Fungal coinfection/superinfection in COVID-19 patients in a tertiary hospital in Mexico / Coinfección o sobreinfección fúngica en pacientes con COVID-19 en un hospital de tercer nivel en México

Introduction: Data on the prevalence of fungal coinfections/superinfections in patients with COVID-19 are limited. Objective: To describe the prevalence of fungal coinfections/superinfections in patients with COVID-19, as well as risk factors and demographic, clinical, and microbiological characteristics. Material and methods: We included patients with a confirmed COVID-19 diagnosis and a confirmed fungal infection hospitalized in the ICU from March 2020 to December 2021. We collected data on age, sex, comorbidities, hospital length of stay (days), laboratory (ferritin) and microbiological results, treatment for COVID-19, antifungal therapy, and outcomes obtained from the clinical records. Results: Only 11 out of 740 patients met the inclusion criteria. The coinfection rate was 0.3% and the superinfection was 1.2%. The most affected population was male adults. The coinfections/superinfections diagnosed were candiduria and candidemia, caused by Candida albicans, C. tropicalis, C. glabrata, C. lusitaniae, and Kluyveromyces marxianus (C. kefyr). In addition, tracheobronchitis due to Aspergillus fumigatus was found. The most used antifungals were fluconazole and caspofungin. The lethality in patients with fungal coinfections was 50% and superinfections, 22%. The length of hospital stay was 11-65 days. Eight patients required mechanical ventilation and six received corticosteroids. The main comorbidity was diabetes mellitus (81.8%). Conclusions: The rate of fungal coinfections/superinfections in COVID-19 patients was low, but the lethality found urges for routine fungal screening in patients with severe COVID-19 to timely detect fungal infections that may further compromise the patient's life.

Introducción: Los datos sobre la prevalencia de coinfecciones o sobreinfecciones fúngicas en pacientes con COVID-19 son limitados. Objetivo: Describir la prevalencia de coinfecciones o sobreinfecciones fúngicas en pacientes con COVID-19, así como los factores de riesgo y las características demográficas, clínicas y microbiológicas. Material y métodos: Se incluyeron pacientes con diagnóstico confirmado de COVID-19, hospitalizados en la unidad de cuidados intensivos y con infección fúngica confirmada entre marzo del 2020 y diciembre del 2021. Del expediente clínico se obtuvieron datos sobre edad, sexo, comorbilidades, días de estancia hospitalaria, resultados de laboratorio (ferritina) y microbiológicos, tratamiento contra COVID-19, terapia antifúngica y desenlace. Resultados: Once de 740 pacientes cumplieron con los criterios de inclusión. La tasa de coinfección fue del 0,3 % y la de sobreinfección fue del 1,2 %. La población más afectada fue la de hombres adultos. Las coinfecciones o sobreinfecciones diagnosticadas fueron candiduria y candidemia, causadas por Candida albicans, C. tropicalis, C. glabrata, C. lusitaniae y Kluyveromyces marxianus (C. kefyr). Además, se encontró una traqueobronquitis por Aspergillus fumigatus. Los antifúngicos más administrados fueron fluconazol y caspofungina. La letalidad en pacientes con coinfecciones fue del 50 % y con sobreinfecciones fúngicas, del 22 %. El tiempo de estancia intrahospitalaria fue de 11 a 65 días. Ocho de los pacientes requirieron asistencia respiratoria mecánica y seis recibieron corticoides. La principal comorbilidad fue diabetes mellitus (81,8 %). Conclusiones: La tasa de coinfecciones o sobreinfecciones por hongos en pacientes con COVID-19 fue baja, pero la letalidad de estas requiere, con urgencia, la realización de pruebas de rutina para detectar hongos en pacientes con COVID-19 grave para diagnosticar oportunamente infecciones fúngicas que puedan comprometer aún más la vida del paciente.

Exploring the potential of chitin and chitosan in nanobiocomposites for fungal immunological detection and antifungal action.

