Clinical characteristics, bacterial coinfections and outcomes in COVID-19-associated pulmonary aspergillosis in a third-level Mexican hospital during the COVID-19 pre-vaccination era.

BACKGROUND: Damage due to respiratory viruses increases the risk of bacterial and fungal coinfections and superinfections. High rates of invasive aspergillosis are seen in severe influenza and COVID-19. This report describes CAPA cases diagnosed during the first wave in the biggest reference centre for severe COVID-19 in Mexico. OBJECTIVES: To describe the clinical, microbiological and radiological characteristics of patients with invasive pulmonary aspergillosis associated with critical COVID-19, as well as to describe the variables associated with mortality. METHODS: This retrospective study identified CAPA cases among individuals with COVID-19 and ARDS, hospitalised from 1 March 2020 to 31 March 2021. CAPA was defined according to ECMM/ISHAM consensus criteria. Prevalence was estimated. Clinical and microbiological characteristics including bacterial superinfections, antifungal susceptibility testing and outcomes were documented. RESULTS: Possible CAPA was diagnosed in 86 patients among 2080 individuals with severe COVID-19, representing 4.13% prevalence. All CAPA cases had a positive respiratory culture for Aspergillus species. Aspergillus fumigatus was the most frequent isolate (64%, n = 55/86). Seven isolates (9%, n = 7/80) were resistant to amphotericin B (A. fumigatus n = 5/55, 9%; A. niger, n = 2/7, 28%), two A. fumigatus isolates were resistant to itraconazole (3.6%, n = 2/55). Tracheal galactomannan values ranged between 1.2 and 4.05, while serum galactomannan was positive only in 11% (n = 3/26). Bacterial coinfection were documented in 46% (n = 40/86). Gram negatives were the most frequent cause (77%, n = 31/40 isolates), from which 13% (n = 4/31) were reported as multidrug-resistant bacteria. Mortality rate was 60% and worse prognosis was seen in older persons, high tracheal galactomannan index and high HbA1c level. CONCLUSIONS: One in 10 individuals with CAPA carry a resistant Aspergillus isolate and/or will be affected by a MDR bacteria. High mortality rates are seen in this population.

Detección y genotipificación de Pneumocystis jirovecii en muestras de pacientes mexicanos VIH positivos y negativos.

INTRODUCTION: Pneumocystis jirovecii is an atypical fungus particularly detected in HIV-positive or transplant patients. OBJECTIVE: To detect and genotype Pneumocystis jirovecii in patient samples from two hospitals in Mexico City. METHOD: Eighty-nine respiratory tract samples, corresponding to 53 patients (30 HIV-positive and 23 HIV-negative) with respiratory symptoms and to 11 healthy individuals included as negative control, were processed. DNA was extracted from the ITS region and amplified by nested polymerase chain reaction from the internal transcribed spacer, with one fragment being obtained at each round (693 and 550 bp). Genotypes and their phylogenetic relationship were determined by sequencing the 550 bp fragment. RESULTS: Forty-eight samples from 30 HIV-positive patients were received from a single hospital, out of which 11 (36.6 %) were positive for Pneumocystis jirovecii. No sample was positive in HIV-negative patients or healthy subjects. The most frequently detected haplotypes were Eg and Em. CONCLUSIONS: The frequency of Pneumocystis jirovecii infection was high in the studied Mexican population. The most common genotype was different from those reported in other countries. It is necessary to address this health problem through early detection of this infection.

INTRODUCCIÓN: Pneumocystis jirovecii es un hongo atípico detectado particularmente en pacientes VIH-positivos o con trasplante. OBJETIVO: Detectar y genotipificar Pneumocystis jirovecii en muestras de pacientes de dos hospitales de la ciudad de México. MÉTODO: Fueron procesadas 89 muestras respiratorias, correspondientes a 53 pacientes (30 VIH positivos y 23 VIH negativos) con sintomatología respiratoria y 11 personas sanas incluidas como control negativo. El DNA fue extraído y amplificado por PCR anidada de la región del espaciador transcrito interno, obteniendo un fragmento en cada ronda (de 693 y 550 pb). Los genotipos y su relación filogenética fueron determinados por secuenciación del fragmento de 550 pb. RESULTADOS: Cuarenta y ocho muestras de 30 pacientes VIH-positivos provenían de un solo hospital, de las cuales 11 (36.6 %) fueron positivas a Pneumocystis jirovecii. Ninguna fue positiva en pacientes VIH-negativos o personas sanas. Los haplotipos detectados con mayor frecuencia fueron Eg y Em. CONCLUSIONES: La frecuencia de infección por Pneumocystis jirovecii fue alta en la población mexicana estudiada. El genotipo más frecuente fue diferente a los reportados en otros países. Es necesario encauzar este problema de salud hacia la detección temprana de esta infección.

Detection of Cytokines and Collectins in Bronchoalveolar Fluid Samples of Patients Infected with Histoplasma capsulatum and Pneumocystis jirovecii.

