“…DNA and RNA from infant and animal faeces is analysed as previously described using microfluidic TaqMan Array cards containing primers and probes for Norovirus GI and GII, adenovirus 40/41, Sapovirus , Enterovirus , Rotavirus, Salmonella enterica , Shigella/EIEC backbone, Shigella/EIEC plasmid, Campylobacter jejuni/coli, Listeria monocytogenes, Clostridium difficile , Helicobacter pylori , enterotoxigenic Escherichia coli LT/ST, enteropathogenic E. coli , enteroaggregative E. coli and Shiga-like toxin-producing E. coli stx1/stx2, Enterocytozoon bieneasi , Giardia , Cryptosporidium spp., Entamoeba histolytica and the MS2 extrinsic control. Most of these pathogens were selected based on prior evidence that they are commonly transmitted in Kenya, with a few like H. pylori and L. monocytogenes being selected based on potential of transmission 68–70. The TaqMan assays are run on a QuantiStudio 12K Flex Real-Time PCR System (ThermoFisher, Chicago, Illinois).…”