1
|
Dao A, Kim HY, Garnham K, Kidd S, Sati H, Perfect J, Sorrell TC, Harrison T, Rickerts V, Gigante V, Alastruey-Izquierdo A, Alffenaar JW, Morrissey CO, Chen SCA, Beardsley J. Cryptococcosis-a systematic review to inform the World Health Organization Fungal Priority Pathogens List. Med Mycol 2024; 62:myae043. [PMID: 38935902 PMCID: PMC11210623 DOI: 10.1093/mmy/myae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/01/2023] [Accepted: 04/27/2024] [Indexed: 06/29/2024] Open
Abstract
Cryptococcosis causes a high burden of disease worldwide. This systematic review summarizes the literature on Cryptococcus neoformans and C. gattii infections to inform the World Health Organization's first Fungal Priority Pathogen List. PubMed and Web of Science were used to identify studies reporting on annual incidence, mortality, morbidity, antifungal resistance, preventability, and distribution/emergence in the past 10 years. Mortality rates due to C. neoformans were 41%-61%. Complications included acute renal impairment, raised intracranial pressure needing shunts, and blindness. There was moderate evidence of reduced susceptibility (MIC range 16-32 mg/l) of C. neoformans to fluconazole, itraconazole, ketoconazole, voriconazole, and amphotericin B. Cryptococcus gattii infections comprised 11%-33% of all cases of invasive cryptococcosis globally. The mortality rates were 10%-23% for central nervous system (CNS) and pulmonary infections, and ∼43% for bloodstream infections. Complications described included neurological sequelae (17%-27% in C. gattii infections) and immune reconstitution inflammatory syndrome. MICs were generally low for amphotericin B (MICs: 0.25-0.5 mg/l), 5-flucytosine (MIC range: 0.5-2 mg/l), itraconazole, posaconazole, and voriconazole (MIC range: 0.06-0.5 mg/l). There is a need for increased surveillance of disease phenotype and outcome, long-term disability, and drug susceptibility to inform robust estimates of disease burden.
Collapse
Affiliation(s)
- Aiken Dao
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Sydney, Australia
- Westmead Clinical School, Westmead Hospital, Sydney, Australia
| | - Hannah Yejin Kim
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
- Department of Pharmacy, Westmead Hospital, Westmead, Australia
| | - Katherine Garnham
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- Sunshine Coast University Hospital, Birtinya, Qld 4575, Australia
| | - Sarah Kidd
- National Mycology Reference Centre, Microbiology and Infectious Diseases, SA Pathology, Adelaide, Australia
| | - Hatim Sati
- AMR Division, World Health Organization, Geneva, Switzerland
| | | | - Tania C Sorrell
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Sydney, Australia
- Westmead Clinical School, Westmead Hospital, Sydney, Australia
| | - Thomas Harrison
- Institute of Infection and Immunity, St George’s University London, London, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | | | - Valeria Gigante
- AMR Division, World Health Organization, Geneva, Switzerland
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Jan-Willem Alffenaar
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- Westmead Clinical School, Westmead Hospital, Sydney, Australia
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - C Orla Morrissey
- Department of Infectious Diseases, Alfred Health, Melbourne, Australia
- Monash University, Department of Infectious Diseases, Melbourne, Victoria, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, Sydney, Australia
| | - Justin Beardsley
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Sydney, Australia
- Westmead Clinical School, Westmead Hospital, Sydney, Australia
| |
Collapse
|
2
|
Gifford H, Rhodes J, Farrer RA. The diverse genomes of Candida auris. THE LANCET. MICROBE 2024:S2666-5247(24)00135-6. [PMID: 38889739 DOI: 10.1016/s2666-5247(24)00135-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024]
Affiliation(s)
- Hugh Gifford
- MRC Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, UK
| | - Johanna Rhodes
- MRC Centre for Global Disease Analysis, Imperial College London, London, UK; Department of Medical Microbiology, Radboudumc, Nijmegen, Netherlands
| | - Rhys A Farrer
- MRC Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, UK.
| |
Collapse
|
3
|
Miyahara A, Umeki A, Sato K, Nomura T, Yamamoto H, Miyasaka T, Tanno D, Matsumoto I, Zong T, Kagesawa T, Oniyama A, Kawamura K, Yuan X, Yokoyama R, Kitai Y, Kanno E, Tanno H, Hara H, Yamasaki S, Saijo S, Iwakura Y, Ishii K, Kawakami K. Innate phase production of IFN-γ by memory and effector T cells expressing early activation marker CD69 during infection with Cryptococcus deneoformans in the lungs. Infect Immun 2024; 92:e0002424. [PMID: 38700335 DOI: 10.1128/iai.00024-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/09/2024] [Indexed: 05/05/2024] Open
Abstract
Cryptococcus deneoformans is a yeast-type fungus that causes fatal meningoencephalitis in immunocompromised patients and evades phagocytic cell elimination through an escape mechanism. Memory T (Tm) cells play a central role in preventing the reactivation of this fungal pathogen. Among these cells, tissue-resident memory T (TRM) cells quickly respond to locally invaded pathogens. This study analyzes the kinetics of effector T (Teff) cells and Tm cells in the lungs after cryptococcal infection. Emphasis is placed on the kinetics and cytokine expression of TRM cells in the early phase of infection. CD4+ Tm cells exhibited a rapid increase by day 3, peaked at day 7, and then either maintained their levels or exhibited a slight decrease until day 56. In contrast, CD8+ Tm cells reached their peak on day 3 and thereafter decreased up to day 56 post-infection. These Tm cells were predominantly composed of CD69+ TRM cells and CD69+ CD103+ TRM cells. Disruption of the CARD9 gene resulted in reduced accumulation of these TRM cells and diminished interferon (IFN) -γ expression in TRM cells. TRM cells were derived from T cells with T cell receptors non-specific to ovalbumin in OT-II mice during cryptococcal infection. In addition, TRM cells exhibited varied behavior in different tissues. These results underscore the importance of T cells, which produce IFN-γ in the lungs during the early stage of infection, in providing early protection against cryptococcal infection through CARD9 signaling.
Collapse
Grants
- 18H02851, 21H02965 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 19K17920, 21K16314 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP19jm0210073, JP20jm0210073, JP21jm0210073 Japan Agency for Medical Research and Development (AMED)
- ID-014 MSD Life Science Foundation, Public Interest Incorporated Foundation (SD Life Science Foundation)
- 20-02, 21-04 medical mycology research center, chiba university
Collapse
Affiliation(s)
- Anna Miyahara
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Aya Umeki
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Ko Sato
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Toshiki Nomura
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hideki Yamamoto
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Tomomitsu Miyasaka
- Center for Medical Education, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Daiki Tanno
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Ikumi Matsumoto
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Tong Zong
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Takafumi Kagesawa
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Akiho Oniyama
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Kotone Kawamura
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Xiaoliang Yuan
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Rin Yokoyama
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yuki Kitai
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Emi Kanno
- Department of Translational Science for Nursing, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hiromasa Tanno
- Department of Translational Science for Nursing, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hiromitsu Hara
- Department of Immunology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Shinobu Saijo
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Yoichiro Iwakura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Keiko Ishii
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Kazuyoshi Kawakami
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| |
Collapse
|
4
|
Del Olmo V, Gabaldón T. Hybrids unleashed: exploring the emergence and genomic insights of pathogenic yeast hybrids. Curr Opin Microbiol 2024; 80:102491. [PMID: 38833792 DOI: 10.1016/j.mib.2024.102491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Hybridisation is the crossing of two divergent lineages that give rise to offspring carrying an admixture of both parental genomes. Genome sequencing has revealed that this process is common in the Saccharomycotina, where a growing number of hybrid strains or species, including many pathogenic ones, have been recently described. Hybrids can display unique traits that may drive adaptation to new niches, and some pathogenic hybrids have been shown to have higher prevalence over their parents in human and environmental niches, suggesting a higher fitness and potential to colonise humans. Here, we discuss how hybridisation and its genomic and phenotypic outcomes can shape the evolution of fungal species and may play a role in the emergence of new pathogens.
Collapse
Affiliation(s)
- Valentina Del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034 Barcelona, Spain; Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034 Barcelona, Spain; Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain; Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
| |
Collapse
|
5
|
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 the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis. PLoS Biol 2024; 22:e3002682. [PMID: 38843310 PMCID: PMC11185503 DOI: 10.1371/journal.pbio.3002682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/18/2024] [Accepted: 05/17/2024] [Indexed: 06/19/2024] Open
Abstract
In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 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 showed 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. Overall, our findings advance our understanding of genetic 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, United States of America
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sage McGinley-Smith
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Arman W. Mohammad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - 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, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| |
Collapse
|
6
|
de Holanda Fonseca DL, Silva DMWD, de Albuquerque Maranhão FC. Molecular characterization of clinical and environmental isolates from the Cryptococcus neoformans/C. Gattii species complexes of Maceió, Alagoas, Brazil. Braz J Microbiol 2024; 55:1369-1380. [PMID: 38619732 PMCID: PMC11153433 DOI: 10.1007/s42770-024-01313-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/21/2024] [Indexed: 04/16/2024] Open
Abstract
Cryptococcosis is one of the major life-threatening opportunistic/systemic fungal diseases of worldwide occurrence, which can be asymptomatic or establish pneumonia and meningoencephalitis mainly in immunosuppressed patients, caused by the Cryptococcus neoformans and C. gattii species complexes. Acquisition is by inhaling fungal propagules from avian droppings, tree hollows and decaying wood, and the association of the molecular types with geographic origin, virulence and antifungal resistance have epidemiological importance. Since data on cryptococcosis in Alagoas are limited, we sought to determine the molecular types of etiological agents collected from clinical and environmental sources. We evaluated 21 isolates previously collected from cerebrospinal fluid and from environment sources (pigeon droppings and tree hollows) in Maceió-Alagoas (Brazil). Restriction fragment length polymorphism of URA5 gene was performed to characterize among the eight standard molecular types (VNI-VNIV and VGI-VGIV). Among isolates, 66.67% (14) were assigned to C. neoformans VNI - 12 of them (12/14) recovered from liquor and 2 from a tree hollow (2/14). One isolate from pigeon droppings (4.76%) corresponded to C. neoformans VNIV, while five strains from tree hollows and one from pigeon droppings (6, 28.57%) to C. gattii VGII. VNI-type was present in clinical and environmental samples and most C. neoformans infections were observed in HIV-positive patients, while types VNIV and VGII were prevalent in environmental sources in Alagoas. This is the first molecular characterization of Cryptococcus spp. in Alagoas, our study provides additional information on the ecoepidemiology of Cryptococcus spp. in Brazil, contributing to a closer view of the endemic species.
Collapse
Affiliation(s)
| | - Denise Maria Wanderlei da Silva
- Institute of Biological and Health Sciences, Sector of Microbiology, Laboratory of Clinical Microbiology, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Fernanda Cristina de Albuquerque Maranhão
- Institute of Biological and Health Sciences, Sector of Microbiology, Laboratory of Clinical Microbiology, Federal University of Alagoas, Av. Lourival de Melo Mota, S/N, Tabuleiro do Martins, Maceió, 57072-900, Alagoas, Brazil.
| |
Collapse
|
7
|
Kausar MA, Narayan J, Mishra N, Akhter Y, Singh R, Khalifa AM, El-Hag ABM, Ahmed RME, Tyagi N, Mahfooz S. Studying Human Pathogenic Cryptococcus Gattii Lineages by Utilizing Simple Sequence Repeats to Create Diagnostic Markers and Analyzing Diversity. Biochem Genet 2024:10.1007/s10528-024-10812-7. [PMID: 38773043 DOI: 10.1007/s10528-024-10812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/11/2024] [Indexed: 05/23/2024]
Abstract
In this study, we compared the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) among the lineages of human pathogenic Cryptococcus gattii using an in-silico approach to gain a deeper understanding of the structure and evolution of their genomes. C. gattii isolate MF34 showed the highest RA and RD of SSRs in both the genomic and transcriptomic sequences, followed by isolate WM276. In both the genomic (50%) and transcriptomic (65%) sequences, trinucleotide SSRs were the most common SSR class. A motif conservation study found that the isolates had stronger conservation (56.1%) of motifs, with isolate IND107 having the most (5.7%) unique motifs. We discovered the presence of SSRs in genes that are directly or indirectly associated with disease using gene enrichment analysis. Isolate-specific unique motifs identified in this study could be utilized as molecular probes for isolate identification. To improve genetic resources among C. gattii isolates, 6499 primers were developed. These genomic resources developed in this study could help with diversity analysis and the development of isolate-specific markers.
