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Morris AJ, Kim HY, Nield B, Dao A, McMullan B, Alastruey-Izquierdo A, Colombo AL, Heim J, Wahyuningsih R, Le T, Chiller TM, Forastiero A, Chakrabarti A, Harrison TS, Bongomin F, Galas M, Siswanto S, Dagne DA, Roitberg F, Gigante V, Beardsley J, Sati H, Alffenaar JW, Morrissey CO. Talaromyces marneffei, Coccidioides species, and Paracoccidioides species-a systematic review to inform the World Health Organization priority list of fungal pathogens. Med Mycol 2024; 62:myad133. [PMID: 38935909 PMCID: PMC11210613 DOI: 10.1093/mmy/myad133] [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: 09/20/2023] [Revised: 11/18/2023] [Accepted: 12/11/2023] [Indexed: 06/29/2024] Open
Abstract
The World Health Organization, in response to the growing burden of fungal disease, established a process to develop a fungal pathogen priority list. This systematic review aimed to evaluate the epidemiology and impact of infections caused by Talaromyces marneffei, Coccidioides species, and Paracoccidioides species. PubMed and Web of Sciences databases were searched to identify studies published between 1 January 2011 and 23 February 2021 reporting on mortality, complications and sequelae, antifungal susceptibility, preventability, annual incidence, and trends. Overall, 25, 17, and 6 articles were included for T. marneffei, Coccidioides spp. and Paracoccidioides spp., respectively. Mortality rates were high in those with invasive talaromycosis and paracoccidioidomycosis (up to 21% and 22.7%, respectively). Hospitalization was frequent in those with coccidioidomycosis (up to 84%), and while the duration was short (mean/median 3-7 days), readmission was common (38%). Reduced susceptibility to fluconazole and echinocandins was observed for T. marneffei and Coccidioides spp., whereas >88% of T. marneffei isolates had minimum inhibitory concentration values ≤0.015 μg/ml for itraconazole, posaconazole, and voriconazole. Risk factors for mortality in those with talaromycosis included low CD4 counts (odds ratio 2.90 when CD4 count <200 cells/μl compared with 24.26 when CD4 count <50 cells/μl). Outbreaks of coccidioidomycosis and paracoccidioidomycosis were associated with construction work (relative risk 4.4-210.6 and 5.7-times increase, respectively). In the United States of America, cases of coccidioidomycosis increased between 2014 and 2017 (from 8232 to 14 364/year). National and global surveillance as well as more detailed studies to better define sequelae, risk factors, outcomes, global distribution, and trends are required.
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Affiliation(s)
- Arthur J Morris
- Department of Microbiology, Auckland City Hospital, Te Toku Tumai, Grafton, Auckland, New Zealand
| | - Hannah Yejin Kim
- The University of Sydney, Infectious Diseases Institute (Sydney ID), New South Wales, Australia
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
| | - Blake Nield
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Aiken Dao
- The University of Sydney, Infectious Diseases Institute (Sydney ID), New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
- Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Brendan McMullan
- School of Clinical Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Department of Infectious Diseases, Sydney Children’s Hospital, Randwick, New South Wales, Australia
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Arnaldo Lopes Colombo
- Departamento de Medicina, Division of Infectious Diseases, Hospital São Paulo, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Jutta Heim
- Global Antibiotics Research and Development Partnership, Drugs for Neglected Diseases Initiative, Geneva, Switzerland
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Parasitology, Faculty of Medicine, Universitas Kristen, Jakarta, Indonesia
| | - Thuy Le
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC, USA
- Tropical Medicine Research Center for Talaromycosis, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Tom M Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Agustina Forastiero
- Department of Communicable Diseases Prevention, Control and Elimination, Pan American Health Organization,Washington, DC, USA
| | | | - Thomas S Harrison
