Yeast species in the respiratory samples of COVID-19 patients; molecular tracking of Candida auris.

Introduction: Although the existence of Candida species in the respiratory tract is often considered commensal, it is crucial to recognize the significance of Candida colonization in immunocompromised or COVID-19 patients. The emergence of Candida auris as an emerging pathogen further emphasizes the importance of monitoring yeast infection/colonization, particularly in COVID-19 patients. Methods: In this study, respiratory samples mainly from COVID-19 patients, primarily those suspected of having a fungal infection, were cultured on Sabouraud dextrose agar plates and the yeast colonies were identified using a two-step multiplex PCR method. The samples suspected of C. auris underwent specific nested PCR followed by sequence analysis. Results: A total of 199 respiratory samples were collected from 73 women and 126 men, ranging in age from 1.6 to 88 years. Among the patients, 141 had COVID-19, 32 had cancer, 5 were hospitalized in ICU, 2 had chronic obstructive pulmonary disease)COPD(, and others were patients with combination diseases. From these samples, a total of 334 yeast strains were identified. C. albicans (n=132, 39.52%) was the most common species, followed by C. tropicalis (n=67, 20%), C. glabrata (n=56, 16.76%), C. krusei (n=18, 5.4%), C. parapsilosis (n=17, 5.08%), Saccharomyces cerevisiae (n=10, 3%), C. kefyr (n=9, 2.6%), C. dubliniensis (n=7, 2.1%), C. lusitaniae (n=5, 1.5%), C. auris (n=3, 0.9%), C. guilliermondii (n=2, 0.6%), C. rugosa (n=1, 0.3%), C. intermedia (n=1, 0.3%), and Trichosporon spp. (n=1, 0.3%). C. auris was detected in a patient in ICU and two COVID-19 patients. While its presence was confirmed through sequence analysis, our extensive efforts to isolate C. auris were unsuccessful. Conclusion: While C. albicans colonization remains prevalent, our study found no evidence of Candida lung infection. Since the role of Candida colonization in airway secretions remains ambiguous due to limited research, further studies are imperative to shed light on this matter.

Features and evaluation of mucormycosis in COVID-19 patients from two referral hospitals in Iran.

OBJECTIVES: The present study aimed to assess the features, clinical characteristics, and species diversity among patients admitted to referral Hospitals for SARS-CoV-2 pneumonia and mucormycosis in Tehran, Iran, and the relationship between seasonal and species diversity was considered. METHODS: Confirmed COVID-19 patients with a positive reverse-transcriptase real-time (rRT-PCR) test for SARS-CoV2 were primarily included based on clinically suspected mucormycosis infection and confirmed by histopathology and mycology examination of biopsy specimens. The PCR technique was performed by the amplification of the high-affinity iron permease 1 (FTR1) gene for identification and discrimination between Rhizopus arrhizus and non- Rhizopus arrhizus isolates. In contrast, species identification of non-Rhizopus arrhizus was performed by sequencing of ITS rDNA region. RESULTS: Rhino-sino-orbital mucormycosis was identified in the majority of cases (n = 33), with 66 % and 34 % of the cases involving male and female patients, respectively. Rhizopus arrhizus was found to be the most prevalent (84.6 %), followed by Mucor circinelloides (7.6 %). Rhizopus arrhizus was the most prevalent species and present in all the seasons; however, Mucor circinelloides was only present in the autumn. The overall mortality of the total population was 24.6 % (16/ 65); the mortality rates occurring in patients diagnosed with rhino-sino-orbital infection and rhino-sinusal form were 21.4 % and 25 %, respectively. CONCLUSION: CAM can be a serious complication of severe COVID-19, especially in patients with uncontrolled diabetes. It is important to monitor the epidemiology of mucormycosis to raise awareness of the disease and improve diagnosis, treatment and prognosis, particularly in the setting of pandemic.

Gut-Lung Microbiota Characterization in Patients with Non-Small Cell Lung Carcinoma and COVID-19 Coinfection.

BACKGROUND: Non-small cell lung cancer (NSCLC) patients with COVID-19 have an excessive chance of morbidity and mortality. The fecal-nasopharyngeal microbiota compositions of NSCLC patients were assessed in this study. METHODS: In total, 234 samples were collected from 17 NSCLC patients infected with COVID-19, 20 NSCLC patients without confirmed COVID-19, 40 non NSCLC patients with COVID-19, and 40 healthy individuals. RESULTS: In lung microbiota, the abundance of Streptococcus spp. in NSCLC patients with confirmed COVID-19 was significantly higher than the two control groups. Pseudomonas aeruginosa and Staphylococcus aureus were listed as the most frequent pulmonary bacterial groups that colonized COVID-19 patients. In fecal specimens, the numbers of Bacteroidetes, Firmicutes, and Actinobacteria phyla were significantly higher amongst NSCLC patients with COVID-19. NSCLC patients infected with COVID-19 showed lower levels of Lactobacillus spp., Akkermansia muciniphila, and Bifidobacterium spp. The counts of Streptococcus spp., in NSCLC patients with COVID-19 were significantly higher than those of healthy individuals (8.49±0.70 log CFU/g wet feces vs 8.49±0.70 log CFU/g wet feces). Prevotella spp. were enriched in the gut and respiratory tracts of COVID-19 patient groups. The unbiased analysis showed an increment in Enterococcus spp., Streptococcus spp., and Prevotella spp. CONCLUSION: Eventually, it was found that compared to control groups, COVID-19 patients with NSCLC showed diminished gut bacteria diversity and increase in Lactobacillus spp., A. muciniphila, and Bifidobacterium spp. The overgrowth of Enterococcus spp., Streptococcus spp., and Prevotella spp. could be potential predictive biomarkers in the gut-lung axis of NSCLC patients with COVID-19.

Pulmonary Function, Anxiety, Depression, and Sleep Quality after Recovery from COVID-19.

Background: The COVID-19 pandemic has affected human beings worldwide. After recovery from the disease, the pulmonary function and physiological characteristics of COVID-19 patients are not well documented. The current study aims to assess post-COVID-19 lung function, anxiety, depression, and sleep quality within three months after recovery from the disease. Materials and Methods: Ninety-seven patients (21 outpatients and 76 inpatients) with COVID-19 were followed three months after recovery. They were divided into two groups according to the severity of the disease. The spirometric parameters included FEV1, FVC, and FEV1/FVC. A 6-minute walk test (6-MWT) was recorded. Besides, sleep quality using Pittsburgh Sleep Quality Index (PSQI) and mood status in two dimensions of anxiety and depression using the Hospital Anxiety and Depression Scale (HADS) were compared between the groups. Results: More than 70% of the studied population presented at least one of the COVID-19 infection-related symptoms within three months after recovery. spirometric measurements revealed non-significant differences between the patients with severe versus non-severe COVID-19 in terms of FVC (P=0.805), FEV1 (P=0.948), FEV1/FVC (P=0.616), and 6MWT (P=0.409). Based on PSQI, sleep quality was significantly associated with the severity of disease (P=0.031), but HADS assessments were not significant (P>0.05). Conclusion: This study demonstrated that a significant proportion of COVID-19 patients have corona symptoms and abnormal pulmonary function tests three months after recovery. Besides, sleep quality was considerably affected by the severity of the disease and was directly associated with the post-COVID-19 mood of the patients. It seems necessary to consider and control the long-term consequences of this infection regardless of the disease severity.