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Ansari L, Asgari B, Zare R, Zamanizadeh HR. Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran. Int J Syst Evol Microbiol 2023; 73. [PMID: 37676702 DOI: 10.1099/ijsem.0.006028] [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: 09/08/2023] Open
Abstract
During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30T (=IRAN 4042CT=CBS 149737T).
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Affiliation(s)
- Laleh Ansari
- Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Bita Asgari
- Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Rasoul Zare
- Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Hamid Reza Zamanizadeh
- Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Fernández NB, Toranzo A, Farias L, Canteros CE. Mycological diagnosis of paracoccidioidomycosis in a hospital from a nonendemic area: classical and molecular methods. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:132-143. [PMID: 37721907 PMCID: PMC10569774 DOI: 10.7705/biomedica.6888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/05/2023] [Indexed: 09/20/2023]
Abstract
Introduction Paracoccidioidomycosis is a systemic mycosis endemic in Latin America. Climate change and host migration emphasize the need to optimize this infection diagnosis. Objective To evaluate the implementation of Paracoccidioides spp. DNA detection in the mycological diagnosis of patients with suspected paracoccidioidomycosis. Materials and methods It is a retrospective study with laboratory data from patients with clinical suspicion of paracoccidioidomycosis, who consulted a university hospital from a non-endemic area. Results We analyzed the laboratory results of samples from 19 patients with suspected paracoccidioidomycosis. Seventeen out of 19 patients were born in or had visited an endemic area in Latin America. Fourteen adult male patients were confirmed to have paracoccidioidomycosis by conventional diagnosis: the direct examination was positive in 12 samples while fungal growth was found only in 4. Anti-Paracoccidioides spp. antibodies were detected in 10 patients, 8 of them with proven paracoccidioidomycosis. Nested PCR for Paracoccidioides spp. detection was performed on clinical samples from 14 patients, and positive results were obtained for 9 out of 10 patients with the conventional diagnosis of paracoccidioidomycosis. Conclusions The incorporation of molecular techniques to detect Paracoccidioides spp. DNA complements the conventional diagnosis of paracoccidioidomycosis. This tool allows the prescription of antifungal treatment in those cases where the fungus is not observed in the clinical samples.
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Affiliation(s)
- Norma B Fernández
- Laboratorio de Micología, Hospital de Clínicas "José de San Martín", Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Adriana Toranzo
- Servicio Micosis Profundas, Departamento de Micología, INEI-ANLIS "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina.
| | - Luciana Farias
- Laboratorio de Micología, Hospital de Clínicas "José de San Martín", Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Cristina E Canteros
- Departamento de Micología, INEI-ANLIS "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina.
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Zerbato V, Di Bella S, Pol R, D’Aleo F, Angheben A, Farina C, Conte M, Luzzaro F, Luzzati R, Principe L. Endemic Systemic Mycoses in Italy: A Systematic Review of Literature and a Practical Update. Mycopathologia 2023; 188:307-334. [PMID: 37294504 PMCID: PMC10386973 DOI: 10.1007/s11046-023-00735-z] [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: 12/17/2022] [Accepted: 04/02/2023] [Indexed: 06/10/2023]
Abstract
Endemic systemic mycoses such as blastomycosis, coccidioidomycosis, histoplasmosis, talaromycosis, paracoccidioidomycosis are emerging as an important cause of morbidity and mortality worldwide. We conducted a systematic review on endemic systemic mycoses reported in Italy from 1914 to nowadays. We found out: 105 cases of histoplasmosis, 15 of paracoccidioidomycosis, 10 of coccidioidomycosis, 10 of blastomycosis and 3 of talaromycosis. Most cases have been reported in returning travelers and expatriates or immigrants. Thirtytwo patients did not have a story of traveling to an endemic area. Fortysix subjects had HIV/AIDS. Immunosuppression was the major risk factor for getting these infections and for severe outcomes. We provided an overview on microbiological characteristics and clinical management principles of systemic endemic mycoses with a focus on the cases reported in Italy.
