Metagenomic next-generation sequencing of viruses, bacteria, and fungi in the epineurium of the facial nerve with Bell’s palsy patients

Background: Bloodstream infection (BSI) has been one of the biggest headaches for clinicians, as it not only aggravates symptoms but also increases the length of stay, the cost of hospitalization, and the side effects caused by antibiotics. It is an urgent need for clinicians to develop timely and accurate methods to find microorganisms. Currently, the gold standard for diagnosing BSI is blood culture, but it takes three to eight days to produce results, and its positive rate is extremely low. Next-generation sequencing (NGS) has emerged as a better technology desperately needed by doctors and patients to diagnose BSI. Objectives: This study compared NGS and blood culture methods in clinical patients with BSI. Methods: In this study, blood culture and NGS were used to analyze the blood of patients with BSI in different departments of the First Affiliated Hospital of Kunming Medical University. Results: Next-generation sequencing detected 60 pathogens in 63 blood samples, while blood culture detected 15 pathogens in 336 blood samples from 63 patients who were clinically considered to be infected. Pathogens detected by NGS included bacteria, fungi, and viruses, while blood culture only found bacteria and fungi. The positive rates of blood culture diagnosis and NGS diagnosis in BSI patients were 23.8% (15/63) (CI: 13.3% - 34.3%) and 95% (60/63) (CI: 90% - 100%), respectively. Conclusions: Our results showed that NGS creates a new diagnostic platform for patients with BSI. Its wide detection range, high positive rate, and characteristics of rapid detection will benefit patients with BSI.

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Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2020/6839103 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9

Author(s):

Xu Chen ◽

Shuizi Ding ◽

Cheng Lei ◽

Jieli Qin ◽

Ting Guo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Bronchoalveolar Lavage ◽

Bronchoalveolar Lavage Fluid ◽

Human Adenovirus ◽

Lavage Fluid ◽

Diagnostic Value ◽

Next Generation ◽

Barr Virus ◽

Bacteria And Fungi ◽

Generation Sequencing

Background. Metagenomic next-generation sequencing (mNGS) has made a revolution in the mode of pathogen identification. We decided to explore the diagnostic value of blood and bronchoalveolar lavage fluid (BALF) as mNGS samples in pneumonia. Methods. We retrospectively reviewed 467 mNGS results and assessed the diagnostic performance of paired blood and BALF mNGS in 39 patients with pneumonia. Results. For bacteria and fungi, 16 patients had culture-confirmed pathogen diagnosis, while 13 patients were culture-negative. BALF mNGS was more sensitive than blood mNGS (81.3% vs. 25.0%, p=0.003), and the specificity in BALF and blood mNGS was not statistically significant different (76.9% vs. 84.6%, p=0.317). For 10 patients without culture test, treatments were changed in 2 patients. For viruses, Epstein-Barr virus was positive in blood mNGS in 9 patients. Human adenovirus was detected in both BALF and blood mNGS in 3 patients. Conclusion. Our study suggests that BALF mNGS is more sensitive than blood mNGS in detecting bacteria and fungi, but blood also has advantages to identify the pathogens of pneumonia, especially for some viruses.

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Case Report: Next-Generation Sequencing in Diagnosis of Pneumonia Due to Pneumocystis jirovecii and Cytomegalovirus in a Patient With HIV Infection

Frontiers in Medicine ◽

10.3389/fmed.2021.653294 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yirui Xie ◽

Bing Ruan ◽

Lingxiao Jin ◽

Biao Zhu

Keyword(s):

Next Generation Sequencing ◽

Hiv Infection ◽

Lavage Fluid ◽

Pneumocystis Jirovecii ◽

Next Generation ◽

Combined Application ◽

Bacteria And Fungi ◽

Bilateral Lung ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Background: Pulmonary infections remain a significant cause of morbidity and mortality in immunocompromised patients. The pathogens spectrum of pulmonary infection that can affect patients with human immunodeficiency virus (HIV) is wide such as bacterial, fungal, viral, parasitic organisms, and so on. The risk of multi-pathogenic pneumonia is higher in HIV-infected patients. However, the fast and accurate diagnosis of multi-pathogenic pneumonia is challenging because of the limitations of current conventional tests.Case Presentation: Here, we report a case of pneumonia due to Pneumocystis jirovecii and cytomegalovirus (CMV) in a 22-year-old male with newly diagnosed HIV infection. Blood tests revealed a low CD4 count, a chest computed tomography (CT) scan showed extensive ground-glass opacities in the bilateral lung with multiple cavity lesions in the left upper lung. Microscopic examination of stained sputum and bronchoalveolar lavage fluid (BALF) smear specimens did not find any pathogens. There was also no evidence of pathogens known to cause pneumonia in bacteria and fungi culture tests and virus antibodies such as EBV, CMV, and COVID-19. The nucleic acid of CMV in blood was reported by quantitative PCR. Next-generation sequencing (NGS) analysis of BALF specimens identified a large number of P. jirovecii and CMV reads, and confirmed the diagnosis of pneumonia due to P. jirovecii and CMV. Following the patient's treatment with anti-PCP and anti-CMV, the patient was cured and discharged.Conclusions: This case highlights the combined application of NGS in the clinical diagnosis of multi-pathogenic pneumonia in an HIV-infected patient. NGS is proposed as an important adjunctive diagnostic approach for identifying pathogens of multi-pathogenic pneumonia in HIV-infected patients.

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Next-Generation Sequencing

Family Practice News ◽

10.1016/s0300-7073(12)70394-8 ◽

2012 ◽

Vol 42 (9) ◽

pp. 8

Author(s):

PETER HULICK

Keyword(s):

Next Generation Sequencing ◽

Next Generation ◽

Generation Sequencing

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Decision letter for "Detection of recurrent, rare, and novel gene fusions in patients with acute leukemia using next‐generation sequencing approaches"

10.1002/hon.2709/v2/decision1 ◽

2019 ◽

Keyword(s):

Next Generation Sequencing ◽

Acute Leukemia ◽

Gene Fusions ◽

Next Generation ◽

Novel Gene ◽

Generation Sequencing

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Review for "Detection of recurrent, rare, and novel gene fusions in patients with acute leukemia using next‐generation sequencing approaches"

10.1002/hon.2709/v1/review1 ◽

2019 ◽

Author(s):

Vundavalli V Murty

Keyword(s):

Next Generation Sequencing ◽

Acute Leukemia ◽

Gene Fusions ◽

Next Generation ◽

Novel Gene ◽

Generation Sequencing

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Labordiagnostik bei gastrointestinalen Tumoren

Onkologische Welt ◽

10.1055/a-1268-3713 ◽

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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