COVID-19-associated aspergillosis in a Brazilian referral centre: Diagnosis, risk factors and outcomes.

BACKGROUND: COVID-19 patients on mechanical ventilation are at risk to develop invasive aspergillosis. To provide additional data regarding this intriguing entity, we conducted a retrospective study describing risk factors, radiology and prognosis of this emerging entity in a Brazilian referral centre. METHODS: This retrospective study included intubated (≥18 years) patients with COVID-19 admitted from April 2020 until July 2021 that had bronchoscopy to investigate pulmonary co-infections. COVID-19-associated aspergillosis (CAPA) was defined according to the 2020 European Confederation of Medical Mycology/International Society of Human and Animal Mycosis consensus criteria. The performance of tracheal aspirate (TA) cultures to diagnose CAPA were described, as well as the radiological findings, risk factors and outcomes. RESULTS: Fourteen patients (14/87, 16%) had probable CAPA (0.9 cases per 100 ICU admissions). The sensitivity, specificity, positive predictive value and negative predictive value of TA for the diagnosis of CAPA were 85.7%, 73.1%, 46.2% and 95% respectively. Most of the radiological findings of CAPA were classified as typical of invasive pulmonary aspergillosis (64.3%). The overall mortality rate of probable CAPA was 71.4%. Age was the only independent risk factor for CAPA [p = .03; odds ratio (OR) 1.072]. CAPA patients under renal replacement therapy (RRT) may have a higher risk for a fatal outcome (p = .053, hazard ratio 8.047). CONCLUSIONS: CAPA was a prevalent co-infection in our cohort of patients under mechanical ventilation. Older patients had a higher risk to develop CAPA, and a poor prognosis may be associated with RRT.

Comparative Genomics of Nonoutbreak Pseudomonas aeruginosa Strains Underlines Genome Plasticity and Geographic Relatedness of the Global Clone ST235.

Pseudomonas aeruginosa is an important opportunistic pathogen in hospitals, responsible for various infections that are difficult to treat due to intrinsic and acquired antibiotic resistance. Here, 20 epidemiologically unrelated strains isolated from patients in a general hospital over a time period of two decades were analyzed using whole genome sequencing. The genomes were compared in order to assess the presence of a predominant clone or sequence type (ST). No clonal structure was identified, but core genome-based single nucleotide polymorphism (SNP) analysis distinguished two major, previously identified phylogenetic groups. Interestingly, most of the older strains isolated between 1994 and 1998 harbored exoU, encoding a cytotoxic phospholipase. In contrast, most strains isolated between 2011 and 2016 were exoU-negative and phylogenetically very distinct from the older strains, suggesting a population shift of nosocomial P. aeruginosa over time. Three out of 20 strains were ST235 strains, a global high-risk clonal lineage; these carried several additional resistance determinants including aac(6')Ib-cr encoding an aminoglycoside N-acetyltransferase that confers resistance to fluoroquinolones. Core genome comparison with ST235 strains from other parts of the world showed that the three strains clustered together with other Brazilian/Argentinean isolates. Despite this regional relatedness, the individuality of each of the three ST235 strains was revealed by core genome-based SNPs and the presence of genomic islands in the accessory genome. Similarly, strain-specific characteristics were detected for the remaining strains, indicative of individual evolutionary histories and elevated genome plasticity.

Evaluation of two commercial methods for the susceptibility testing of Candida species: Vitek 2(R) and Sensititre YeastOne(R) / Evaluación de dos métodos comerciales para el estudio de la sensibilidad a los antifúngicos de especies de Candida: Vitek 2(R) y Sensititre YeastOne(R)

