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Revista Espanola de Quimioterapia :... Aug 2023
Topics: Humans; Prevotella; Lung Diseases; Bacteroidaceae Infections
PubMed: 37184104
DOI: 10.37201/req/001.2023 -
Journal of Thoracic Disease Oct 2019Culture-independent methods such as quantitative polymerase chain reaction (qPCR) are more sensitive for detecting pathogens than conventional culture. This study aimed...
Potential clinical utility of multiple target quantitative polymerase chain reaction (qPCR) array to detect microbial pathogens in patients with chronic obstructive pulmonary disease (COPD).
BACKGROUND
Culture-independent methods such as quantitative polymerase chain reaction (qPCR) are more sensitive for detecting pathogens than conventional culture. This study aimed to test the clinical potential of a multiple target qPCR array in identifying sputum pathogens, compared to traditional culture.
METHODS
Forty chronic obstructive pulmonary disease (COPD) patients provided spontaneous sputum and blood samples during an exacerbation event (n=25 patients) and in stable state (n=15 patients). Sputum was processed and analysed by microscopy, culture and sensitivity testing (MCS) to identify living microbial isolates, and multiple target qPCR (44 targets for bacterial and fungal pathogens and antibiotic resistance genes), and 16S rRNA gene sequencing.
RESULTS
Six microbial isolates (5 bacterial, 1 fungal) were cultured from 20 exacerbation and 10 stable patient sputum samples. Four of these microbial isolates had their presence in patient sputum confirmed by qPCR. All bacterial targets detected by qPCR were further confirmed by 16S rRNA gene sequencing at a genus level. qPCR identified significantly more bacterial pathogens than culture (P<0.001). The most prevalent bacterial species identified by qPCR were (72% of patients), (40%), (32%) and (17%). Microbial species diversity and richness were not significantly different between samples obtained from exacerbating and clinically stable cases. 16S rRNA gene sequencing identified (P=0.022, FDR =0.043 AUC =0.72) as a significantly different bacterial OTU (operational taxonomic units) in exacerbation sputum samples compared to stable state samples.
CONCLUSIONS
Multiple target qPCR was more sensitive for detection of sputum pathogens in COPD patients than conventional culture. 16S rRNA gene sequencing confirmed the identity at a genus level of all bacterial targets detected by qPCR, as well as identifying bacterial OTUs that could potentially be used to distinguish between exacerbation and stable COPD disease states. Multiple target qPCR pathogen detection in the sputum of COPD patients warrants further investigation to determine how it may influence COPD clinical management.
PubMed: 31737352
DOI: 10.21037/jtd.2019.10.39 -
BMC Infectious Diseases Sep 2021Descending necrotizing mediastinitis (DNM) is one of the most virulent forms of mediastinitis. The main causes of high mortality in DNM are believed to stem from...
BACKGROUND
Descending necrotizing mediastinitis (DNM) is one of the most virulent forms of mediastinitis. The main causes of high mortality in DNM are believed to stem from difficulty and delay in the diagnosis. Fast and accurate identification of pathogens is important for the treatment of these patients. Metagenomics next-generation sequencing (mNGS) is a powerful tool to identify all kinds of pathogens, especially for rare and complex infections.
CASE PRESENTATION
A 64-year-old male patient was admitted to the intensive care unit (ICU) with unconsciousness, dyspnea, and swelling in the mandible and neck. Computed tomography (CT) scan results combined with clinical laboratory examination indicated DNM. Vancomycin and imipenem were used, and vacuum sealing drainage was applied for debridement and drainage of the infected area. The positive mNGS results of drainage fluid confirmed the presence of mixed infection caused by Streptococcus anginosus, Prevotella oris, and several other anaerobes. The antibiotics were adjusted to piperacillin/tazobactam and tinidazole according to the mNGS results and antimicrobial susceptibility testing of cultured pathogens. After 11 days of antibiotic therapy, the infection symptoms of the neck and mediastinum improved, and the patient was transferred out of the ICU on the 26 day after negative result of drainage fluid culture.
CONCLUSION
This case suggested that mNGS is a promising technology for precise and fast pathogens identification with high sensitivity, which may guide the diagnosis of infectious diseases in the future trend.