Chitin is a polymer of N-acetylglucosamine and an essential component of the fungal cell wall. Chitosan is the deacetylated form of chitin and is also important for maintaining the integrity of this structure. Both polysaccharides are widely distributed in nature and have been shown to have a variety of applications in biomedicine, including their potential in immune sensing and as potential antifungal agents. In addition, chitin has been reported to play an important role in the pathogen-host interaction, involving innate and adaptive immune responses. This paper will explore the role of chitin and chitosan when incorporated into nanobiocomposites to improve their efficacy in detecting fungi of medical interest and inhibiting their growth. Potential applications in diagnostic and therapeutic medicine will be discussed, highlighting their promise in the development of more sensitive and effective tools for the early diagnosis of fungal infections. This review aims to highlight the importance of the convergence of nanotechnology and biology in addressing public health challenges.

Primary Vitrectomy versus Tap and Inject for Fungal Endophthalmitis: Meta-Analysis and Comparison with Data from a Reference Centre.

PURPOSE: We aimed to compare the visual outcomes after pars plana vitrectomy (PPV) versus tap and inject (T&I) in fungal endophthalmitis (FE) reported in the literature and to compare the findings from the literature with data from a reference centre. METHODS: We performed a systematic review and meta-analysis of studies reporting the use of PPV versus T&I in FE. We also performed a retrospective review of the clinical records of patients with endophthalmitis from a reference centre in Colombia. RESULTS: We included 13 studies with 334 eyes; 53.59% received PPV and 46.4% received T&I. The overall relative risk of improving ≥ 2 lines in PPV versus T&I was 0.98 (95% confidence interval [CI] 0.80-1.22; p = 0.88) with a mean difference of final visual acuity of 0.26 (95% CI 0.12-0.63; p = 0.18). There were no significant differences in subgroup analysis. Data from the reference centre included 32 endophthalmitis cases, 15.6% of which had a fungal aetiology (80% received PPV and 20% T&I). There were no significant differences in the subgroup analysis. CONCLUSIONS: Based on the findings from the literature and the reference centre, T&I is noninferior to PPV. This is the first meta-analysis in the literature evaluating these effects in FE. It is necessary to execute new prospective randomised controlled studies in patients with endophthalmitis.

Infecciones fúngicas en otorrinolaringología: revisión de la literatura / Fungal infections in otolaryngology: literature review

Ante el aumento a nivel mundial de condiciones inmunosupresoras, la incidencia de enfermedades fúngicas que afectan órganos y sistemas propios del estudio otorrinolaringológico va en alza. Entre estas patologías es posible encontrar la candidiasis orofaríngea, laringitis fúngica, otomicosis, y distintos tipos de rinosinusitis. El estudio de los aspectos clínicos, agentes causantes y mecanismos patogénicos de estas enfermedades será fundamental para la práctica médica de los tiempos por venir.

With the worldwide increase of immunosuppressive conditions, the incidence of fungal diseases affecting organs and systems of otorhinolaryngological study is on the rise. Among these pathologies it is possible to find oropharyngeal candidiasis, fungal laryngitis, otomycosis, and different types of rhinosinusitis. The study of the clinical aspects, causative agents and pathogenic mechanisms of these diseases will be fundamental for the medical practice of the times to come.

Identification and production of novel potential pathogen-specific biomarkers for diagnosis of histoplasmosis.

IMPORTANCE: Histoplasmosis is considered one of the most important mycoses due to the increasing number of individuals susceptible to develop severe clinical forms, particularly those with HIV/AIDS or receiving immunosuppressive biological therapies, the high mortality rates reported when antifungal treatment is not initiated in a timely manner, and the limitations of conventional diagnostic methods. In this context, there is a clear need to improve the capacity of diagnostic tools to specifically detect the fungal pathogen, regardless of the patient's clinical condition or the presence of other co-infections. The proposed novel pathogen-specific biomarkers have the potential to be used in immunodiagnostic platforms and antifungal treatment monitoring in histoplasmosis. In addition, the bioinformatics strategy used in this study could be applied to identify potential diagnostic biomarkers in other models of fungal infection of public health importance.

