NIHR | Manchester Biomedical Research Centre

UK-wide implementation of a novel NHS diagnostic test using pyrosequencing

Research funded by Manchester BRC has led to UK-wide implementation of a novel NHS diagnostic test that uses pyrosequencing (a method of identifying genetic markers in DNA), to identify the right treatment for people with aspergillosis.

Aspergillosis is a serious respiratory infection caused by Aspergillus mould that can affect people with a weakened immune system, damaged lungs or allergies. Invasive aspergillosis (IA) can cause death within a few days to weeks, while chronic pulmonary aspergillosis (CPA) and allergic bronchopulmonary aspergillosis (ABPA) are progressive conditions causing gradual destruction of airways.

Aspergillosis rates have increased in recent years, with 200,000 CPA and 1,062,000 ABPA cases in Europe alone, and 50-85 per cent CPA mortality within 5 years.

Standard treatment is the triazole class of antifungal drugs. However, growing numbers of studies show a transcontinental trend in resistance to these medicines due to long treatment courses (CPA requires at least six months therapy) and agricultural use – with a slow rate of new treatments available.

Professor Malcolm Richardson, NIHR Manchester BRC project lead in fungal research and Consultant Clinical Scientist in Mycology at Wythenshawe Hospital said: “Early and accurate diagnosis of antifungal resistance is vital to improve patient outcomes now, and in the future. This is why Manchester BRC set out to find a way to detect this antifungal resistance in patients with aspergillosis that could be applied as part of routine clinical care.”

The research compared the pyrosequencing technique against high volume cultures (HVC).

HVCs are grown in the laboratory from mould present in a patient’s sputum (saliva and mucus). It can take 10 days for enough culture to grow for analysis of antifungal resistance and in some case the culture might not grow at all. The pyrosequencing procedure can be carried out from start to finish in three to four days


The novel pyrosequencing test analyses the genetic molecules (DNA) of the Aspergillus mould, taken directly from a patient’s sputum and can detect mutations in the fungus that reveal if it will be resistant to certain antifungal drugs.

In one comparison example, around 50 per cent of samples from patients with CPA who were failing on treatment did not grow a culture so conventional antifungal testing was not possible. However, pyrosequencing allowed detection of mutations in the DNA of Aspergillus directly in the clinical sample.

The National Aspergillosis Centre (NAC) consults on approximately 500 CPA patients annually. Dr Caroline Baxter, Acting Clinical Director of the NHS National Aspergillosis Centre (NAC) said: “The importance of the introduction of this test in the NHS cannot be underestimated, not just for the clear patient benefits it brings, but for the major impact it has on the long-standing challenge of early detection of antifungal resistance. This test allows for prompt recognition of antifungal resistance and will quickly give doctors the information they need to plan the most effective treatment for their patients.”

The test was accredited by UKAS in summer 2019. The NHS Mycology Reference Centre Manchester (MRCM) is delivering the service for UK and European clinical teams and is ideally positioned to provide this diagnostic as it provides fungal diagnostics as a hub laboratory to several UK satellite aspergillosis clinics.

The MRCM and the NAC are currently in discussions with NHS England Specialist Services Commissioners regarding the expansion of these services.

Deciphering Aspergillus fumigatus cyp51A-mediated triazole resistance by pyrosequencing of respiratory specimens has been published in the Journal of Antimicrobial Chemotherapy.