Lumena Pereira Machado Siqueira

Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo

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Viviane Mazo Fávero Gimenes

Universidade de São Paulo

Gil Benard

Universidade de São Paulo

Roseli Santos de Freitas

Universidade de São Paulo

João Nóbrega de Almeida

Universidade Federal de São Paulo

Flávia Rossi

Universidade de São Paulo

Gilda Maria Bárbaro Del Negro

Universidade de São Paulo

Márcia de Souza Carvalho Melhem

Instituto Adolfo Lutz

Adriana Lopes Motta

Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo

Arnaldo Lopes Colombo

Universidade Federal de São Paulo

Tânia Sueli de Andrade

Instituto Adolfo Lutz

Cooperative Institutions

Universidade de São Paulo

Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo

Instituto Adolfo Lutz

Universidade Estadual Paulista (Unesp)

Instituto de Medicina Avançada

Hospital São Paulo

Universidade Federal de São Paulo

Instituto de Medicina Tropical

Instituto de Infectologia Emílio Ribas

Secretaria da Saúde

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Comparing the phenotypic, genotypic, and proteomic identification of Trichosporon species: A globally emerging yeast of medical importance

Medical Mycology (2021)

Bruna Rossini Lara Bruno Braidotti de Camargo Claudete Rodrigues Paula Diniz Pereira Leite Hans Garcia Garces

Trichosporon spp. are widely distributed in the nature, comprising species that inhabit different ecological niches and can be found in the water, soil, and body surface of animals and humans. Such microorganisms have been classically associated with superficial infections; however, in the last decades, they have also been related to disseminated infections in immunocompromised patients, behaving as opportunistic agents, which demands rapid and accurate species identification for efficient therapy. Concordance level between the traditional phenotypic method and the molecular technique (gold standard) in the identification of all 59 Trichosporon samples was 59.3%. Identification concordance between MALDI-TOF spectrometry and the molecular technique was 71.2%. No isolate of environmental origin was identifiable by MALDI-TOF mass spectrometry (MS), and 100% of such environmental isolates were discordant for IGS region sequencing and phenotypic characterization. Both comparisons evidenced greatest concordance in the identification of T. asahii. The species T. debeurmannianum, T. dermatis, T. venhuisii and T. insectorum were not properly identified by both MALDI-TOF MS and the phenotypic technique. MALDI-TOF MS, in particular, seems to be appropriate to investigate yeasts of the genus Trichosporon; however, database updates are still necessary, especially for species that are not common in the clinical routine. With the aim of helping understand the aspects involved in early and accurate diagnosis of infections caused by this opportunistic agent, the present study compared the phenotypic, molecular (IGS region) and mass-spectrometry (MALDI-TOF) identification of 59 yeasts of the genus Trichosporon which had clinical and environmental origin and were kept in a mycology collection.The present study compared the phenotypic, genotypic, and mass-spectrometry (MALDI-TOF) identification of 59 yeasts of the genus Trichosporon. MALDI-TOF MS, in particular, seems to be appropriate to investigate this yeasts when compared to a molecular technique (gold standard).

Trichosporon

Concordance

Identification

10.1093/mmy/myab050

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Citations (9)

Evaluating VITEK MS for the identification of clinically relevant Aspergillus species

Medical Mycology (2019)

Fernanda M Américo Lumena Pereira Machado Siqueira Gilda Maria Bárbaro Del Negro Viviane Mazo Fávero Gimenes Mario Roberto S Trindade

Aspergillus spp. identification has become more relevant in clinical practice since azole-resistant cryptic species have been related to invasive fungal infections. Conventional morphologic identification is not able to discriminate Aspergillus species, and DNA sequencing is not feasible for clinical laboratories. MALDI-TOF mass spectrometry is an emergent technology that has been explored to provide fast and accurate identification of microorganisms, including clinically relevant moulds. However, only a few studies have explored the platform VITEK MS for the identification of Aspergillus species. Hence, we provided additional data regarding the performance of the VITEK MS system for the identification of Aspergillus species, including azole-resistant ones. We also improved the RUO system by adding additional spectral profiles from well-identified Aspergillus strains belonging to different noncryptic and cryptic species. The IVD library correctly identified 91.6% of the organisms at genus and section level, and 84.7% at species level, including the azole-resistant Aspergillus lentulus and Aspergillus calidoustus. The organisms belonging to Aspergillus cryptic species had only 31.2% of correct species identification. The RUO library plus our in-house SuperSpectra correctly identified 100% of the organisms at genus and section level and 91.6% at species level. Among organisms belonging to Aspergillus cryptic species, 68.7% had correct species identification. Some closely related Aspergillus cryptic species showed similar spectral profiles and were difficult to be differentiated.