Esporotricose em felinos domésticos: revisão de literatura / Sporotrichosis in domestic felines: literature review

A Esporotricose é uma micose subcutânea de caráter zoonótico causada pelo fungo Sporothrix schenckii que habita o solo, palhas, vegetais e também madeiras, podendo ser transmitido por meio de materiais contaminados, como farpas ou espinhos. Contudo os animais infectados e em especial os gatos, também transmitem a doença, por meio de arranhões, mordidas e contato direto com pele lesionada. Nos mamíferos, o quadro clínico apresenta-se na forma crônica ou aguda com o surgimento de lesões cutâneas. A doença é considerada um problema de saúde pública, pois afeta a população de áreas endêmicas. O presente trabalho foi delineado para analisar a manifestação da doença em gatos domésticos, revisando sinais clínicos, diagnóstico, prevenção, tratamento e também faz um alerta para a sua importância em saúde pública.(AU)

Sporotrichosis is a zoonotic subcutaneous mycosis caused by the fungus Sporothrix schenckii that inhabits the soil, straw, vegetables and also wood, and can be transmitted through contaminated materials, such as splinters or thorns. However, infected animals, and especially cats, also transmit the disease through scratches, bites and direct contact with injured skin. In mammals, the clinical picture is chronic or acute with the appearance of skin lesions. The disease is considered a public health problem, as it affects the population of endemic areas. The present work was designed to analyze the manifestation of the disease in domestic cats, reviewing clinical signs, diagnosis, prevention, treatment and also makes an alert for its importance in public health. Educational measures are needed to make the population aware of the effects of waste on One Health.(AU)

Una experiencia de siete años en el laboratorio de Micología del Hospital de Pediatría Juan P. Garrahan / A seven-year experience in the Mycology Laboratory of Hospital de Pediatría Juan P. Garrahan

En noviembre del año 2015 nos incorporamos al Laboratorio de Micología del Servicio de Microbiología del Hospital Garrahan. En este breve resumen queremos compartir los avances logrados a través de nuestra experiencia durante siete años de trabajo profesional. Debido a los diagnósticos realizados y su complejidad, consideramos que el Hospital Garrahan, sus pacientes y la comunidad toda necesitan contar con un laboratorio de Micología que responda a sus necesidades. Creemos haber iniciado un camino que esperamos continúe y culmine con la creación de la Unidad de Micología (AU)

In November 2015 we joined the Mycology Laboratory of the Microbiology Service of the Hospital Garrahan. In this brief summary we want to share the advances achieved through our experience during seven years of professional work. Due to the diagnosis made and their complexity, we believe that the Hospital Garrahan, its patients and the entire community, need to have a Mycology laboratory that responds to their requirements. We believe we have started a path that we hope will continue and culminate with the creation of the Mycology Unit (AU)

COVID-19 associated rhinomaxillary mucormycosis: a case series and review of literature

During COVID-19 pandemic, fulminant deep fungal infection started emerging in India, known as Mucormycosis. This type of mucormycosis was termed as COVID-19 associated mucormycosis (CAM). These patients had previous history of COVID-19 infection. Such cases were mainly reported in immunocompromised patients such as patients with poorly controlled diabetes and chronic renal diseases etc. Rhinomaxillary mucormycosis is an aggressive, fulminant, fatal deep fungal infection of head and neck region. Early diagnosis and prompt treatment can reduce the mortality and morbidity associated with the disease; hence we present case series of rhinomaxillary mucormycosis to create awareness amongst dental surgeons

Fungal Bloodstream Co-infection by Trichosporon asahii in a COVID-19 Critical Patient: Case Report and Literature Review.

Opportunistic infections are serious complications in critically ill COVID-19 patients, especially co-infections with bacterial and fungal agents. Here we report a rare case of bloodstream co-infection by Trichosporon asahii, an emerging yeast, and Acinetobacterbaumannii, an opportunistic nosocomial pathogen, both multidrug resistant, in a tertiary hospital from southern Brazil. A review of the literature regarding similar cases is also included. Treatment with multiple antimicrobials failed, and the patient progressed to death four days after the diagnosis of bacteremia and fungemia.