Collapse
Affiliation(s)
- Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Ha'il, Hail, 2440, Saudi Arabia.
| | - Jitendra Narayan
- CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
| | - Nishtha Mishra
- Department of Chemistry, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Rajeev Singh
- Department of Environmental Science, Jamia Millia Islamia Central University, New Delhi, 110025, India
| | - Amany Mohammed Khalifa
- Department of Pathology, College of Medicine, University of Ha'il, Hail, 2440, Saudi Arabia
| | | | | | - Neetu Tyagi
- Bone Biology Laboratory, Department of Physiology, University of Louisville, Louisville, USA
| | - Sahil Mahfooz
- Department of Industrial Microbiology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009, India.
| |
Collapse
|
8
|
Uppar A, Andiperumal Raj P, Veenakumari HB, Arghadip S, Dawn Bharath R, S N. Disseminated cerebral cryptococcoma mimicking glioblastoma - A case report.". Indian J Med Microbiol 2024; 49:100609. [PMID: 38735642 DOI: 10.1016/j.ijmmb.2024.100609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/14/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
Abstract
We discuss a rare instance of cryptococcoma caused by Cryptococcus gattii in a 55-year-old woman initially treated for suspected COVID bronchopneumonia. The diagnosis posed a challenge due to vague symptoms and unclear imaging findings suggesting malignancy. Postoperative samples confirmed the presence of Cryptococcus gattii through culture of brain tissue and blood. Appropriate therapy was initiated, but despite treatment, it led to a fatal outcome. The case emphasizes the crucial role of microbiologist in early diagnosis of fungal infections of Central Nervous System. Additionally, the delayed diagnosis in immunocompetent individuals highlights the critical need for early recognition and intervention to mitigate potentially fatal outcomes.
Collapse
Affiliation(s)
- Akshata Uppar
- Department of Neuromicrobiology, NIMHANS, Bengaluru, 29, India
| | | | - H B Veenakumari
- Department of Neuromicrobiology, NIMHANS, Bengaluru, 29, India
| | | | - Rose Dawn Bharath
- Neuroimaging and Interventional Radiology, NIMHANS, Bengaluru, 29, India
| | - Nagarathna S
- Department of Neuromicrobiology, NIMHANS, Bengaluru, 29, India.
| |
Collapse
|
9
|
Omura M, Satoh K, Tamura T, Komori A, Makimura K. Molecular epidemiological investigation of Cryptococcus spp. carried by captive koalas ( Phascolarctos cinereus) in Japan. Microbiol Spectr 2024; 12:e0290323. [PMID: 38411053 DOI: 10.1128/spectrum.02903-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii cause cryptococcosis, a systemic mycosis that infects a wide range of species. Recent molecular biological investigations have allowed for the genotyping of these species, providing more detailed information on their pathogenicity and infection routes. Koalas (Phascolarctos cinereus) are frequently colonized by Cryptococcus spp., but molecular epidemiological studies have yet to be conducted in Japan. Here, we conducted multi-locus sequence typing (MLST) analysis on Cryptococcus spp. colonization isolates obtained from all koalas kept in seven parks across Japan. Out of 46 koalas examined, 10 (22%) were positive for C. gattii and 3 (6.5%) were positive for C. neoformans. All C. gattii isolates belonged to molecular type VGI and were either sequence type (ST) 51 or a novel ST, and all C. neoformans isolates belonged to molecular type VNI and ST23. Despite the frequent movement of koalas between parks, the STs were relatively park-specific, suggesting that the floor of the rearing barns is a source of infection and may act as a reservoir. MLST analysis confirmed that C. gattii was transported, established, and spread by koalas in areas where C. gattii was not originally present. MLST analysis is considered useful in assessing the pathogenicity and tracing the transmission routes of Cryptococcus spp. carried by koalas.IMPORTANCEThis is the first study to conduct a multi-locus sequence typing analysis on Cryptococcus spp. carried by captive koalas in Japan. Cryptococcosis remains a globally high-fatality fungal infection in humans, and captive koalas are known to carry a high percentage of Cryptococcus spp. Through this research, the molecular types and transmission routes of Cryptococcus spp. carried by koalas have been elucidated, revealing the potential role of enclosure flooring as a reservoir. It has been confirmed that Cryptococcus gattii, which is not endemic in Japan, has become established through koalas and is spreading to new individuals in Japan. This study is believed to provide valuable insights into koala conservation and contribute to the One Health approach for Cryptococcosis, a zoonotic infection.
Collapse
Affiliation(s)
- Miki Omura
- Laboratory of Medical Mycology, Graduate School of Medicine, Teikyo University, Tokyo, Japan
| | - Kazuo Satoh
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
| | - Takashi Tamura
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
| | - Aya Komori
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
| | - Koichi Makimura
- Laboratory of Medical Mycology, Graduate School of Medicine, Teikyo University, Tokyo, Japan
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
| |
Collapse
|
10
|
Hallas-Mølle M, Burow M, Henrissat B, Johansen KS. Cryptococcus neoformans: plant-microbe interactions and ecology. Trends Microbiol 2024:S0966-842X(24)00059-3. [PMID: 38519353 DOI: 10.1016/j.tim.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
While the opportunistic human pathogens Cryptococcus neoformans and Cryptococcus gattii are often isolated from plants and plant-related material, evidence suggests that these Cryptococcus species do not directly infect plants. Studies find that plants are important for Cryptococcus mating and dispersal. However, these studies have not provided enough detail about how plants and these fungi interact, especially in ways that could show the fungi are capable of causing disease. This review synthesizes recent findings from studies utilizing different plant models associated with the ecology of C. neoformans and C. gattii. Unanswered questions about their environmental role are highlighted. Overall, current research indicates that Cryptococcus utilizes plants as a substrate rather than harming them, arguing against Cryptococcus as a genuine plant pathogen. We hypothesize that plants represent reservoirs that aid dispersal, not hosts vulnerable to infection.
Collapse
Affiliation(s)
- Magnus Hallas-Mølle
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Meike Burow
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kgs, Lyngby, Denmark
| | - Katja Salomon Johansen
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark.
| |
Collapse
|
11
|
Mbangiwa T, Sturny-Leclère A, Lechiile K, Kajanga C, Boyer-Chammard T, Hoving JC, Leeme T, Moyo M, Youssouf N, Lawrence DS, Mwandumba H, Mosepele M, Harrison TS, Jarvis JN, Lortholary O, Alanio A. Development and validation of quantitative PCR assays for HIV-associated cryptococcal meningitis in sub-Saharan Africa: a diagnostic accuracy study. THE LANCET. MICROBE 2024; 5:e261-e271. [PMID: 38342110 PMCID: PMC10914677 DOI: 10.1016/s2666-5247(23)00362-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 09/27/2023] [Accepted: 10/26/2023] [Indexed: 02/13/2024]
Abstract
BACKGROUND HIV-associated cryptococcal meningitis is the second leading cause of AIDS-related deaths, with a 10-week mortality rate of 25-30%. Fungal load assessed by colony-forming unit (CFU) counts is used as a prognostic marker and to monitor response to treatment in research studies. PCR-based assessment of fungal load could be quicker and less labour-intensive. We sought to design, optimise, and validate quantitative PCR (qPCR) assays for the detection, identification, and quantification of Cryptococcus infections in patients with cryptococcal meningitis in sub-Saharan Africa. METHODS We developed and validated species-specific qPCR assays based on DNA amplification of QSP1 (QSP1A specific to Cryptococcus neoformans, QSP1B/C specific to Cryptococcus deneoformans, and QSP1D specific to Cryptococcus gattii species) and a pan-Cryptococcus assay based on a multicopy 28S rRNA gene. This was a longitudinal study that validated the designed assays on cerebrospinal fluid (CSF) of 209 patients with cryptococcal meningitis at baseline (day 0) and during anti-fungal therapy (day 7 and day 14), from the AMBITION-cm trial in Botswana and Malawi (2018-21). Eligible patients were aged 18 years or older and presenting with a first case of cryptococcal meningitis. FINDINGS When compared with quantitative cryptococcal culture as the reference, the sensitivity of the 28S rRNA was 98·2% (95% CI 95·1-99·5) and of the QSP1 assay was 90·4% (85·2-94·0) in CSF at day 0. Quantification of the fungal load with QSP1 and 28S rRNA qPCR correlated with quantitative cryptococcal culture (R2=0·73 and R2=0·78, respectively). Both Botswana and Malawi had a predominant C neoformans prevalence of 67% (95% CI 55-75) and 68% (57-73), respectively, and lower C gattii rates of 21% (14-31) and 8% (4-14), respectively. We identified ten patients that, after 14 days of treatment, harboured viable but non-culturable yeasts based on QSP1 RNA detection (without any positive CFU in CSF culture). INTERPRETATION QSP1 and 28S rRNA assays are useful in identifying Cryptococcus species. qPCR results correlate well with baseline quantitative cryptococcal culture and show a similar decline in fungal load during induction therapy. These assays could be a faster alternative to quantitative cryptococcal culture to determine fungal load clearance. The clinical implications of the possible detection of viable but non-culturable cells in CSF during induction therapy remain unclear. FUNDING European and Developing Countries Clinical Trials Partnership; Swedish International Development Cooperation Agency; Wellcome Trust/UK Medical Research Council/UKAID Joint Global Health Trials; and UK National Institute for Health Research.
Collapse
Affiliation(s)
- Tshepiso Mbangiwa
- Botswana-Harvard Health Partnership, Gaborone, Botswana; Institut Pasteur, Université Paris Cité, Translational Mycology Group, Centre National de Référence Mycoses Invasives et Antifongiques, Department of Mycology, Paris, France; Institute of Infectious Disease and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Aude Sturny-Leclère
- Institut Pasteur, Université Paris Cité, Translational Mycology Group, Centre National de Référence Mycoses Invasives et Antifongiques, Department of Mycology, Paris, France
| | | | - Cheusisime Kajanga
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Kamuzu University of Health Science, Blantyre, Malawi
| | - Timothée Boyer-Chammard
- Institut Pasteur, Université Paris Cité, Translational Mycology Group, Centre National de Référence Mycoses Invasives et Antifongiques, Department of Mycology, Paris, France; Department of Infectious Diseases and Tropical Medicine, Centre Hospitalier d'Ajaccio, Ajaccio, France
| | - Jennifer C Hoving
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; AFRICA CMM Medical Mycology Research Unit, Institute of Infectious Disease and Molecular Medicine (IDM), Cape Town, South Africa
| | - Tshepo Leeme
- Botswana-Harvard Health Partnership, Gaborone, Botswana
| | - Melanie Moyo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Kamuzu University of Health Science, Blantyre, Malawi
| | - Nabila Youssouf
- Botswana-Harvard Health Partnership, Gaborone, Botswana; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - David S Lawrence
- Botswana-Harvard Health Partnership, Gaborone, Botswana; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Henry Mwandumba
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Liverpool School of Tropical Medicine, Liverpool, UK
| | - Mosepele Mosepele
- Botswana-Harvard Health Partnership, Gaborone, Botswana; Department of Internal Medicine, University of Botswana, Gaborone, Botswana
| | - Thomas S Harrison
- Centre for Global Health, Institute for Infection and Immunity, St George's University of London, London, UK; Clinical Academic Group in Infection, St George's University Hospitals NHS Foundation Trust, London, UK; MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Joseph N Jarvis
- Botswana-Harvard Health Partnership, Gaborone, Botswana; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Olivier Lortholary
- Institut Pasteur, Université Paris Cité, Translational Mycology Group, Centre National de Référence Mycoses Invasives et Antifongiques, Department of Mycology, Paris, France; Necker Pasteur Centre for Infectious Diseases and Tropical Médicine, Hôpital Universitaire Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, Université Paris Cité, Translational Mycology Group, Centre National de Référence Mycoses Invasives et Antifongiques, Department of Mycology, Paris, France; Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010, Paris, France.
| |
Collapse
|
12
|
Cogliati M, Chidebelu PE, Hitchcock M, Chen M, Rickerts V, Ackermann S, Desnos Ollivier M, Inácio J, Nawrot U, Florek M, Kwon-Chung KJ, Yang DH, Firacative C, Puime CA, Escandon P, Bertout S, Roger F, Xu J. Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids. Fungal Genet Biol 2024; 170:103861. [PMID: 38128716 DOI: 10.1016/j.fgb.2023.103861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Hybrid AD strains of the human pathogenic Cryptococcus neoformans species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the Cryptococcus research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.
