A wide array of non-pathogenic and pathogenic E. coli with phylogenetic intermixing, and high prevalence of shared multidrug resistances amongst livestock, humans, meat and environment are present in a poultry farm and the contracted slaughterhouse.
(A) Overview of the study design and cohort information. 154 human, animal, meat and environmental samples were collected at each of three time points (denoted t1-3 and l1-3) over two independent 6-weeks broiler production cycles over one farm as well as the abattoir linked to this farm in China. The total number and type of isolates cultured and sequenced by host and host body site are shown. (B) Maximum likelihood phylogenetic tree of the whole cohort based on core genome of the 154 isolates with recombination correction, cultured from the human, animal and environmental and meat samples collected from the farm and slaughterhouse. Phylogroups (inner ring), sequence types, clonal complex, collection time points, host type and resistance profile (outer ring) are shown around the outside of tree. EAEC and EPEC isolates indicated by ⁕ and ⁕⁕ respectively. (C) Numbers of susceptible and resistant isolates, based on antimicrobial susceptibility testing by broth microdilution, for each of a panel of 26 antimicrobials encompassing nine different antimicrobial groups.