Diversity among antimicrobial resistant E. coli isolated from Irish retail meats

Background and Objectives Antimicrobial resistance is recognised globally as a major public health concern. The role of food in the dissemination of these important antimicrobial resistant bacteria is examined in this study. ... [ view full abstract ]

Background and Objectives
Antimicrobial resistance is recognised globally as a major public health concern. The role of food in the dissemination of these important antimicrobial resistant bacteria is examined in this study.
Methods
A total of 600 raw meat samples were purchased from retail outlets throughout the island of Ireland from November 2013 to September 2014. All samples were screened for the presence of antimicrobial resistant E. coli (AREC) and 496 AREC isolates were detected. All AREC isolates were characterised by a series of phenotypic and genotypic tests and based on these results 96 isolates were selected for whole genome sequencing. Isolate genomes were hosted in and analysis was performed using a local installation of BIGSdb.
Results
In total 46 sequence types (STs) and 12 clonal complexes and 61 ribosomal sequence types (rSTs) were identified. rST-1544 accounted for 15% of isolates and an association with source was apparent with 92.9% of rST-1544 from chicken samples (13/14). A total of 4981 loci were compared for all genomes and the fewest differences (n=39) were found in two chicken meat isolates within the rST-1544 grouping. None of the rST-1544 group were ESBL producers.
Conclusions
AREC E. coli found in Irish retail meats were relatively diverse with over half being ESBL producers. Interrogation of whole genome databases for emerging antimicrobial resistance determinants provides a rapid low cost approach to evaluate the extent of dissemination prior to recognition and will become more powerful as databases expand.