Collapse
Affiliation(s)
- M Cogliati
- Lab. Medical Mycology, Dept. Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy.
| | - P E Chidebelu
- Department of Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - M Hitchcock
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - M Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Chanzheng Hospital, Second Military Medical University, Shanghai, China
| | | | | | - M Desnos Ollivier
- Institut Pasteur, Université de Paris, CNRS UMR2000, Molecular Mycology Unit, National Reference Center for Invasive Mycoses and Antifungals, Paris, France
| | - J Inácio
- School of Applied Sciences, University of Brighton, Brighton, UK
| | - U Nawrot
- Department of Pharmaceutical Microbiology and Parasitology, Wroclaw Medical University, Wroclaw, Poland
| | - M Florek
- Department of Pathology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - K J Kwon-Chung
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases NIH, Bethesda, USA
| | - D-H Yang
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases NIH, Bethesda, USA
| | - C Firacative
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad de Rosario, Bogotá, Colombia
| | - C A Puime
- Unidad de Parasitología y Micología, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo, Uruguay
| | - P Escandon
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - S Bertout
- Laboratoire de Parasitologie et Mycologie Médicale, UMI 233 TransVIHMI, University of Montpellier, IRD, INSERM, Montpellier, France
| | - F Roger
- Laboratoire de Parasitologie et Mycologie Médicale, UMI 233 TransVIHMI, University of Montpellier, IRD, INSERM, Montpellier, France
| | - J Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
13
|
Melhem MSC, Leite Júnior DP, Takahashi JPF, Macioni MB, Oliveira LD, de Araújo LS, Fava WS, Bonfietti LX, Paniago AMM, Venturini J, Espinel-Ingroff A. Antifungal Resistance in Cryptococcal Infections. Pathogens 2024; 13:128. [PMID: 38392866 PMCID: PMC10891860 DOI: 10.3390/pathogens13020128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Antifungal therapy, especially with the azoles, could promote the incidence of less susceptible isolates of Cryptococcus neoformans and C. gattii species complexes (SC), mostly in developing countries. Given that these species affect mostly the immunocompromised host, the infections are severe and difficult to treat. This review encompasses the following topics: 1. infecting species and their virulence, 2. treatment, 3. antifungal susceptibility methods and available categorical endpoints, 4. genetic mechanisms of resistance, 5. clinical resistance, 6. fluconazole minimal inhibitory concentrations (MICs), clinical outcome, 7. environmental influences, and 8. the relevance of host factors, including pharmacokinetic/pharmacodynamic (PK/PD) parameters, in predicting the clinical outcome to therapy. As of now, epidemiologic cutoff endpoints (ECVs/ECOFFs) are the most reliable antifungal resistance detectors for these species, as only one clinical breakpoint (amphotericin B and C. neoformans VNI) is available.
Collapse
Affiliation(s)
- Marcia S C Melhem
- Graduate Program in Sciences, Secretary of Health, São Paulo 01246-002, SP, Brazil
- Graduate Program in Infectious and Parasitic Diseases, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
- Graduate Program in Tropical Diseases, State University of São Paulo, Botucatu 18618-687, SP, Brazil
| | | | - Juliana P F Takahashi
- Graduate Program in Infectious and Parasitic Diseases, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
- Pathology Division, Adolfo Lutz Institute, São Paulo 01246-002, SP, Brazil
| | | | | | - Lisandra Siufi de Araújo
- Graduate Program in Infectious and Parasitic Diseases, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
- Central Public Health Laboratory-LACEN, Mycology Unit, Adolfo Lutz Institut, São Paulo 01246-002, SP, Brazil
| | - Wellington S Fava
- Graduate Program in Infectious and Parasitic Diseases, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Lucas X Bonfietti
- Central Public Health Laboratory-LACEN, Mycology Unit, Adolfo Lutz Institut, São Paulo 01246-002, SP, Brazil
| | - Anamaria M M Paniago
- Graduate Program in Infectious and Parasitic Diseases, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - James Venturini
- Graduate Program in Infectious and Parasitic Diseases, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Ana Espinel-Ingroff
- Central Public Health Laboratory-LACEN, Campo Grande 79074-460, MS, Brazil
- VCU Medical Center, Richmond, VA 23284, USA
| |
Collapse
|
14
|
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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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
|
15
|
Barrs VR, Beczkowski PM, Talbot JJ, Hobi S, Teoh SN, Hernandez Muguiro D, Shubitz LF, Sandy J. Invasive Fungal Infections and Oomycoses in Cats: 1. Diagnostic approach. J Feline Med Surg 2024; 26:1098612X231219696. [PMID: 38189288 PMCID: PMC10949879 DOI: 10.1177/1098612x231219696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
CLINICAL RELEVANCE In contrast to superficial fungal infections, such as dermatophytosis, invasive fungal infections (IFIs) are characterised by penetration of tissues by fungal elements. Disease can spread locally within a region or can disseminate haematogenously or via the lymphatics. The environment is the most common reservoir of infection. Since fungal spores are airborne, indoor cats are also susceptible to IFIs. Some environmental fungi are ubiquitous and present globally, while others are endemic or hyperendemic within specific geographic regions. Zoonotic pathogens include Microsporum canis, Sporothrix schenckii and Sporothrix brasiliensis. AIM In the first of a two-part article series, the approach to the investigation of feline IFIs and oomycoses is reviewed. As well as tips for diagnosis, and information on the ecological niche and distribution of fungal pathogens, the review covers clinical presentation of the most common IFIs, including cryptococcosis, histoplasmosis, blastomycosis, coccidioidomycosis, sporotrichosis, phaeohyphomycosis, aspergillosis and dermatophytic pseudomycetoma, as well as the oomycoses pythiosis, lagenidiosis and paralagenidiosis. In Part 2, the spectrum of activity, mechanisms of action, pharmacokinetic and pharmacodynamic properties and adverse effects of antifungal drugs are reviewed, and the treatment and prognosis for specific IFIs and oomycoses are discussed. EVIDENCE BASE The review draws on published evidence and the authors' combined expertise in feline medicine, mycology, dermatology, clinical pathology and anatomical pathology.
Collapse
Affiliation(s)
- Vanessa R Barrs
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
- Centre for Animal Health and Welfare, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
| | - Paweł M Beczkowski
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
| | | | - Stefan Hobi
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
| | - Shu Ning Teoh
- Veterinary Specialists Aotearoa, Henderson, Auckland, New Zealand
| | | | - Lisa F Shubitz
- Valley Fever Center for Excellence, The University of Arizona, AZ, USA
| | - Jeanine Sandy
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
| |
Collapse
|
16
|
Ordaya EE, Abu Saleh OM, Vergidis P, Deml SM, Wengenack NL, Fida M. Temporal trends in antifungal susceptibility of Cryptococcus neoformans isolates from a reference laboratory in the United States, 2011-2021. Mycoses 2024; 67:e13691. [PMID: 38214377 DOI: 10.1111/myc.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 12/17/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND There are no established clinical breakpoints for antifungal agents against Cryptococcus species; however, epidemiological cut-off values can help distinguish wild-type (WT) isolates without any acquired resistance from non-WT strains, which may harbour resistance mechanisms. PATIENTS/METHODS We describe the trends of antifungal MICs and percentages of WT C. neoformans species complex (CNSC) isolates processed in our reference laboratory from November 2011 to June 2021. There were only nine isolates in 2011, thus, we included them in the year 2012 for data analysis. Clinical data is also described when available. RESULTS We identified 632 CNSC, the majority collected from blood (n = 301), cerebrospinal fluid (n = 230), and respiratory (n = 71) sources. The overall percentage of WT isolates for amphotericin B (AMB), 5-flucytosine, and fluconazole was 77%, 98%, and 91%, respectively. We noticed a statistically significant change in the percentage of AMB WT isolates over the years, with 98% of isolates being WT in 2012 compared to 79% in 2021 (p < .01). A similar change was not observed for other antifungal agents. Clinical data was available for 36 patients, primarily non-HIV immunocompromised patients with disseminated cryptococcosis. There were no statistically significant differences in the clinical characteristics and outcomes between patients with WT (58.3%) versus non-WT (41.7%) isolates, but we noticed higher mortality in patients infected with an AMB non-WT CNSC isolate. CONCLUSIONS We observed an increase in the percentage of AMB non-WT CNSC isolates in the past decade. The clinical implications of this finding warrant further evaluation in larger studies.
Collapse
Affiliation(s)
- Eloy E Ordaya
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Omar M Abu Saleh
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Paschalis Vergidis
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sharon M Deml
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nancy L Wengenack
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Madiha Fida
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
17
|
Kebabonye K, Jongman M, Loeto D, Moyo S, Choga W, Kasvosve I. Determining Potential Link between Environmental and Clinical Isolates of Cryptococcus neoformans/Cryptococcus gattii Species Complexes Using Phenotypic and Genotypic Characterisation. MYCOBIOLOGY 2023; 51:452-462. [PMID: 38179115 PMCID: PMC10763847 DOI: 10.1080/12298093.2023.2272380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 10/10/2023] [Indexed: 01/06/2024]
Abstract
Opportunistic infections due to Cryptococcus neoformans and C. gattii species complexes continue to rise unabated among HIV/AIDS patients, despite improved antifungal therapies. Here, we collected a total of 20 environmental and 25 presumptive clinical cryptococcal isolates from cerebrospinal fluid (CSF) samples of 175 patients enrolled in an ongoing clinical trial Ambition 1 Project (Botswana-Harvard Partnership). Identity confirmation of the isolates was done using MALDI-TOF MS and PCR. We describe the diversity of the isolates by PCR fingerprinting and sequencing (Oxford Nanopore Technology) of the intergenic spacer region. Mating types of the isolates were determined by amplification of the MAT locus. We report an unusual prevalence of 42.1% of C. neoformans x C. deneoformans hybrids Serotype AD (n = 16), followed by 39.5% of C. neoformans Serotype A (n = 15), 5.3% of C. deneoformans, Serotype D (n = 2), 7.9% of C. gattii (n = 3), and 5.3% of C. tetragattii (n = 2) in 38 representative isolates that have been characterized. Mating type-specific PCR performed on 38 representative environmental and clinical isolates revealed that 16 (42.1%) were MATa/MATα hybrids, 17 (44.7%) were MATα, and five (13.2%) possessed MATa mating type. We used conventional and NGS platforms to demonstrate a potential link between environmental and clinical isolates and lay a foundation to further describe mating patterns/history in Botswana.
Collapse
Affiliation(s)
- Kenosi Kebabonye
- School of Health Allied Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Mosimanegape Jongman
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Daniel Loeto
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- School of Health Allied Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
- School of Health Systems of Public Health, University of Pretoria, Pretoria, South Africa
| | - Wonderful Choga
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ishmael Kasvosve
- School of Health Allied Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| |
Collapse
|
18
|
Borman AM, Johnson EM. Changes in fungal taxonomy: mycological rationale and clinical implications. Clin Microbiol Rev 2023; 36:e0009922. [PMID: 37930182 PMCID: PMC10732072 DOI: 10.1128/cmr.00099-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/13/2023] [Indexed: 11/07/2023] Open
Abstract
Numerous fungal species of medical importance have been recently subjected to and will likely continue to undergo nomenclatural changes as a result of the application of molecular approaches to fungal classification together with abandonment of dual nomenclature. Here, we summarize those changes affecting key groups of fungi of medical importance, explaining the mycological (taxonomic) rationale that underpinned the changes and the clinical relevance/importance (where such exists) of the key nomenclatural revisions. Potential mechanisms to mitigate unnecessary taxonomic instability are suggested, together with approaches to raise awareness of important changes to minimize potential clinical confusion.
Collapse
Affiliation(s)
- Andrew M. Borman
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| | - Elizabeth M. Johnson
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| |
Collapse
|
19
|
Zhang L, Wang S, Hong N, Li M, Liu Y, Zhou T, Peng Y, Hu C, Li X, Zhang Z, Guo M, Cogliati M, Hitchcock M, Xu J, Chen M, Liao G. Genotypic diversity and antifungal susceptibility of Cryptococcus neoformans species complex from China, including the diploid VNIII isolates from HIV-infected patients in Chongqing region. Med Mycol 2023; 61:myad119. [PMID: 37985734 DOI: 10.1093/mmy/myad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023] Open
Abstract
Although previous studies on the genotypic diversity and antifungal susceptibility of the Cryptococcus neoformans species complex (CNSC) isolates from China revealed ST5 genotype isolates being dominant, the information about the CNSC isolates from Chinese HIV-infected patients is limited. In this study, 171 CNSC isolates from HIV-infected patients in the Chongqing region of Southwest China were genotyped using the International Society for Human and Animal Mycology-multilocus sequence typing consensus scheme, and their antifungal drug susceptibilities were determined following CLSI M27-A3 guidelines. Among 171 isolates, six sequence types (STs) were identified, including the dominant ST5 isolates, the newly reported ST15, and four diploid VNIII isolates (ST632/ST636). Moreover, a total of 1019 CNSC isolates with STs and HIV-status information were collected and analyzed from Mainland China in the present study. A minimum spanning analysis grouped these 1019 isolates into three main subgroups, which were dominated by the ST5 clonal complex (CC5), followed by the ST31 clonal complex (CC31) and ST93 clonal complex (CC93). The trend of resistance or decreasing susceptibility of clinical CNSC isolates to azole agents within HIV-infected patients from the Chongqing region is increasing, especially resistance to fluconazole.