Background: An increased incidence of fungal infections caused by Candida species, especially Candida glabrata and Candida krusei, which are less susceptible to azoles, has been observed. Standardized susceptibility testing is essential for clinical management and for monitoring the epidemiology of resistance. Aims: We evaluated the performance of two different susceptibility testing commercial methods, Vitek 2(R) and Sensititre YeastOne(R), and compared them with the standard broth microdilution method (CLSI). Methods: A total of 80 isolates of several Candida species (Candida albicans, Candida parapsilosis complex, Candida tropicalis, C. glabrata and C. krusei) were selected for this study. Results: We analyzed the categorical agreement (CA) between the methods, stratifying the disagreements. The average CA between the methods was 96.3% for Vitek 2(R) and 84% for Sensititre YeastOne(R). No very major errors were observed. Major errors and minor errors were found for all the isolates tested. With the azoles, both Vitek 2(R) and Sensititre YeastOne(R) had good and similar performance levels, except for C. tropicalis and C. krusei (Sensititre YeastOne(R) showed low CA, 56.2%). With the echinocandins, both methods showed good performance for C. albicans, C. parapsilosis and C. tropicalis. However, we observed important discrepancies for C. krusei with caspofungin: Vitek 2(R) had 100% CA while Sensititre YeastOne(R) had only 25%. With amphotericin B, both Vitek 2(R) and Sensititre YeastOne(R) had good performance with high CA. Conclusions: Despite the limited isolates tested, we concluded that both methods have good performance and are reliable for antifungal susceptibility testing. However, caspofungin activity against C. krusei and C. glabrata should be interpreted carefully when using Sensititre YeastOne(R) because we observed a low CA

Antecedentes: La incidencia de infecciones fúngicas provocadas por especies de Candida, especialmente por Candida glabrata y Candida krusei, menos sensibles a los azoles, ha ido en aumento. Los métodos estandarizados de estudio de la sensibilidad a los antifúngicos son fundamentales para el manejo clínico y para un mejor seguimiento de la epidemiología de la resistencia. Objetivos: Se evaluó la actividad de dos métodos comerciales diferentes para el estudio de la sensibilidad in vitro a los antifúngicos, Vitek 2(R) y Sensititre YeastOne(R), y se compararon con la técnica estándar de microdilución en caldo del CLSI. Métodos: Para este estudio se seleccionó un total de 80 cepas aisladas de varias especies de Candida (Candida albicans, Candida parapsilosis, Candida tropicalis, C. glabrata y C. krusei). Resultados: Se analizó la concordancia categórica (CC) entre los métodos y se estratificaron los desacuerdos. La CC media entre los métodos fue del 96,3% para Vitek 2(R) y del 84% para Sensititre YeastOne(R). No se observaron errores muy altos. Se encontraron errores mayores y menores en todos los aislamientos probados. Con los azoles, tanto Vitek 2(R) como YeastOne(R) presentaron rendimientos buenos y similares, excepto para C. tropicalis y C. krusei (Sensititre YeastOne(R) mostró baja CC, el 56,2%). Con las equinocandinas, los dos métodos mostraron buen rendimiento para C. albicans, C. parapsilosis y C. tropicalis. Sin embargo, se observaron discrepancias importantes para C. krusei con la caspofungina: Vitek 2(R) presentó el 100% de CC, mientras que Sensititre YeastOne(R) solo el 25%. Para la anfotericina B, Vitek 2(R) y Sensititre YeastOne(R) presentaron un buen rendimiento con una CC alta. Conclusiones: Aunque el número de cepas aisladas probadas fue limitado, concluimos que los dos métodos tienen un buen rendimiento y son fiables para la prueba de sensibilidad antifúngica. Sin embargo, la actividad de la caspofungina frente a C. krusei y C. glabrata mediante el método Sensititre YeastOne(R) debe interpretarse cuidadosamente, ya que se observa un valor bajo de CC

Evaluation of two commercial methods for the susceptibility testing of Candida species: Vitek 2® and Sensititre YeastOne®.

BACKGROUND: An increased incidence of fungal infections caused by Candida species, especially Candida glabrata and Candida krusei, which are less susceptible to azoles, has been observed. Standardized susceptibility testing is essential for clinical management and for monitoring the epidemiology of resistance. AIMS: We evaluated the performance of two different susceptibility testing commercial methods, Vitek 2® and Sensititre YeastOne®, and compared them with the standard broth microdilution method (CLSI). METHODS: A total of 80 isolates of several Candida species (Candida albicans, Candida parapsilosis complex, Candida tropicalis, C. glabrata and C. krusei) were selected for this study. RESULTS: We analyzed the categorical agreement (CA) between the methods, stratifying the disagreements. The average CA between the methods was 96.3% for Vitek 2® and 84% for Sensititre YeastOne®. No very major errors were observed. Major errors and minor errors were found for all the isolates tested. With the azoles, both Vitek 2® and Sensititre YeastOne® had good and similar performance levels, except for C. tropicalis and C. krusei (Sensititre YeastOne® showed low CA, 56.2%). With the echinocandins, both methods showed good performance for C. albicans, C. parapsilosis and C. tropicalis. However, we observed important discrepancies for C. krusei with caspofungin: Vitek 2® had 100% CA while Sensititre YeastOne® had only 25%. With amphotericin B, both Vitek 2® and Sensititre YeastOne® had good performance with high CA. CONCLUSIONS: Despite the limited isolates tested, we concluded that both methods have good performance and are reliable for antifungal susceptibility testing. However, caspofungin activity against C. krusei and C. glabrata should be interpreted carefully when using Sensititre YeastOne® because we observed a low CA.