Species complex

Identification

10.1093/mmy/myz066

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Citations (13)

Evaluation of Vitek MS for Differentiation of Cryptococcus neoformans and Cryptococcus gattii Genotypes

Journal of Clinical Microbiology (2018)

Lumena Pereira Machado Siqueira Viviane Mazo Fávero Gimenes Roseli Santos de Freitas Márcia de Souza Carvalho Melhem Lucas Xavier Bonfietti

Cryptococcus neoformans and Cryptococcus gattii are the main pathogenic species of invasive cryptococcosis among the Cryptococcus species. Taxonomic studies have shown that these two taxa have different genotypes or molecular types with biological and ecoepidemiological peculiarities. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been proposed as an alternative method for labor-intensive methods for C. neoformans and C. gattii genotype differentiation. However, Vitek MS, one of the commercial MALDI-TOF MS instruments, has not been yet been evaluated for this purpose. Thus, we constructed an in-house database with reference strains belonging to the different C. neoformans (VNI, VNII, VNIII, and VNIV) and C. gattii (VGI, VGII, VGIII, and VGIV) major molecular types by using the software Saramis Premium (bioMérieux, Marcy-l'Etoile, France). Then, this new database was evaluated for discrimination of the different genotypes. Our in-house database provided correct identification for all C. neoformans and C. gattii genotypes; however, due to the intergenotypic mass spectral similarities, a careful postanalytic evaluation is necessary to provide correct genotype identification.

Cryptococcus gattii

10.1128/jcm.01282-18

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Significance of Aspergillus spp. isolation in defining cases of COVID-19 Associated Pulmonary Aspergillosis – CAPA

The Brazilian Journal of Infectious Diseases (2023)

Tiago Alexandre Cocio Lumena Pereira Machado Siqueira Katie Cristina Takeuti Riciluca Viviane Mazo Fávero Gimenes Tânia Sueli de Andrade

COVID-19-Associated Pulmonary Aspergillosis (CAPA) is a relatively common complication in patients with severe forms of the disease caused by the SARS-CoV-2 virus. Diagnosing and confirming CAPA is challenging. In this study, Aspergillus spp. isolation in respiratory specimens from patients with COVID-19 was evaluated for identifying cases of CAPA. In 2020‒2021, 17 Aspergillus spp. were isolated from 15 COVID-19 patients admitted to a university hospital in Brazil. Patient records were retrospectively reviewed to obtain clinical-epidemiological data and other markers of Aspergillus spp. infection and then compared with the ECMM/ISHAM criteria for defining CAPA. Probable CAPA was defined in 5/10 patients, who had Aspergillus spp. isolated from Bronchoalveolar Lavage (BAL) or a positive galactomannan blood test. Additionally, anti-Aspergillus antibodies were detected in two of these patients, during active or follow-up phases of CAPA. In another seven patients with Aspergillus spp. isolated from tracheobronchial aspirate or sputum, CAPA was presumed, mainly due to deterioration of clinical conditions and new lung imaging suggestive of fungal infection. Antifungal agents to control CAPA, particularly voriconazole, were used in 9/15 cases. In cases of probable CAPA and remaining patients, clinical conditions and comorbidities were similar, with lethality being high, at 60% and 71%, respectively. The number of CAPA cases defined by scientific criteria was lower than that assumed in the clinical context. This was largely due to the lack of BAL collection for fungal culture and the non-intensive use of other markers of invasive aspergillosis. The isolation of Aspergillus spp. in different respiratory specimens should alert clinicians to the diagnosis of CAPA.

