First isolation of Ascotricha chartarum from bronchoalveolar lavage of two patients with respiratory infections in Kuwait
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PROVIDER: PRJEB26989 | ENA |
REPOSITORIES: ENA
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Project description:Ascotricha chartarum is a rare human pathogen. We describe the isolation and characterization of A. chartarum from bronchoalveolar lavage samples of two patients with underlying pulmonary infections. The identity of both isolates was established by typical phenotypic characteristics and by sequencing of the internal transcribed spacer region and D1/D2 domains of recombinant DNA and β-tubulin gene fragment. The demonstration of branched, septate hyphae in direct microscopic examination of both the specimens and isolation of the fungus in pure cultures suggest its aetiologic role in the disease process. Because of phenotypic similarities of A. chartarum with Chaetomium spp. and other Chaetomium-like fungi, the application of molecular methods is needed for its accurate identification. Although in the absence of histopathologic evidence the aetiologic role of A. chartarum could not be established unequivocally, nonetheless, in view of the rarity of its isolation from clinical specimens and demonstration of hyphal elements in bronchoalveolar lavage sample, this report assumes considerable significance. It serves to create awareness about environmental fungi that previously have missed attention but may play a role in respiratory infections.
| S-EPMC6363919 | biostudies-literature
Project description:ObjectiveMetagenomic next-generation sequencing (mNGS) has the potential to overcome the shortcomings of traditional culture methods. This study aimed to assess the diagnostic value of mNGS in patients with lower respiratory tract infections (LRTIs).MethodsThis retrospective observational study sequentially enrolled 47 patients with LRTIs admitted to Shenzhen Hospital of Southern Medical University between February 2019 and November 2020. Pathogens in bronchoalveolar lavage fluid (BALF) samples were investigated to compare diagnoses by mNGS with culture methods.ResultsCompared with culture methods, mNGS had a diagnostic sensitivity of 80% and a specificity of 35.13% with an agreement rate of 44.68% between these two methods. mNGS significantly increased the pathogen detection rate.ConclusionsmNGS may show some advantages in identifying a wide range of LRTI pathogens, improving the sensitivity for viruses and atypical pathogens. The clinical application of NGS technology is worth looking forward to.
| S-EPMC9087262 | biostudies-literature
Project description:ObjectiveTo assess the association between commonly obtained endoscopic and serologic data and bronchoalveolar lavage pepsin assay (BAL) results in children with chronic cough.Study designWe performed a retrospective chart review of 72 children with a BAL pepsin obtained through our Aerodigestive Center over an 18-month period. BAL outcomes include evidence of viral, bacterial, or fungal infection, presence of lipid-laden macrophages, and cytology (eosinophils, neutrophils, and lymphocytes). Gastrointestinal outcomes include esophagogastroduodenoscopy (EGD) and pH impedance probe findings. Other characteristics include serum eosinophils, neutrophils, and lymphocytes; spirometry; FeNO; and IgE.ResultsSeventy-two patients underwent BAL pepsin testing. Median age was 4.9 years, 30.6% had severe persistent asthma, and 59.2% were on reflux medication. There was an association between positive BAL pepsin assay and positive viral panel (p = .002) or fungal culture (p = .027). No significant association found between positive BAL bacterial culture; BAL cytology; the presence of BAL lipid-laden macrophages; IgE; spirometry; FeNO; CBC neutrophil, eosinophil, or lymphocytes; pH impedance testing parameters; or EGD pathology.ConclusionsBAL pepsin is associated with a positive BAL viral PCR or fungal culture. Lack of correlation between pepsin-positivity and pH-impedance parameters or EGD pathology suggests microaspiration may be due to an acute event (such as a respiratory infection) rather than chronic gastroesophageal reflux disease. This may be especially true in the presence of a positive viral panel or fungal culture when a BAL pepsin is obtained.
