract
Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. aurisIMPORTANCE In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology.
Collapse
Affiliation(s)
- Nancy A Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - José F Muñoz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Elizabeth L Berkow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Xiao Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rory M Welsh
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Kaitlin Forsberg
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Rodney Adam
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Alexandre Alanio
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Université de Paris, Paris, France
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Sahar Althawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | - Ronen Ben-Ami
- Infectious Diseases Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Belinda Calvo
- Department of Infectious Diseases, School of Medicine, Universidad del Zulia, Maracaibo, Venezuela
| | - Marie Desnos-Ollivier
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Paris, France
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Dianne Gardam
- Department of Microbiology, PathWest Laboratory Medicine FSH Network, Fiona Stanley Hospital, Murdoch, Australia
| | - Revathi Gunturu
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Christopher H Heath
- Department of Microbiology, PathWest Laboratory Medicine FSH Network, Fiona Stanley Hospital, Murdoch, Australia
- Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Australia
- Infectious Diseases, Royal Perth Hospital, Perth, Australia
- Faculty of Health & Medical Sciences, University of Western Australia, Crawley, Washington, Australia
| | - Oliver Kurzai
- German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Jena, Germany
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Ronny Martin
- German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Jena, Germany
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Anastasia P Litvintseva
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | | |
Collapse
|
48
|
Abstract
Over the past decade, Candida auris has emerged as an urgent threat to public health. Initially reported from cases of ear infections in Japan and Korea, C. auris has since been detected around the world. While whole-genome sequencing has been extensively used to trace the genetic relationships of the global emergence and local outbreaks, a recent report in mBio describes a targeted genotyping method as a rapid and inexpensive method for classifying C. auris isolates (T. de Groot, Y. Puts, I. Berrio, A. Chowdhary, and J. F. Meis, mBio 11:e02971-19, https://doi.org/10.1128/mBio.02971-19, 2020).
Collapse
Affiliation(s)
| | - Alexandre Alanio
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Groupe Hospitalier Saint-Louis Lariboisière Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université de Paris, Paris, France
| |
Collapse
|
49
|
Ma L, Chen Z, Huang DW, Cissé OH, Rothenburger JL, Latinne A, Bishop L, Blair R, Brenchley JM, Chabé M, Deng X, Hirsch V, Keesler R, Kutty G, Liu Y, Margolis D, Morand S, Pahar B, Peng L, Van Rompay KKA, Song X, Song J, Sukura A, Thapar S, Wang H, Weissenbacher-Lang C, Xu J, Lee CH, Jardine C, Lempicki RA, Cushion MT, Cuomo CA, Kovacs JA. Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of Multiple Pneumocystis Species. mBio 2020; 11:e02878-19. [PMID: 32127451 PMCID: PMC7064768 DOI: 10.1128/mbio.02878-19] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/16/2020] [Indexed: 12/23/2022] Open
Abstract
Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multicopy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins and provide a detailed description of the classification, unique characteristics, and phylogenetic relatedness of five Msg families. We further describe, for the first time, the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests multiple functions for this superfamily rather than just conferring antigenic variation to allow immune evasion as previously believed. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.IMPORTANCEPneumocystis continues to be a major cause of disease in humans with immunodeficiency, especially those with HIV/AIDS and organ transplants, and is being seen with increasing frequency worldwide in patients treated with immunodepleting monoclonal antibodies. Annual health care associated with Pneumocystis pneumonia costs ∼$475 million dollars in the United States alone. In addition to causing overt disease in immunodeficient individuals, Pneumocystis can cause subclinical infection or colonization in healthy individuals, which may play an important role in species preservation and disease transmission. Our work sheds new light on the diversity and complexity of the msg superfamily and strongly suggests that the versatility of this superfamily reflects multiple functions, including antigenic variation to allow immune evasion and optimal adaptation to host environmental conditions to promote efficient infection and transmission. These findings are essential to consider in developing new diagnostic and therapeutic strategies.
Collapse
Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Zehua Chen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Da Wei Huang
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jamie L Rothenburger
- Department of Pathobiology, Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Ontario, Canada
| | | | - Lisa Bishop
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert Blair
- Tulane National Primate Research Center, Tulane University, New Orleans, Louisiana, USA
| | - Jason M Brenchley
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Magali Chabé
- Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Xilong Deng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rebekah Keesler
- California National Primate Research Center, University of California, Davis, Davis, California, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel Margolis
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Serge Morand
- Institut des Sciences de l'Evolution, Université de Montpellier 2, Montpellier, France
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University, New Orleans, Louisiana, USA
| | - Li Peng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, California, USA
| | - Xiaohong Song
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Antti Sukura
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Sabrina Thapar
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Honghui Wang
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Chao-Hung Lee
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Claire Jardine
- Department of Pathobiology, Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Ontario, Canada
| | - Richard A Lempicki
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Melanie T Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Christina A Cuomo
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
50
|
Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell 2020; 180:816. [PMID: 32084344 PMCID: PMC7201975 DOI: 10.1016/j.cell.2020.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|