AMR research using Functional Metagenomics and Wastewater Samples
The Charles lab has brought together knowledge from wastewater surveillance projects as well as functional metagenomics to launch studies into Antimicrobial Resistance (AMR). Currently these projects involve making metagenomic libraries from wastewater samples to query through functional metagenomics any resistance to a selection of antibiotics including ampicillin, kanamycin, tetracycline, imipenem, meropenem, and vancomycin. Phenotypic screening of these libraries in an E. coli host in combination with both Nanopore and Illumina sequencing is used to examine the landscape of AMR present in municipal wastewater that could not otherwise be captured through direct culture of resistant organisms (the primary method for clinical isolates).
The WW-AMR team is currently expanding host selection for these metagenomic libraries to include organisms such as Pseudomonas, Moraxella, and Bacillus to allow screening of additional antibiotics and cross-validation of found resistance genes.
This work is supported through an NSERC Alliance grant, in partnership with the Doxey lab, public health partners from York region and the Region of Waterloo, as well as the Ontario Ministry for Environment, Conservation, and Parks.