MICROBIAL TECHNOLOGY


information encoded in each amplification event (via real-time data), to identify the nature of nucleic acid molecules. The utility of a reliable and accurate high-level multiplexing capability in the diagnostic laboratory is clear.


Issues in sexual health Returning to the area of STIs mentioned above, a recent analysis by The Guardian of English council spending on sexual health services found national cuts of more than a third since 2013, despite a rise in consultations for STIs.3


English An acute case of gonococcal urethritis (Gram staining).


We are fortunate that Dr Alicia Demirjian from Evelina London Children’s Hospital and UKHSA has agreed to speak and explain the new five-year plan to us. Dr Demirjian is a consultant in paediatric infectious diseases and immunology at Evelina London Children’s Hospital, Guy’s and St Thomas’ NHS Foundation Trust, where she is the lead for paediatric antimicrobial stewardship, and deputy lead for infection prevention and control. In addition, she is a consultant epidemiologist in the UKHSA’s Healthcare-Associated Infection & Antimicrobial Resistance division and is an expert on the new five-year plan. In the previous article of this two- we described advances in


part review,2


rapid sequencing developed by Adela Alcolea-Medina, Lead, Next-Generation Sequencing, Infection Sciences, Synovis, St Thomas’ Hospital, London leading to the development of a unified metagenomic method for rapid detection of bacteria, fungi and viruses in clinical samples, but it should not be forgotten that PCR as a diagnostic tool, although well-established, is also rapidly advancing.


Multiplexing capability in diagnostics


Dr Rodriguez Manzano, Associate Professor in the Department of Infectious Disease at Imperial College London will be describing his work on infections and AMR using, among other approaches, a machine-learning method to develop high-level multiplexing in qPCR and dPCR. Dr Manzano is also a member of the National Institute for Health and Care Research (NIHR) Unit in Healthcare- Associated Infections and Antimicrobial Resistance, a partnership between Imperial College and the UKHSA,


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where he contributes to shaping the UK’s strategy for addressing the critical issue of AMR. The technology he and his unit have developed enables accurate multiplexing (up to 21 targets in a single well has been demonstrated). The patented approach enables the recognition of primer-characteristic molecular signatures. Hopefully this will lead to truly affordable solutions in established molecular tests, by effectively extracting the kinetic and thermodynamic information from existing real-time data. There is a huge amount of information contained in these data which is not visible to the end user in the clinical laboratory but is normally just seen in the form of a positive or negative result. This technology should enhance diagnostic performance and has the potential to vastly increase throughput by identifying multiple nucleic acid targets in a single amplification reaction. It is compatible with a wide range of amplification chemistries (eg probe-based, intercalating dyes, and isothermal reactions), and hence can be seamlessly integrated with various laboratory workflows. Multiplexing offers a solution that reduces the requirements in physical space, time- to-result, and volume of reagents and sample.


In the microbiology laboratory,


fluorescent probes are often used as markers and the number of targets is often limited by optical instrumentation and the small range of different wavelengths available for reporting. Alternative methods of detection such as post-amplification analysis may require lengthy gel-electrophoresis or expensive sequencing approaches. The technology leverages machine learning to automatically learn target-specific


councils spent £9.58 a head on sexual health services – including STI testing and treatment, contraception, and advice – in 2022–23, compared with £14.41 in 2013– 14, after taking inflation into account. The result of this is that people are being hospitalised for sexual health conditions that are easily treatable in local clinics. Nationally, the number of gonorrhoea and syphilis cases reached a record last year, with 146 gonorrhoea diagnoses per 100,000 people. That was up from 58 in 2013, while syphilis diagnoses increased from 6.4 to 15.4. Hospital figures show admissions for syphilis and Chlamydia doubled between 2013–14 and 2022–23, while gonorrhoea admissions tripled. Advice, prevention and promotion services have seen the largest cuts to funding, with net spending down 44% since councils were made responsible for public health in 2013. Meanwhile, STI testing and treatment fell by 33% and contraception spending fell by 30%. Of course, some of this fall in funding may be as a direct result of the more widespread introduction of cheaper tests that can be performed by online requesting of a test kit without the need for clinic attendance. It remains to be seen if the ambitious targets of the UKHSA AMR plan can be realised in the face of such cuts, which are of course not confined to the field of STI testing, treatment and contact tracing. The rise in the unnecessary hospitalisation of patients with disseminated gonococcal infection (DGI) referred to above poses its own particular problems. Diagnosis often has to rely on 16s rRNA sequencing of molecular specimens rather than culture. Here, there is no cultured isolate for phenotypic antimicrobial susceptibility testing (AST), therefore selection of an appropriate antibiotic therapy for DGI, or in other gonorrhoea infections where ceftriaxone is contraindicated, is challenging and relies on molecular methods.


Molecular approaches Dr Michelle Cole, Interim Head of the STI Reference Laboratory, UKHSA, will be reviewing some of the molecular


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