MICROBIAL TECHNOLOGY
ongoing but reassuringly in 701 samples to date only one case of ceftriaxone resistance has been detected. While the study continues, these early data suggest that there is not currently a high level of undetected ceftriaxone-resistant gonorrhoea widely circulating in the UK. Dr Cole provided an insightful and thought-provoking update on antimicrobial resistance in STIs. It demonstrated both the importance of real-time surveillance and the role that molecular techniques can have in providing both epidemiological data and detecting resistance mechanisms. This is particularly crucial in pathogens that either do not grow easily or at all in culture and those for which culture recovery rates are low due to their fastidious nature.
Mycoplasma genitalium is increasingly
recognised as a pathogen of concern in this area. As the organism is difficult to culture, its diagnosis and resistance detection are generally determined through molecular techniques. This has shown very high levels of resistance to azithromycin, which is the first- line treatment. Similarly high levels of macrolide resistance have been confirmed in Treponema pallidum. Antimicrobial resistance in STIs remains a topic of significant concern, one which
is unlikely to go away any time soon, and will require coordination between many different strands of healthcare to control and mitigate.
Towards practical metagenomics
After lunch Adela Alcolea-Medina, Lead, Next-Generation Sequencing, Infection Sciences, Synnovis, St Thomas’ Hospital, London, who had previously spoken at a BSMT meeting two years ago, presented her evaluation of a single unified metagenomic method for the rapid detection of bacteria, fungi and viruses in clinical samples, which has just been published.1
This method also had
the potential to detect AMR genes. As it is now well known, next-generation sequencing allows thousands to billions of DNA fragments to be simultaneously and independently sequenced. In theory, this should allow an ‘agnostic’ approach for the detection of pathogens, and sequencing all the nucleic acids present in the sample should provide an unbiased answer regardless of any preheld beliefs on the likely pathogen. One of the problems is that current methods for clinical metagenomics with a short turnaround time are only able to detect DNA- or RNA-containing microorganisms, but not both. Existing
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methods for the detection of RNA and DNA tend to take several days to provide results. This is mainly due to the huge quantity of human DNA in clinical samples, which is orders of magnitude higher than that of any pathogen. The method adopted by the St Thomas’ group is to deplete human DNA in the sample before sequencing, thus increasing sensitivity and reducing turnaround time. Details of the methods are described in the forthcoming paper in Nature Communications Medicine, but essentially use a low- speed centrifugation step to sediment human cells and then endonuclease treatment of the supernatant. This is followed by DNA and RNA extraction, a reverse transcriptase step leading to double-strand synthesis of DNA. A simple library preparation is followed by sequencing using the Oxford Nanopore technology. This involves very low capital expenditure as it does not need the purchase of a large, standalone DNA sequencer. Preliminary results can be obtained after as little as 30 minutes sequencing and there is no need to batch a large number of samples together to achieve economies of scale. Adela Alcolea-Medina described some uses of the method in clinical applications during the monkeypox
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3 Immediate stabilisation of the calprotectin 3 Transportation stability for 7 days at ambient
3 On receipt it is ready to vortex, centrifuge and load onto the analyser
3 Survey has demonstrated high acceptance and ease of use for patients
3 Study has shown good correlation with the lab method
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alphalabs.co.uk/calex-pack Phone: 023 8048 3000 Email:
sales@alphalabs.co.uk WWW.PATHOLOGYINPRACTICE.COM AUGUST 2024 01- CALEX Patient Packs - Updated July
2024.indd 1 11/07/2024 15:59:25 17
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