Clusters of patients with candidaemia due to genotypes of Candida albicans and Candida parapsilosis: differences in frequency between hospitals

The presence of clusters (identical genotypes infecting different patients) suggests patient-to-patient transmission or a common source for strains. We report the results of a genotyping study based on microsatellite markers of Candida albicans (n = 179) and Candida parapsilosis (n = 76) causing candidaemia, to assess and compare the percentage of patients grouped in clusters during the study period (January 2010 to December 2012). The study was performed in two large tertiary hospitals in Madrid, Spain. We detected 145 C. albicans genotypes (21 in clusters) and 63 C. parapsilosis genotypes (seven in clusters). Clusters involved two to seven patients each. Most of the clusters in the two centres involved two patients for both species, but the number of patients included in each cluster differed between hospitals. Considering both species, the percentage of patients per cluster ranged from 19% to 38% (p < 0.05) in Hospital A and B respectively. Up to 2.9% of genotypes were present in both hospitals. Clusters of C. albicans and C. parapsilosis genotypes causing candidaemia differed between hospitals, suggesting differences in strain transmission. Occasionally, the same genotypes were found in patients admitted to different hospitals located in the same city

Estructura poblacional de "Streptococcus pneumoniae" con resistencia a los macrólidos asociada a bombas de eflujo (genes mef) y mecanismos duales [genes mef y erm (B)]

Streptococcus pneumoniae constituye un patógeno relevante en la patología infecciosa. Asimismo, es paradigma en el estudio de la evolución de la resistencia a los antimicrobianos y en el estudio de la estructura poblacional en los que la utilización de los antimicrobianos y la implantación de políticas de vacunación han determinado modificaciones relevantes en los últimos años. El presente trabajo está encaminado a analizar la relación entre resistencia y clonalidad en S. pneumoniae, utilizando como modelo y ejes principales la resistencia a los macrólidos, el análisis de la estructura poblacional mediante las técnicas de MLST y repPCR asi como de las estructuras genéticas que vehiculizan los genes de resistencia a los macrólidos. Los objetivos del presente trabajo han sido: 1. Determinar la resistencia a los macrólidos entre los aislados de S. pneumoniae de origen no invasivo y de hemocultivos, obtenidos en dos periodos de tiempo diferentes (colección prevacunal recogida entre 1999 y 2003 y colección obtenida en la época en que la vacuna conjugada heptavalente estaba implantada, entre los años 2000 y 2007). 2. Determinar las resistencias asociadas a otros antibióticos entre los aislados de S. pneumoniae resistentes a los macrólidos. 3. Describir los genes y fenotipos de resistencia asociados a los macrólidos así como a la tetraciclina entre los aislados seleccionados. 4. Determinar la estructura poblacional de los aislados de S. pneumoniae con amplificación positiva para los genes mef mediante diferentes técnicas de tipado. 5. Evaluar la aplicación del sistema semiautomático DiversiLab R para el tipado de aislados de S. pneumoniae resistentes a los macrólidos. 6. Emplear diferentes índices matemáticos para medir la diversidad genética y la distribución de esta en los aislados de S. pneumoniae resistentes a los macrólidos. 7. Determinar la presencia de elementos derivados de Tn916 en los aislados de S.pneumoniae resistentes a los macrólidos

Fungi in Bronchiectasis: A Concise Review

Although the spectrum of fungal pathology has been studied extensively in immunosuppressed patients, little is known about the epidemiology, risk factors, and management of fungal infections in chronic pulmonary diseases like bronchiectasis. In bronchiectasis patients, deteriorated mucociliary clearance—generally due to prior colonization by bacterial pathogens—and thick mucosity propitiate, the persistence of fungal spores in the respiratory tract. The most prevalent fungi in these patients are Candida albicans and Aspergillus fumigatus; these are almost always isolated with bacterial pathogens like Haemophillus influenzae and Pseudomonas aeruginosa, making very difficult to define their clinical significance. Analysis of the mycobiome enables us to detect a greater diversity of microorganisms than with conventional cultures. The results have shown a reduced fungal diversity in most chronic respiratory diseases, and that this finding correlates with poorer lung function. Increased knowledge of both the mycobiome and the complex interactions between the fungal, viral, and bacterial microbiota, including mycobacteria, will further our understanding of the mycobiome’s relationship with the pathogeny of bronchiectasis and the development of innovative therapies to combat it

The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives.

Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities' structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host's physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas

Invasive Pulmonary Aspergillosis in Patients with and without SARS-CoV-2 Infection

The recent European Confederation of Medical Mycology (ECMM) and the International Society for Human and Animal Mycology (ISHAM) 2020 consensus classification proposes criteria to define coronavirus 2019 (COVID-19)-associated invasive pulmonary aspergillosis (CAPA), including mycological evidence obtained via non-bronchoscopic lavage. Given the low specificity of radiological findings in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, this criterion makes it difficult to differentiate between invasive pulmonary aspergillosis (IPA) and colonization. This unicenter and retrospective study includes 240 patients with isolates of any Aspergillus species in any respiratory samples during a 20-month study (140 IPA and 100 colonization). Mortality was high in the IPA and colonization groups (37.1% and 34.0%, respectively; p = 0.61), especially in patients with SARS-CoV-2 infection, where mortality was higher in colonized patients (40.7% vs. 66.6.%; p: 0.021). Multivariate analysis confirmed the following variables to be independently associated with increased mortality: age &gt; 65 years, acute or chronic renal failure at diagnosis, thrombocytopenia (&lt;100,000 platelets/&micro;L) at admission, inotrope requirement, and SARS-CoV-2 infection, but not the presence of IPA. This series shows that the isolation of Aspergillus spp. in respiratory samples, whether associated with disease criteria or not, is associated with high mortality, especially in patients with SARS-CoV-2 infection, and suggests an early initiation of treatment given its high mortality rate

The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives

Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities&rsquo; structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host&rsquo;s physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas

<i>Candida</i> Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant <i>C. parapsilosis</i>

Background: Candidaemia and invasive candidiasis are typically hospital-acquired. Genotyping isolates from patients admitted to different hospitals may be helpful in tracking clones spreading across hospitals, especially those showing antifungal resistance. Methods: We characterized Candida clusters by studying Candida isolates (C. albicans, n = 1041; C. parapsilosis, n = 354, and C. tropicalis, n = 125) from blood cultures (53.8%) and intra-abdominal samples (46.2%) collected as part of the CANDIMAD (Candida in Madrid) study in Madrid (2019–2021). Species-specific microsatellite markers were used to define the genotypes of Candida spp. found in a single patient (singleton) or several patients (cluster) from a single hospital (intra-hospital cluster) or different hospitals (widespread cluster). Results: We found 83 clusters, of which 20 were intra-hospital, 49 were widespread, and 14 were intra-hospital and widespread. Some intra-hospital clusters were first detected before the onset of the COVID-19 pandemic, but the number of clusters increased during the pandemic, especially for C. parapsilosis. The proportion of widespread clusters was significantly higher for genotypes found in both compartments than those exclusively found in either the blood cultures or intra-abdominal samples. Most C. albicans- and C. tropicalis-resistant genotypes were singleton and presented exclusively in either blood cultures or intra-abdominal samples. Fluconazole-resistant C. parapsilosis isolates belonged to intra-hospital clusters harboring either the Y132F or G458S ERG11p substitutions; the dominant genotype was also widespread. Conclusions: the number of clusters—and patients involved—increased during the COVID-19 pandemic mainly due to the emergence of fluconazole-resistant C. parapsilosis genotypes