Critical Assessment of Metagenome Interpretation: the second round of challenges

Nature Methods, Год журнала: 2022, Номер 19(4), С. 429 - 440

Опубликована: Апрель 1, 2022

Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative Critical Assessment Metagenome Interpretation (CAMI). The CAMI II challenge engaged community to assess methods on realistic complex datasets with long- short-read sequences, created computationally from around 1,700 new known genomes, as well 600 plasmids viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due long-read data. Related strains still challenging assembly genome recovery through binning, was quality latter. Profilers markedly matured, taxon profilers binners excelling at higher bacterial ranks, but underperforming viruses Archaea. Clinical pathogen detection revealed a need improve reproducibility. Runtime memory usage analyses identified efficient programs, including top performers other metrics. identify challenges guide researchers selecting analyses.

Язык: Английский

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Clinical Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-Free DNA for the Diagnosis of Infectious Diseases: A Multicenter Retrospective Cohort Study

Clinical Infectious Diseases, Год журнала: 2020, Номер 72(2), С. 239 - 245

Опубликована: Янв. 13, 2020

Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as an attractive diagnostic modality allowing broad-range pathogen detection, noninvasive sampling, and earlier diagnosis. However, little is known about its real-world clinical impact used in routine practice.We performed a retrospective cohort study all patients for whom mNGS (Karius test) was indications at 5 United States institutions over 1.5 years. Comprehensive records review performed, standardized assessment the based on treating team's interpretation Karius results patient management established.A total 82 tests were evaluated from 39 (47.6%) adults 43 (52.4%) children 53 (64.6%) immunocompromised patients. positivity rate 50 (61.0%), with 25 (50.0%) showing 2 or more organisms (range, 2-8). The test led to positive 6 (7.3%), negative 3 (3.7%), no 71 (86.6%), indeterminate (2.4%). Cases result involved bacteria and/or fungi but not viruses parasites. In 10 who underwent 16 additional repeated tests, only 1 associated impact.The currently practice limited. Further studies are needed identify high-yield populations, define complementary role conventional microbiological methods, discern how best integrate into current testing algorithms.

Язык: Английский

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Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

BMC Microbiology, Год журнала: 2021, Номер 21(1)

Опубликована: Янв. 26, 2021

Abstract Background Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing the 16S ribosomal RNA (rRNA) gene proven to be a powerful strategy for taxonomic classification bacteria. This study aims improve method full-length rRNA analysis using nanopore long-read sequencer MinION™. We compared it conventional short-read mock community human fecal samples. Results modified our existing protocol amplicon by A new library construction with an optimized primer set overcame PCR-associated bias enabled across broad range species. performance gut microbiota composition. The relative abundance dominant genera was highly similar between sequencing. At species level, MinION™ had better resolution discriminating members particular taxa such as Bifidobacterium , allowing accurate representation sample Conclusions Our present microbiome study, comparing discriminatory power sequencing, clearly illustrated analytical advantage gene.

Язык: Английский

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Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

GigaScience, Год журнала: 2019, Номер 8(8)

Опубликована: Июль 30, 2019

Abstract Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well track the population levels established or endemic pests. Where these traps have low specificity and capture non-target species in excess target pests, need extensive specimen sorting identification creates a major diagnostic bottleneck. While recent development standardized molecular diagnostics has partly alleviated this requirement, single per reaction nature methods does not readily scale sheer number insects trapped programmes. Consequently, lists often restricted few high-priority allowing unanticipated avoid detection potentially establish populations. DNA metabarcoding recently emerged method conducting simultaneous, multi-species complex mixed communities may lend itself ideally rapid bulk trap samples. Moreover, high-throughput sequencing platforms could enable multiplexing hundreds diverse samples on flow cell, thereby providing means dramatically up terms both quantity that can be processed concurrently pest targeted. In review literature, we explore how tailored context highlight unique technical regulatory challenges must considered when implementing technologies into sensitive applications.

Язык: Английский

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Drug-Resistant Fungi: An Emerging Challenge Threatening Our Limited Antifungal Armamentarium

Antibiotics, Год журнала: 2020, Номер 9(12), С. 877 - 877

Опубликована: Дек. 8, 2020

The high clinical mortality and economic burden posed by invasive fungal infections (IFIs), along with significant agricultural crop loss caused various species, has resulted in the widespread use of antifungal agents. Selective drug pressure, attributes, host- drug-related factors have counteracted efficacy limited systemic drugs changed epidemiological landscape IFIs. Species belonging to Candida, Aspergillus, Cryptococcus, Pneumocystis are among pathogens showing notable rates resistance. Drug-resistant fungi from environment increasingly identified settings. Furthermore, we a understanding class-specific resistance mechanisms emerging Candida species. establishment stewardship programs both fields inclusion species identification, susceptibility testing, therapeutic monitoring practices clinic can minimize emergence drug-resistant fungi. New featuring promising profiles great promise treat setting. Mitigating tolerance, prelude resistance, also requires development effective fungal-specific adjuvants be used combination antifungals.

