scholarly journals Utility of Whole-Genome Next-Generation Sequencing of Plasma in Identifying Opportunistic Infections in HIV/AIDS

2019 ◽  
Vol 13 (1) ◽  
pp. 7-11 ◽  
Author(s):  
Yang Zhou ◽  
Vagish Hemmige ◽  
Sudeb C. Dalai ◽  
David K. Hong ◽  
Kenneth Muldrew ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Opportunistic Infections ◽  
Case Series ◽  
Whole Genome ◽  
Next Generation ◽  
Invasive Procedures ◽  
First Case ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Hiv Aids

Background:AIDS-associated Opportunistic Infections (OIs) have significant morbidity and mortality and can be diagnostically challenging, requiring invasive procedures as well as a combination of culture and targeted molecular approaches.Objective:We aimed to demonstrate the clinical utility of Next-generation Sequencing (NGS) in pathogen identification; NGS is a maturing technology enabling the detection of miniscule amounts of cell-free microbial DNA from the bloodstream.Methods:We utilized a novel Next-generation Sequencing (NGS) test on plasma samples to diagnose a series of HIV-associated OIs that were diagnostically confirmed through conventional microbial testing.Results:In all cases, NGS test results were available sooner than conventional testing. This is the first case series demonstrating the utility of whole-genome NGS testing to identify OIs from plasma in HIV/AIDS patients.Conclusion:NGS approaches present a clinically-actionable, comprehensive means of diagnosing OIs and other systemic infections while avoiding the labor, expense, and delays of multiple tests and invasive procedures.

scholarly journals Rare Presentation of Toxoplasma Pneumonitis in the Absence of Neurological Symptoms in an AIDS Patient and Use of Next-Generation Sequencing for Diagnosis

2020 ◽  
Author(s):  
Moni Roy ◽  
Nikhut Siddique ◽  
Bindu Bathina ◽  
Sharjeel Ahmad
Keyword(s):  
Next Generation Sequencing ◽  
Opportunistic Infections ◽  
Miliary Tuberculosis ◽  
Neurological Symptoms ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Next Generation ◽  
Rare Presentation ◽  
Immunodeficiency Syndrome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Toxoplasma gondii is a known cause of encephalitis in human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) patients. Toxoplasma pneumonitis is a manifestation of extracerebral toxoplasmosis and can be clinically indistinguishable from other opportunistic infections including Pneumocystis jirovecii pneumonia (PJP) and miliary tuberculosis. In this case report, Toxoplasma pneumonitis and disseminated toxoplasmosis was diagnosed using next-generation sequencing (NGS) and polymerase chain reaction (PCR) assessment. NGS can detect microbial cell-free DNA (cfDNA) circulating in the plasma of over 1,000 pathogens. This case is a rare presentation of Toxoplasma pneumonitis in the absence of neurological symptoms and we discuss the use of NGS of microbial cfDNA and PCR tests that may be utilized for the timely diagnosis of such challenging cases.

scholarly journals Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018

2019 ◽  
Vol 24 (2) ◽  
Author(s):  
Anja Berger ◽  
Alexandra Dangel ◽  
Tilmann Schober ◽  
Birgit Schmidbauer ◽  
Regina Konrad ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Corynebacterium Diphtheriae ◽  
Whole Genome ◽  
Next Generation ◽  
Insect Bites ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

scholarly journals Next-Generation Sequencing-Based Molecular Diagnosis of Choroideremia

2015 ◽  
Vol 6 (2) ◽  
pp. 246-250 ◽  
Author(s):  
Kayo Shimizu ◽  
Akio Oishi ◽  
Maho Oishi ◽  
Ken Ogino ◽  
Satoshi Morooka ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Retinal Detachment ◽  
Macular Hole ◽  
Molecular Diagnosis ◽  
Novel Mutation ◽  
Case Series ◽  
Next Generation ◽  
Macular Hole Retinal Detachment ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

We screened patients with choroideremia using next-generation sequencing (NGS) and identified a novel mutation and a known mutation in the CHM gene. One patient presented an atypical fundus appearance for choroideremia. Another patient presented macular hole retinal detachment in the left eye. The present case series shows the utility of NGS-based screening in patients with choroideremia. In addition, the presence of macular hole in 1 of the 2 patients, together with a previous report, indicated the susceptibility of patients with choroideremia to macular hole.

scholarly journals Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 641
Author(s):  
Manasi Majumdar ◽  
Cristina Celma ◽  
Elaine Pegg ◽  
Krunal Polra ◽  
Jake Dunning ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sensitivity And Specificity ◽  
Severe Disease ◽  
Clinical Samples ◽  
Whole Genome ◽  
Next Generation ◽  
Coding Region ◽  
Diagnostic Laboratory ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

There are increasing concerns of infections by enteroviruses (EVs) causing severe disease in humans. EV diagnostic laboratory methods show differences in sensitivity and specificity as well as the level of genetic information provided. We examined a detection method for EVs based on next generation sequencing (NGS) analysis of amplicons covering the entire capsid coding region directly synthesized from clinical samples. One hundred and twelve clinical samples from England; previously shown to be positive for EVs, were analyzed. There was high concordance between the results obtained by the new NGS approach and those from the conventional Sanger method used originally with agreement in the serotypes identified in the 83 samples that were typed by both methods. The sensitivity and specificity of the NGS method compared to those of the conventional Sanger sequencing typing assay were 94.74% (95% confidence interval, 73.97% to 99.87%) and 97.85% (92.45% to 99.74%) for Enterovirus A, 93.75% (82.80% to 98.69%) and 89.06% (78.75% to 95.49%) for Enterovirus B, 100% (59.04% to 100%) and 98.10% (93.29% to 99.77%) for Enterovirus C, and 100% (75.29% to 100%) and 100% (96.34% to 100%) for Enterovirus D. The NGS method identified five EVs in previously untyped samples as well as additional viruses in some samples, indicating co-infection. This method can be easily expanded to generate whole-genome EV sequences as we show here for EV-D68. Information from capsid and whole-genome sequences is critical to help identifying the genetic basis for changes in viral properties and establishing accurate spatial-temporal associations between EV strains of public health relevance.

#40: Next-generation Sequencing Improves the Diagnosis of Uncommon Infection in children with Hematologic Malignancies: A Case Series Study

2021 ◽  
Vol 10 (Supplement_1) ◽  
pp. S2-S2
Author(s):  
Mi Zhou ◽  
Peifang Xiao ◽  
Hailong He ◽  
Jun Lu ◽  
Jie Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Symptoms ◽  
Case Series ◽  
Hematologic Malignancies ◽  
Next Generation ◽  
Promising Tool ◽  
Case Series Study ◽  
Next Generation Sequencing Ngs ◽  
Series Study ◽  
Generation Sequencing

Abstract Background Children with hematological malignancies are at high risk of infection. Various kinds of pathogens may cause infection in these patients. The effect of traditional methods on these patients is not ideal. Methods This was a case series study. The cases of five patients with clinical symptoms of pulmonary infection. Next-generation sequencing (NGS) was used to identify pathogens in these 5 patients. Results Uncommon pathogens were detected in five patients. Case information are shown in Table 1. Conclusion NGS may serve as a promising tool for rapid and accurate etiological diagnosis, which could greatly improve the diagnosis of uncommon infection in children with hematologic malignancies.

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