Practical training in molecular DNA diagnostics

Russ Stothard, Jaco Verweij, Lucas Cunningham and Mike Osei-Atweneboana

Developing our research theme on molecular diagnostics for soil-transmitted helminthiasis and schistosomiasis, COUNTDOWN organised a 1-week practical training session on real-time PCR assays within the laboratory of Mike Osei-Atweneboana.

The course was attended by 16 researchers from the Noguchi Memorial Institute for Medical Research (NMIMR), Ghana Health Services (GHS) and Council for Scientific and Industrial Research (CSIR), which aimed to consolidate and develop their existing experience and skills. The course started on the afternoon of 14th March with formal introductions from Drs Mike Osei-Atweneboana, Nana Biritwum and Margaret Gyapong, then overview lectures by Russ and Jaco on the importance of molecular diagnostics and its application within the COUNTDOWN consortium.

The week was divided into daily lectures with ample time at-the-bench for hands on training in: genomic DNA extraction from stool, design and application of TaqMan® assays for detection of parasites and pathogens, actual data collection using duplex/multiplex assay formats on a test panel of known samples and discussion on the optimisation of TaqMan® assays. Both Jaco and Lucas were able to each provide ‘tips-and-tricks’ with general trouble shooting advice on each method used. The importance of good laboratory practice was stressed throughout. This covered how the laboratory should be organised and how each workflow should be arranged to minimise contamination; how an appropriate inventory system should be developed to track the clinical results as each assay was performed.

Typically, as each laboratory/researcher has a slightly different way of doing things adhering to best clinical practice can be problematic. Putting theory into practice in sub-Saharan Africa settings is even more challenging for there are often daily hurdles both in logistics and infrastructures to overcome. We experienced several first-hand, for example, after torrential rains on the Monday evening, downed trees on the CSIR site cut laboratory electrical grid supplies needing essential outside repairs. Throughout the morning and the following day alternative power supplies, featuring both solar and portable generators, were used.

Strengthening the collaboration between the CSIR and NMIMR after initial visit of Dr Emily Adams last summer, we made a visit to see Drs John Odoom and Jacob Barnor and discuss the Polio screening programme. By good fortune we also met with new colleagues at NMIMR who were using real-time PCR to examine cervical biopsies for Human Papilloma Virus (HPV). It came as a surprise that they were unaware of female genital schistosomiasis (FGS). This was likely due to the traditional division between virology and parasitology but by adding real-time PCR assays it would be possible to tackle FGS in routine screening of biopsy material using this DNA detection platform.

Bridging this health services gap with a newly identified solution, and using assays taught in our course, we would hope to provide a more holistic appraisal of genito-urinary tract disease in Ghana. Undoubtedly, this could give a new overview of FGS in Ghanaian women and identify their currently unmet treatment needs for schistosomiasis. On further discussions later in the week with Dr Kofi Effah, a gynaecologist working in Battor, Lake Volta Region, there is an exciting opportunity for COUNTDOWN to foster much greater concerted action on FGS across the Ghanaian health sector.

The importance of good preparation in quality clinical diagnostics

It is said that prior planning prevents poor performance, so we were pleased to be joined in Liverpool by our colleague Jaco Verweij who is supporting the qPCR workshop which will take place in Ghana later in the month. As head of the clinical molecular diagnostics facility at Tilburg, Dr Verweij has developed an automated laboratory system that is capable of processing 100,000 samples a year with 45 multiplex DNA assays targeting a wide range of pathogens from multiple sample sources from blood to faecal.

As well as leading this state of the art molecular lab in the Netherlands he shares the same vision as COUNTDOWN, in terms of the need to scale up capacity in the Africa region.  During molecular workshops in Africa, he helped others to specialise in the use of Taqman® multiplex assays to identify some of the more damaging worm infections: from schistosomiasis to soil-transmitted helminthiasis.  With a higher diagnostic specificity and sensitivity than traditional parasitological methods these Taqman® assays use real-time polymerase chain reaction (qPCR) platforms. Adopting these methods allows for the development of a more detailed and accurate epidemiological picture several worm infections, strongyloidiasis in particular.

At the Ghana workshop a series of seminars and laboratory work will give the participants the skills and background knowledge to carry out faecal DNA extraction, qPCR, and the subsequent analysis of the results. The workshop will lay the ground work in skills development for the subsequent COUNTDOWN milestones for both the filariasis and helminth work as well as providing the skilled staff at the Global Polio Laboratory Network and the Council for Scientific and Industrial Research with the opportunity to increase their diagnostic horizons. We look forward to an exciting and productive trip that will sow the seeds for future work in the country.