Performance of the dipstick screening test as a predictor of negative urine culture.

OBJECTIVE: To investigate whether the urine dipstick screening test can be used to predict urine culture results. METHODS: A retrospective study conducted between January and December 2014 based on data from 8,587 patients with a medical order for urine dipstick test, urine sediment analysis and urine culture. Sensitivity, specificity, positive and negative predictive values were determined and ROC curve analysis was performed. RESULTS: The percentage of positive cultures was 17.5%. Nitrite had 28% sensitivity and 99% specificity, with positive and negative predictive values of 89% and 87%, respectively. Leukocyte esterase had 79% sensitivity and 84% specificity, with positive and negative predictive values of 51% and 95%, respectively. The combination of positive nitrite or positive leukocyte esterase tests had 85% sensitivity and 84% specificity, with positive and negative predictive values of 53% and 96%, respectively. Positive urinary sediment (more than ten leukocytes per microliter) had 92% sensitivity and 71% specificity, with positive and negative predictive values of 40% and 98%, respectively. The combination of nitrite positive test and positive urinary sediment had 82% sensitivity and 99% specificity, with positive and negative predictive values of 91% and 98%, respectively. The combination of nitrite or leukocyte esterase positive tests and positive urinary sediment had the highest sensitivity (94%) and specificity (84%), with positive and negative predictive values of 58% and 99%, respectively. Based on ROC curve analysis, the best indicator of positive urine culture was the combination of positives leukocyte esterase or nitrite tests and positive urinary sediment, followed by positives leukocyte and nitrite tests, positive urinary sediment alone, positive leukocyte esterase test alone, positive nitrite test alone and finally association of positives nitrite and urinary sediment (AUC: 0.845, 0.844, 0.817, 0.814, 0.635 and 0.626, respectively). CONCLUSION: A negative urine culture can be predicted by negative dipstick test results. Therefore, this test may be a reliable predictor of negative urine culture. OBJETIVO: Verificar se a triagem de urina por fitas reativas é capaz de predizer a cultura de urina. Métodos Estudo retrospectivo realizado entre janeiro e dezembro de 2014 com 8.587 pacientes, com solicitação médica de triagem de urina (fita), sedimento urinário e cultura de urina. FORAM ANALISADOS: sensibilidade, especificidade, valor preditivo positivo, valor preditivo negativo e curva ROC. RESULTADOS: Foram positivas 17,5% das culturas. O nitrito apresentou sensibilidade de 28% e especificidade de 99%. O valor preditivo positivo foi de 89% e o valor preditivo negativo de 87%. Esterase apresentou sensibilidade de 79% e especificidade de 84%. Valor preditivo positivo e valor preditivo negativo foram de 51% e 95%, respectivamente. A combinação de nitrito ou esterase positivos apresentou sensibilidade de 85% e especificidade de 84%. Valor preditivo positivo e valor preditivo negativo foram, respectivamente, 53% e 96%. O sedimento positivo (mais de dez leucócitos por microlitro) apresentou sensibilidade de 92% e especificidade de 71%. O valor preditivo positivo foi 40% e o negativo, 98%. A combinação de nitrito e sedimento urinário positivos apresentou sensibilidade de 82% e especificidade de 99%. Os valores preditivos positivo e negativo foram 91% e 98%, respectivamente. Para o nitrito ou esterase positivos mais os leucócitos positivos, a sensibilidade foi de 94% e a especificidade de 84%. O valor preditivo positivo foi de 58% e o negativo foi de 99%. Com base na curva ROC, o melhor indicador de urocultura positiva foi a associação entre a esterase ou nitrito positivos na fita mais os leucócitos positivos no sedimento, seguido por nitrito e esterase positivos, sedimento urinário positivo isolado, esterase positiva isolada, nitrito positivo isolado e, finalmente, pela associação entre nitrito e sedimento urinário positivos (AUC: 0,845, 0,844, 0,817, 0,814, 0,635 e 0,626, respectivamente). CONCLUSÃO: Uma urocultura negativa pode ser prevista com resultados negativos na fita. Portanto, este teste pode ser um preditor confiável de urocultura negativa.

