Detection of aerobe–anaerobe mixed infection by metagenomic next-generation sequencing in an adult suffering from descending necrotizing mediastinitis

Abstract 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 26th 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.

Download Full-text

A Novel Method for Microsatellite Instability Detection by Liquid Biopsy Based on Next- Generation Sequencing

Current Bioinformatics ◽

10.2174/1574893615666200324133451 ◽

2020 ◽

Vol 15 ◽

Author(s):

Zheng Jiang ◽

Hui Liu ◽

Siwen Zhang ◽

Jia Liu ◽

Weitao Wang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Instability ◽

Liquid Biopsy ◽

Tumor Tissue ◽

High Sensitivity ◽

Next Generation ◽

Tissue Samples ◽

Next Generation Sequencing Technology ◽

Medication Selection ◽

Generation Sequencing

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through puncture or surgery, which causes injury and risk of concurrent disease, further illustrating the need for MSI detection by liquid biopsy. Methods: We propose an analytic method using paired plasma/leukocyte samples and MSI detection using next-generation sequencing technology. Based on the theoretical progress of oncogenesis, we hypothesized that the microsatellite site length in plasma equals the combination of the distribution of tumor tissue and leukocytes. Thus, we defined a window-judgement method to identify whether biomarkers were stable. Results: Compared to traditional PCR as the standard, we evaluated three methods in 20 samples (MSI-H:3/MSS:17): peak shifting method using tissue vs. leukocytes, peak shifting method using plasma vs. leukocytes, and our method using plasma vs. leukocytes. Compared to traditional PCR, we observed a sensitivity of 100%, 0%, and 100%, and a specificity of 100.00%, 94.12%, and 88.24%, respectively. Conclusion: Our method has the advantage of possibly detecting MSI in a liquid biopsy and provides a novel direction for future studies to increase the specificity of the method.

Download Full-text

Next-generation sequencing as a clinical laboratory tool for describing different microbiotas: an urgent need for future paediatric practice

Archives of Disease in Childhood ◽

10.1136/archdischild-2021-321683 ◽

2021 ◽

pp. archdischild-2021-321683

Author(s):

Richard Hansen ◽

Mona Bajaj-Elliott ◽

Georgina L Hold ◽

Konstantinos Gerasimidis ◽

Tariq H Iqbal ◽

...

Keyword(s):

Next Generation Sequencing ◽

Clinical Laboratory ◽

Next Generation ◽

Paediatric Practice ◽

Laboratory Tool ◽

Generation Sequencing

Download Full-text

Detection of Coccidioides posadasii in a patient with meningitis using metagenomic next-generation sequencing: a case report

BMC Infectious Diseases ◽

10.1186/s12879-021-06661-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yuqiao Mao ◽

Xia Li ◽

Haibo Lou ◽

Xiaoyu Shang ◽

Yanjun Mai ◽

...

Keyword(s):

Next Generation Sequencing ◽

Los Angeles ◽

Systemic Infection ◽

High Sensitivity ◽

Pathological Examination ◽

Next Generation ◽

Coccidioides Posadasii ◽

Dimorphic Fungi ◽

Almost All ◽

Generation Sequencing

Abstract Background Coccidioidomycosis is a systemic infection caused by dimorphic fungi Coccidioides spp. endemic to Southwestern United States and Central and South America. A history of residence and travel in these areas is essential for the diagnostic of coccidioidomycosis, which has highly variable symptoms ranging from asymptomatic to severe, disseminated infection, and even death. Immunocompromised patients of coccidioidomycosis experience a high risk of dissemination, chronic infection, and mortality. Meningitis is one of the most deleterious coccidioidomycosis and can cause various life-threatening complications. Case presentation Here we report a case of Coccidioides posadasii meningitis in a 49-year-old female who returned to China after one and a half years residence in Los Angeles, USA. The repeated routine cultures using CSF for bacteria or fungi were all negative. To hunt for an infectious etiology, the state-of-the-art technology metagenomic next-generation sequencing (mNGS) was then utilized, suggesting Coccidioides posadasii. Organizational pathological examination and polymerase-chain-reaction (PCR) results subsequently confirmed the mNGS detection. Conclusion To our knowledge, cases for coccidioidal meningitis have been rarely reported in China. While global travelling may spread this disease across continents and make the diagnosis more difficult. mNGS can detect almost all known pathogens with high sensitivity and specificity, especially for uncommon pathogen, such as Coccidioides posadasii in China.