Galactomannan

Clinical Significance

10.1016/j.bjid.2023.102793

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First report of tinea corporis caused by Arthroderma benhamiae in Brazil

Brazilian Journal of Microbiology (2019)

Roseli Santos de Freitas Thaís Helena Proença de Freitas Lumena Pereira Machado Siqueira Viviane Mazo Fávero Gimenes Gil Benard

Tinea Capitis

Griseofulvin

Dermatomycosis

Etiology

10.1007/s42770-019-00141-y

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Citations (12)

RECARACTERIZAÇÃO DE LINHAGENS DO COMPLEXO SPOROTHRIX SCHENCKII DO NÚCLEO DE COLEÇÕES DE MICRO-ORGANISMOS POR MEIO DA METODOLOGIA MALDITOF COM CONSTRUÇÃO DE BANCO IN-HOUSE

Jane de Jesus da Silveira Moreira Nicolas Vieira Guerra Castilho Tânia Sueli de Andrade Lumena Pereira Machado Siqueira

Resumo: A esporotricose é uma doença zoonótica causada pelo fungo termodimórfico Sporothrix schenckii, que afeta principalmente humanos e gatos, mas, pode acometer também outros animais de sangue quente. A transmissão ocorre por contato traumático com fontes contaminadas, como mordeduras ou arranhaduras de animais infectados e vegetação contaminada. O aumento progressivo dos casos levou à sua classificação como notificação compulsória no estado de São Paulo, especialmente devido à emergência do agente etiológico Sporothrix brasiliensis, que se mostrou mais patogênico que o Sporothrix schenckii. Isso enfatiza a importância do trabalho epidemiológico para rastrear e caracterizar as espécies do complexo Sporothrix schenckii. Nos centros de referência, como o Instituto Adolfo Lutz, utiliza-se a metodologia de sequenciamento e PCR de regiões alvo para identificar corretamente as espécies de Sporothrix sp. e monitorar o aumento epidemiológico das diferentes linhagens. No entanto, os métodos moleculares, como PCR e sequenciamento Sanger, enfrentam o desafio do alto custo, tornando o MALDI-TOF uma alternativa viável. Contudo, o uso de bancos comerciais é limitado pela similaridade dos perfis proteômicos das espécies e pela falta de atualização com novas linhagens. O objetivo deste estudo foi criar uma biblioteca interna para recaracterizar as espécies Sporothrix brasiliensis, Sporothrix globosa, Sporothrix mexicana e Sporothrix schenckii do acervo do Núcleo de Coleções de Micro-organismos pela metodologia de MALDI-TOF. O banco in-house foi criado e obteve sensibilidade de 96,15% na identificação correta dos micro-organismos, comparando com os resultados obtidos por meio de métodos moleculares de PCR multiplex e sequenciamento Sanger, com escore médio de 2,32 na comparação dos espectros das linhagens validadas pelo banco in-house, possibilitando desta forma o uso do banco como ferramenta diagnóstica para a vigilância e novos estudos.

10.53934/agronfy-2025-02-17

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Citations (0)

Evaluating and Improving Vitek MS for Identification of Clinically Relevant Species of Trichosporon and the Closely Related Genera Cutaneotrichosporon and Apiotrichum

Journal of Clinical Microbiology (2017)

João Nóbrega de Almeida Viviane M. Favero Gimenes Elaine Cristina Francisco Lumena Pereira Machado Siqueira Renato K. G. de Almeida

Trichosporon species are relevant etiologic agents of hospital-acquired infections. High mortality rates are attributed to Trichosporon deep-seated infections in immunocompromised individuals, making fast and accurate species identification relevant for hastening the discovery of best-targeted therapy. Recently, Trichosporon taxonomy has been reassessed, and three genera have been proposed for the pathogenic species: Trichosporon, Cutaneotrichosporon, and Apiotrichum Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has replaced old phenotypic methods for microorganism identification in clinical laboratories, but spectral profile databases have to be evaluated and improved for optimal species identification performance. Vitek MS (bioMérieux) is one of the commercially available MALDI-TOF MS platforms for pathogen identification, and its spectral profile databases remain poorly evaluated for Trichosporon, Cutaneotrichosporon, and Apiotrichum species identification. We herein evaluated and improved Vitek MS for the identification of the main clinical relevant species of Trichosporon, Cutaneotrichosporon, and Apiotrichum using a large set of strains and isolates belonging to different yeast collections in Brazil and France.

Trichosporon

Identification

Species Identification

10.1128/jcm.00461-17

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Citations (34)

A neglected disease. Human sporotrichosis in a densely populated urban area in São Paulo, Brazil: clinical–epidemiological and therapeutic aspects

Brazilian Journal of Microbiology (2022)

Amanda Azevedo Bittencourt Luiza Keiko Matsuka Oyafuso Roberta Figueiredo Cavalin Renata Bacic Palhares Gil Benard

Sporothrix schenckii

Contact tracing

Sporothrix

10.1007/s42770-022-00713-5

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Citations (10)