Multiparametric assay of screening for the diagnosis of mycoses of interest in Public Health: standardization of methodology / Ensaio multiparamétrico de triagem para diagnóstico de micoses de interesse em Saúde Pública: padronização da metodologia

The standardization and validation of a multiplex assay requires the combination of important parameters such as sensitivity and specificity, acceptable levels of performance, robustness, and reproducibility. We standardized a multiparametric Dot-blot aimed at the serological screening of paracoccidioidomycosis, histoplasmosis, and aspergillosis. A total of 148 serum were evaluated: 10 from healthy subjects, 36 from patients with paracoccidioidomycosis, 62 from patients with histoplasmosis, and 40 from patients with aspergillosis. It was found that the multiparametric Dot-blot showed a high percentage of cross-reactivity. However, when evaluated individually, in the serological screening of histoplasmosis, a good performance was observed when compared to the double immunodiffusion assay, considered the gold standard test, with 100% co-positivity and 83.3% co-negativity. The performance of serological screening for aspergillosis was not satisfactory when compared to double immunodiffusion, showing 71.4% co-positivity and 100% co-negativity. The evaluation of the stability of nitrocellulose membranes showed that membranes sensitized with H. capsulatum antigen remained stable for 90 days and those sensitized with A. fumigatus antigen for 30 days. We conclude that the use of crude antigens was not suitable for the standardization of the multiparametric Dot-blot assay, due to the high cross-reactivity, and that further tests should be performed with purified proteins (AU).

A padronização e validação de um ensaio multiplex requer a combinação de parâmetros importantes, como sensibilidade e especificidade, níveis aceitáveis de desempenho, robustez e reprodutibilidade. Este trabalho padronizou um Dot-blot multiparamétrico visando a triagem sorológica da paracoccidioidomicose, histoplasmose e aspergilose. Foram avaliadas 148 amostras de soro: 10 de indivíduos saudáveis, 36 de pacientes com paracoccidioidomicose, 62 de pacientes com histoplasmose e 40 de pacientes com aspergilose. Verificou-se que o Dot-blot multiparamétrico apresentou elevado percentual de reatividade cruzada. Entretanto, quando avaliado individualmente, na triagem sorológica da histoplasmose observou-se bom desempenho quando comparado ao ensaio de imunodifusão dupla, considerado o teste padrão ouro, com 100% de co-positividade e 83,3% de co-negatividade. O desempenho da triagem sorológica da aspergilose não foi satisfatório quando comparado a imunodifusão dupla, apresentando 71,4% de co-positividade e 100% de co-negatividade. A avaliação da estabilidade das membranas de nitrocelulose mostrou que membranas sensibilizadas com antígeno de H. capsulatum permaneceram estáveis por 90 dias e as sensibilizadas com antígeno de A. fumigatus, por 30 dias. Concluímos que o uso de antígenos brutos não foi adequado para a padronização do ensaio de Dot-blot multiparamétrico, devido ao alto índice de reatividade cruzada, e que novos testes devem ser realizados com proteínas purificadas (AU).

The current state of Clinical Mycology in Eastern and South-Eastern Europe.

The ability of medical centers in Eastern and South-Eastern Europe to diagnose and treat fungal infections remains unknown. In order to investigate that, here we conducted a cross-sectional online survey, released at both The International Society for Human & Animal Mycology (ISHAM) and European Confederation of Medical Mycology (ECMM) websites. A total of 31 institutions responded to the questionnaire. Most centers (87.1%, n = 27) had access to Aspergillus spp. ELISA galactomannan testing as well as to Cryptococcus spp. antigen testing (83.9%, n = 26). Serological tests were mostly available for Aspergillus species (80.6%, n = 25); and most institutions reported access to mold-active antifungal drugs (83.9%; n = 26), but 5-flucytosine was available to only 29% (n = 9) of the participant centers. In conclusion, this study represents the first attempt to document the strengths and limitations of the Eastern and South-Eastern European region for diagnosing and treating fungal diseases. LAY SUMMARY: Our article is about the availability of diagnostic and treatments tools related to fungal infections in the countries of Eastern and South-Eastern region. Surveys like these are important to understand the gaps and point towards the fungal infections as a global health issue.

Fungal diagnostic testing and therapy: navigating the neutropenic period in children with high-risk leukemia.

