Point of care genomic tests in infectious disease

17 June 2019

This blog was written by Simran Goyal, a fourth year medical student at the University of Cambridge. Simran was on placement for her Student Selected Component (SSC) with us between 10 December 2018 and 8 February 2019 

Identifying the organisms responsible for many infectious diseases can rely on slow and costly laboratory methods. Faster methods of diagnosis could enable more prompt delivery of the right treatment, save costs to the healthcare system, and promote better infection control.

The principal aim of point-of-care (POC) tests is to support clinical decision-making by providing test results within a short timeframe. Consideration is needed as to whether such devices can be feasibly introduced into clinical practice and whether they are really more cost-effective than current methods.

What are point-of-care genomic tests for infectious diseases?

Public Health England defines POC tests as a “medical diagnostic test, performed at or near the site of patient care, undertaken by healthcare professionals who may not be trained laboratory staff. It is a test to support clinical decision making, and for which the results can be available in real time, usually in less than 90 minutes”. Most available POC genomic devices provide limited results indicating the presence or absence of a certain pathogen or antimicrobial resistance gene. Higher resolution devices are also being developed that sequence the whole genome, providing more information about the pathogen, such as its strain, known virulence factors and antimicrobial resistance genes. However these devices are not yet quick enough for POC use – current POC tests closest to clinical implementation provide limited results, but within the required timeframes. 

Potential uses of point-of-care testing

Identifying the cause of disease

Current practice: Lab-based phenotypic testing of bacteria requires bacteria to be grown in culture, which can take hours to days. Genomic approaches such as lab-based PCR are more commonly used for viruses.

Potential of POC: Speed is crucial in a clinical setting where decisions regarding patient management need to be made rapidly for optimal outcomes and to prevent the spread of infectious disease. Current technologies can test for a wide range of pathogens from different clinical samples, and yield results within an hour, with less than a minute of hands-on time (Cepheid, BioMerieux).

This technology could be used in GP practices, hospitals and pharmacies, allowing prompt diagnosis and treatment with antimicrobial drugs where appropriate.

Informing clinicians of which antimicrobial treatments to avoid

Current practice: Identifying antimicrobial resistance profiles is done by testing the susceptibility of bacteria to a range of antibiotic therapies in vitro.

Potential of POCTs: POC tests are fast and culture-free, unlike phenotypic methods which require organisms to be grown before tests can be carried out. Currently, they can be used to identify specified resistance genes. For example, Cepheid have developed the Xpert CARBA-R real-time PCR assay that allows rapid detection of organisms resistant to the antibiotic carbapenem – an antibiotic of last resort – indicating that strict infection control measures must implemented. Through curation of a centralised quality-controlled genetic database, more resistance genes may be discovered in bacterial genomes which could increase the clinical utility of POC tests in future.

The potential value of such a POC device is recognised by the £10m Longitudinal Prize fund that rewards a competitor who can develop a POC test to conserve antibiotics for future generations. The test must be accurate, rapid, affordable and easy to use anywhere in the world.

Strain tracking and outbreak surveillance

Potential of POC tests: Genomic technologies could be used in combination with epidemiology to help identify the source of a disease and its transmission between people, which can be used to inform infection control strategies. POC methods for surveillance are advantageous in urgent situations, such as tracking the source of influenza or MRSA outbreaks, or during the Ebola crisis.

Strain tracking would require high-resolution sequence data, in comparison to the other discrete POC tests already discussed. Currently, there is no test that can sequence the full genome of a pathogen quickly enough to be called point-of-care. Oxford Nanopore Technologies have developed a portable sequencing device called MinION which, although currently for research use only, could be used in clinical settings in the future. Using the MinION device, a research team developed a rapid sequencing pipeline which enabled phylogenetic analysis of human influenza viruses and tracking of disease transmission within 24 hours, demonstrating how scientists are developing methods to reduce turnaround time for WGS.  

POC tests in practice

Influenza

Pilots and randomised controlled trials of POC devices for diagnosing influenza have been conducted in a number of hospitals in the UK, with positive results. For example, Kingston Hospital adopted the Cobas Influenza A/B PCR-based test in winter 2017/18, which yielded benefits for bed management, targeted antiviral treatment, antimicrobial stewardship and infection control. The test has since been implemented into the emergency department and acute assessment unit at Kingston Hospital.

Other centres at which POC testing has been implemented include University Hospital Southampton Foundation NHS Trust, Sheffield Teaching Hospital NHS Trust, Public Health Wales and the Scottish Health Protection Network.

Although benefits have been reported from early-adopters of the POC technology, there is currently insufficient evidence on the cost-effectiveness of POCT testing to warrant wider implementation. Additionally, such benefits may be achieved by other means, for example through reconfiguration of existing services.

Clostridium difficile infection

A study conducted in a central London hospital has demonstrated the value of POC testing for detecting Clostridium difficile infection in shorter timeframes, which had the effect of reducing the time between sampling and availability of results from 18 hours to 1.85 hours. Staff reported that the device developed by Cepheid was easy-to-use and aided more effective bed management. In future, a device that screens for a broader range of pathogens could speed up the differentiation between infectious and non-infectious causes of diarrhoea.

Conclusions

Integrating POC devices into clinical practice has been shown to be feasible with many reported benefits. As well as hospitals, pharmacies are an accessible health provider where POC tests could have the greatest impact on patient care and containing the spread of infectious disease. However, more evidence is needed to assess the true benefit and cost-effectiveness of POC devices in clinical practice.

With expansion of pathogen genomic databases and continued improvements of POC technology to address the challenges of cost, speed, accuracy and ease-of-use, POC testing technology may yet have a place in infectious disease diagnostics in the future.


 

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