Topics: Coinfection; High-Throughput Nucleotide Sequencing; Humans; Male; Mediastinitis; Metagenomics; Middle Aged; Necrosis; Prevotella
PubMed: 34479479
DOI: 10.1186/s12879-021-06624-4 -
Cureus May 2020Empyema necessitasis (EN) also referred to as empyema necessitans (EN) is a rare complication of empyema that can involve soft tissues outside the pleural cavity and can...
Empyema necessitasis (EN) also referred to as empyema necessitans (EN) is a rare complication of empyema that can involve soft tissues outside the pleural cavity and can lead to brachial plexus injury. Although, brachial plexus injury most commonly occurs as a result of trauma, inflammation, or malignancies, but it has been rarely seen in EN. We are reporting a rare and challenging case of empyema necessitasis (EN) causing impingement of brachial plexus in a 42-year-old, type 2 diabetic patient, who initially presented to the hospital with left-sided pleuritic chest pain and acute onset of left upper limb weakness. Urgent CT brain ruled out an acute neurological insult. Chest radiograph and contrast-enhanced CT thorax revealed left-sided loculated effusion. MRI of the left upper limb showed impingement of brachial plexus by the inflammatory process of surrounding effusion. Ultrasound-guided aspiration of the encapsulated fluid was performed and culture analysis of the fluid was remarkable for Prevotella oris (sensitive strain) growth. After drainage of the infected fluid and with a prolonged course of antibiotics, the patient's neurological symptoms improved significantly. Hospital course was uncomplicated and further follow-up was unremarkable for any deterioration. Our objective is to emphasize on the prompt management with close follow-up in EN, which can present with life-threatening complications as seen in our case. Any delay can compromise the patient's health. As per our limited knowledge, this case has not been reported in the literature.
PubMed: 32596084
DOI: 10.7759/cureus.8267 -
BMC Microbiology May 2024We evaluated whether the sputum bacterial microbiome differs between nontuberculous mycobacteria pulmonary disease (NTM-PD) patients with stable disease not requiring... (Comparative Study)
Comparative Study
BACKGROUND
We evaluated whether the sputum bacterial microbiome differs between nontuberculous mycobacteria pulmonary disease (NTM-PD) patients with stable disease not requiring antibiotic treatment and those requiring antibiotics.
METHODS
We collected sputum samples from 21 clinically stable NTM-PD patients (stable group) and 14 NTM-PD patients needing antibiotic treatment (treatment group). We also obtained 13 follow-up samples from the stable group. We analyzed the 48 samples using 16S rRNA gene sequencing (V3-V4 region) and compared the groups.
RESULTS
In the linear discriminant analysis effect size (LEfSe) analysis, the species Porphyromonas pasteri, Haemophilus parahaemolyticus, Prevotella nanceiensis, and Gemella haemolysans were significantly more prevalent in the sputum of the stable group compared to the treatment group. No taxa showed significant differences in alpha-/beta-diversity or LEfSe between the 21 baseline and 13 follow-up sputum samples in the stable group. In the stable group, the genus Bergeyella and species Prevotella oris were less common in patients who achieved spontaneous culture conversion (n = 9) compared to those with persistent NTM positivity (n = 12) (effect size 3.04, p = 0.039 for Bergeyella; effect size 3.64, p = 0.033 for P. oris). In the treatment group, H. parainfluenzae was more common in patients with treatment success (n = 7) than in treatment-refractory patients (n = 7) (effect size 4.74, p = 0.013).
CONCLUSIONS
Our study identified distinct bacterial taxa in the sputum of NTM-PD patients based on disease status. These results suggest the presence of a microbial environment that helps maintain disease stability.
Topics: Humans; Sputum; Male; Female; Microbiota; Aged; Mycobacterium Infections, Nontuberculous; RNA, Ribosomal, 16S; Middle Aged; Anti-Bacterial Agents; Bacteria; Nontuberculous Mycobacteria; DNA, Bacterial; Lung Diseases
PubMed: 38760693
DOI: 10.1186/s12866-024-03308-2