Collapse
Affiliation(s)
- Lanyu Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Saisai Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Nan Hong
- Department of Dermatology, Jinling Hospital, School of Medicine of Nanjing University, Nanjing, China
| | - Muyuan Li
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Yiting Liu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Tao Zhou
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Yan Peng
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Changhua Hu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Xiaoxu Li
- The Medical Research Institute (MRI), Southwest University, Chongqing, China
| | - Zhen Zhang
- Department of Clinical Laboratory, Chongqing General Hospital, Chongqing, China
| | - Mengzhu Guo
- Department of Dermatology, General Hospital of Southern Theatre Command, Guangzhou, China
| | - Massimo Cogliati
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy
| | - Megan Hitchcock
- Department of Biology, McMaster University, Hamilton, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Canada
| | - Min Chen
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Shanghai, China
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
- The Medical Research Institute (MRI), Southwest University, Chongqing, China
| |
Collapse
|
20
|
Fraser B, Munawar M, Halani S, Sabur N. Disseminated Cryptococcus neoformans presenting with an isolated pleural effusion in a patient receiving temozolomide and long-term steroids. BMJ Case Rep 2023; 16:e256255. [PMID: 37993145 PMCID: PMC10668160 DOI: 10.1136/bcr-2023-256255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
Cryptococcus neoformans is a ubiquitous environmental organism found worldwide. Infection with this organism occurs predominantly in immunocompromised hosts, including persons living with HIV or those with impaired cellular immunity. Cryptococcal pleural effusions have been described in cases with extensive pulmonary involvement. Here we present the case of a woman receiving temozolomide and steroids for glioblastoma multiforme, who developed cough and dyspnoea and was found to have an uncomplicated pleural effusion. Pleural fluid culture grew Cryptococcus neoformans with negative culture on bronchoalveolar lavage. High serum cryptococcal antigen titre of 1:64 prompted lumbar puncture which demonstrated positive cerebrospinal fluid for Cryptococcus neoformans She was treated with liposomal amphotericin B and flucytosine, followed by consolidation and maintenance therapy with fluconazole. Pleural involvement in the absence of pulmonary involvement has rarely been reported. We review pulmonary and radiographic manifestations of cryptococcal infection, when to assess for disseminated infection, and management principles.
Collapse
Affiliation(s)
- Brooke Fraser
- Medicine, University of Toronto, Toronto, Ontario, Canada
- Infectious Diseases, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Maha Munawar
- Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sheliza Halani
- Medicine, University of Toronto, Toronto, Ontario, Canada
- Infectious Diseases, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Natasha Sabur
- Medicine, University of Toronto, Toronto, Ontario, Canada
- Respirology, St Michael's Hospital, Toronto, Ontario, Canada
| |
Collapse
|
21
|
Bive BZ, Sacheli R, Mudogo CN, Zakayi PK, Bontems S, Lelo GM, Hayette MP. Correlation of antifungal susceptibility and sequence types within Cryptococcus neoformans VNI from HIV patients, and ERG11 gene polymorphism. J Mycol Med 2023; 33:101428. [PMID: 37651769 DOI: 10.1016/j.mycmed.2023.101428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/21/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023]
Abstract
INTRODUCTION Here we tested the correlation between minimum inhibitory concentrations (MICs) of major antifungal agents and sequence types (STs) within Cryptococcus neoformans VNI isolates, and explored the ERG11 gene of included strains. MATERIALS AND METHODS We analysed 23 C. neoformans strains categorised into two groups according to the distribution of the ST profile in Kinshasa clinics (Democratic Republic of Congo): major ST [ST93 (n = 15)], and less common STs [ST659 (n = 2), ST5 (n = 2), ST4 (n = 1), ST 53 (n = 1), ST31 (n = 1), and ST69 (n = 1)]. The MICs of the major antifungal agents [amphotericin B (AMB), 5-fluorocytosine (5FC) and fluconazole (FCZ)] were determined following EUCAST guidelines. ERG11 gene sequences were extracted from whole genome sequence of the isolates and compared with the wild-type gene sequence of the C. neoformans VNI. RESULTS Although major ST isolates appeared to have lower median MICs for AMB and 5FU than less common ST isolates (0.50 vs. 0.75 mg/L for AMB, 2 vs. 4 mg/L for 5FU, respectively), FCZ susceptibility was similar in both groups (4 mg/L) (p-value >0.05). The susceptibility profile of C. neoformans strains separately considered did not significantly affect the patients' clinical outcomes (p-value >0.05). Furthermore, two structural modalities of the ERG11 gene were observed: (1) that of the reference gene, and (2) that containing two exonic silent point substitutions, and one intronic point substitution located in a sequence potentially involved in pre-mRNA splicing (c.337-22C > T); with no association with the MICs of the isolates (p-value >0.05). CONCLUSIONS The lack of association/correlation found in this study calls for further investigations to better understand the mechanisms of C. neoformans resistance to antifungal agents.
Collapse
Affiliation(s)
- Bive Zono Bive
- Molecular Biology Service, Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo; Department of Clinical Microbiology, National Reference Center for Mycosis, Center for Interdisciplinary Research on Medicines, University of Liege, Liege, Belgium.
| | - Rosalie Sacheli
- Department of Clinical Microbiology, National Reference Center for Mycosis, Center for Interdisciplinary Research on Medicines, University of Liege, Liege, Belgium
| | - Celestin Nzanzu Mudogo
- Molecular Biology Service, Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Pius Kabututu Zakayi
- Molecular Biology Service, Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Sébastien Bontems
- Department of Clinical Microbiology, Laboratory of Virology and Immunology, Center for Interdisciplinary Research on Medicines, University of Liege, Liege, Belgium
| | - Georges Mvumbi Lelo
- Molecular Biology Service, Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Marie-Pierre Hayette
- Department of Clinical Microbiology, National Reference Center for Mycosis, Center for Interdisciplinary Research on Medicines, University of Liege, Liege, Belgium
| |
Collapse
|
22
|
Cumagun PM, Moore MK, McCarty TP, McGwin G, Pappas PG. Cryptococcal Meningoencephalitis in Phenotypically Normal Patients. Pathogens 2023; 12:1303. [PMID: 38003768 PMCID: PMC10674724 DOI: 10.3390/pathogens12111303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 11/26/2023] Open
Abstract
Cryptococcosis is an invasive fungal infection found worldwide that causes significant morbidity and mortality among a broad range of hosts. There are approximately 223,000 new cases of cryptococcosis annually throughout the world, and at least 180,000 deaths are attributed to this infection each year. Most of these are due to complications of cryptococcal meningoencephalitis among HIV-infected patients in resource-limited environments. The majority of individuals diagnosed with cryptococcosis have underlying conditions associated with immune dysfunction such as HIV, solid organ transplant, hematologic malignancy, organ failure syndromes, and/or the use of immunosuppressive agents such as glucocorticosteroids and biologic agents. In most clinical series, there is a small proportion of patients with cryptococcosis who are phenotypically normal; that is, they have no clinically obvious predisposition to disease. Cryptococcal meningoencephalitis (CME) presentation and management differ substantially between these normal individuals and their immunocompromised counterparts. In this review, we will focus on CME in the phenotypically normal host and underscore differences in the clinical presentation, management, outcome, and potential risk factors for these patients compared to immunocompromised persons who develop this potential devastating invasive fungal infection.
Collapse
Affiliation(s)
- Pia M. Cumagun
- Department of Medicine, Division of Infectious Diseases, The University of Alabama at Birmingham, Birmingham, AL 35294, USA; (P.M.C.)
| | | | - Todd P. McCarty
- Department of Medicine, Division of Infectious Diseases, The University of Alabama at Birmingham, Birmingham, AL 35294, USA; (P.M.C.)
| | - Gerald McGwin
- Department of Epidemiology, School of Public Health, University of Alabama, Birmingham, AL 35294, USA
| | - Peter G. Pappas
- Department of Medicine, Division of Infectious Diseases, The University of Alabama at Birmingham, Birmingham, AL 35294, USA; (P.M.C.)
| |
Collapse
|
23
|
Kobayashi Y, Kayamori A, Aoki K, Shiwa Y, Matsutani M, Fujita N, Sugita T, Iwasaki W, Tanaka N, Takashima M. Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny. BMC Genomics 2023; 24:609. [PMID: 37821828 PMCID: PMC10568926 DOI: 10.1186/s12864-023-09718-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/05/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Since DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided fungal identification; however, a barcode sequence alone is often insufficient. Thus, multi-gene- or whole-genome-based methods were developed. We previously isolated Basidiomycota yeasts classified in the Trichosporonales. Some strains were described as Cutaneotrichosporon cavernicola and C. spelunceum, whereas strain HIS471 remained unidentified. We analysed the genomes of these strains to elucidate their taxonomic relationship and genetic diversity. RESULTS The long-read-based assembly resulted in chromosome-level draft genomes consisting of seven chromosomes and one mitochondrial genome. The genome of strain HIS471 has more than ten chromosome inversions or translocations compared to the type strain of C. cavernicola despite sharing identical ITS barcode sequences and displaying an average nucleotide identity (ANI) above 93%. Also, the chromosome synteny between C. cavernicola and the related species, C. spelunceum, showed significant rearrangements, whereas the ITS sequence identity exceeds 98.6% and the ANI is approximately 82%. Our results indicate that the relative evolutionary rates of barcode sequences, whole-genome nucleotide sequences, and chromosome synteny in Cutaneotrichosporon significantly differ from those in the model yeast Saccharomyces. CONCLUSIONS Our results revealed that the relative evolutionary rates of nucleotide sequences and chromosome synteny are different among fungal clades, likely because different clades have diverse mutation/repair rates and distinct selection pressures on their genomic sequences and syntenic structures. Because diverse syntenic structures can be a barrier to meiotic recombination and may lead to speciation, the non-linear relationships between nucleotide and synteny diversification indicate that sequence-level distances at the barcode or whole-genome level are not sufficient for delineating species boundaries.
Collapse
Affiliation(s)
- Yuuki Kobayashi
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
| | - Ayane Kayamori
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Keita Aoki
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Nobuyuki Fujita
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Masako Takashima
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
| |
Collapse
|
24
|
Serna-Espinosa BN, Forero-Castro M, Morales-Puentes ME, Parra-Giraldo CM, Escandón P, Sánchez-Quitian ZA. First report of environmental isolation of Cryptococcus and Cryptococcus-like yeasts from Boyacá, Colombia. Sci Rep 2023; 13:15755. [PMID: 37735454 PMCID: PMC10514045 DOI: 10.1038/s41598-023-41994-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 09/04/2023] [Indexed: 09/23/2023] Open
Abstract
The Cryptococcus genus comprises more than 100 species, of which C. neoformans and C. gattii are the leading cause of cryptococcosis. The distribution of C. gattii and C. neoformans species complexes has been extensively studied and widely reported globally. Other species such as Naganishia albida, Papiliotrema laurentii, and Papiliotrema flavescens have been reported as pathogenic yeasts. Since there are no reports of environmental isolation in the Boyacá region (Colombia), this study aimed to isolate and characterize Cryptococcus and Cryptococcus-like yeasts from pigeon feces, Eucalyptus, and olive trees distributed in the municipalities of Tunja and Ricaute Alto. The environmental data was recovered, and the isolations obtained were identified by microscopy, biochemical test, MALDI-TOF MS, URA5-RFLP, and sequencing of the ITS and LSU loci. For the 93 pigeon dropping samples collected in Tunja, 23 yielded to C. neoformans, 3 to N. globosa, 2 N. albida and 1 to P. laurentii. Of the 1188 samples collected from olive trees, 17 (1.43%) positive samples were identified as C. gattii species complex (4), C. neoformans species complex (2), P. laurentii (3), N. albida (2), N. globosa (5) and P. flavescens (1). Likewise, specimens of C. neoformans presented molecular type VNI and molecular type VNII; for C. gattii the molecular types found were VGIII and one VGIV by URA5-RFLP but VGIII by MALDI-TOF and sequencing of the ITS and LSU. Therefore, it can be concluded that the species of Cryptococcus, Naganishia and Papiliotrema genera, are present in the environment of Boyacá, and show a predilection for climate conditions that are typical of this region.