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Affiliation(s)
- Verena Zerbato
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), Piazza dell’Ospitale 1, 34125 Trieste, Italy
| | - Stefano Di Bella
- Clinical Department of Medical, Surgical and Health Sciences, Trieste University, 34149 Trieste, Italy
| | - Riccardo Pol
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), Piazza dell’Ospitale 1, 34125 Trieste, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Unit, Great Metropolitan Hospital “Bianchi Melacrino Morelli”, 89124 Reggio Calabria, Italy
| | - Andrea Angheben
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore - Don Calabria Hospital, 37024 Negrar di Valpolicella, Verona, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST “Papa Giovanni XXIII”, 24127 Bergamo, Italy
| | - Marco Conte
- Microbiology and Virology Unit, Great Metropolitan Hospital “Bianchi Melacrino Morelli”, 89124 Reggio Calabria, Italy
| | - Francesco Luzzaro
- Clinical Microbiology and Virology Unit, “A. Manzoni” Hospital, 23900 Lecco, Italy
| | | | - Roberto Luzzati
- Clinical Department of Medical, Surgical and Health Sciences, Trieste University, 34149 Trieste, Italy
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, “S. Giovanni di Dio” Hospital, 88900 Crotone, Italy
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Laux K, Teixeira MDM, Barker B. Love in the time of climate change: A review of sexual reproduction in the order Onygenales. Fungal Genet Biol 2023; 167:103797. [PMID: 37100376 DOI: 10.1016/j.fgb.2023.103797] [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: 09/10/2022] [Revised: 02/02/2023] [Accepted: 04/03/2023] [Indexed: 04/28/2023]
Abstract
Life-threatening infections caused by fungi in the order Onygenales have been rising over the last few decades. Increasing global temperature due to anthropogenic climate change is one potential abiotic selection pressure that may explain the increase in infections. The generation of genetically novel offspring with novel phenotypes through the process of sexual recombination could allow fungi to adapt to changing climate conditions. The basic structures associated with sexual reproduction have been identified in Histoplasma, Blastomyces, Malbranchea, and Brunneospora. However, for Coccidioides and Paracoccidioides, the actual structural identification of these processes has yet to be identified despite having genetic evidence that suggests sexual recombination is occurring in these organisms. This review highlights the importance of assessing sexual recombination in the order Onygenales as a means of understanding the mechanisms these organisms might employ to enhance fitness in the face of a changing climate and provides details regarding the known reproductive mechanisms in the Onygenales.
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Affiliation(s)
- Klaire Laux
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA.
| | - Marcus de Melo Teixeira
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA; Nùcleo de Medicina Tropical, University of Brasilia, Universitário Darcy Ribeiro, s/n -Asa Norte, Brasília, DF 70910-900, Brazil
| | - Bridget Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA.
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Genetic Diversity of Human Fungal Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023. [DOI: 10.1007/s40588-023-00188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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Peçanha-Pietrobom PM, Tirado-Sánchez A, Gonçalves SS, Bonifaz A, Colombo AL. Diagnosis and Treatment of Pulmonary Coccidioidomycosis and Paracoccidioidomycosis. J Fungi (Basel) 2023; 9:218. [PMID: 36836333 PMCID: PMC9959547 DOI: 10.3390/jof9020218] [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: 12/21/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Coccidioidomycosis (CM) and paracoccidioidomycosis (PCM) are systemic mycoses that are highly endemic in Latin America and have recently been included on the World Health Organization (WHO) Fungal Priority Pathogens List. Coccidioides immitis and Coccidioides posadasii are recognized as etiological agents of CM, with peculiarities in their geographic distribution. The genus Paracoccidioides now includes Paracoccidioides lutzii and the Paracoccidioides brasiliensis complex, which encompasses four phylogenetic species. In both diseases, pulmonary signs and symptoms are the main reasons for patients to seek medical assistance, and they are frequently misdiagnosed as tuberculosis. In this paper, we present a critical view of the strategies for diagnosis and clinical management of CM and PCM. Over the past few decades, there has been an increase in the number of reports of endemic fungal infections in areas previously thought to be "non-endemic" due to climate change and increased travel, among other factors. Learning to recognize their main epidemiological aspects and clinical manifestations is crucial so that clinicians can include them in the differential diagnosis of lung disease and avoid late diagnosis.
