Relating Antimicrobial Resistance and Virulence in Surface Water E. coli (Data and Code)

This project aimed to assess the relationship between antimicrobial resistance (AMR) and virulence in Escherichia coli isolated from surface waters in Eastern North Carolina, some from sites downstream of commercial hog operations (CHOs) and some from background sites. AMR presence for a collection of resistances was determined previously by Kirby Bauer disc diffusion (see Christenson et al. 2022, link below). To account for spatial and temporal variation, a subset of matched pairs was created (n = 254, 127 pairs) by matching each isolate resistant to at least one antibiotic to a completely susceptible isolate from the same sample date and site (i.e., same sample). Virulence presence for a collection of virulence genes was determined in the subset of isolates by traditional PCR. The data for AMR and virulence assays are binary and as such, logistic regressions were performed to assess potential relationships between carriage of AMR traits and virulence genes. Additionally, multiple isolates from the same sample possessing identical AMR and virulence (as determined by the current work) profiles were assumed to be genetic clones. Groups of assumed clones were “collapsed” by choosing one representative via random number generator and removing the others, along with their respective matches (n = 174, 87 pairs; 67 swine pairs, 20 background pairs). The main datasets, as well as tabs for creating the matched pairs, running multicollinearity tests, and other data processing are included in the "LaMontagne_ABR..." Excel spreadsheet. The "Collapsed" spreadsheet includes a single table of the collapsed dataset in an R-ready format. The R code for running the logistic regressions and related processing on the collapsed ("Regressions_Collapsed_2") and uncollapsed ("Regressions") datasets are included below. The data reveal a negative relationship between AMR and virulence in these isolates, particularly between virulence gene STa (astA) and tetracycline resistance