Collapse
Affiliation(s)
- Briggith-Nathalia Serna-Espinosa
- Facultad de Ciencias, Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Tunja, Boyacá, Colombia
| | - Maribel Forero-Castro
- Facultad de Ciencias, Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Tunja, Boyacá, Colombia
| | - María Eugenia Morales-Puentes
- Facultad de Ciencias, Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Tunja, Boyacá, Colombia
| | - Claudia Marcela Parra-Giraldo
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, 110231, Colombia
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Calle 26 # 51-20, Bogotá, D.C., Colombia
| | - Zilpa Adriana Sánchez-Quitian
- Grupo de Investigación Gestión Ambiental, Facultad de Ciencias e Ingeniería, Departamento de Biología y Microbiología, Universidad de Boyacá, Carrera 2ª Este No. 64-169, Tunja, Boyacá, Colombia.
| |
Collapse
|
25
|
de Oliveira Kocerginsky P, Dos Santos Soares PH, Lyra HFS, Cadena PG, de Lima-Neto RG, Pontes-Filho NT, Lima-Filho JVM, Costa-Júnior SD, Neves RP, Cavalcanti IMF, Santos-Magalhães NS. Efficacy and non-toxicity of ciclopirox olamine-loaded liposomes against Cryptococcus neoformans clinical isolates. Braz J Microbiol 2023; 54:1513-1521. [PMID: 37540461 PMCID: PMC10484888 DOI: 10.1007/s42770-023-01071-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
The aim of this study was to evaluate the efficacy and non-toxicity of ciclopirox olamine-loaded liposomes against Cryptococcus neoformans clinical isolates. Initially, 24-1 fractional experimental design was carried out to obtain an optimized formulation of liposomes containing CPO (CPO-LipoC), which were then used to prepare stealth liposomes (CPO-LipoS). Liposomal formulations were characterized by their mean size diameter, polydispersity index (PDI), and drug encapsulation efficiency (EE%). Immunosuppressed mice were exposed to CPO-LipoS at 0.5 mg/kg/day for 14 days to verify possible histopathological alterations in the liver and kidneys. Immunosuppressed mice infected with C. neoformans were treated with CPO-LipoS at 0.5 mg/kg/day for 14 days to quantify the fungal burden in spleen, liver, lungs, and brain. CPO-LipoS presented a mean size diameter, PDI, and EE% of 101.4 ± 0.7 nm, 0.307, and 96.4 ± 0.9%, respectively. CPO-LipoS was non-toxic for the liver and kidneys of immunosuppressed mice. At the survival curve, all infected animals submitted to treatment with CPO-LipoS survived until the end of the experiment. Treatment with CPO-LipoS reduced C. neoformans cells in the spleen (59.3 ± 3.4%), liver (75.0 ± 3.6%), lungs (75.7 ± 6.7%), and brain (54.2 ± 3.2%). CPO-LipoS exhibit antifungal activity against C. neoformans, and the encapsulation of CPO into stealth liposomes allows its use as a systemic drug for treating cryptococcosis.
Collapse
Affiliation(s)
- Patrícia de Oliveira Kocerginsky
- Biosciences Center, Laboratory of Medical Mycology, Federal University of Pernambuco (UFPE), Av Reitor Joaquim Amazonas, S/N, Cidade Universitária, Recife, PE, 50740-570, Brazil
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Pedro Henrique Dos Santos Soares
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Hannah Ferreira Soares Lyra
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Pabyton Gonçalves Cadena
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
- Department of Animal Morphology and Physiology, Federal Rural University of Pernambuco (UFRPE), Rua Dom Manoel de Medeiros, S/N, Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - Reginaldo Gonçalves de Lima-Neto
- Biosciences Center, Laboratory of Medical Mycology, Federal University of Pernambuco (UFPE), Av Reitor Joaquim Amazonas, S/N, Cidade Universitária, Recife, PE, 50740-570, Brazil
- Health Sciences Center, Department of Tropical Medicine, Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Nicodemos Teles Pontes-Filho
- Center for Health Sciences, Department of Pathology, Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - José Vitor Moreira Lima-Filho
- Department of Biology, Federal Rural University of Pernambuco (UFRPE), Rua Dom Manoel de Medeiros, 401, Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - Sérgio Dias Costa-Júnior
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Rejane Pereira Neves
- Biosciences Center, Laboratory of Medical Mycology, Federal University of Pernambuco (UFPE), Av Reitor Joaquim Amazonas, S/N, Cidade Universitária, Recife, PE, 50740-570, Brazil
| | - Isabella Macário Ferro Cavalcanti
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
- Academic Center of Vitória (CAV), Laboratory of Microbiology and Immunology, Vitória de Santo Antão, Federal University of Pernambuco (UFPE), Rua Alto Do Reservatório, S/N, Vitória de Santo Antão, PE, Brazil.
| | - Nereide Stela Santos-Magalhães
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
| |
Collapse
|
26
|
Andrade-Silva LE, Vilas-Boas A, Ferreira-Paim K, Andrade-Silva J, Santos DDA, Ferreira TB, Borges AS, Mora DJ, Melhem MDSC, Silva-Vergara ML. Genotyping Analysis of Cryptococcus deuterogattii and Correlation with Virulence Factors and Antifungal Susceptibility by the Clinical and Laboratory Standards Institute and the European Committee on Antifungal Susceptibility Testing Methods. J Fungi (Basel) 2023; 9:889. [PMID: 37754997 PMCID: PMC10532325 DOI: 10.3390/jof9090889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 09/28/2023] Open
Abstract
Data about the relationship between their molecular types, virulence factors, clinical presentation, antifungal susceptibility profile, and outcome are still limited for Cryptococcus deuterogattii. This study aimed to evaluate the molecular and phenotypic characteristics of 24 C. deuterogattii isolates from the southeast region of Brazil. The molecular characterization was performed by multilocus sequence typing (MLST). The antifungal susceptibility profile was obtained according to CLSI-M27-A3 and EUCAST-EDef 7.1 methods. The virulence factors were evaluated using classic techniques. The isolates were divided into four populations. The molecular analysis suggests recombinant events in most of the groups evaluated. Resistance and susceptibility dose-dependent to fluconazole were evidenced in four isolates (16%) by EUCAST and in four isolates (16%) by CLSI methods. The agreement at ±two dilutions for both methods was 100% for itraconazole, ketoconazole, and voriconazole, 96% for amphotericin B, and 92% for fluconazole. Significant differences in virulence factor expression and antifungal susceptibility to itraconazole and amphotericin B were found. The mixed infection could be suggested by the presence of variable sequence types, differences in virulence factor production, and decreased antifungal susceptibility in two isolates from the same patient. The data presented herein corroborate previous reports about the molecular diversity of C. deuterogattii around the world.
Collapse
Affiliation(s)
- Leonardo Euripedes Andrade-Silva
- Infectious Diseases Unit, Internal Medicine Department, Federal University of Triangulo Mineiro, Uberaba 38001-170, MG, Brazil; (A.V.-B.); (K.F.-P.); (J.A.-S.); (T.B.F.); (M.L.S.-V.)
| | - Anderson Vilas-Boas
- Infectious Diseases Unit, Internal Medicine Department, Federal University of Triangulo Mineiro, Uberaba 38001-170, MG, Brazil; (A.V.-B.); (K.F.-P.); (J.A.-S.); (T.B.F.); (M.L.S.-V.)
| | - Kennio Ferreira-Paim
- Infectious Diseases Unit, Internal Medicine Department, Federal University of Triangulo Mineiro, Uberaba 38001-170, MG, Brazil; (A.V.-B.); (K.F.-P.); (J.A.-S.); (T.B.F.); (M.L.S.-V.)
| | - Juliana Andrade-Silva
- Infectious Diseases Unit, Internal Medicine Department, Federal University of Triangulo Mineiro, Uberaba 38001-170, MG, Brazil; (A.V.-B.); (K.F.-P.); (J.A.-S.); (T.B.F.); (M.L.S.-V.)
| | - Daniel de Assis Santos
- Microbiology Department, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Thatiana Bragine Ferreira
- Infectious Diseases Unit, Internal Medicine Department, Federal University of Triangulo Mineiro, Uberaba 38001-170, MG, Brazil; (A.V.-B.); (K.F.-P.); (J.A.-S.); (T.B.F.); (M.L.S.-V.)
| | - Aercio Sebastião Borges
- Infectious Diseases Unit, Internal Medicine Department, Federal University of Uberlândia, Uberlândia 38496-017, MG, Brazil
| | - Delio Jose Mora
- Center of Health Sciences, Federal University of Sul da Bahia, Teixeira de Freitas 85866-000, BA, Brazil;
| | | | - Mario Léon Silva-Vergara
- Infectious Diseases Unit, Internal Medicine Department, Federal University of Triangulo Mineiro, Uberaba 38001-170, MG, Brazil; (A.V.-B.); (K.F.-P.); (J.A.-S.); (T.B.F.); (M.L.S.-V.)
| |
Collapse
|
27
|
Kakizaki MIT, Melhem MDESC. CRYPTOCOCCOSIS: A bibliographic narrative review on antifungal resistance. AN ACAD BRAS CIENC 2023; 95:e20220862. [PMID: 37466540 DOI: 10.1590/0001-3765202320220862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/15/2022] [Indexed: 07/20/2023] Open
Abstract
Cryptococcosis is an infectious fungal disease widely studied for its epidemiological importance in the context of public health, given the high morbidity and mortality associated with this invasive fungal infection. Many cases of the disease present clinical resistance and progress to death, even in the presence of antifungal therapy. The prolonged use of triazole drugs to maintain the treatment of cryptococcosis in AIDS patients, can lead to selective pressure from mutant strains, among other resistance mechanisms, justifying the poor clinical evolution of some cases. In this study, a narrative review of the literature on the occurrence of antifungal resistance in cryptococcosis agents was performed. Publications from 2010 to 2022 that address this topic were selected using Google Scholars and Scopus website. Data from the studies were analyzed for the values of minimum inhibitory concentration (MIC) of drugs used in the management of cryptococcosis. The review showed that the highest MIC values occurred for voriconazole, especially against C. neoformans. It is concluded that there is a lack of studies with statistical analysis of the data obtained, in order to provide a better dimensioning of the resistance rates of cryptococcosis agents to different antifungal agents, both in geographical and temporal context.
Collapse
Affiliation(s)
- Maria Ismênia T Kakizaki
- Instituto de Assistência Médica ao Servidor Público Estadual: Iamspe, Setor de Oncologia e Hematologia, Rua Pedro de Toledo, 1800, Vila Clementino, 04039-901 São Paulo, SP, Brazil
| | - Marcia DE S C Melhem
- Departmento de Micologia, Associado de pesquisa sênior, Instituto Adolfo Lutz, Av. Dr. Arnaldo, 355, Cerqueira César, 01246-000 São Paulo, SP, Brazil
- Universidade Federal do Mato Grosso do Sul, Departamento de Medicina, Av. Costa e Silva, s/n, Pioneiros, 79070-900 Campo Grande, MS, Brazil
| |
Collapse
|
28
|
Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, Mead ME, Roberts CD, Raja HA, Li Y, Colabardini AC, de Castro PA, dos Reis TF, Canóvas D, Sanchez RL, Lagrou K, Torrado E, Rodrigues F, Oberlies NH, Zhou X, Goldman GH, Rokas A. Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547508. [PMID: 37461539 PMCID: PMC10350022 DOI: 10.1101/2023.07.03.547508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Cryptic fungal pathogens pose significant identification and disease management challenges due to their morphological resemblance to known pathogenic species while harboring genetic and (often) infectionrelevant trait differences. The cryptic fungal pathogen Aspergillus latus, an allodiploid hybrid originating from Aspergillus spinulosporus and an unknown close relative of Aspergillus quadrilineatus within section Nidulantes, remains poorly understood. The absence of accurate diagnostics for A. latus has led to misidentifications, hindering epidemiological studies and the design of effective treatment plans. We conducted an in-depth investigation of the genomes and phenotypes of 44 globally distributed isolates (41 clinical isolates and three type strains) from Aspergillus section Nidulantes. We found that 21 clinical isolates were A. latus; notably, standard methods of pathogen identification misidentified all A. latus isolates. The remaining isolates were identified as A. spinulosporus (8), A. quadrilineatus (1), or A. nidulans (11). Phylogenomic analyses shed light on the origin of A. latus, indicating one or two hybridization events gave rise to the species during the Miocene, approximately 15.4 to 8.8 million years ago. Characterizing the A. latus pangenome uncovered substantial genetic diversity within gene families and biosynthetic gene clusters. Transcriptomic analysis revealed that both parental genomes are actively expressed in nearly equal proportions and respond to environmental stimuli. Further investigation into infection-relevant chemical and physiological traits, including drug resistance profiles, growth under oxidative stress conditions, and secondary metabolite biosynthesis, highlight distinct phenotypic profiles of the hybrid A. latus compared to its parental and closely related species. Leveraging our comprehensive genomic and phenotypic analyses, we propose five genomic and phenotypic markers as diagnostics for A. latus species identification. These findings provide valuable insights into the evolutionary origin, genomic outcome, and phenotypic implications of hybridization in a cryptic fungal pathogen, thus enhancing our understanding of the underlying processes contributing to fungal pathogenesis. Furthermore, our study underscores the effectiveness of extensive genomic and phenotypic analyses as a promising approach for developing diagnostics applicable to future investigations of cryptic and emerging pathogens.