- Institute for Infection and Immunity, and Clinical Academic Group in Infection and Immunity, St. George’s, University of London, and St. George’s University Hospitals NHS Foundation Trust, London, UK
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Felix Bongomin
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Gulu University, Gulu, Uganda
| | - Marcelo Galas
- Antimicrobial Resistance Special Program, Communicable Diseases and Environmental Determinants of Health, Pan American Health Organization, Washington, DC, USA
| | - Siswanto Siswanto
- World Health Organization, South-East Asia Region Office, New Delhi, India
| | - Daniel Argaw Dagne
- Department of Control of Neglected Tropical Diseases, World Health Organization, Geneva, Switzerland
| | - Felipe Roitberg
- Department of Noncommunicable Diseases, World Health Organization, Geneva, Switzerland
| | - Valeria Gigante
- Impact Initiatives and Research Coordination Unit, Global Coordination Department, Antimicrobial Resistance Division, World Health Organization, Geneva, Switzerland
| | - Justin Beardsley
- The University of Sydney, Infectious Diseases Institute (Sydney ID), New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Hatim Sati
- Impact Initiatives and Research Coordination Unit, Global Coordination Department, Antimicrobial Resistance Division, World Health Organization, Geneva, Switzerland
| | - Jan-Willem Alffenaar
- The University of Sydney, Infectious Diseases Institute (Sydney ID), New South Wales, Australia
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
| | - Catherine Orla Morrissey
- Department of Infectious Diseases, The Alfred and Monash University, Melbourne, Victoria, Australia
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de Brito EDCA, França ADO, Siqueira IV, Félix VLT, Rezende AA, Amorim BC, da Silva SER, Mendes RP, Weber SS, Paniago AMM. Analysis and Interpretation of Automated Blood Count in the Treatment of Chronic Paracoccidioidomycosis. J Fungi (Basel) 2024; 10:317. [PMID: 38786672 PMCID: PMC11122400 DOI: 10.3390/jof10050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Blood count is crucial for assessing bone marrow's cell production and differentiation during infections, gaging disease severity, and monitoring therapeutic responses. The profile of blood count in chronic forms of paracoccidioidomycosis (PCM) has been insufficiently explored. To better understand the changes in hematological cells in different stages of the PCM chronic form, we evaluated the blood count, including immature blood cells in automated equipment, before and during the treatment follow-up of 62 chronic PCM patients. Predominantly male (96.8%) with an average age of 54.3 (standard deviation SD 6.9) years, participants exhibited pre-treatment conditions such as anemia (45.2%), monocytosis (38.7%), and leukocytosis (17.7%), which became less frequent after clinical cure. Anemia was more prevalent in severe cases. Notably, hemoglobin and reticulocyte hemoglobin content increased, while leukocytes, monocytes, neutrophils, immature granulocytes, and platelets decreased. Chronic PCM induced manageable hematological abnormalities, mainly in the red blood series. Monocytosis, indicating monocytes' role in PCM's immune response, was frequent. Post-treatment, especially after achieving clinical cure, significant improvements were observed in various hematological indices, including immature granulocytes and reticulocyte hemoglobin content, underscoring the impact of infection on these parameters.
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Affiliation(s)
- Eliana da Costa Alvarenga de Brito
- Graduate Program in Infectious and Parasitic Diseases, Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (E.d.C.A.d.B.); (A.d.O.F.); (B.C.A.)
| | - Adriana de Oliveira França
- Graduate Program in Infectious and Parasitic Diseases, Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (E.d.C.A.d.B.); (A.d.O.F.); (B.C.A.)
| | - Igor Valadares Siqueira
- Scientific Initiation CNPq, Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (I.V.S.); (V.L.T.F.); (A.A.R.); (S.E.R.d.S.)
| | - Vinícius Lopes Teodoro Félix
- Scientific Initiation CNPq, Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (I.V.S.); (V.L.T.F.); (A.A.R.); (S.E.R.d.S.)