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Affiliation(s)
| | - Andrés Tirado-Sánchez
- Dermatology Service & Mycology Department, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City 06726, Mexico
- Internal Medicine Department, Hospital General de Zona 29, Instituto Mexicano del Seguro Social, Mexico City 07950, Mexico
| | - Sarah Santos Gonçalves
- Department of Pathology, Infectious Diseases Postgraduate Program, Federal University of Espírito Santo (UFES), Vitoria 29043900, Brazil
| | - Alexandro Bonifaz
- Internal Medicine Department, Hospital General de Zona 29, Instituto Mexicano del Seguro Social, Mexico City 07950, Mexico
| | - Arnaldo Lopes Colombo
- Department of Medicine, Division of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04039032, Brazil
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Gerrits van den Ende B, Rodrigues AM, Hahn RC, Hagen F. A surprising finding: The curious case of a tongue lesion misdiagnosed as paracoccidioidomycosis. Rev Iberoam Micol 2023; 40:10-14. [PMID: 36690509 DOI: 10.1016/j.riam.2022.11.002] [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: 08/10/2022] [Revised: 11/08/2022] [Accepted: 11/23/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Paracoccidioidomycosis is an endemic mycosis caused by members of the Paracoccidioides genus. Brazil remains the focus area and, to a lesser extent, the disease has been reported from Argentina, Colombia and Venezuela. AIMS A Venezuelan Paracoccidioides brasiliensis strain, isolated from a patient diagnosed with chronic multifocal paracoccidioidomycosis, was subjected to whole genome sequencing to provide more insight about Paracoccidioides outside the endemic focus area. METHODS P. brasiliensis strain CBS 118890 was whole genome sequenced using nanopore; library preparation with the 'native barcoding genomic DNA kit' was followed by sequencing on Flongle and MinION flowcells. Batches of strain CBS 118890 were re-identified by sequencing the internal transcribed spacer (ITS) region, and final identification was made based on phylogenetic analysis. RESULTS Surprisingly, the Venezuelan P. brasiliensis strain CBS 118890 turned out to be a Nannizziopsis species. The batches of this strain were ITS sequenced followed by phylogenetic analysis and resulted in the final identification of Nannizziopsis arthrosporioides. CONCLUSIONS Nannizziopsis infections are commonly seen in a wide variety of reptiles, but are particularly rare in human infections. This case underlines the need for molecular characterization of cases that clinically mimic paracoccidioidomycosis but that are serologically negative for Paracoccidioides.
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Affiliation(s)
| | - 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, Brazil; Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil; Júlio Muller University Hospital - Ebserh, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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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: 3] [Impact Index Per Article: 1.5] [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: 0] [Impact Index Per Article: 0] [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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Jofre GI, Singh A, Mavengere H, Sundar G, D'Agostino E, Chowdhary A, Matute DR. An Indian lineage of Histoplasma with strong signatures of differentiation and selection. Fungal Genet Biol 2022; 158:103654. [PMID: 34942368 DOI: 10.1016/j.fgb.2021.103654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 01/04/2023]
Abstract
Histoplasma, a genus of dimorphic fungi, is the etiological agent of histoplasmosis, a pulmonary disease widespread across the globe. Whole genome sequencing has revealed that the genus harbors a previously unrecognized diversity of cryptic species. To date, studies have focused on Histoplasma isolates collected in the Americas with little knowledge of the genomic variation from other localities. In this report, we report the existence of a well-differentiated lineage of Histoplasma occurring in the Indian subcontinent. The group is differentiated enough to satisfy the requirements of a phylogenetic species, as it shows extensive genetic differentiation along the whole genome and has little evidence of gene exchange with other Histoplasma species. Next, we leverage this genetic differentiation to identify genetic changes that are unique to this group and that have putatively evolved through rapid positive selection. We found that none of the previously known virulence factors have evolved rapidly in the Indian lineage but find evidence of strong signatures of selection on other alleles potentially involved in clinically-important phenotypes. Our work serves as an example of the importance of correctly identifying species boundaries to understand the extent of selection in the evolution of pathogenic lineages. IMPORTANCE: Whole genome sequencing has revolutionized our understanding of microbial diversity, including human pathogens. In the case of fungal pathogens, a limiting factor in understanding the extent of their genetic diversity has been the lack of systematic sampling. In this piece, we show the results of a collection in the Indian subcontinent of the pathogenic fungus Histoplasma, the causal agent of a systemic mycosis. We find that Indian samples of Histoplasma form a distinct clade which is highly differentiated from other Histoplasma species. We also show that the genome of this lineage shows unique signals of natural selection. This work exemplifies how the combination of a robust sampling along with population genetics, and phylogenetics can reveal the precise genetic changes that differentiate lineages of fungal pathogens.