Collapse
Affiliation(s)
- Jacob L. Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Sonja Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Rafael W. Bastos
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology and Parasitology, Bioscience Center, Federal University of Rio Grande do Norte, Natal-RN, Brazil
| | - Charu Balamurugan
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - David Rinker
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Matthew E. Mead
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Christopher D. Roberts
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Huzefa A. Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Ana Cristina Colabardini
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David Canóvas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Rafael Luperini Sanchez
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Egídio Torrado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B’s-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B’s-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Nicholas H. Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| |
Collapse
|
29
|
Gomes RMODS, da Silva KJG, Ferreira LC, Arantes TD, Theodoro RC. Distribution and Polymorphisms of Group I Introns in Mitochondrial Genes from Cryptococcus neoformans and Cryptococcus gattii. J Fungi (Basel) 2023; 9:629. [PMID: 37367565 DOI: 10.3390/jof9060629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
The species complexes Cryptococcus neoformans and Cryptococcus gattii are the causative agents of cryptococcosis. Virulence and susceptibility to antifungals may vary within each species according to the fungal genotype. Therefore, specific and easily accessible molecular markers are required to distinguish cryptic species and/or genotypes. Group I introns are potential markers for this purpose because they are polymorphic concerning their presence and sequence. Therefore, in this study, we evaluated the presence of group I introns in the mitochondrial genes cob and cox1 in different Cryptococcus isolates. Additionally, the origin, distribution, and evolution of these introns were investigated by phylogenetic analyses, including previously sequenced introns for the mtLSU gene. Approximately 80.5% of the 36 sequenced introns presented homing endonucleases, and phylogenetic analyses revealed that introns occupying the same insertion site form monophyletic clades. This suggests that they likely share a common ancestor that invaded the site prior to species divergence. There was only one case of heterologous invasion, probably through horizontal transfer to C. decagattii (VGIV genotype) from another fungal species. Our results showed that the C. neoformans complex has fewer introns compared to C. gattii. Additionally, there is significant polymorphism in the presence and size of these elements, both among and within genotypes. As a result, it is impossible to differentiate the cryptic species using a single intron. However, it was possible to differentiate among genotypes within each species complex, by combining PCRs of mtLSU and cox1 introns, for C. neoformans species, and mtLSU and cob introns for C. gattii species.
Collapse
Affiliation(s)
| | | | - Leonardo Capistrano Ferreira
- Institute of Tropical Medicine, Universidade Federal do Rio Grande do Norte, Natal 59064-741, RN, Brazil
- Department of Biochemistry, Center of Bioscience, Universidade Federal do Rio Grande do Norte, Natal 59064-741, RN, Brazil
| | - Thales Domingos Arantes
- Institute of Tropical Pathology and Public Health, Universidade Federal de Goiás, Goiânia 74605-050, GO, Brazil
| | - Raquel Cordeiro Theodoro
- Institute of Tropical Medicine, Universidade Federal do Rio Grande do Norte, Natal 59064-741, RN, Brazil
- Department of Cell Biology and Genetics, Center of Bioscience, Universidade Federal do Rio Grande do Norte, Natal 59064-741, RN, Brazil
| |
Collapse
|
30
|
Mixão V, Nunez-Rodriguez JC, Del Olmo V, Ksiezopolska E, Saus E, Boekhout T, Gacser A, Gabaldón T. Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens. BMC Biol 2023; 21:105. [PMID: 37170256 PMCID: PMC10173528 DOI: 10.1186/s12915-023-01608-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Hybrids are chimeric organisms with highly plastic heterozygous genomes that may confer unique traits enabling the adaptation to new environments. However, most evolutionary theory frameworks predict that the high levels of genetic heterozygosity present in hybrids from divergent parents are likely to result in numerous deleterious epistatic interactions. Under this scenario, selection is expected to favor recombination events resulting in loss of heterozygosity (LOH) affecting genes involved in such negative interactions. Nevertheless, it is so far unknown whether this phenomenon actually drives genomic evolution in natural populations of hybrids. To determine the balance between selection and drift in the evolution of LOH patterns in natural yeast hybrids, we analyzed the genomic sequences from fifty-five hybrid strains of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis, which derived from at least six distinct natural hybridization events. RESULTS We found that, although LOH patterns in independent hybrid clades share some level of convergence that would not be expected from random occurrence, there is an apparent lack of strong functional selection. Moreover, while mitosis is associated with a limited number of inter-homeologous chromosome recombinations in these genomes, induced DNA breaks seem to increase the LOH rate. We also found that LOH does not accumulate linearly with time in these hybrids. Furthermore, some C. orthopsilosis hybrids present LOH patterns compatible with footprints of meiotic recombination. These meiotic-like patterns are at odds with a lack of evidence of sexual recombination and with our inability to experimentally induce sporulation in these hybrids. CONCLUSIONS Our results suggest that genetic drift is the prevailing force shaping LOH patterns in these hybrid genomes. Moreover, the observed LOH patterns suggest that these are likely not the result of continuous accumulation of sporadic events-as expected by mitotic repair of rare chromosomal breaks-but rather of acute episodes involving many LOH events in a short period of time.
Collapse
Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Present address: Genomics and Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Valentina Del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ewa Ksiezopolska
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Attila Gacser
- Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE "Lendület" Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
| |
Collapse
|
31
|
Espinel-Ingroff A, Cantón E. Methods for Antifungal Susceptibility Testing of the Cryptococcus neoformans/ C. gattii Complex: Strengths and Limitations. J Fungi (Basel) 2023; 9:jof9050542. [PMID: 37233253 DOI: 10.3390/jof9050542] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
When method-dependent categorical endpoints are available, namely either BPs or ECVs, MICs could aid in selecting the best treatment agent(s). BPs can categorize an isolate as either susceptible or resistant while the ECVs/ECOFFs can distinguish the wild type (WT, no known resistance mechanisms) from the Non-WT (NWT, harboring resistant mechanisms). Our literature review focused on the Cryptococcus species complex (SC) and the available methods and categorization endpoints. We also covered the incidence of these infections as well as the numerous Cryptococcus neoformans SC and C. gattii SC genotypes. The most important agents to treat cryptococcal infections are fluconazole (widely used), amphotericin B, and flucytosine. We provide data from the collaborative study that defined CLSI fluconazole ECVs for the most common cryptococcal species or genotypes and modes. EUCAST ECVs/ECOFFs are not yet available for fluconazole. We have summarized the incidence of cryptococccal infections (2000-2015) where fluconazole MICs were obtained by reference and commercial antifungal susceptibility tests. This occurrence is documented all over the world and those fluconazole MICs are mostly categorized by available CLSI ECVs/BPs as "resistant" instead of non-susceptible strains, including those by the commercial methods. As expected, the agreement between the CLSI and commercial methods is variable because SYO and Etest data could yield low/variable agreement (<90%) versus the CLSI method. Therefore, since BPs/ECVs are species and method dependent, why not gather sufficient MICs by commercial methods and define the required ECVs for these species?
Collapse
Affiliation(s)
| | - Emilia Cantón
- Severe Infection Research Group, Health Research Institute Hospital La Fe, 46026 Valencia, Spain
| |
Collapse
|
32
|
Macrae C, Ellis J, Keddie SH, Falconer J, Bradley J, Keogh R, Baerenbold O, Hopkins H, Jarvis JN. Diagnostic performance of the IMMY cryptococcal antigen lateral flow assay on serum and cerebrospinal fluid for diagnosis of cryptococcosis in HIV-negative patients: a systematic review. BMC Infect Dis 2023; 23:209. [PMID: 37024842 PMCID: PMC10080957 DOI: 10.1186/s12879-023-08135-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND The incidence of cryptococcosis amongst HIV-negative persons is increasing. Whilst the excellent performance of the CrAg testing in people living with HIV is well described, the diagnostic performance of the CrAg LFA has not been systematically evaluated in HIV-negative cohorts on serum or cerebrospinal fluid. METHODS We performed a systematic review to characterise the diagnostic performance of IMMY CrAg® LFA in HIV-negative populations on serum and cerebrospinal fluid. A systematic electronic search was performed using Medline, Embase, Global Health, CENTRAL, WoS Science Citation Index, SCOPUS, Africa-Wide Information, LILACS and WHO Global Health Library. Studies were screened and data extracted from eligible studies by two independent reviewers. A fixed effect meta-analysis was used to estimate the diagnostic sensitivity and specificity. RESULTS Of 447 records assessed for eligibility, nine studies met our inclusion criteria, including 528 participants overall. Amongst eight studies that evaluated the diagnostic performance of the IMMY CrAg® LFA on serum, the pooled median sensitivity was 96% (95% Credible Interval (CrI) 68-100%) with a pooled specificity estimate of 96% (95%CrI 84-100%). Amongst six studies which evaluated the diagnostic performance of IMMY CrAg® LFA on CSF, the pooled median sensitivity was 99% (95%CrI 95-100%) with a pooled specificity median of 99% (95%CrI 95-100%). CONCLUSIONS This review demonstrates a high pooled sensitivity and specificity for the IMMY CrAg® LFA in HIV-negative populations, in keeping with findings in HIV-positive individuals. The review was limited by the small number of studies. Further studies using IMMY CrAg® LFA in HIV-negative populations would help to better determine the diagnostic value of this test.
Collapse
Affiliation(s)
- Catriona Macrae
- Infectious Diseases Unit, NHS Lanarkshire, University Hospital Monklands, Monkscourt Avenue, Airdrie, ML6 0JS UK
| | - Jayne Ellis
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
- Infectious Diseases Institute, Makerere University, PO Box 22418, Kampala, Uganda
| | - Suzanne H. Keddie
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Jane Falconer
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - John Bradley
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Ruth Keogh
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Oliver Baerenbold
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Heidi Hopkins
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Joseph N. Jarvis
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| |
Collapse
|
33
|
Zhao Y, Ye L, Zhao F, Zhang L, Lu Z, Chu T, Wang S, Liu Z, Sun Y, Chen M, Liao G, Ding C, Xu Y, Liao W, Wang L. Cryptococcus neoformans, a global threat to human health. Infect Dis Poverty 2023; 12:20. [PMID: 36932414 PMCID: PMC10020775 DOI: 10.1186/s40249-023-01073-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Emerging fungal pathogens pose important threats to global public health. The World Health Organization has responded to the rising threat of traditionally neglected fungal infections by developing a Fungal Priority Pathogens List (FPPL). Taking the highest-ranked fungal pathogen in the FPPL, Cryptococcus neoformans, as a paradigm, we review progress made over the past two decades on its global burden, its clinical manifestation and management of cryptococcal infection, and its antifungal resistance. The purpose of this review is to drive research efforts to improve future diagnoses, therapies, and interventions associated with fungal infections. METHODS We first reviewed trends in the global burden of HIV-associated cryptococcal infection, mainly based on a series of systematic studies. We next conducted scoping reviews in accordance with the guidelines described in the Preferred Reporting Items for Systematic Reviews and Meta-analyses extension for Scoping Reviews using PubMed and ScienceDirect with the keyword Cryptococcus neoformans to identify case reports of cryptococcal infections published since 2000. We then reviewed recent updates on the diagnosis and antifungal treatment of cryptococcal infections. Finally, we summarized knowledge regarding the resistance and tolerance of C. neoformans to approved antifungal drugs. RESULTS There has been a general reduction in the estimated global burden of HIV-associated cryptococcal meningitis since 2009, probably due to improvements in highly active antiretroviral therapies. However, cryptococcal meningitis still accounts for 19% of AIDS-related deaths annually. The incidences of CM in Europe and North America and the Latin America region have increased by approximately two-fold since 2009, while other regions showed either reduced or stable numbers of cases. Unfortunately, diagnostic and treatment options for cryptococcal infections are limited, and emerging antifungal resistance exacerbates the public health burden. CONCLUSION The rising threat of C. neoformans is compounded by accumulating evidence for its ability to infect immunocompetent individuals and the emergence of antifungal-resistant variants. Emphasis should be placed on further understanding the mechanisms of pathogenicity and of antifungal resistance and tolerance. The development of novel management strategies through the identification of new drug targets and the discovery and optimization of new and existing diagnostics and therapeutics are key to reducing the health burden.
Collapse
Affiliation(s)
- Youbao Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China.
| | - Leixin Ye
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Fujie Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Lanyue Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhenguo Lu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Tianxin Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Siyu Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Zhanxiang Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Yukai Sun
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Min Chen
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Shanghai, 200003, China
| | - Guojian Liao
- The Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Chen Ding
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, Liaoning, China
| | - Yingchun Xu
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Shanghai, 200003, China
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100039, China.
| |
Collapse
|
34
|
Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
Collapse
Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| |
Collapse
|
35
|
Hitchcock M, Xu J. Global Analyses of Multi-Locus Sequence Typing Data Reveal Geographic Differentiation, Hybridization, and Recombination in the Cryptococcus gattii Species Complex. J Fungi (Basel) 2023; 9:jof9020276. [PMID: 36836390 PMCID: PMC9967412 DOI: 10.3390/jof9020276] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 02/22/2023] Open
Abstract
Cryptococcus gattii species complex (CGSC) is a basidiomycete haploid yeast and globally distributed mammalian pathogen. CGSC is comprised of six distinct lineages (VGI, VGII, VGIII, VGIV, VGV, and VGVI); however, the geographical distribution and population structure of these lineages is incompletely described. In this study, we analyze published multi-locus sequence data at seven loci for 566 previously recorded sequence types (STs) encompassing four distinct lineages (VGI, VGII, VGIII, and VGIV) within the CGSC. We investigate indicators of both clonal dispersal and recombination. Population genetic analyses of the 375 STs representing 1202 isolates with geographic information and 188 STs representing 788 isolates with ecological source data suggested historically differentiated geographic populations with infrequent long-distance gene flow. Phylogenetic analyses of sequences at the individual locus and of the concatenated sequences at all seven loci among all 566 STs revealed distinct clusters largely congruent with four major distinct lineages. However, 23 of the 566 STs (4%) each contained alleles at the seven loci belonging to two or more lineages, consistent with their hybrid origins among lineages. Within each of the four major lineages, phylogenetic incompatibility analyses revealed evidence for recombination. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across all samples. Together, our results suggest evidence for historical geographical differentiation, sexual recombination, hybridization, and both long-distance and localized clonal expansion in the global CGSC population.