| | - Amanda Alves Rezende
- Scientific Initiation CNPq, Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (I.V.S.); (V.L.T.F.); (A.A.R.); (S.E.R.d.S.)
| | - Bárbara Casella Amorim
- Graduate Program in Infectious and Parasitic Diseases, Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (E.d.C.A.d.B.); (A.d.O.F.); (B.C.A.)
| | - Suzane Eberhart Ribeiro da Silva
- Scientific Initiation CNPq, Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (I.V.S.); (V.L.T.F.); (A.A.R.); (S.E.R.d.S.)
| | - Rinaldo Poncio Mendes
- Department of Tropical Diseases, Botucatu Medical School, São Paulo State University, Botucatu 18618-687, SP, Brazil;
| | - Simone Schneider Weber
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil;
| | - Anamaria Mello Miranda Paniago
- Graduate Program in Infectious and Parasitic Diseases, Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (E.d.C.A.d.B.); (A.d.O.F.); (B.C.A.)
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Rodrigues AM, Hagen F, Puccia R, Hahn RC, de Camargo ZP. Paracoccidioides and Paracoccidioidomycosis in the 21st Century. Mycopathologia 2023; 188:129-133. [PMID: 36633737 DOI: 10.1007/s11046-022-00704-y] [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: 10/04/2022] [Accepted: 12/16/2022] [Indexed: 01/13/2023]
Abstract
Paracoccidioidomycosis (PCM) defines a broad spectrum of human and animal diseases caused by Paracoccidioides species (Onygenales). In the twenty-first century, Paracoccidioides advanced from a monotypic taxon to a genus that harbors seven species, including P. brasiliensis sensu stricto, P. americana, P. restrepiensis, P. venezuelensis, P. lutzii, P. loboi, and P. cetii. Classic PCM, acquired upon inhalation of propagules from P. brasiliensis sensu stricto, P. americana, P. restrepiensis, P. venezuelensis, and P. lutzii, affects the human lungs and may progress to systemic granulomatous disease with tegumentary and visceral involvement. On the other hand, PCM loboi and PCM ceti caused by the unculturable P. loboi and P. cetii are subcutaneous mycoses, typically observed as keloid lesions in humans and dolphins. Such heterogeneity highlights the importance of recognizing species boundaries in Paracoccidioides to gain insights into the ecology, evolution, clinical features, and mitigation strategies to tackle the advance of PCM.
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Affiliation(s)
- Anderson Messias Rodrigues
- Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil.
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil.
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Rosana Puccia
- Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - Rosane Christine Hahn
- Medical Mycology Laboratory/Investigation, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, MT, 78060900, Brazil
- Júlio Muller Hospital, EBSERH, Cuiabá, MT, Brazil
| | - Zoilo Pires de Camargo
- Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
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Pinheiro BG, Pôssa AP, Ricci G, Nishikaku AS, Hagen F, Hahn RC, de Camargo ZP, Rodrigues AM. Development of a Multiplex qPCR Assay for Fast Detection and Differentiation of Paracoccidioidomycosis Agents. J Fungi (Basel) 2023; 9:jof9030358. [PMID: 36983526 PMCID: PMC10057483 DOI: 10.3390/jof9030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Classic paracoccidioidomycosis (PCM) is a potentially deadly neglected tropical systemic mycosis caused by members of the Paracoccidioides brasiliensis complex (P. brasiliensis s. str., P. americana, P. restrepiensis, and P. venezuelensis) and P. lutzii. The laboratorial diagnosis of PCM relies on observing pathognomonic structures such as the “steering wheel” or “Mickey Mouse” shape in the direct mycological examination, fresh biopsied tissue in 10% KOH, histopathological analysis, and/or the isolation of the fungus in culture. However, these procedures are time-consuming and do not allow for the speciation of Paracoccidioides due to overlapping morphologies. Here, we propose a new one-tube multiplex probe-based qPCR assay to detect and recognize agents of the P. brasiliensis complex and P. lutzii. Primers (Paracoco-F and Paracoco-R) and TaqMan probes (PbraCx-Fam, Plu-Ned, and Paracoco-Vic) were developed to target the rDNA (ITS2/28S) in the Paracoccidioides genome. A panel of 77 Paracoccidioides isolates revealed a 100% specificity (AUC = 1.0, 95% CI 0.964–1.000, p < 0.0001) without cross-reacting with other medically relevant fungi or human and murine DNA. The lower limit of detection was 10 fg of gDNA and three copies of the partial rDNA amplicon. Speciation using qPCR was in perfect agreement with AFLP and TUB1-RFLP markers (kappa = 1.0). As a proof of concept, we assessed a panel of 16 formalin-fixed and paraffin-embedded specimens from histopathologically confirmed PCM patients to reveal a significant sensitivity of 81.25% and specificity of 100% (AUC = 0.906 ± 0.05, 95% CI = 0.756–0.979, p < 0.0001, Youden index J = 0.8125). Our assay achieved maximum sensitivity (100%) and specificity (100%) using fresh clinical samples (n = 9) such as sputum, bronchoalveolar lavage, and tissue fragments from PCM patients (AUC = 1.0, 95% CI 0.872–1.000, p < 0.0001, Youden index J = 1.0). Overall, our qPCR assay simplifies the molecular diagnosis of PCM and can be easily implemented in any routine laboratory, decreasing a critical bottleneck for the early treatment of PCM patients across a vast area of the Americas.
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Affiliation(s)
- Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Ana Paula Pôssa
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Giannina Ricci
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr. Ivo Ricci, São Carlos 13561-020, Brazil
| | - Angela Satie Nishikaku
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr. Ivo Ricci, São Carlos 13561-020, Brazil
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá 78060-900, Brazil
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá 78048-902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
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Hahn RC, Hagen F, Mendes RP, Burger E, Nery AF, Siqueira NP, Guevara A, Rodrigues AM, de Camargo ZP. Paracoccidioidomycosis: Current Status and Future Trends. Clin Microbiol Rev 2022; 35:e0023321. [PMID: 36074014 PMCID: PMC9769695 DOI: 10.1128/cmr.00233-21] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Paracoccidioidomycosis (PCM), initially reported in 1908 in the city of São Paulo, Brazil, by Adolpho Lutz, is primarily a systemic and neglected tropical mycosis that may affect individuals with certain risk factors around Latin America, especially Brazil. Paracoccidioides brasiliensis sensu stricto, a classical thermodimorphic fungus associated with PCM, was long considered to represent a monotypic taxon. However, advances in molecular taxonomy revealed several cryptic species, including Paracoccidioides americana, P. restrepiensis, P. venezuelensis, and P. lutzii, that show a preference for skin and mucous membranes, lymph nodes, and respiratory organs but can also affect many other organs. The classical diagnosis of PCM benefits from direct microscopy culture-based, biochemical, and immunological assays in a general microbiology laboratory practice providing a generic identification of the agents. However, molecular assays should be employed to identify Paracoccidioides isolates to the species level, data that would be complemented by epidemiological investigations. From a clinical perspective, all probable and confirmed cases should be treated. The choice of treatment and its duration must be considered, along with the affected organs, process severity, history of previous treatment failure, possibility of administering oral medication, associated diseases, pregnancy, and patient compliance with the proposed treatment regimen. Nevertheless, even after appropriate treatment, there may be relapses, which generally occur 5 years after the apparent cure following treatment, and also, the mycosis may be confused with other diseases. This review provides a comprehensive and critical overview of the immunopathology, laboratory diagnosis, clinical aspects, and current treatment of PCM, highlighting current issues in the identification, treatment, and patient follow-up in light of recent Paracoccidioides species taxonomic developments.