Performance of the dipstick screening test as a predictor of negative urine culture / Desempenho da fita de urina como resultado presuntivo para cultura de urina negativa

ABSTRACT Objective To investigate whether the urine dipstick screening test can be used to predict urine culture results. Methods A retrospective study conducted between January and December 2014 based on data from 8,587 patients with a medical order for urine dipstick test, urine sediment analysis and urine culture. Sensitivity, specificity, positive and negative predictive values were determined and ROC curve analysis was performed. Results The percentage of positive cultures was 17.5%. Nitrite had 28% sensitivity and 99% specificity, with positive and negative predictive values of 89% and 87%, respectively. Leukocyte esterase had 79% sensitivity and 84% specificity, with positive and negative predictive values of 51% and 95%, respectively. The combination of positive nitrite or positive leukocyte esterase tests had 85% sensitivity and 84% specificity, with positive and negative predictive values of 53% and 96%, respectively. Positive urinary sediment (more than ten leukocytes per microliter) had 92% sensitivity and 71% specificity, with positive and negative predictive values of 40% and 98%, respectively. The combination of nitrite positive test and positive urinary sediment had 82% sensitivity and 99% specificity, with positive and negative predictive values of 91% and 98%, respectively. The combination of nitrite or leukocyte esterase positive tests and positive urinary sediment had the highest sensitivity (94%) and specificity (84%), with positive and negative predictive values of 58% and 99%, respectively. Based on ROC curve analysis, the best indicator of positive urine culture was the combination of positives leukocyte esterase or nitrite tests and positive urinary sediment, followed by positives leukocyte and nitrite tests, positive urinary sediment alone, positive leukocyte esterase test alone, positive nitrite test alone and finally association of positives nitrite and urinary sediment (AUC: 0.845, 0.844, 0.817, 0.814, 0.635 and 0.626, respectively). Conclusion A negative urine culture can be predicted by negative dipstick test results. Therefore, this test may be a reliable predictor of negative urine culture.

RESUMO Objetivo Verificar se a triagem de urina por fitas reativas é capaz de predizer a cultura de urina. Métodos Estudo retrospectivo realizado entre janeiro e dezembro de 2014 com 8.587 pacientes, com solicitação médica de triagem de urina (fita), sedimento urinário e cultura de urina. Foram analisados sensibilidade, especificidade, valor preditivo positivo, valor preditivo negativo e curva ROC. Resultados Foram positivas 17,5% das culturas. O nitrito apresentou sensibilidade de 28% e especificidade de 99%. O valor preditivo positivo foi de 89% e o valor preditivo negativo de 87%. Esterase apresentou sensibilidade de 79% e especificidade de 84%. Valor preditivo positivo e valor preditivo negativo foram de 51% e 95%, respectivamente. A combinação de nitrito ou esterase positivos apresentou sensibilidade de 85% e especificidade de 84%. Valor preditivo positivo e valor preditivo negativo foram, respectivamente, 53% e 96%. O sedimento positivo (mais de dez leucócitos por microlitro) apresentou sensibilidade de 92% e especificidade de 71%. O valor preditivo positivo foi 40% e o negativo, 98%. A combinação de nitrito e sedimento urinário positivos apresentou sensibilidade de 82% e especificidade de 99%. Os valores preditivos positivo e negativo foram 91% e 98%, respectivamente. Para o nitrito ou esterase positivos mais os leucócitos positivos, a sensibilidade foi de 94% e a especificidade de 84%. O valor preditivo positivo foi de 58% e o negativo foi de 99%. Com base na curva ROC, o melhor indicador de urocultura positiva foi a associação entre a esterase ou nitrito positivos na fita mais os leucócitos positivos no sedimento, seguido por nitrito e esterase positivos, sedimento urinário positivo isolado, esterase positiva isolada, nitrito positivo isolado e, finalmente, pela associação entre nitrito e sedimento urinário positivos (AUC: 0,845, 0,844, 0,817, 0,814, 0,635 e 0,626, respectivamente). Conclusão Uma urocultura negativa pode ser prevista com resultados negativos na fita. Portanto, este teste pode ser um preditor confiável de urocultura negativa.