Collapse
|
36
|
Patiño LH, Muñoz M, Ramírez AL, Vélez N, Escandón P, Parra-Giraldo CM, Ramírez JD. A Landscape of the Genomic Structure of Cryptococcus neoformans in Colombian Isolates. J Fungi (Basel) 2023; 9:jof9020135. [PMID: 36836249 PMCID: PMC9959405 DOI: 10.3390/jof9020135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
Cryptococcus neoformans species complexes are recognized as environmental fungi responsible for lethal meningoencephalitis in immunocompromised individuals. Despite the vast knowledge about the epidemiology and genetic diversity of this fungus in different regions of the world, more studies are necessary to comprehend the genomic profiles across South America, including Colombia, considered to be the second country with the highest number of Cryptococcosis. Here, we sequenced and analyzed the genomic architecture of 29 Colombian C. neoformans isolates and evaluated the phylogenetic relationship of these strains with publicly available C. neoformans genomes. The phylogenomic analysis showed that 97% of the isolates belonged to the VNI molecular type and the presence of sub-lineages and sub-clades. We evidenced a karyotype without changes, a low number of genes with copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs). Additionally, a difference in the number of SNPs between the sub-lineages/sub-clades was observed; some were involved in crucial fungi biological processes. Our study demonstrated the intraspecific divergence of C. neoformans in Colombia. These findings provide evidence that Colombian C. neoformans isolates do not probably require significant structural changes as adaptation mechanisms to the host. To the best of our knowledge, this is the first study to report the whole genome sequence of Colombian C. neoformans isolates.
Collapse
Affiliation(s)
- Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Angie Lorena Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Nórida Vélez
- Unidad de Proteómica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá 111321, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28001 Madrid, Spain
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Claudia-Marcela Parra-Giraldo
- Unidad de Proteómica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá 111321, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28001 Madrid, Spain
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: or ; Tel.: +1-(332)-2344161
| |
Collapse
|
37
|
Kidd SE, Abdolrasouli A, Hagen F. Fungal Nomenclature: Managing Change is the Name of the Game. Open Forum Infect Dis 2023; 10:ofac559. [PMID: 36632423 PMCID: PMC9825814 DOI: 10.1093/ofid/ofac559] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/18/2022] [Indexed: 01/09/2023] Open
Abstract
Fungal species have undergone and continue to undergo significant nomenclatural change, primarily due to the abandonment of dual species nomenclature in 2013 and the widespread application of molecular technologies in taxonomy allowing correction of past classification errors. These have effected numerous name changes concerning medically important species, but by far the group causing most concern are the Candida yeasts. Among common species, Candida krusei, Candida glabrata, Candida guilliermondii, Candida lusitaniae, and Candida rugosa have been changed to Pichia kudriavzevii, Nakaseomyces glabrata, Meyerozyma guilliermondii, Clavispora lusitaniae, and Diutina rugosa, respectively. There are currently no guidelines for microbiology laboratories on implementing changes, and there is ongoing concern that clinicians will dismiss or misinterpret laboratory reports using unfamiliar species names. Here, we have outlined the rationale for name changes across the major groups of clinically important fungi and have provided practical recommendations for managing change.
Collapse
Affiliation(s)
- Sarah E Kidd
- Correspondence: Sarah E. Kidd, BMedSc(Hons), PhD , National Mycology Reference Centre, SA Pathology, Frome Road, Adelaide, South Australia 5000, Australia ()
| | - Alireza Abdolrasouli
- Department of Medical Microbiology, King's College Hospital, London, United Kingdom,Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|
38
|
Taverna CG, Arias BA, Firacative C, Vivot ME, Szusz W, Vivot W, Mazza M, Córdoba SB, Canteros CE. Genotypic Diversity and Antifungal Susceptibility of Clinical Isolates of Cryptococcus Gattii Species Complex from Argentina. Mycopathologia 2023; 188:51-61. [PMID: 36609823 DOI: 10.1007/s11046-022-00705-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/24/2022] [Indexed: 01/09/2023]
Abstract
The aim of this study was to determine the genotypic diversity of 22 Cryptococcus gattii species complex clinical isolates from Argentina and to place these genotypes within the diversity of clinical, veterinary and environmental isolates from Latin America. Mating type and antifungal susceptibility of the isolates were also determined. By URA5-RFLP, nine isolates were identified as molecular type VGI, 10 as VGII, one as VGIII and two as VGIV. Multilocus sequence typing (MSLT), following the International Society for Human and Animal Mycology (ISHAM) consensus MLST scheme, was used to determine the genotypic diversity. Our results suggest that, in Argentina, VGI isolates have low genetic diversity, while VGII isolates have high genetic diversity. Both isolates identified as VGIV by URA5-RFLP were genotyped by MLST as belonging to the currently named VGVI clade. From all isolates, eight sequence types (STs) were unique for Argentina, while five STs have been reported already in other countries, being of high interest the genotypes ST20 and ST7 since they belong to the subtypes VGIIa and VGIIb, respectively, which are associated with hypervirulent strains responsible for outbreaks in North America. To note, geographical analysis showed that some genotypes may be associated with some regions in Argentina. Most isolates were MATα, but we are reporting one isolate MATa for the first time in the country. Antifungal susceptibility tests showed that itraconazole, voriconazole and posaconazole had high activity against all isolates, while amphotericin B, fluconazole and 5-fluorocytosine were the least active drugs against all studied isolates.
Collapse
Affiliation(s)
- Constanza Giselle Taverna
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina.
| | - Barbara Abigail Arias
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Firacative
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad de Rosario, Bogotá, Colombia
| | - Matías Ezequiel Vivot
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Wanda Szusz
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Walter Vivot
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariana Mazza
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Susana Beatriz Córdoba
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Cristina Elena Canteros
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
39
|
Jenks JD, Aneke CI, Al-Obaidi MM, Egger M, Garcia L, Gaines T, Hoenigl M, Thompson GR. Race and ethnicity: Risk factors for fungal infections? PLoS Pathog 2023; 19:e1011025. [PMID: 36602962 DOI: 10.1371/journal.ppat.1011025] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Racial and ethnic identities, largely understood as social rather than biologic constructs, may impact risk for acquiring infectious diseases, including fungal infections. Risk factors may include genetic and immunologic differences such as aberrations in host immune response, host polymorphisms, and epigenomic factors stemming from environmental exposures and underlying social determinants of health. In addition, certain racial and ethnic groups may be predisposed to diseases that increase risk for fungal infections, as well as disparities in healthcare access and health insurance. In this review, we analyzed racial and ethnic identities as risk factors for acquiring fungal infections, as well as race and ethnicity as they relate to risk for severe disease from fungal infections. Risk factors for invasive mold infections such as aspergillosis largely appear related to environmental differences and underlying social determinants of health, although immunologic aberrations and genetic polymorphisms may contribute in some circumstances. Although black and African American individuals appear to be at high risk for superficial and invasive Candida infections and cryptococcosis, the reasons for this are unclear and may be related to underling social determinants of health, disparities in access to healthcare, and other socioeconomic disparities. Risk factors for all the endemic fungi are likely largely related to underlying social determinants of health, socioeconomic, and health disparities, although immunologic mechanisms likely play a role as well, particularly in disseminated coccidioidomycosis.
Collapse
Affiliation(s)
- Jeffrey D Jenks
- Durham County Department of Public Health, Durham, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Chioma Inyang Aneke
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Mohanad M Al-Obaidi
- Division of Infectious Diseases, Department of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Matthias Egger
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
| | - Lorena Garcia
- Department of Public Health Sciences, UC Davis School of Medicine, Davis, California, United States of America
| | - Tommi Gaines
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California, San Diego, California, United States of America
| | - Martin Hoenigl
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California, San Diego, California, United States of America
| | - George R Thompson
- University of California Davis Center for Valley Fever, Sacramento, California, United States of America
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, California, United States of America
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
| |
Collapse
|
40
|
Beardsley J, Dao A, Keighley C, Garnham K, Halliday C, Chen SCA, Sorrell TC. What's New in Cryptococcus gattii: From Bench to Bedside and Beyond. J Fungi (Basel) 2022; 9:jof9010041. [PMID: 36675862 PMCID: PMC9865494 DOI: 10.3390/jof9010041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Cryptococcus species are a major cause of life-threatening infections in immunocompromised and immunocompetent hosts. While most disease is caused by Cryptococcus neoformans, Cryptococcus gattii, a genotypically and phenotypically distinct species, is responsible for 11-33% of global cases of cryptococcosis. Despite best treatment, C. gattii infections are associated with early mortality rates of 10-25%. The World Health Organization's recently released Fungal Priority Pathogen List classified C. gattii as a medium-priority pathogen due to the lack of effective therapies and robust clinical and epidemiological data. This narrative review summarizes the latest research on the taxonomy, epidemiology, pathogenesis, laboratory testing, and management of C. gattii infections.
Collapse
Affiliation(s)
- Justin Beardsley
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Correspondence:
| | - Aiken Dao
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Caitlin Keighley
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
| | - Katherine Garnham
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Sunshine Coast University Hospital, Sunshine Coast University, Birtinya, QLD 4575, Australia
| | - Catriona Halliday
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Institute of Clinical Pathology and Medical Research (ICPMR), NSW Health Pathology, Sydney, NSW 2145, Australia
| | - Sharon C.-A. Chen
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Institute of Clinical Pathology and Medical Research (ICPMR), NSW Health Pathology, Sydney, NSW 2145, Australia
| | - Tania C. Sorrell
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| |
Collapse
|
41
|
Saidykhan L, Onyishi CU, May RC. The Cryptococcus gattii species complex: Unique pathogenic yeasts with understudied virulence mechanisms. PLoS Negl Trop Dis 2022; 16:e0010916. [PMID: 36520688 PMCID: PMC9754292 DOI: 10.1371/journal.pntd.0010916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of Cryptococcus gattii/neoformans species complex are the etiological agents of the potentially fatal human fungal infection cryptococcosis. C. gattii and its sister species cause disease in both immunocompetent and immunocompromised hosts, while the closely related species C. neoformans and C. deneoformans predominantly infect immunocompromised hosts. To date, most studies have focused on similarities in pathogenesis between these two groups, but over recent years, important differences have become apparent. In this review paper, we highlight some of the major phenotypic differences between the C. gattii and neoformans species complexes and justify the need to study the virulence and pathogenicity of the C. gattii species complex as a distinct cryptococcal group.
Collapse
Affiliation(s)
- Lamin Saidykhan
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- Division of Physical and Natural Science, University of The Gambia, Brikama Campus, West Coast Region, The Gambia
| | - Chinaemerem U. Onyishi
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Robin C. May
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
| |
Collapse
|
42
|
Ssebambulidde K, Anjum SH, Hargarten JC, Chittiboina P, Shoham S, Seyedmousavi S, Marr KA, Hammoud DA, Billioux BJ, Williamson PR. Treatment recommendations for non-HIV associated cryptococcal meningoencephalitis including management of post-infectious inflammatory response syndrome. Front Neurol 2022; 13:994396. [PMID: 36530631 PMCID: PMC9751747 DOI: 10.3389/fneur.2022.994396] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/04/2022] [Indexed: 08/29/2023] Open
Abstract
Cryptococcal meningoencephalitis (CM) continues to cause major morbidity and mortality in a range of patients such as those immunosuppressed from HIV and with biologic immunosuppressants, including treatments of autoimmunity, malignancies, and conditioning regimens for transplantation. It is currently the most common cause of non-viral meningitis in the United States. Infections in previously healthy patients also develop with autoantibodies to granulocyte-macrophage colony stimulating factor or with monogenetic defects. In all populations, mortality and significant long-term morbidity occur in 30-50% despite therapy, and immune reconstitution and post-infectious inflammatory response syndromes complicate management. To help with these difficult cases, we present here a practical tutorial of the care of a range of patients with CM in the absence of HIV/AIDS.
Collapse
Affiliation(s)
- Kenneth Ssebambulidde
- Translational Mycology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Seher H. Anjum
- Translational Mycology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jessica C. Hargarten
- Translational Mycology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Prashant Chittiboina
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States
| | - Shmuel Shoham
- Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Seyedmojtaba Seyedmousavi
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Kieren A. Marr
- Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Dima A. Hammoud
- Center for Infectious Disease Imaging (CIDI), Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Bridgette Jeanne Billioux
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Peter R. Williamson
- Translational Mycology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
43
|
Gene expression profiles of ERG11, MDR1 and AFR1 in Cryptococcus neoformans var.grubbi from HIV patients. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2022; 42:697-706. [PMID: 36511671 PMCID: PMC9818250 DOI: 10.7705/biomedica.6519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Indexed: 12/14/2022]
Abstract
Introduction: Fluconazole is the most used antifungal drug for prevention and treatment of Cryptococcus spp. infections, the etiological agent of cryptococcosis. Resistance to fluconazole among Cryptococcus neoformans isolates can lead to treatment failure and generate relapses.
