What question did this study set out to answer?

To demonstrate the use of whole genome sequencing for detecting antimicrobial resistance genes in multiply resistant bacteria.

February 22, 2026

In-house whole genome sequencing of multiply resistant bacteria by Oxford Nanopore to detect antimicrobial resistance genes: proof of concept

Key Points

To demonstrate the use of whole genome sequencing for detecting antimicrobial resistance genes in multiply resistant bacteria.
In-house whole genome sequencing performed using Oxford Nanopore technology.
Targeted detection of antimicrobial resistance genes in clinical samples.
Assessment of typical turnaround times compared to traditional PCR methods.
Whole genome sequencing enables faster identification of antimicrobial resistance genes.
It provides a potential solution to missed detection of new or imported AMR genes.
Results facilitate improved infection prevention and control practices.

Abstract

Multiply resistant organisms (MROs) are of increasing global concern. Patients colonised with MROs may have harder-to-treat infections, increased complications, longer hospital stays, higher morbidity and higher mortality. Detection of antimicrobial resistance (AMR) genes can help inform infection prevention and control practices, detect clusters/outbreaks, and inform antibiotic choice for the individual patient. However, these tests are typically performed by PCR, so may miss new or imported AMR genes, and whole genome sequencing is expensive and somewhat slow for non-reference laboratories, with 1–2-week turnaround times being typical.

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Cite This Study

Prabhakar et al. (Sun,) studied this question.

synapsesocial.com/papers/699a534bfdaf4e3c1268eec5 https://doi.org/https://doi.org/10.1016/j.pathol.2026.01.324

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