Язык: Английский

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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

Briefings in Bioinformatics, Год журнала: 2020, Номер 22(2), С. 616 - 630

Опубликована: Окт. 8, 2020

Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding evolution of infectious agents, investigating spread transmission chains outbreaks, as well facilitating development effective rapid molecular diagnostic tests contributing to hunt treatments vaccines. The ongoing COVID-19 pandemic poses one greatest global threats modern history has already caused severe social economic costs. efficient methods reconstruct genomic sequence SARS-CoV-2, etiological agent COVID-19, fundamental design devise measures mitigate diffusion pandemic. Diverse approaches can, testified by number available sequences, be applied SARS-CoV-2 genomes. However, each technology approach its own advantages limitations. In current review, we will provide a brief, but hopefully comprehensive, account currently platforms methodological We also present an outline repositories databases that access data associated metadata. Finally, offer general advice guidelines appropriate sharing deposition metadata, suggest more standardized integration future SARS-CoV-2-related would greatly facilitate struggle against this new pathogen. hope our 'vademecum' production handling data, contribute objective.

Язык: Английский

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Healthcare-associated infections in adult intensive care unit patients: Changes in epidemiology, diagnosis, prevention and contributions of new technologies

Intensive and Critical Care Nursing, Год журнала: 2022, Номер 70, С. 103227 - 103227

Опубликована: Март 3, 2022

Язык: Английский

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Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Nature Microbiology, Год журнала: 2020, Номер 5(3), С. 443 - 454

Опубликована: Янв. 13, 2020

Язык: Английский

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The diagnostic value of metagenomic next⁃generation sequencing in infectious diseases

BMC Infectious Diseases, Год журнала: 2021, Номер 21(1)

Опубликована: Янв. 13, 2021

Abstract Background Although traditional diagnostic techniques of infection are mature and price favorable at present, most them time-consuming with a low positivity. Metagenomic next⁃generation sequencing (mNGS) was studied widely because identification typing all pathogens not rely on culture retrieving DNA without bias. Based this background, we aim to detect the difference between mNGS method, explore relationship results severity, prognosis infectious patients. Methods 109 adult patients were enrolled in our study Shanghai Tenth People’s Hospital from October 2018 December 2019. The results, negative predictive values, positive false rate, pathogen sample types analyzed by using both methods. Then, samples clinical information 93 infected group (ID) collected. According whether detected pathogens, ID divided into 67 cases 26 cases. Peripheral blood leukocytes, C-reactive protein (CRP), procalcitonin (PCT) neutrophil counts measured, concentrations IL-2, IL-4, IL-6, TNF-α, IL-17A, IL-10 INF-γ serum determined ELISA. correlation detection severity illness, hospitalization days, mortality analyzed. Results assigned (ID, 92/109, 84.4%), non-infected (NID, 16/109, 14.7%), unknown (1/109, 0.9%). Blood abundant type 37 cases, followed bronchoalveolar lavage fluid 36 tissue, sputum, pleural effusion, cerebrospinal (CSF), pus, bone marrow nasal swab. In group, majority diagnosed lower respiratory system infections (73/109, 67%), bloodstream infections, effusion central nervous infections. sensitivity significantly higher than that method (67.4% vs 23.6%; P < 0.001), especially ( = 0.002), 0.001) sputum 0.037), while specificity different (68.8% 81.3%; 0.41). number hospitals stays 28-day-motality those statistically significant 0.05). Age multivariate logistic analyses mNGS. Conclusions found had blood, samples. And hospital stay, 28-day-mortality, which means nucleic acid sequences may be potential high-risk factor for poor has value. MNGS should used more early diagnosis future.

Язык: Английский

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A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready?

Frontiers in Microbiology, Год журнала: 2020, Номер 10

Опубликована: Янв. 14, 2020

Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously-ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection identification of the causative agent, resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation results should be according context. Where IFD differential diagnosis, panfungal PCR assays allow rapid detection/identification species directly from specimens with specificity; sensitivity also high when hyphae seen specimen paraffin-embedded tissue. Aspergillus on blood fractions screening high- risk haematology patients negative positive predictive values 94% 70%, respectively two obtained. The standardisation, commercialisation has now enabled direct comparison between laboratories commercial offering simultaneous common azole mutations. Candida not as well standardised only FDA-approved system (T2Candida) detecting five most species; whilst T2Candida outperforms culture candidaemia, its role routine diagnostics defined. There growing use Mucorales-specific detect selected genera fractions. Quantitative real-time Pneumocystis jirovecii PCRs replaced microscopy immunofluorescent stains many distinguishing infection may problematic non HIV-infected patients. For isolates, DNA barcoding dual loci (ITS TEF1α) offer optimal accuracy next generation sequencing technologies highly discriminatory analysis genetic diversity outbreak investigation, drug characterisation. Advances molecular will further enhance diagnostics.

Язык: Английский

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