Children, adolescents, and young adults receiving intensive chemotherapy for acute myeloid leukemia or high-risk or relapsed acute lymphoblastic leukemia sustain prolonged periods of neutropenia that predispose them to invasive fungal disease (IFD). For many decades the standard of care for these patients was to initiate empirical antifungal therapy after a period of prolonged fever and neutropenia. Recent publications have yielded important evidence on the utility of different diagnostic and therapeutic approaches aimed at reducing the impact of IFD among these patients during these vulnerable periods. This case-based review highlights and interprets the published data to provide context for the IFD diagnostic and therapeutic recommendations proposed in multiple published guidelines. Personalized approaches are offered at points where evidence is lacking. Time points where specific knowledge gaps exist are identified along the clinical trajectory of the prolonged neutropenic period to illustrate areas for future investigation.

Recent developments in less known and multi-resistant fungal opportunists.

Fungal infections have increased in recent years due to host factors, such as oncohaematological and transplant-related disorders, immunosuppressive therapy, and AIDS. Additionally, molecular and proteomic facilities have become available to identify previously unrecognizable opportunists. For these reasons, reports on less-known and recalcitrant mycoses, such as those caused by black fungi, hyaline filamentous fungi, coelomycetes, Mucorales, and non-Candida yeasts have emerged. In this review, novel taxonomy in these groups, which often are multi-resistant to one or several classes of antifungals, is discussed. Clinical presentations, diagnosis and current treatment of some major groups are summarised.

Microbiological profile in chronic granulomatous disease patients in a single Brazilian primary immunodeficiency center.

BACKGROUND: Chronic granulomatous disease (CGD) is a rare primary immunodeficiency. Infections of lung, skin, lymph nodes, and liver are the hallmark of CGD and frequently the initial manifestation of the disease. The aim of the present paper is to describe the sites of infections and their causative agents in 38 pediatric patients with CGD. METHODS: This retrospective, single-center cohort study included CGD patients followed at the allergy and immunology unit of a tertiary hospital in São Paulo, Brazil over the last 40 years. Sites of infections and their causative agents were described. RESULTS: Thirty-eight patients were included (36 males). The median age of onset of symptoms was 45 days (ranging from 7 days-7 years), and the median age at diagnosis was 23 months (ranging from 1 month-12 years). In all, 31.6% of the patients reported a family history of child deaths and 21% (eight cases) had another male family member with CGD. The most common infections were pneumonia (81.6%), skin infections (50.0%), adenitis (42.1%), and liver abscess (23.7%); 188 cultures were positive (85.6% bacteria; 14.4% fungi). The most prevalent bacterial agents were Staphylococcus sp. (12.4%), Staphylococcus aureus (11.2%), and Klebsiella pneumoniae (9.3%). Aspergillus sp. and Candida sp. were 56% and 22.2% of the isolated fungi, respectively. Mycobacterium tuberculosis was isolated in 5.6% and Mycobacterium bovis in one patient (0.9%). CONCLUSION: Staphylococcus sp., Staphylococcus aureus, and Aspergillus sp. were the most frequent agents found in this cohort. M. tuberculosis should be considered in endemic area. Detection of infectious agents drives to the adequate treatment and benefits the evolution of patients with CGD.

Deep mycoses and pseudomycoses of the foot: a single-center retrospective study of 160 cases, in a tertiary-care center in Mexico.

BACKGROUND: Deep mycoses and pseudomycoses (DMP) may cause significant disability and even death; however, the reports regarding these diseases, mainly affecting the foot, are scarce. OBJECTIVE: To describe the epidemiological, clinical, and diagnostic characteristics of DMP of the foot in 160 patients. METHODS: A retrospective and observational study of DMP affecting the foot was carried out in a tertiary-care center in Mexico for 20 years (from January 2000 to December 2019). Cases with confirmatory microbiological studies were included; the identification of the isolated fungi was based on the forms of reproduction. For actinomycetes, morphological analysis in an automated system ATB Vitek® 1574 (Biomèrieux) was used. The fungi were identified by PCR, using several primers from the ITS regions and for actinomycetes in the 16S rRNA region. Data from histopathological studies were also collected. RESULTS: One hundred and sixty proven cases of DMP of the foot were included. The cases were categorized into nine types of infections including mycetoma (actinomycetoma and eumycetoma) in 102 cases (63.7%); sporotrichosis in 21 cases (13.1%); chromoblastomycosis, 18 cases (11.2%); phaeohyphomycosis, 3 cases (1.8%); histoplasmosis, 12 cases (7.5%); coccidioidomycosis 2 cases (1.2%) and botryomycosis and nocardiosis with one case respectively (0.6%). Most cases developed after traumatic implantation (147 cases, 91.8%). One hundred fifteen cases (71.8%) were men. The evolution was chronic in 125 cases (78.2%); bone involvement was observed in 64 cases (40%). Parasitic forms were observed In 139 cases (86.8%). The isolation and identification of the etiological agents were confirmed in all cases. CONCLUSION: The main DMP affecting the foot were infections due to traumatic implantation; most were endemic mycoses. The clinical characteristics and the evolution of the diseases are easily misdiagnosed, and thus, diagnostic tests are usually required.