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Affiliation(s)
- Gaston I Jofre
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Ashutosh Singh
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Heidi Mavengere
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Gandhi Sundar
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Emmanuel D'Agostino
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Anuradha Chowdhary
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States.
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Andrade-Silva J, Andrade-Silva LE, Paes HC, Alves L, Rosa A, Tenório BG, Ferreira MS, Felipe MSS, Teixeira MDM, Silva-Vergara ML. Molecular epidemiology of Paracoccidiodes spp. recovered from patients with paracoccidioidomycosis in a teaching hospital from Minas Gerais State of Brazil. PLoS Negl Trop Dis 2021; 15:e0009956. [PMID: 34843484 PMCID: PMC8659327 DOI: 10.1371/journal.pntd.0009956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/09/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
Introduction Paracoccidioidomycosis (PCM) is caused by several species of the Paracoccidioides genus which can be differentiated by interspecific genetic variations, morphology and geographic distribution. Intraspecific variability correlation with clinical and epidemiological aspects of these species still remains unclear. This study aimed to sequence the loci GP43, exon 2 and ARF of 23 clinical isolates of Paracoccidioides spp. from patients in the Southeast Region of Brazil. Methodology and main findings GenBank was used to compare the present (23) with previous described sequences (151) that included ARF and GP43. It was identified a high polymorphism rate among the 23 isolates in comparison to the other 151. Among the isolates, 22 (95.66%) were S1/P. brasiliensis and 1 (4.34%) was identified as PS2/P. americana. A total of 45 haplotypes were found as follows: 19 from S1/P. brasiliensis (13 from the present study), 15 from P. lutzii, 6 from PS2/P. americana (1 from the present study), 3 from PS3/P. restrepiensis and 2 from PS4/P. venezuelensis. Moreover, exclusive haplotypes according to clinical origin and geographical area were found. S1/P. brasiliensis (HD = 0.655 and K = 4.613) and P. lutzii (HD = 0.649 and K = 2.906) presented the highest rate of polymorphism among all species, from which 12 isolates of the present study were clustered within S1b/P. brasiliensis. The GP43 locus showed a higher variability and was found to be the main reason for the species differentiation. Conclusions The results herein decribed show a high intraspecific genetic variability among S1/P. brasiliensis isolates and confirm the predominance of this species in the Southeast region of Brazil. The finding of exclusive haplotypes according to clinical origin and geographical area would suggest correlation between the molecular profile with the clinical form and geographic origin of patients with PCM. Paracoccidioidomycosis (PCM) is one of the most important systemic mycosis of Latin America. This disease can be caused by Paracoccidioides lutzii and four different phylogenetic species: S1/Paracoccidioides brasiliensis sensu stricto that harboring S1a and S1b, PS2/Paracoccidioides americana, PS3/Paracoccidioides restrepiensis and PS4/Paracoccidioides venezuelensis. Some of these species show differences in their main geographic region of predominance such as PS2/P. americana that can be found in Venezuela and Southern Brazil; PS3/P. restrepiensis and PS4/P. venezuelensis which are distributed in Colombia and Venezuela. However, and due to their wide geographical distribution, the species S1/P. brasiliensis and P. lutzii overlapping ecological niches and can be found in different regions of Brazil and other Latin American countries. Regarding eco-epidemiological aspects, the habitat is believed to be the soil due to the predominance of the disease among rural workers who become infected by inhaling infectious propagules during their farm activities. According to other authors, these species could have relation with the different PCM clinical presentation. This study aimed to describe the molecular epidemiology associated with clinical and epidemiological data of Paracoccidiodes spp. in the Minas Gerais State, located in the Southeast region, Brazil. Among the 23 isolates herein evaluated, 22 were S1/P. brasiliensis and 1 was identified as PS2/P. americana. A total of 45 haplotypes were found when these isolates were compared with other 151 deposited in the Genbank. The preliminar finding of exclusive haplotypes according to clinical origin and geographical area would suggest correlation between the molecular profile with the clinical form and geographic origin of patients with PCM. The GP43 locus showed a higher variability and was found to be the main promotor of species differentiation. The results herein described pointed out a high intraspecific genetic variability among S1/P. brasiliensis isolates and confirm the predominance of this species in the Southeast region of Brazil.
