scholarly journals Beware of pharyngeal Fusobacterium nucleatum in COVID-19

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lirong Bao ◽  
Cheng Zhang ◽  
Jinglu Lyu ◽  
Caixia Yan ◽  
Ranran Cao ◽  
...  
Keyword(s):  
Gastrointestinal Disease ◽  
Area Under The Curve ◽  
Fusobacterium Nucleatum ◽  
Opportunistic Pathogen ◽  
Next Generation ◽  
Opportunistic Pathogens ◽  
Promising Candidate ◽  
Viral Respiratory Infection ◽  
Generation Sequencing ◽  
Viral Respiratory

Abstract Background Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker of gut eubiosis/dysbiosis to some extent. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS). Results Pharyngeal F. n was significantly increased in COVID-19 patients, and it was higher in male than female patients. Increased abundance of pharyngeal F. n was associated with a higher risk of a positive SARS-CoV-2 test (adjusted OR = 1.32, 95% CI = 1.06 ~ 1.65, P < 0.05). A classifier to distinguish COVID-19 patients from the healthy controls based on the pharyngeal F. n was constructed and achieved an area under the curve (AUC) of 0.843 (95% CI = 0.688 ~ 0.940, P < 0.001). However, the level of fecal F. n and fecal F. p remained unaltered between groups. Besides, mNGS showed that the pharyngeal swabs of COVID-19 patients were dominated by opportunistic pathogens. Conclusions Pharyngeal but not fecal F. n was significantly increased in COVID-19 patients, clinicians should pay careful attention to potential coinfection. Pharyngeal F. n may serve as a promising candidate indicator for COVID-19.

scholarly journals Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

2016 ◽  
Vol 54 (4) ◽  
pp. 980-987 ◽  
Author(s):  
Sarah Mollerup ◽  
Jens Friis-Nielsen ◽  
Lasse Vinner ◽  
Thomas Arn Hansen ◽  
Stine Raith Richter ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Propionibacterium Acnes ◽  
Opportunistic Pathogen ◽  
Next Generation Sequencing Data ◽  
Clinical Samples ◽  
Next Generation ◽  
Sequencing Data ◽  
Tissue Samples ◽  
Content Type ◽  
Generation Sequencing

Propionibacterium acnesis the most abundant bacterium on human skin, particularly in sebaceous areas.P. acnesis suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence ofP. acnesDNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions ofP. acnesDNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples.P. acnesreads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show thatP. acnescan be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully whenP. acnesis detected in clinical samples. We advocate that detection ofP. acnesalways be accompanied by experiments validating the association between this bacterium and any clinical condition.

scholarly journals Case Report: A Severe and Multi-Site Nocardia farcinica Infection Rapidly and Precisely Identified by Metagenomic Next-Generation Sequencing

2021 ◽  
Vol 8 ◽  
Author(s):  
Mengfan Jiao ◽  
Xiang Deng ◽  
Hongfu Yang ◽  
Junqiang Dong ◽  
Jun Lv ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Venous Blood ◽  
Opportunistic Pathogen ◽  
Diagnosis And Treatment ◽  
Next Generation ◽  
Nocardia Farcinica ◽  
Negative Results ◽  
Golden Standard ◽  
Immunosuppressed Patients ◽  
Generation Sequencing

Nocardia genus is an aerobic, gram-positive, and opportunistic pathogen, which mainly affects cell-mediated immunosuppressed patients. Early diagnosis and treatment greatly improve prognosis. However, the limitation of golden standard-bacterial culture exists. Here, we report a 61-year-old male with pneumonia, sepsis and intermuscular abscesses induced by Nocardia farcinica. Venous blood culture reported negative results. Former improper diagnosis and treatment did not improve his condition. With the assistant of metagenomic next-generation sequencing, the pathogen was identified as Nocardia farcinica. He was then applied with accurate treatment and had a remarkable clinical and radiological improvement.

scholarly journals DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Takehiro Matsubara ◽  
Junichi Soh ◽  
Mizuki Morita ◽  
Takahiro Uwabo ◽  
Shuta Tomida ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Characteristic Curve ◽  
Area Under The Curve ◽  
Poor Quality ◽  
Next Generation ◽  
Tissue Samples ◽  
Rna Integrity ◽  
Rna Quality ◽  
Pcr Product ◽  
Generation Sequencing

