Escherichia coli Genome sequencing and assembly

A four-year surveillance diarrhea study (from January 2010 to July 2014) was conducted in 890 children <5-year-old that sought medical care for acute community-acquired diarrhea in Yucatan, Mexico. Stool samples from these children were analyzed for the presence of DEP, Campylobacter spp., Salmonella sp., Shigella spp., Vibrio cholerae sp. and rotavirus. The genomes of ten Diffusely Adherent E. coli (DAEC) and nine Enteroaggregative E. coli (EAEC) strains isolated from the most severe cases of this study were selected for whole genome sequencing, together with one EAEC strain isolated from a 56-year-old adult patient with acute diarrhea and one commensal E. coli from a healthy 2-year-old girl. These genomes were analyzed together with 85 previously sequenced E. coli genomes to study their phylogenetic distribution and the prevalence of different virulence genes among Diarrheagenic E. coli pathotypes (DEP).