Dr. Thushan de Silva, Dr. Abdul Karim Sesay, Helen Brotherton, and Prof. Beate Kampmann of the Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine have received a Grand Challenges Exploration Award to develop a novel metagenomic approach to detect infectious pathogens in hospitalised preterm neonates in The Gambia.
In order to identify and treat existing and emergent infectious disease efficiently, clinicians and the global health community must have access to accurate and timely estimates of disease burden and distribution. Traditionally, summaries of these data have been manually reported by national health ministries from regional clinical data, aggregated from local health centers

Recognizing barriers for adoption of next-generation sequencing in global health, the Bill & Melinda Gates Foundation has partnered with the Chan Zuckerberg Biohub and the Chan Zuckerberg Initiative to enable patients in low- and middle-resource settings to benefit from cutting-edge pathogen detection and discovery.

Over one million neonates die from complications of being born too soon each year, with a substantial proportion caused by infections, including multi-drug resistant (MDR) Enterobacteriaceae. Rapid and accurate diagnostics need to be urgently developed for timely and effective treatment, to block disease spread and improve neonatal outcomes.

The team, led by Dr. de Silva, will test the potential for next generation sequencing to overcome this challenge by conducting a pilot study using carriage and invasive samples from hospitalised preterm neonates with suspected infections, nested within an ongoing MRCG at LSHTM based clinical trial (eKMC; clinicaltrials.gov NCT 0355598), conducted at the national neonatal unit at the Edward Francis Small Teaching Hospital by Dr. Brotherton and her team.

The iSeq100 next generation sequencing platform will be provided as part of the grant and will add to the expanding genomic capacity at MRC Unit The Gambia at LSHTM. The team will optimise protocols for detecting pathogens from a range of sample types and develop methods to specifically detect MDR-Enterobacteriaceae. MRCG at LSHTM scientific staff will receive highly specialised training in bio-sample preparation and sequencing at the Chan-Zuckerberg Biohub, in addition to learning to use the open-source IDseq software.

In addition to generating much needed local data on aetiology of neonatal infections, the team plans to use the pilot study findings to develop national and regional neonatal surveillance networks to perform next generation sequencing for insight into MDR-Enterobacteriacae carriage and invasive disease.

The Grand Challenges is an initiative fostering innovation to solve key global health and development problems. Each initiative is an experiment in the use of challenges to focus innovation on making an impact. Individual challenges address some of the same problems, but from differing perspectives.