Download Full-text

Implementation of Cloud based Next Generation Sequencing data analysis in a clinical laboratory

BMC Research Notes ◽

10.1186/1756-0500-7-314 ◽

2014 ◽

Vol 7 (1) ◽

pp. 314 ◽

Cited By ~ 15

Author(s):

Getiria Onsongo ◽

Jesse Erdmann ◽

Michael D Spears ◽

John Chilton ◽

Kenneth B Beckman ◽

...

Keyword(s):

Data Analysis ◽

Next Generation Sequencing ◽

Clinical Laboratory ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Generation Sequencing ◽

Sequencing Data Analysis

Download Full-text

Abstract 1506: Mutant enrichment by ICE COLD-PCR prior to the next-generation sequencing enables high sensitivity and high throughput detection of cancer biomarkers in patient samples

10.1158/1538-7445.am2014-1506 ◽

2014 ◽

Author(s):

Rui Lin ◽

Sarah Cherubin ◽

Courtney Cubrich ◽

Grant Wu ◽

Ben Legendre ◽

...

Keyword(s):

Next Generation Sequencing ◽

High Throughput ◽

High Sensitivity ◽

Cancer Biomarkers ◽

Next Generation ◽

High Throughput Detection ◽

Generation Sequencing

Download Full-text

Using Machine Learning to Identify True Somatic Variants from Next-Generation Sequencing

Clinical Chemistry ◽

10.1373/clinchem.2019.308213 ◽

2019 ◽

Vol 66 (1) ◽

pp. 239-246 ◽

Cited By ~ 1

Author(s):

Chao Wu ◽

Xiaonan Zhao ◽

Mark Welsh ◽

Kellianne Costello ◽

Kajia Cao ◽

...

Keyword(s):

Machine Learning ◽

Next Generation Sequencing ◽

Clinical Laboratory ◽

Next Generation ◽

Single Nucleotide Variants ◽

Test Set ◽

Clinical Laboratories ◽

Bona Fide ◽

Validation Set ◽

Generation Sequencing

Abstract BACKGROUND Molecular profiling has become essential for tumor risk stratification and treatment selection. However, cancer genome complexity and technical artifacts make identification of real variants a challenge. Currently, clinical laboratories rely on manual screening, which is costly, subjective, and not scalable. We present a machine learning–based method to distinguish artifacts from bona fide single-nucleotide variants (SNVs) detected by next-generation sequencing from nonformalin-fixed paraffin-embedded tumor specimens. METHODS A cohort of 11278 SNVs identified through clinical sequencing of tumor specimens was collected and divided into training, validation, and test sets. Each SNV was manually inspected and labeled as either real or artifact as part of clinical laboratory workflow. A 3-class (real, artifact, and uncertain) model was developed on the training set, fine-tuned with the validation set, and then evaluated on the test set. Prediction intervals reflecting the certainty of the classifications were derived during the process to label “uncertain” variants. RESULTS The optimized classifier demonstrated 100% specificity and 97% sensitivity over 5587 SNVs of the test set. Overall, 1252 of 1341 true-positive variants were identified as real, 4143 of 4246 false-positive calls were deemed artifacts, whereas only 192 (3.4%) SNVs were labeled as “uncertain,” with zero misclassification between the true positives and artifacts in the test set. CONCLUSIONS We presented a computational classifier to identify variant artifacts detected from tumor sequencing. Overall, 96.6% of the SNVs received definitive labels and thus were exempt from manual review. This framework could improve quality and efficiency of the variant review process in clinical laboratories.

Download Full-text

Digital PCR—An Emerging Technology with Broad Applications in Microbiology

Clinical Chemistry ◽

10.1373/clinchem.2019.304048 ◽

2019 ◽

Vol 66 (1) ◽

pp. 117-123 ◽

Cited By ~ 11

Author(s):

Stephen J Salipante ◽

Keith R Jerome

Keyword(s):

Next Generation Sequencing ◽

Quantitative Pcr ◽

Clinical Microbiology ◽

Clinical Laboratory ◽

Digital Pcr ◽

Emerging Technology ◽

Next Generation ◽

Powerful Technique ◽

Advantages And Disadvantages ◽

Generation Sequencing

Abstract BACKGROUND The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR. CONTENT Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing. SUMMARY dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.

Download Full-text