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Affiliation(s)
- Rosane Christine Hahn
- Medical Mycology Laboratory/Investigation, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
- Júlio Muller Hospital, EBSERH, Cuiabá, Mato Grosso, Brazil
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Rinaldo Poncio Mendes
- Faculdade de Medicina de Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- Faculdade de Medicina, Federal University of Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Eva Burger
- Department of Microbiology and Immunology, Federal University of Alfenasgrid.411180.d (UNIFAL), Alfenas, Minas Gerais, Brazil
| | - Andreia Ferreira Nery
- Medical Mycology Laboratory/Investigation, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
- Júlio Muller Hospital, EBSERH, Cuiabá, Mato Grosso, Brazil
| | - Nathan Pereira Siqueira
- Medical Mycology Laboratory/Investigation, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Armando Guevara
- Medical Mycology Laboratory/Investigation, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
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Paracoccidioidomycosis: What We Know and What Is New in Epidemiology, Diagnosis, and Treatment. J Fungi (Basel) 2022; 8:jof8101098. [PMID: 36294662 PMCID: PMC9605487 DOI: 10.3390/jof8101098] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a systemic mycosis endemic to Latin America caused by thermodimorphic fungi of the genus Paracoccidioides. In the last two decades, enhanced understanding of the phylogenetic species concept and molecular variations has led to changes in this genus’ taxonomic classification. Although the impact of the new species on clinical presentation and treatment remains unclear, they can influence diagnosis when serological methods are employed. Further, although the infection is usually acquired in rural areas, the symptoms may manifest years or decades later when the patient might be living in the city or even in another country outside the endemic region. Brazil accounts for 80% of PCM cases worldwide, and its incidence is rising in the northern part of the country (Amazon region), owing to new settlements and deforestation, whereas it is decreasing in the south, owing to agriculture mechanization and urbanization. Clusters of the acute/subacute form are also emerging in areas with major human intervention and climate change. Advances in diagnostic methods (molecular and immunological techniques and biomarkers) remain scarce, and even the reference center’s diagnostics are based mainly on direct microscopic examination. Classical imaging findings in the lungs include interstitial bilateral infiltrates, and eventually, enlargement or calcification of adrenals and intraparenchymal central nervous system lesions are also present. Besides itraconazole, cotrimoxazole, and amphotericin B, new azoles may be an alternative when the previous ones are not tolerated, although few studies have investigated their use in treating PCM.
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Ricci G, Campanini EB, Nishikaku AS, Puccia R, Marques M, Bialek R, Rodrigues AM, Batista WL. PbGP43 Genotyping Using Paraffin-Embedded Biopsies of Human Paracoccidioidomycosis Reveals a Genetically Distinct Lineage in the Paracoccidioides brasiliensis Complex. Mycopathologia 2021; 187:157-168. [PMID: 34870754 DOI: 10.1007/s11046-021-00608-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/12/2021] [Indexed: 11/26/2022]
Abstract
Paracoccidioidomycosis (PCM) is a systemic mycosis caused by a group of cryptic species embedded in the Paracoccidioides brasiliensis complex and Paracoccidioides lutzii. Four species were recently inferred to belong to the P. brasiliensis complex, but the high genetic diversity found in both human and environmental samples have suggested that the number of lineages may be higher. This study aimed to assess the 43-kilodalton glycoprotein genotypes (PbGP43) in paraffin-embedded samples from PCM patients to infer the phylogenetic lineages of the P. brasiliensis complex responsible for causing the infection. Formalin-fixed, paraffin-embedded (FFPE) tissue samples from patients with histopathological diagnosis of PCM were analyzed. DNAs were extracted and amplified for a region of the second exon of the PbGP43 gene. Products were sequenced and aligned with other PbGP43 sequences available. A haplotype network and the phylogenetic relationships among sequences were inferred. Amino acid substitutions were investigated regarding the potential to modify physicochemical properties in the proteins. Six phylogenetic lineages were identified as belonging to the P. brasiliensis complex. Two lineages did not group with any of the four recognized species of the complex, and, interestingly, one of them comprised only FFPE samples. A coinfection involving two lineages was found. Five parsimony-informative sites were identified and three of them showed radical non-synonymous substitutions with the potential to promote changes in the protein. This study expands the knowledge regarding the genetic diversity existing in the P. brasiliensis complex and shows the potential of FFPE samples in species identification and in detecting coinfections.