Diagnóstico micológico por técnicas no convencionales en el siglo XXI / Mycological diagnosis by non-conventional techniques in the 21st century

Introducción: En la actualidad las infecciones fúngicas representan un problema para la salud humana. Las infecciones causadas por especies patógenas de hongos registran un incremento constante y se ubican entre el cuarto y décimo lugar como causa de muerte, particularmente en las unidades de cuidado intensivo. Un diagnóstico adecuado y precoz impacta directamente en la morbilidad y mortalidad asociadas a estas. Objetivo: Describir las principales técnicas de diagnóstico no convencional de las enfermedades fúngicas más frecuentes, en especial las relacionadas con el diagnóstico serológico y molecular. Métodos: Se realizó una revisión de la literatura científica sobre el tema, publicada entre 2000 y 2019. Se revisaron un total de 63 trabajos. Como motores de búsqueda se emplearon Google y Google Scholar. Se revisaron las bases de datos Medline, PubMed, Science Direct, BUCea y SciELO. Análisis y síntesis de la información: Las técnicas serológicas se emplean en el diagnóstico de las micosis invasivas o sistémicas por ser fáciles, rápidas y confiables. La detección de anticuerpos tiene utilidad limitada en el diagnóstico de las micosis invasivas debido a que la respuesta puede estar retrasada, reducida o no existir en pacientes inmunocomprometidos. La detección de componentes no antigénicos liberados por los hongos durante la infección y la secuenciación de ácidos nucleicos fúngicos son otras opciones para el diagnóstico de las micosis. Conclusiones: El desarrollo biotecnológico aporta nuevas herramientas que incrementan las oportunidades de identificación de las micosis. En la actualidad se disponen de métodos basados tanto en la detección de marcadores inmunológicos como de elementos moleculares específicos. La eficacia de las herramientas no convencionales para el diagnóstico depende de la correcta combinación de estas(AU)

Introduction: Fungal infections are a current human health problem. Infections caused by pathogenic fungal species constantly increase in number, and are ranked between the fourth and tenth leading causes of death, particularly in intensive care units. Early accurate diagnosis has a direct impact on the morbidity and mortality of fungal infections. Objective: Describe the main non-conventional diagnostic techniques for the most common fungal diseases, especially those related to serological and molecular diagnosis. Methods: A review was conducted of the scientific literature about the topic published between the years 2000 and 2019. A total 63 publications were reviewed. The search engines used were Google and Google Scholar. The databases Medline, PubMed, Science Direct, BUCea and SciELO were reviewed. Data analysis and synthesis: Serological techniques are used for the diagnosis of invasive or systemic mycoses because they are easy, fast and reliable. The detection of antibodies has a limited usefulness in invasive mycosis diagnosis, for the response may be delayed, reduced or inexistent in immunocompromised patients. Detection of non-antigenic components released by fungi during infection and sequencing of fungal nucleic acids are other mycosis diagnosis options. Conclusions: Biotechnological development contributes new tools increasing mycosis identification opportunities. Methods are currently available which are based on detection of immunological markers and specific molecular elements. The efficacy of non-conventional diagnostic tools depends on their appropriate combination(AU)

Isothermal nucleic acid amplification techniques for detection and identification of pathogenic fungi: A review.