Poor quality of biological samples will result in an inaccurate analysis of next-generation sequencing (NGS). Therefore, methods to accurately evaluate sample integrity are needed. Among methods for evaluating RNA quality, the RNA integrity number equivalent (RINe) is widely used, whereas the DV200, which evaluates the percentage of fragments of >200 nucleotides, is also used as a quality assessment standard. In this study, we compared the RINe and DV200 RNA quality indexes to determine the most suitable RNA index for the NGS analysis. Seventy-one RNA samples were extracted from formalin-fixed paraffin-embedded tissue samples (n=30), fresh-frozen samples (n=25), or cell lines (n=16). After assessing RNA quality using the RINe and DV200, we prepared two kinds of stranded mRNA sequencing libraries. Finally, we calculated the correlation between each RNA quality index and the amount of library product (1st PCR product per input RNA). The DV200 measure showed stronger correlation with the amount of library product than the RINe (R2=0.8208 for the DV200 versus 0.6927 for the RINe). Receiver operating characteristic curve analyses revealed that the DV200 was the better marker for predicting efficient library production than the RINe using a threshold of >10 ng/ng for the amount of the 1st PCR product per input RNA (cutoff value for the RINe and DV200, 2.3 and 66.1%; area under the curve, 0.99 and 0.91; sensitivity, 82% and 92%; and specificity, 93% and 100%, respectively). Our results indicate that NGS libraries prepared using RNA samples with the DV200 value>66.1% exhibit greater sensitivity and specificity than those prepared with the RINe values>2.3. These findings suggest that the DV200 is superior to the RINe, especially for low-quality RNA, because it is a more consistent assessment of the amount of the 1st NGS library product per input.

scholarly journals Next-Generation Sequencing Analysis of Root Canal Microbiota Associated with a Severe Endodontic-Periodontal Lesion

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1461
Author(s):  
Alessio Buonavoglia ◽  
Gianvito Lanave ◽  
Michele Camero ◽  
Marialaura Corrente ◽  
Antonio Parisi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Population ◽  
Clinical Manifestations ◽  
Fusobacterium Nucleatum ◽  
Sequencing Analysis ◽  
Next Generation ◽  
Bacterial Migration ◽  
Next Generation Sequencing Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

A patient with an unusual endo-periodontal lesion, without coronal decay or damage, likely caused by a deep periodontal lesion with subsequent endodontic bacterial migration, required medical care. Next-generation sequencing (NGS) was used to assess the endodontic microbiota in vestibular and palatal canals after tooth extraction, evidencing a predominant population (Fusobacterium nucleatum) in one endodontic canal, and a mixed bacterial population with six major populations almost equally distributed in the other endodontic canal (F. nucleatum, Porphyromonas gingivalis, P. endodontis, Parvimonas, Peptostreptococcus stomatis, Prevotella multiformis). These data could suggest different, separated ecologic niches in the same endodontic system, with potentially different pathogenicity levels, clinical manifestations and prognoses for every single canal of the same tooth.

scholarly journals Clinical Application of Metagenomic Next-Generation Sequencing for Suspected Infections in Patients With Primary Immunodeficiency Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenjing Tang ◽  
Yu Zhang ◽  
Chong Luo ◽  
Lina Zhou ◽  
Zhiyong Zhang ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Next Generation Sequencing ◽  
Primary Immunodeficiency ◽  
Primary Immunodeficiency Disease ◽  
Next Generation ◽  
Opportunistic Pathogens ◽  
Pathogen Identification ◽  
Conventional Methods ◽  
Immunodeficiency Disease ◽  
Generation Sequencing

BackgroundInfections are the major cause of morbidity and mortality in patients with primary immunodeficiency disease (PID). Timely and accurate microbiological diagnosis is particularly important in these patients. Metagenomic next-generation sequencing (mNGS) has been used for pathogen detection recently. However, few reports describe the use of mNGS for pathogen identification in patients with PID.ObjectiveTo evaluate the utility of mNGS for detecting pathogens in patients with PID, and to compare it with conventional microbiological tests (CMT).MethodsThis single center retrospective study investigated the diagnostic performance of mNGS for pathogens detection in PID patients and compared it with CMT. Sixteen PID patients with suspected infection were enrolled, and medical records were analyzed to extract detailed clinical characteristics such as gene variation, immune status, microbial distribution, time-consuming of mNGS and CMT, treatment, and outcomes.ResultsmNGS identified pathogenic microbe in 93.75% samples, compared to 31.25% for culture and 68.75% for conventional methods, and detected an extra 18 pathogenic microorganisms including rare opportunistic pathogens and Mycobacterium tuberculosis. Pathogen identification by mNGS required 48 hours, compared with bacterial culture for 3-7 days and even longer for fungus and Mycobacterium tuberculosis culture.ConclusionsmNGS has marked advantages over conventional methods for pathogenic diagnosis, particularly opportunistic pathogens and mixed infections, in patients with PID. This method might enable clinicians to make more timely and targeted therapeutic decisions, thereby improving the prognosis of these patients.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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