| S-EPMC8327477 | biostudies-literature
Project description:Lower respiratory tract infections (LRTIs) diagnosis is challenging because noninfectious diseases mimic its clinical features. The altered host response and respiratory microbiome following LRTIs have the potential to differentiate LRTIs from noninfectious respiratory diseases (non-LRTIs). Patients suspected of having LRTIs are retrospectively enrolled and a clinical metatranscriptome test is performed on bronchoalveolar lavage fluid (BALF). Transcriptomic and metagenomic analysis profiled the host response and respiratory microbiome in patients with confirmed LRTI (n = 126) or non-LRTIs (n = 75). Patients with evidenced LRTIs exhibited enhanced pathways on chemokine and cytokine response, neutrophile recruitment and activation, along with specific gene modules linked to LRTIs status and key blood markers. Moreover, LRTIs patients exhibited reduced diversity and evenness in the lower respiratory microbiome, likely driven by an increased abundance of bacterial pathogens. Host marker genes are selected, and classifiers are developed to distinguish patients with LRTIs, non-LRTIs, and indeterminate status, achieving an area under the receiver operating characteristic curve of 0.80 to 0.86 and validated in a subsequently enrolled cohort. Incorporating respiratory microbiome features further enhanced the classifier's performance. In summary, a single metatranscriptome test of BALF proved detailed profiles of host response and respiratory microbiome, enabling accurate LRTIs diagnosis.
| S-EPMC11809327 | biostudies-literature
Project description:Nocardiae are Gram-positive, filamentous, aerobic, relatively slow-growing, and weakly acid-fast bacteria which cause nocardiosis in humans. We describe a 53-year-old patient with chronic bronchitis referred to Al-Zahra Hospital, Isfahan. A bronchial washing sample was taken from the patient. A Nocardia-like microorganism was detected in microscopic evaluation. Based on the phenotypic and 16S rRNA gene sequencing, the isolate was identified as Nocardia thailandica. The patient was treated with trimethoprim-sulfamethoxazole and linezolid. This is the first report of the isolation of Nocardia thailandica from Iran.
| S-EPMC6123558 | biostudies-literature
Project description:Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, P < 0.001), coincidence (90.34% vs 35.17%, P < 0.001), and negative predictive value (80.00% vs 13.21%, P < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, P < 0.001). Streptococcus pneumoniae as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as Mycobacterium tuberculosis and non-tuberculous. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
| S-EPMC11302328 | biostudies-literature
Project description:ObjectivesDiagnosis of pneumonia is challenging in critically ill, intubated patients due to limited diagnostic modalities. Endotracheal aspirate (EA) cultures are standard of care in many ICUs; however, frequent EA contamination leads to unnecessary antibiotic use. Nonbronchoscopic bronchoalveolar lavage (NBBL) obtains sterile, alveolar cultures, avoiding contamination. However, paired NBBL and EA sampling in the setting of a lack of gold standard for airway culture is a novel approach to improve culture accuracy and limit antibiotic use in the critically ill patients.DesignWe designed a pilot study to test respiratory culture accuracy between EA and NBBL. Adult, intubated patients with suspected pneumonia received concurrent EA and NBBL cultures by registered respiratory therapists. Respiratory culture microbiology, cell counts, and antibiotic prescribing practices were examined.SettingWe performed a prospective pilot study at the Cleveland Clinic Main Campus Medical ICU in Cleveland, Ohio for 22 months from May 2021 through March 2023.Patients or subjectsThree hundred forty mechanically ventilated patients with suspected pneumonia were screened. Two hundred fifty-seven patients were excluded for severe hypoxia (Fio2 ≥ 80% or positive end-expiratory pressure ≥ 12 cm H2O), coagulopathy, platelets less than 50,000, hemodynamic instability as determined by the treating team, and COVID-19 infection to prevent aerosolization of the virus.InterventionsAll 83 eligible patients were enrolled and underwent concurrent EA and NBBL.Measurements and main resultsMore EA cultures (42.17%) were positive than concurrent NBBL cultures (26.51%, p = 0.049), indicating EA contamination. The odds of EA contamination increased by eight-fold 24 hours after intubation. EA was also more likely to be contaminated with oral flora when compared with NBBL cultures. There was a trend toward decreased antibiotic use in patients with positive EA cultures if paired with a negative NBBL culture. Alveolar immune cell populations were recovered from NBBL samples, indicating successful alveolar sampling. There were no major complications from NBBL.ConclusionsNBBL is more accurate than EA for respiratory cultures in critically ill, intubated patients. NBBL provides a safe and effective technique to sample the alveolar space for both clinical and research purposes.
| S-EPMC10656098 | biostudies-literature
Project description:It has been reported that repeated intra-tracheal instillation of S. chartarum spores induced significant pulmonary arterial remodeling in mice, which resulted in pathological changes like human pulmonary arterial hypertension (PAH) and elevation right ventricle systolic pressure. Then, we used microarrays to know the complex molecular mechanisms that underlie pathogenesis of PAH.
2010-07-29 | GSE23178 | GEO