BACKGROUND: Fungal infections have increased during the last years due to the AIDS epidemic and immunosuppressive therapies. The available diagnostic methods, such as culture, histopathology and serology, have several drawbacks regarding sensitivity, specificity and time-consuming, while molecular methods are still expensive and dependent on many devices. In order to overcome these challenges, isothermal nucleic acid amplification techniques (INAT) arose as promising diagnostic methods for infectious diseases. OBJECTIVE: This review aimed to present and discuss the main contributions of the isothermal nucleic acid amplification techniques applied in medical mycology. METHODS: Papers containing terms for each INAT (NASBA, RCA, LAMP, CPA, SDA, HAD or PSR) and the terms 'mycoses' or 'disease, fungal' were obtained from National Center for Biotechnology Information database until August 2019. RESULTS: NASBA, RCA, LAMP and PSR are the INAT reported in the literature for detection and identification of pathogenic fungi. Despite the need of a previous conventional PCR, the RCA technique might also be used for genotyping or cryptic species differentiation, which may be important for the treatment of certain mycoses; nevertheless, LAMP is the most used INAT for pathogen detection. CONCLUSION: Among all INATs herein reviewed, LAMP seems to be the most appropriate method for fungal detection, since it is affordable, sensitive, specific, user-friendly, rapid, robust, equipment-free and deliverable to end-users, fulfilling all ASSURED criteria of the World Health Organization for an ideal diagnostic method.

Endemic mycoses: epidemiology and diagnostic strategies.

INTRODUCTION: The global frequency of endemic mycoses has considerably increased, mainly due to environmental changes, population growth in endemic areas, and the increase in HIV-related immunosuppressed status. Among the most frequent endemic mycoses are coccidioidomycosis in semi-desert climates, and paracoccidioidomycosis, and histoplasmosis in tropical climates. The inoculum can enter the host through the airway or directly through the skin. Lymphatic and hematogenous spread may involve the skin. AREAS COVERED: In this article, we provide up-to-date epidemiological and diagnostic data on major (histoplasmosis, paracoccidioidomycosis, coccidioidomycosis, blastomycosis) and minor (talaromycosis, adiaspiromycosis, emergomycosis) endemic mycoses. EXPERT OPINION: Endemic mycoses include diseases with a localized endemic area, and a few of them converge. These mycoses all have in common the airway involvement and can cause pulmonary symptoms following initial asymptomatic infection. Among the risk groups to acquire these mycoses are travelers from endemic areas, archeologists, speleologists, and immigrants. Promising and useful diagnostic tools have been developed in endemic mycoses; however, most of them are not standardized or available in low-income countries.

Comparison of Matrix-assisted Laser Desorption Ionization Time-of-flight Mass Spectrometry (MALDI-TOF MS) and the Vitek 2 System for Routine Identification of Clinically Relevant Bacteria and Yeast.

OBJECTIVE: In this study, we compared the observed agreement and correlation of the Vitek 2 system with the biomarker-based MALDI-TOF MS identification results of bacteria and yeast on a routine basis. METHODS: Clinical isolates collected from two years were included. Isolates were identified using the Vitek 2 system and MALDI-TOF MS. The percent of observed agreements and the kappa coefficient (κ) with its corresponding 95% interval confidence were calculated between both results. When species-level biotyper identifications matched a member of a group, complex, or one of the species of a slashing call, the identification was considered correct for agreement calculations. RESULTS: The 4,238 recruited isolates included 2,669 gram-negative bacteria, 1,479 gram-positive bacteria, and 90 yeast. Among gram-negative bacteria, the most frequent species identified were Escherichia coli (κ=0.983), Acinetobacter baumannii complex (κ=0.979), Klebsiella pneumoniae (κ=0.972), and Pseudomonas aeruginosa (κ=0.970). Among Staphylococcal species, Staphylococcus aureus was the most frequently species detected (κ=0.986), followed by S. epidermidis (κ=0.904). For enterococcal species, Enterococcus faecalis (κ=0.882) and Enterococcus faecium (κ=0.849) were the most frequently detected. For yeasts, the more common species were Candida albicans (κ=0.888), followed by Candida tropicalis (κ=0.946) and Candida glabrata (κ=1.000). CONCLUSIONS: According to our results, when antimicrobial susceptibility tests are performed using Vitek 2 cards, the most common pathogens are correctly identified for the most frequent clinical isolates.