MICROBIAL TECHNOLOGY
detecting all bacteria, DNA and RNA viruses and fungi in one simple, unified workflow. Additionally, bioinformatic analysis of sequencing data derived from metagenomics can predict antimicrobial resistance profiles, facilitating tailored treatment strategies and contributing to global efforts to combat antimicrobial resistance within the One Health framework. Results are obtainable within seven to eight hours. A trial of the use of the method is currently under way in several different ICUs in London, and she will present data on how the use of the method has helped patient management. In theory, clinical metagenomics (CMg) has the potential to revolutionise infectious disease diagnostics by rapidly identifying and characterising all pathogenic microorganisms in clinical samples within a few hours. This should be particularly helpful in lower respiratory tract infections (LRTI) that are serious and can be caused by a broad range of known and emerging bacterial, fungal and viral pathogens. The current diagnostic approach using a combination of culture for bacteria and targeted PCR for viruses, supplemented by antigen detection and other tests, is often unsatisfactory. It requires multiple assays, provides staggered results, and ultimately incomplete information, which causes residual uncertainty around diagnosis and patient and antibiotic management. Moreover, samples are typically processed in separate clinical microbiology and virology laboratories and may need additional testing by reference laboratories if a rarer or fastidious pathogen is suspected. One stage that is crucial is depletion of the human DNA, which may be present in very high concentration. There are many challenges to achieving this objective, given the heterogeneity of human samples and the need to focus on identifying DNA and RNA pathogens that have many different sizes and structures and are nearly always present in low abundance compared with the host’s cells.
Several human DNA depletion methods have been developed to increase sensitivity and reduce turnaround time (TAT) for detecting either DNA or RNA organisms in clinical samples using metagenomic techniques. These methods include physical separation by differential centrifugation, lysis of human cells using saponin, or other chaotropic agents. These methods allow bacteria, fungi or viruses to be successfully sequenced following human DNA depletion, but never all at the same time due to sample heterogeneity and fundamental differences in microbial cell morphology and abundance observed in clinical samples.
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Session chair Professor Brian Duerden (left) in discussion with this year’s speaker Ivor Mitchelmore in the trade show during a break in last year’s conference programme.
In this novel approach, a unified metagenomic method utilises a mechanical human DNA depletion method that allows detection of bacteria, fungi and viruses present in a sample. It uses bead-beating to selectively disrupt human cells and release human nucleic acid for enzymatic digestion, prior to microbial cell lysis and nucleic acid extraction, followed by reverse transcription and DNA PCR amplification before real-time nanopore sequencing. The innovative approach involves a slow centrifugation step and mechanical lysis via bead-beating. This technique effectively depletes human DNA while preserving microbial DNA and RNA. Coupled with nanopore sequencing, this approach streamlines the workflow, providing clinically actionable information within a seven-hour timeframe. This innovative metagenomic
approach holds promise in overcoming existing limitations. It offers a technically straightforward method for robust respiratory pathogen detection. The prospect of a single, unified metagenomic test holds significant utility in clinical settings. It provides rapid and comprehensive results, informing initial treatment decisions, local infection control, and national surveillance. While challenges such as cost, validation and accreditation persist, this workflow represents a substantial step forward in unlocking the full clinical potential of metagenomics in infectious disease diagnostics.
This rapidly emerging field of
RDTs using metagenomics in clinical microbiology presents both enormous opportunities but major challenges in implementation in the clinical laboratory. Addressing issues related to reagent DNA contamination, the removal of human DNA from specimens and cost barriers is imperative for the successful integration of metagenomics into routine clinical diagnostics. While continued research and technical improvements
will take place, the major challenges are arguably now in the area of validation and standardisation to further establish the clinical utility of metagenomics, and ensure that it contributes to improved patient outcomes and public health to the fullest possible extent. Nevertheless, we are conscious that for much of the world, there is no access to any laboratory facility for diagnostic tests, let alone RDTs. In complete contrast to the talk by Adela Alcolea- Medina, Ivor Mitchelmore, formerly chief biomedical scientist in microbiology at Luton and Dunstable Hospital, will talk about his experiences in helping to set up a laboratory from scratch in India, and how access to even the most basic blood culture system can have a major impact.
n This year’s conference is dedicated to the memory of Mahsa Amini, an Iranian student about to start a degree in microbiology but was arrested on 13 September 2022 for ‘improperly wearing the mandatory head covering’. She died in police custody several days later.
There will be another article written by BSMT chairman Dr Mark Wilks in the April issue of Pathology in Practice looking at some of the themes of the other talks. As always, this year’s BSMT conference will have a full trade show with 20 of the most innovative companies attending to present the latest developments and newest equipment to talk to delegates about what their company can offer laboratories.
The conference provides scientists the opportunity to discuss and debate their experiences and there will be ample opportunity to question the experts! Registration is now open. Book now to catch the early bird rate! Check the BSMT website (
https://www.bsmt.org.uk) to register and for updates to the programme.
www.bsmt.org.uk FEBRUARY 2024
WWW.PATHOLOGYINPRACTICE.COM
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