Agnostic sequencing for detection of viral pathogens

NPG Gauthier, SD Chorlton, M Krajden… - Clinical microbiology …, 2023 - Am Soc Microbiol
The advent of next-generation sequencing (NGS) technologies has expanded our ability to
detect and analyze microbial genomes and has yielded novel molecular approaches for …

Next-generation sequencing in clinical microbiology: are we there yet?

SL Mitchell, PJ Simner - Clinics in laboratory medicine, 2019 - labmed.theclinics.com
Next-generation sequencing (NGS) is a method that allows for high-throughput, massively
parallel sequencing of thousands to billions of DNA fragments independently and …

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

I Allali, RE Abotsi, LA Tow, L Thabane, HJ Zar… - Microbiome, 2021 - Springer
Background The role of the human microbiome in health and disease is an emerging and
important area of research; however, there is a concern that African populations are under …

Surveillance and diagnosis of west nile virus in the face of flavivirus cross-reactivity

Y Lustig, D Sofer, ED Bucris, E Mendelson - Frontiers in microbiology, 2018 - frontiersin.org
West Nile Virus (WNV) is an arthropod-borne flavivirus whose zoonotic cycle includes both
mosquitoes and birds as amplifiers and humans and horses as dead-end hosts. In recent …

Navigating clinical utilization of direct-from-specimen metagenomic pathogen detection: clinical applications, limitations, and testing recommendations

LM Filkins, AL Bryson, SA Miller, SL Mitchell - Clinical chemistry, 2020 - academic.oup.com
Background Metagenomic next generation sequencing (mNGS) is becoming increasingly
available for pathogen detection directly from clinical specimens. These tests use target …

Validation of the VirCapSeq-VERT system for differential diagnosis, detection, and surveillance of viral infections

V Kapoor, T Briese, A Ranjan… - Journal of Clinical …, 2024 - Am Soc Microbiol
There is a need in clinical microbiology and public health for assays that enable sensitive
and rapid detection of infectious agents. Next Generation Sequencing (NGS) is increasingly …

Metagenomics to assist in the diagnosis of bloodstream infection

AL Greninger, SN Naccache - The journal of applied laboratory …, 2019 - academic.oup.com
Background Metagenomic next-generation sequencing (mNGS) has emerged as a
promising technology that enables pan-pathogen detection from any source. However …

BacCapSeq: a platform for diagnosis and characterization of bacterial infections

OM Allicock, C Guo, AC Uhlemann, S Whittier… - MBio, 2018 - Am Soc Microbiol
We report a platform that increases the sensitivity of high-throughput sequencing for
detection and characterization of bacteria, virulence determinants, and antimicrobial …

Use of quantitative metagenomics next-generation sequencing to confirm fever of unknown origin and infectious disease

Y Dong, Y Gao, Y Chai, S Shou - Frontiers in Microbiology, 2022 - frontiersin.org
A body temperature> 38.3° C that lasts≥ 3 weeks and lacks a clear diagnosis after 1 week
of standard hospital examination and treatment is called “fever of unknown origin”(FUO) …

Viral capture sequencing detects unexpected viruses in the cerebrospinal fluid of adults with meningitis

F McGill, R Tokarz, EC Thomson, A Filipe, S Sameroff… - Journal of Infection, 2022 - Elsevier
Objectives Many patients with meningitis have no aetiology identified leading to
unnecessary antimicrobials and prolonged hospitalisation. We used viral capture …