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Affiliation(s)
- Juliana Andrade-Silva
- Infectious Diseases Unit, Internal Medicine Department, Triangulo Mineiro Federal University, Uberaba, Brazil
| | | | - Hugo Costa Paes
- Faculty of Medicina, University of Brasília, Brasília, Brazil
| | - Lucas Alves
- Faculty of Medicina, University of Brasília, Brasília, Brazil
| | - Adair Rosa
- Faculty of Medicina, University of Brasília, Brasília, Brazil
| | | | - Marcelo Simão Ferreira
- Infectious diseases Unit, Internal Medicine Department Federal University of Uberlândia, Uberlândia, Brazil
| | | | | | - Mario León Silva-Vergara
- Infectious Diseases Unit, Internal Medicine Department, Triangulo Mineiro Federal University, Uberaba, Brazil
- * E-mail:
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12
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Vilela R, Huebner M, Vilela C, Vilela G, Pettersen B, Oliveira C, Mendoza L. The taxonomy of two uncultivated fungal mammalian pathogens is revealed through phylogeny and population genetic analyses. Sci Rep 2021; 11:18119. [PMID: 34518564 PMCID: PMC8438014 DOI: 10.1038/s41598-021-97429-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/18/2021] [Indexed: 01/21/2023] Open
Abstract
Ever since the uncultivated South American fungal pathogen Lacazia loboi was first described 90 years ago, its etiology and evolutionary traits have been at the center of endless controversies. This pathogen infects the skin of humans and as long believed, dolphin skin. However, recent DNA analyses of infected dolphins placed its DNA sequences within Paracoccidioides species. This came as a surprise and suggested the human and dolphin pathogens may be different species. In this study, population genetic analyses of DNA from four infected dolphins grouped this pathogen in a monophyletic cluster sister to P. americana and to the other Paracoccidioides species. Based on the results we have emended the taxonomy of the dolphin pathogen as Paracoccidioides cetii and P. loboi the one infecting human. Our data warn that phylogenetic analysis of available taxa without the inclusion of unusual members may provide incomplete information for the accurate classification of anomalous species.
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Affiliation(s)
- Raquel Vilela
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, MI, 48824, USA
- Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, 31270, Brazil
| | - Marianne Huebner
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, 48824, USA
| | - Camila Vilela
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, MI, 48824, USA
| | - Gabriella Vilela
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, MI, 48824, USA
| | - Bruno Pettersen
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, MI, 48824, USA
| | - Claudia Oliveira
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, MI, 48824, USA
| | - Leonel Mendoza
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, MI, 48824, USA.
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
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Seki Kioshima E, de Souza Bonfim de Mendonça P, de Melo Teixeira M, Grenier Capoci IR, Amaral A, Vilugron Rodrigues-Vendramini FA, Lauton Simões B, Rodrigues Abadio AK, Fernandes Matos L, Soares Felipe MS. One Century of Study: What We Learned about Paracoccidioides and How This Pathogen Contributed to Advances in Antifungal Therapy. J Fungi (Basel) 2021; 7:106. [PMID: 33540749 PMCID: PMC7913102 DOI: 10.3390/jof7020106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 02/08/2023] Open
Abstract
Paracoccidioidomycosis (PCM) is a notable fungal infection restricted to Latin America. Since the first description of the disease by Lutz up to the present day, Brazilian researchers have contributed to the understanding of the life cycle of this pathogen and provided the possibility of new targets for antifungal therapy based on the structural and functional genomics of Paracoccidioides. In this context, in silico approaches have selected molecules that act on specific targets, such as the thioredoxin system, with promising antifungal activity against Paracoccidioides. Some of these are already in advanced development stages. In addition, the application of nanostructured systems has addressed issues related to the high toxicity of conventional PCM therapy. Thus, the contribution of molecular biology and biotechnology to the advances achieved is unquestionable. However, it is still necessary to transcend the boundaries of synthetic chemistry, pharmaco-technics, and pharmacodynamics, aiming to turn promising molecules into newly available drugs for the treatment of fungal diseases.