Objective: To evaluate the expression profiles of the AFR1, MDR1 and ERG11 genes in C. neoformans var. grubii clinical isolates during the in vitro response to fluconazole induction.
Materials and methods: Fourteen C. neoformans var. grubii isolates recovered from HIV patients were studied, in which 6 showed sensitivities to fluconazole and 8 decreased sensitivity. The expression levels of ERG11, AFR1 and MDR1 genes were determined by real-time PCR from extracted mRNA.
Results: AFR1 and MDR1 genes from C. neoformans var. grubii were overexpressed in fluconazole resistant isolates, whereas ERG11 maintains homogeneous expression in all
the evaluated resistance phenotypes of C. neoformans var. grubii isolates.
Conclusions: The overexpression of AFR1 and MDR1 genes, which codify for efflux pumps, contributes to fluconazole resistance in the studied isolates. However, the resistance patterns in this fungus and the relapse cases in HIV patients cannot be attributed solely to the exposure to the drug. Heteroresistance and the emerging resistance (resistance through other ERG genes), might be other mechanisms involved in this phenomenon, which must be studied in these isolations.
Collapse
|
44
|
Zhang J, Wang Z, Chen Y, Zhou Z, Yang Q, Fu Y, Zhao F, Li X, Chen Q, Fang L, Jiang Y, Yu Y. Antifungal susceptibility and molecular characteristics of Cryptococcus spp. based on whole-genome sequencing in Zhejiang Province, China. Front Microbiol 2022; 13:991703. [PMID: 36466641 PMCID: PMC9712201 DOI: 10.3389/fmicb.2022.991703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/31/2022] [Indexed: 06/05/2024] Open
Abstract
Cryptococcus spp. is a complex species that often causes cryptococcosis, which is one of the most common opportunistic infections in adults living with HIV and has very high morbidity and mortality rates. This study aimed to investigate the antifungal susceptibility profiles and epidemiological characteristics of the Cryptococcus neoformans species complex (CNSC) and the Cryptococcus gattii species complex (CGSC) in Zhejiang Province, China. A total of 177 CNSC and 3 CGSC isolates were collected, and antifungal susceptibility was tested by FUNGUS 3 and verified with an E-test. Moreover, multiple classification methods and genomic analyses were performed. The majority of the isolates (96.11%) were C. neoformans (formerly C. neoformans var. grubii) (ST5-VNI-A-α). Our study highlights that most of the patients with cryptococcosis were non-HIV patients in China, and nearly half of them did not have underlying diseases that led to immune insufficiency. Most of the Cryptococcus spp. isolates in this study were sensitive to common antifungal drugs. Two 5-flucytosine (5-FC)-resistant strains were identified, and FUR1 mutation was detected in the 5-FC-resistant isolates. Typing based on whole-genome sequencing (WGS) showed better discrimination than that achieved with multilocus sequence typing (MLST) and indicated a clear population structure. A phylogenetic analysis based on WGS included more genomic information than traditional classification methods.
Collapse
Affiliation(s)
- Junli Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Zhengan Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Qing Yang
- Department of Clinical Laboratory, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Fu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Feng Zhao
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Qiong Chen
- Department of Clinical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Fang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| |
Collapse
|
45
|
Weiss ZF, DiCarlo JE, Basta DW, Kent S, Liakos A, Baden L, Brigl M, Kanjilal S, Cañete-Gibas C, Wiederhold NP, Basu SS. Hidden in plain sight: urinary Cryptococcus neoformans missed by routine diagnostics in a patient with acute leukemia. Ann Clin Microbiol Antimicrob 2022; 21:49. [PMID: 36371203 PMCID: PMC9655867 DOI: 10.1186/s12941-022-00540-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022] Open
Abstract
Cryptococcuria is a rare manifestation of localized cryptococcal disease. We present a case of Cryptococcus neoformans urinary tract infection in an immunocompromised host missed by routine laboratory workup. The patient had negative blood cultures, a negative serum cryptococcal antigen (CrAg), and “non-Candida yeast” growing in urine culture that was initially dismissed as non-pathogenic. The diagnosis was ultimately made by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) from a repeat urine culture after transfer to a tertiary care center. Cryptococcus should be considered in the differential of refractory urinary tract infections growing non-Candida yeast.
Collapse
|
46
|
Hitchcock M, Xu J. Analyses of the Global Multilocus Genotypes of the Human Pathogenic Yeast Cryptococcus neoformans Species Complex. Genes (Basel) 2022; 13:2045. [PMID: 36360282 PMCID: PMC9691084 DOI: 10.3390/genes13112045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/18/2023] Open
Abstract
Cryptococcus neoformans species complex (CNSC) is a globally distributed human opportunistic yeast pathogen consisting of five major molecular types (VNI, VNII, VNB, VNIII and VNIV) belonging to two species, C. neoformans (VNI, VNII and VNB, collectively called serotype A) and C. deneoformans (VNIV, commonly called serotype D), and their hybrids (VNIII, serotype AD). Over the years, many studies have analyzed the geographical distribution and genetic diversity of CNSC. However, the global population structure and mode of reproduction remain incompletely described. In this study, we analyze the published multilocus sequence data at seven loci for CNSC. The combined sequences at the seven loci identified a total of 657 multilocus sequence types (STs), including 296 STs with known geographic information, representing 4200 non-redundant isolates from 31 countries and four continents. Among the 296 STs, 78 and 52 were shared among countries and continents, respectively, representing 3643 of the 4200 isolates. Except for the clone-corrected serotype D sample among countries, our analysis of the molecular variance of the 4200 isolates revealed significant genetic differentiations among countries and continents in populations of CNSC, serotype A, and serotype D. Phylogenetic analyses of the concatenated sequences of all 657 STs revealed several large clusters corresponding to the major molecular types. However, several rare but distinct STs were also found, representing potentially novel molecular types and/or hybrids of existing molecular types. Phylogenetic incompatibility analyses revealed evidence for recombination within all four major molecular types-VNI, VNII, VNIV and VNB-as well as within two VNB subclades, VNBI and VNBII, and two ST clusters around the most common STs, ST5 and ST93. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across most samples. Together, our results suggest evidence for historical differentiation, frequent recent gene flow, clonal expansion and recombination within and between lineages of the global CNSC population.
Collapse
Affiliation(s)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| |
Collapse
|
47
|
Wang H, Yan S, Liu Y, Li Y, Cui G, Ma X. Metagenomic next-generation sequencing assists in the diagnosis of Cryptococcus pneumonia: Case series and literature review. Front Public Health 2022; 10:971511. [PMID: 36408040 PMCID: PMC9672815 DOI: 10.3389/fpubh.2022.971511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Pulmonary cryptococcosis (PC) was once thought to occur only in patients with immune deficiencies, such as tested positive for the Human Immunodeficiency Virus (HIV). However, in recent years, it has been discovered that more than half of the patients with PC in our nation are individuals with normal immune function. As more and more PC cases are recorded, our diagnosis and treatment approaches, as well as our understanding of PC, are gradually improving. In reality, most PC patients still have a high incidence of misdiagnosis on their initial visit. It is primarily linked to the diverse clinical manifestations, atypical imaging findings, and inaccurate diagnostic approaches. Methods The research was conducted from 2019 to 2020. We performed traditional microbiological testing and mNGS on sample from patients with fever of Pulmonary nodules or lung infections. Furthermore, we collected patients' baseline information, clinical features, laboratory and imaging examination results, diagnosis, treatment and outcome. In the end, we confirmed three cases of PC using biopsy and mNGS. Conclusion Our data demonstrates that mNGS can be utilized as an auxiliary method for PC diagnosis. Early mNGS aids in the identification of pathogens, enabling early diagnosis and treatment, as well as a reduction in the rate of misdiagnosis and illness progression.
Collapse
Affiliation(s)
- Huifen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Su Yan
- Health Management Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangying Cui
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Guangying Cui
| | - Xiaoxu Ma
- Department of Respiratory Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Xiaoxu Ma
| |
Collapse
|
48
|
Howard-Jones AR, Sparks R, Pham D, Halliday C, Beardsley J, Chen SCA. Pulmonary Cryptococcosis. J Fungi (Basel) 2022; 8:1156. [PMID: 36354923 PMCID: PMC9696922 DOI: 10.3390/jof8111156] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 07/25/2023] Open
Abstract
Pulmonary cryptococcosis describes an invasive lung mycosis caused by Cryptococcus neoformans or Cryptococcus gattii complex. It is often a high-consequence disease in both immunocompromised and immunocompetent populations, and may be misdiagnosed as pulmonary malignancy, leading to a delay in therapy. Epidemiology follows that of cryptococcal meningoencephalitis, with C. gattii infection more common in certain geographic regions. Diagnostic tools include histopathology, microscopy and culture, and the detection of cryptococcal polysaccharide antigen or Cryptococcus-derived nucleic acids. All patients with lung cryptococcosis should have a lumbar puncture and cerebral imaging to exclude central nervous system disease. Radiology is key, both as an adjunct to laboratory testing and as the initial means of detection in asymptomatic patients or those with non-specific symptoms. Pulmonary cryptococcomas (single or multiple) may also be associated with disseminated disease and/or cryptococcal meningitis, requiring prolonged treatment regimens. Optimal management for severe disease requires extended induction (amphotericin B and flucytosine) and consolidation therapy (fluconazole) with close clinical monitoring. Susceptibility testing is of value for epidemiology and in regions where relatively high minimum inhibitory concentrations to azoles (particularly fluconazole) have been noted. Novel diagnostic tools and therapeutic agents promise to improve the detection and treatment of cryptococcosis, particularly in low-income settings where the disease burden is high.
Collapse
Affiliation(s)
- Annaleise R. Howard-Jones
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rebecca Sparks
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - David Pham
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Catriona Halliday
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Justin Beardsley
- Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
- Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
49
|
Sato K, Kawakami K. PAMPs and Host Immune Response in Cryptococcal Infection. Med Mycol J 2022; 63:133-138. [DOI: 10.3314/mmj.22.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Ko Sato
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine
| | - Kazuyoshi Kawakami
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine
| |
Collapse
|
50
|
Becerra-Álvarez P, Escandón P, Lizarazo J, Quirós-Gómez Ó, Firacative C. Cryptococcus neoformans- and Cryptococcus gattii-specific IgG, IgA and IgM differ among children and adults with and without cryptococcosis from Colombia. Med Mycol 2022; 60:6692868. [PMID: 36066645 DOI: 10.1093/mmy/myac067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cryptococcus neoformans (Cn) and Cryptococcus gattii (Cg) cause cryptococcosis, a life-threatening systemic mycosis of global distribution affecting mainly immunocompromised adults. Although a humoral response occurs during cryptococcosis, the role of antibody production against this mycosis is not fully understood. We aimed to determine total and specific antibodies against cryptococcal protein antigens in sera from people with and without diagnosis of cryptococcosis from Colombia. Using ELISA, total and specific levels of immunoglobulin (Ig)G, IgA and IgM were determined in sera from children and adults with (n = 109) and without (n = 119) cryptococcosis. Specific antibodies were those binding Cn- and Cg-protein antigens. In general, the mean of the total IgG production was higher in cryptococcosis patients than in controls (13 942.32 vs. 6459.91 µg/ml), while levels of IgA (488.13 vs. 1564.53 µg/ml) and IgM (775.69 vs. 1014.72 µg/ml) were higher in controls than in cryptococcosis patients (p ≤ 0.05). In patients with cryptococcosis, total IgG, IgA and IgM levels were higher in HIV + compared with HIV- (p ≤ 0.05). Specific antibodies tended to be higher in cryptococcosis patients than in controls and in adults than in children, with a positive correlation between antibody reactivity and age. All immunoglobulins were more reactive against Cn-proteins than Cg-proteins. Overall, a positive weak correlation between total and specific antibodies was found, although not always statistically significant. In patients with cryptococcosis from Colombia, the levels of immunoglobulins, total and specific, differ with respect to people without cryptococcosis. Variations in antibody production among adults and children with cryptococcosis and between Cn- and Cg-protein antigens were as well established. Our findings encourage further studies to determine the role of humoral immunity for host defence against cryptococcosis.
Collapse
Affiliation(s)
- Paola Becerra-Álvarez
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Patricia Escandón
- Group of Microbiology, National Institute of Health, Bogota, Colombia
| | - Jairo Lizarazo
- Internal Medicine Department, Hospital Universitario Erasmo Meoz, Universidad de Pamplona, Cúcuta, Colombia
| | - Óscar Quirós-Gómez
- Group of Epidemiology and Biostatistics, Universidad CES, Medellin, Colombia
| | - Carolina Firacative
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| |
Collapse
|