Paul Cardenas-Aldaz, MD, PhD, MSc

GHES LMIC Fellow 2018-2019

FELLOWSHIP SITE: Universidad San Francisco, Quito, Ecuador
U.S. INSTITUTION: University of california, berkeley

Project Title: Metagenome, Reistome Analysis and Animal Food Production 

There is very little research about the role of small- and large-scale food-animal production in transmitting antimicrobial resistance (AMR) to communities in low- and middle-income countries (LMICs). For that reason, the proposed collaborative study to be carried out by USFQ and colleagues from the University of Michigan and the Public Health Institute will aim to determine the extent to which small- and large-scale food-animal production contributes to the spread of AMR in children in an LMIC (Ecuador). We will prospectively study the exchange of multi-drug resistant E. coli and mobile genetic elements between food-animals and children living in peri-urban parishes east of Quito, and additionally I will apply a culture-independent method (i.e. metagenomics) approach to analyze a broad set of AMR genes within the whole microbial community of child and animal fecal samples. I would be able to measure the abundance of AMR genes (as well as other virulence genes) to study changes in the resistome of children and animals. The results obtained could be contrasted with the ones obtained from the cultured E. coli isolates in terms of AMR gene abundance, genotype and diversity. Also, it would be possible to develop a fuller picture of the AMR genes present within the mixed microbial community. When contrasting human and animal fecal samples, this metagenomics approach could allow us to understand the commonalities in AMR genes between these two groups and would build off of study of E. coli populations by providing a more comprehensive assessment of how the AMR genes move within human and domestic animal communities.