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Affiliation(s)
- Erika Seki Kioshima
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - Patrícia de Souza Bonfim de Mendonça
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília (UnB), Brasilia, Distrito Federal 70910-900, Brazil;
| | - Isis Regina Grenier Capoci
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - André Amaral
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia 74690-900, Brazil;
| | - Franciele Abigail Vilugron Rodrigues-Vendramini
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - Bruna Lauton Simões
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - Ana Karina Rodrigues Abadio
- Faculty of Agricultural Social Sciences, Mato Grosso State University, Nova Mutum, Mato Grosso 78450-000, Brazil;
| | - Larissa Fernandes Matos
- Faculty of Ceilandia, University of Brasília (UnB), Brasília, Distrito Federal 72220-275, Brazil;
- Program in Microbial Biology, Institute of Biological Sciences, University of Brasília, Brasília 70910-900, Brazil
| | - Maria Sueli Soares Felipe
- Program of Genomic Sciences and Biotechnology, Catholic University of Brasilia, Brasília 70790-160, Brazil;
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Bagagli E, Matute DR, Garces HG, Tenório BG, Garces AG, Alves LGDB, Yamauchi DH, Hrycyk MF, Barker BM, Teixeira MDM. Paracoccidioides brasiliensis Isolated from Nine-Banded Armadillos ( Dasypus novemcinctus) Reveal Population Structure and Admixture in the Amazon Basin. J Fungi (Basel) 2021; 7:54. [PMID: 33467393 PMCID: PMC7829815 DOI: 10.3390/jof7010054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
Paracoccidioidomycosis is an endemic fungal disease to Latin America caused by at least five species-level genotypes of Paracoccidioides, named P. lutzii, P. brasiliensis (S1a and S1b populations), P. americana, P. restrepiensis, and P. venezuelensis. In this manuscript, we report on Paracoccidioides sp. sampling efforts in armadillos from two different areas in Brazil. We sequenced the genomes of seven Paracoccidioides isolates and used phylogenomics and populations genetics for genotyping. We found that P. brasiliensis and P. lutzii are both present in the Amazon region. Additionally, we identified two Paracoccidioides isolates that seem to be the result of admixture between divergent populations within P. brasiliensis sensu stricto. Both of these isolates were recovered from armadillos in a P. lutzii endemic area in Midwestern Brazil. Additionally, two isolates from human patients also show evidence of resulting from admixture. Our results suggest that the populations of P. brasiliensis sensu stricto exchange genes in nature. More generally, they suggest that population structure and admixture within species is an important source of variation for pathogenic fungi.
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Affiliation(s)
- Eduardo Bagagli
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista/UNESP, Botucatu SP 18618-691, Brazil; (E.B.); (H.G.G.); (A.G.G.); (D.H.Y.)
| | | | - Hans Garcia Garces
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista/UNESP, Botucatu SP 18618-691, Brazil; (E.B.); (H.G.G.); (A.G.G.); (D.H.Y.)
| | - Bernardo Guerra Tenório
- Faculdade de Medicina, Universidade de Brasília, Brasília DF 70910-900, Brazil; (B.G.T.); (L.G.d.B.A.)
| | - Adalberto Garcia Garces
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista/UNESP, Botucatu SP 18618-691, Brazil; (E.B.); (H.G.G.); (A.G.G.); (D.H.Y.)
| | | | - Danielle Hamae Yamauchi
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista/UNESP, Botucatu SP 18618-691, Brazil; (E.B.); (H.G.G.); (A.G.G.); (D.H.Y.)
| | - Marluce Francisca Hrycyk
- Faculdade de Ciências Biológicas e Agrárias, Universidade do Estado de Mato Grosso, Campus de Alta Floresta, Alta Floresta MT 78580-000, Brazil;
| | - Bridget Marie Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Marcus de Melo Teixeira
- Faculdade de Medicina, Universidade de Brasília, Brasília DF 70910-900, Brazil; (B.G.T.); (L.G.d.B.A.)
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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