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Affiliation(s)
- Giannina Ricci
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr Ivo Ricci, São Carlos, SP, Brazil.
- Departamento de Patologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Angela Satie Nishikaku
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr Ivo Ricci, São Carlos, SP, Brazil
| | - Rosana Puccia
- Disciplina de Biologia Celular, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Mariângela Marques
- Faculdade de Medicina de Botucatu, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Ralf Bialek
- LADR GmbH MVZ Dr, Kramer & Kollegen, Lauenburger Straße 67, 21502, Geesthacht, Germany
| | - Anderson Messias Rodrigues
- Disciplina de Biologia Celular, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Wagner Luiz Batista
- Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo, Campus Diadema, São Paulo, SP, Brazil
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Roberto T, de Carvalho J, Beale M, Hagen F, Fisher M, Hahn R, de Camargo Z, Rodrigues A. Exploring genetic diversity, population structure, and phylogeography in Paracoccidioides species using AFLP markers. Stud Mycol 2021; 100:100131. [PMID: 34934463 PMCID: PMC8645518 DOI: 10.1016/j.simyco.2021.100131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation of Paracoccidioides propagules from the environment. The main agents include members of the P. brasiliensis complex (phylogenetically-defined species S1, PS2, PS3, and PS4) and P. lutzii. DNA-sequencing of protein-coding loci (e.g., GP43, ARF, and TUB1) is the reference method for recognizing Paracoccidioides species due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity within Paracoccidioides. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotyping Paracoccidioides species. The bioinformatic analysis generated 144 in silico AFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC/MseI-CT and #2 EcoRI-AT/MseI-CT). The combinations #1 and #2 were used in vitro to genotype 165 Paracoccidioides isolates recovered from across a vast area of South America. Considering the overall scored AFLP markers in vitro (67-87 fragments), the values of polymorphism information content (PIC = 0.3345-0.3456), marker index (MI = 0.0018), effective multiplex ratio (E = 44.6788-60.3818), resolving power (Rp = 22.3152-34.3152), discriminating power (D = 0.5183-0.5553), expected heterozygosity (H = 0.4247-0.4443), and mean heterozygosity (H avp = 0.00002-0.00004), demonstrated the utility of AFLP markers to speciate Paracoccidioides and to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability among P. brasiliensis complex and P. lutzii (PhiPT = 0.651-0.658, P < 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for P. brasiliensis s. str. (χ2 = 1.025; P = 0.3113), P. venezuelensis (χ2 = 0.692; P = 0.4054), and P. lutzii (χ2 = 0.027; P = 0.8694), supporting random mating within each species. In contrast, skewed distributions were found for P. americana (χ2 = 8.909; P = 0.0028) and P. restrepiensis (χ2 = 4.571; P = 0.0325) with a preponderance of MAT1-1. Geographical distributions confirmed that P. americana, P. restrepiensis, and P. lutzii are more widespread than previously thought. P. brasiliensis s. str. is by far the most widely occurring lineage in Latin America countries, occurring in all regions of Brazil. Our new DNA fingerprint assay proved to be rapid, reproducible, and highly discriminatory, to give insights into the taxonomy, ecology, and epidemiology of Paracoccidioides species, guiding disease-control strategies to mitigate PCM.
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Affiliation(s)
- T.N. Roberto
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - J.A. de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - M.A. Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - F. Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - M.C. Fisher
- MRC Center for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - R.C. Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, 78060900, Brazil
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá, 78048902, Brazil
| | - Z.P. de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
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