Analysis of ESKAPEE Pathogens in a Longitudinal Study of Mother and Child Fecal Microbiomes

Background and Question
Enteric pathogens are major causes of mortality worldwide, especially in children in industrializing countries (1–3). Bacteria such as Enterococcus faecium, Escherichia coli, Salmonella enterica, and viral pathogens such as Norovirus, can be responsible for these infections. These microbes represent major global threats to human health, with E. faecium and E. coli being members of the “ESKAPEE” group (E. faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and E. coli), pathogens with high infection and mortality rates and high rates of antibiotic resistance (4). Early infection with enteric pathogens can have profound effects on child development, including both cognitive and physical, and chronic downstream effects such as diarrhea, which can significantly alter the patient’s microbiome or result in death. There have been some recent efforts to characterize the impacts of enteric pathogens, such as E. coli, on childhood infections (1,3,5), which have uncovered unexpected co-occurrence of bacterial pathogens and commensals in the gut, as well as other effects, but the routes of infection in children and the effects of specific pathogens on microbiome changes remain largely unknown. We therefore aim to characterize enteric infections in early childhood via use of metagenomics, namely the route of acquisition, and how timing of infection affects subsequent growth and development of both the child and its microbiome. Metagenomic sequencing is untargeted in this application, allowing for a comprehensive analysis of all microbes within a sample. This will allow us to not only examine specific enteric pathogens of interest, but also the overall microbiome profile of study subjects.