Histoplasmosis and pneumocystosis co-infections have been reported mainly in immunocompromised humans and in wild animals. The immunological response to each fungal infection has been described primarily using animal models; however, the host response to concomitant infection is unknown. The present work aimed to evaluate the pulmonary immunological response of patients with pneumonia caused either by Histoplasma capsulatum, Pneumocystis jirovecii, or their co-infection. We analyzed the pulmonary collectin and cytokine patterns of 131 bronchoalveolar lavage samples, which included HIV and non-HIV patients infected with H. capsulatum, P. jirovecii, or both fungi, as well as healthy volunteers and HIV patients without the studied fungal infections. Our results showed an increased production of the surfactant protein-A (SP-A) in non-HIV patients with H. capsulatum infection, contrasting with HIV patients (p < 0.05). Significant differences in median values of SP-A, IL-1ß, TNF-α, IFN-γ, IL-18, IL-17A, IL-33, IL-13, and CXCL8 were found among all the groups studied, suggesting that these cytokines play a role in the local inflammatory processes of histoplasmosis and pneumocystosis. Interestingly, non-HIV patients with co-infection and pneumocystosis alone showed lower levels of SP-A, IL-1ß, TNF-α, IFN-γ, IL-18, IL-17A, and IL-23 than histoplasmosis patients, suggesting an immunomodulatory ability of P. jirovecii over H. capsulatum response.

Histoplasma capsulatum and Pneumocystis jirovecii coinfection in hospitalized HIV and non-HIV patients from a tertiary care hospital in Mexico.

BACKGROUND: Histoplasma capsulatum and Pneumocystis jirovecii are respiratory fungal pathogens that principally cause pulmonary disease. Coinfection with both pathogens is scarcely reported. This study detected this coinfection using specific molecular methods for each fungus in the bronchoalveolar lavage (BAL) of patients from a tertiary care hospital. MATERIALS AND METHODS: BAL samples from 289 hospitalized patients were screened by PCR with specific markers for H. capsulatum (Hcp100) and P. jirovecii (mtLSUrRNA and mtSSUrRNA). The presence of these pathogens was confirmed by the generated sequences for each marker. The clinical and laboratory data for the patients were analyzed using statistical software. RESULTS: The PCR findings separated three groups of patients, where the first was represented by 60 (20.8%) histoplasmosis patients, the second by 45 (15.6%) patients with pneumocystosis, and the last group by 12 (4.2%) patients with coinfection. High similarity among the generated sequences of each species was demonstrated by BLASTn and neighbor-joining algorithms. The estimated prevalence of H. capsulatum and P. jirovecii coinfection was higher in HIV patients.

Detección y genotipificación de Pneumocystis jirovecii en muestras de pacientes mexicanos VIH positivos y negativos / Detection and genotyping of Pneumocystis jirovecii in samples from HIV positive and negative Mexican patients

Resumen Introducción: Pneumocystis jirovecii es un hongo atípico detectado particularmente en pacientes VIH-positivos o con trasplante. Objetivo: Detectar y genotipificar Pneumocystis jirovecii en muestras de pacientes de dos hospitales de la ciudad de México. Método: Fueron procesadas 89 muestras respiratorias, correspondientes a 53 pacientes (30 VIH positivos y 23 VIH negativos) con sintomatología respiratoria y 11 personas sanas incluidas como control negativo. El DNA fue extraído y amplificado por PCR anidada de la región del espaciador transcrito interno, obteniendo un fragmento en cada ronda (de 693 y 550 pb). Los genotipos y su relación filogenética fueron determinados por secuenciación del fragmento de 550 pb. Resultados: Cuarenta y ocho muestras de 30 pacientes VIH-positivos provenían de un solo hospital, de las cuales 11 (36.6 %) fueron positivas a Pneumocystis jirovecii. Ninguna fue positiva en pacientes VIH-negativos o personas sanas. Los haplotipos detectados con mayor frecuencia fueron Eg y Em. Conclusiones: La frecuencia de infección por Pneumocystis jirovecii fue alta en la población mexicana estudiada. El genotipo más frecuente fue diferente a los reportados en otros países. Es necesario encauzar este problema de salud hacia la detección temprana de esta infección.

Abstract Introduction: Pneumocystis jirovecii is an atypical fungus particularly detected in HIV-positive or transplant patients. Objective: To detect and genotype Pneumocystis jirovecii in patient samples from two hospitals in Mexico City. Method: Eighty-nine respiratory tract samples, corresponding to 53 patients (30 HIV-positive and 23 HIV-negative) with respiratory symptoms and to 11 healthy individuals included as negative control, were processed. DNA was extracted from the ITS region and amplified by nested polymerase chain reaction from the internal transcribed spacer, with one fragment being obtained at each round (693 and 550 bp). Genotypes and their phylogenetic relationship were determined by sequencing the 550 bp fragment. Results: Forty-eight samples from 30 HIV-positive patients were received from a single hospital, out of which 11 (36.6 %) were positive for Pneumocystis jirovecii. No sample was positive in HIV-negative patients or healthy subjects. The most frequently detected haplotypes were Eg and Em. Conclusions: The frequency of Pneumocystis jirovecii infection was high in the studied Mexican population. The most common genotype was different from those reported in other countries. It is necessary to address this health problem through early detection of this infection.