Using PCR in microbiome research

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Using PCR in microbiome research

The make-up and balance of the microbiome (the total of all the microorganisms that live in or on us) is taking a more and more significant role in human health, with links to periodontitis, obesity, cardiovascular disease and inflammatory bowel disease, as well as potentially life-threatening infections such as Clostridium difficile. Researchers at the Mayo Clinic in the US have used PCR (polymerase chain reaction) to find out more about C difficile in the gut, as well as looking at the potential of the technology to help prevent infection in hospital.

Scanning electron micrograph of C difficile bacteria from a stool sample - image credit: CDC/Lois S. Wiggs (PHIL #6260)

Scanning electron micrograph of C difficile bacteria from a stool sample – image credit: CDC/Lois S. Wiggs (PHIL #6260)

Clostridium difficile is naturally found in the gut in around 3% of the adult population, and in seven out of 10 babies. Normally it is kept in balance by other bacteria, but in some situations, such as after antibiotic treatment, the levels of C difficile get out of control. This can lead to severe diarrhoea and pseudomembranous colitis, which can be life-threatening. C difficile is the leading cause of healthcare-associated diarrhoea.

In the study, which was published in AJIC: American Journal of Infection Control, patients without symptoms of C difficile infection who were admitted to a Minnesota tertiary care hospital had their stools tested for toxigenic C difficile. This used a real-time PCR assay to detect tcdC, a factor that regulates the bacteria’s expression of toxins. Around one in 10 of the people tested were positive for toxigenic C difficile, meaning that they were carrying the bacteria but showed no symptoms. The researchers also looked at the risk factors that may increase people’s risk of carrying the bug, and the top ones were recent hospitalization, chronic dialysis and corticosteroid use.

It’s important to know which patients are carrying Clostridium difficile so that they can be monitored for signs of diarrhoea and be treated early, and so that staff can take infection prevention measures to avoid transmitting the bacteria to other vulnerable patients. Knowing about the risk factors could mean that the focus is on these patients, who make up half of the hospital population but three-quarters of the C difficile carriers, rather than having to screen all patients on admission. This would cut costs and save time for laboratory and healthcare staff, and save patients having to go through stool sample collection unnecessarily.

Previous tests for C difficile have been lengthy and labour-intensive, but using real-time PCR could make routine testing feasible, both for research purposes and for practical clinical applications.


Suzanne Elvidge is a freelance science, biopharma, business and health writer with more than 20 years of experience. She has written for a range of online and print publications including FierceBiomarkers, FierceDrugDelivery, European Life Science, the Journal of Life Sciences (now the Burrill Report), In Vivo, Life Science Leader, Nature Biotechnology, New Scientist, PR Week and Start-Up. She specialises in writing on pharmaceuticals, biotechnology, healthcare, science, lifestyle and green living, but can write on any topic given enough tea and chocolate biscuits. She lives just beyond the neck end of nowhere in the Peak District with her second-hand bookseller husband and two second-hand cats.

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