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Primary production environment is considered as reservoir of  Escherichia coli  contamination of produce.  E. coli  is classified into eight phylogroups which differ in ecological niches, evolutionary history, and phenotypic properties. To understand the population genetic structure and composition of  E. coli  in primary production environments in Metro Manila, Philippines, a total of 80  E. coli  recovered from irrigation water, soil, vegetables, and feces of cat, carabao, chicken, dog, and goat were allocated into distinct phylogroups based on the presence and absence of genetic markers. Results showed that the most prevalent phylogroup was B1 (71.3%), followed by A (18.6%), D (6.3%), B2 (1.3%), E (1.3%), and an unknown phylogroup (1.3%). The most prevalent genetic marker was  arpA , followed by TspE4.C2,  yjaA , and  chuA . The carbapenem resistance of 24  E. coli  isolates representing different phylogroups was also evaluated. Intriguingly, all isolates exhibited uniform susceptibility. This is the first report to provide insights into the phylogroup structure and composition, as well as carbapenem resistance of  E. coli  from primary production in the Philippines, which highlights possible source of and solution for gastrointestinal and enteric diseases.

Phylogroup typing and carbapenem resistance of Escherichia coli from agricultural samples in Metro Manila, Philippines