Environmental_reservoirs_of_Salmonella_Typhi_3

Background Standard food, water and environmental microbiology methods require the use of a three-step approach; two sequential broth cultures (enrichment and then selection) followed by culture on solid media prior to identification by biochemistry and serology. These methods have not been optimized for the isolation of S. Typhi, which is likely to be out-competed by E. coli. Although PCR has been used to infer the presence of S. Typhi in water (Karkey 2016) it is uncertain what the presence of DNA in water means and without the ability to culture bacteria, the latency of the pathogen in its environmental niche cannot be determined. Identification of viable bacteria in the environment is key to informing vaccine models. Goals and approaches 1. Novel microbiological approaches to isolating S. Typhi from the environment We will explore are a number of novel approaches that might facilitate the isolation of S. Typhi from the environment, including: (i)Large volume water filtration; permitting water volumes to be cultured that are x100 greater than in the past (ii)Techniques using novel culture media and procedures in collaboration developed at Sanger. (iii)The use of immunomagnetic bead separation to concentrate the low bacterial numbers (iv)The investigation of novel protist reservoirs i.e. Bodo saltans These techniques will be developed in the UK national Food, Water and Environment Laboratory at Public Health England, London, using spiked sewage samples from the UK, before being deployed in Malawi. 2. Using dynamic and geospatial modelling to inform sampling strategy and interpret results Preliminary spatial investigation: IDM will use existing data from an ongoing case control study funded by BMGF, plus geospatial and genomic data, to generate hypotheses to frame environmental sampling regarding areas of highest risk due to elevation, flow accumulation, or behavioral/demographic factors. Sampling site prioritization: Based on previously developed Polio sampling strategies, IDM will design an iterative sampling process integrating population density, water usage patterns, elevation and waterways, the typhoid case burden and S. Typhi genomics to maximize sampling resources and distinguish flows from reservoirs.