Within-host Escherichia coli diversity in Nairobi.

This investigation explores the intra- and inter-species diversity and strain sharing of Escherichia coli in co-habiting humans and livestock in Nairobi, Kenya. Across six different households, putative E. coli is isolated in 2015 using eosin methylene blue agar from faecal samples or rectal swabs from two adult humans, one chicken and one goat. In 2016 ten putative E. coli colonies from each individual are resurrected and subject to additional culture-based identification using CHROMagar (France) one specimen is negative for E. coli on CHROMagar and excluded from further investigations. The remaining specimens are subject to whole genome sequencing via the Illumina HiSeq 2500. A total of 252 isolates are sequenced (231 in this investigation and 21 in BioProject PRJEB32607), including seven experimental replicates, three technical replicates, and three control specimens. Three specimens fail initial quality checks; one is identified as mixed species (E. coli and Proteus sp.) and two have insufficient read numbers. An additional specimen fails de novo assembly. Excluding the mixed-species specimen, all low-quality specimens are subject to re-sequencing on the Illumina Miseq, V3 2x300bp cartridge. One re-sequenced specimen again fails de novo assembly and is excluded from further analysis. De-duplication of replicates leaves 238 unique study specimens.