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Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing.
APMIS
January 2025
Department of Laboratory Medicine, Clinical Microbiology Örebro University Hospital and Faculty of Medicine and Health at Örebro University, Örebro, Sweden.
Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation.
View Article and Find Full Text PDFMultiple introductions of NRCS-A to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey.
Microb Genom
January 2025
Department of Microbiology, Oxford University Hospitals, Oxford, UK.
The NRCS-A strain has emerged as a global cause of late-onset sepsis associated with outbreaks in neonatal intensive care units (NICUs) whose transmission is incompletely understood. Demographic and clinical data for 45 neonates with and 90 with other coagulase-negative staphylococci (CoNS) isolated from sterile sites were reviewed, and clinical significance was determined. isolated from 27 neonates at 2 hospitals between 2017 and 2022 underwent long-read (ONT) (=27) and short-read (Illumina) sequencing (=18).
View Article and Find Full Text PDFA Comparison of Causative Pathogens in Bone and Prosthetic Joint Infections: Implications for Antimicrobial Therapy.
Antibiotics (Basel)
November 2024
The Bone Infection Unit, Nuffield Orthopaedic Centre, Oxford University Hospitals, Oxford OX3 7HE, UK.
: The microbiological profile of bone and joint infections is important for determining the empiric choice of both systemic and local antimicrobial therapy. This study assessed whether there was a difference in the bacterial species that were isolated on culture in osteomyelitis (OM), fracture-related infection (FRI) or prosthetic joint infection (PJI). This was a retrospective, observational cohort study of patients who had surgical intervention for PJI or OM or FRI with a positive microbial culture between 2019 and 2022.
View Article and Find Full Text PDFThe importance of microbiology reference laboratories and adequate funding for infectious disease surveillance.
Lancet Digit Health
December 2024
Nuffield Department of Population Health, University of Oxford, Oxford, UK. Electronic address:
Microbiology reference laboratories perform a crucial role within public health systems. This role was especially evident during the COVID-19 pandemic. In this Viewpoint, we emphasise the importance of microbiology reference laboratories and highlight the types of digital data and expertise they provide, which benefit national and international public health.
View Article and Find Full Text PDFComprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology.
Genome Med
December 2024
Institute of Population of Health Sciences, National Health Research Institutes, Miaoli County, Zhunan, Taiwan.
Background: Blood cultures are essential for diagnosing bloodstream infections, but current phenotypic tests for antimicrobial resistance (AMR) provide limited information. Oxford Nanopore Technologies introduces nanopore sequencing with adaptive sampling, capable of real-time host genome depletion, yet its application directly from blood cultures remains unexplored. This study aimed to identify pathogens and predict AMR using nanopore sequencing.
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