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Background  Enteroaggregative (EAEC) and Shiga-toxin producing  Escherichia coli  (STEC) are a major cause of diarrhea worldwide.  E. coli  carrying both virulence factors characteristic for EAEC and STEC and producing extended-spectrum beta-lactamase caused severe and protracted disease during an outbreak of  E. coli  O104:H4 in Europe in 2011. We assessed the opportunities for  E. coli  carrying the  aggR  and  stx  genes to emerge in ‘backyard’ farms in south-east Asia.    Results  Faecal samples collected from 204 chicken farms; 204 farmers and 306 age- and gender-matched individuals not exposed to poultry farming were plated on MacConkey agar plates with and without antimicrobials being supplemented. Sweep samples obtained from MacConkey agar plates without supplemented antimicrobials were screened by multiplex PCR for the detection of the  stx1 ,  stx2  and  aggR  genes. One chicken farm sample each (0.5 %) contained the  stx1  and the  aggR  gene. Eleven (2.4 %) human faecal samples contained the  stx1  gene, 2 samples (0.4 %) contained  stx2  gene, and 31 (6.8 %) contained the  aggR  gene. From 46 PCR-positive samples, 205  E. coli  isolates were tested for the presence of  stx1 ,  stx2 ,  aggR ,  wzx  O104  and  fliC  H4  genes. None of the isolates simultaneously contained the four genetic markers associated with  E. coli  O104:H4 epidemic strain ( aggR ,  stx2 ,  wzx   O104   and  fliC   H4  ). Of 34 EAEC, 64.7 % were resistant to 3 rd -generation cephalosporins.    Conclusion  These results indicate that in southern Vietnam, the human population is a more likely reservoir of  aggR  and  stx  gene carrying  E. coli  than the chicken population. However, conditions for transmission of isolates and/or genes between human and animal reservoirs resulting in the emergence of highly virulent  E. coli  strains are still favorable, given the nature of‘backyard’ farms in Vietnam.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-016-0827-z) contains supplementary material, which is available to authorized users.

Colonization of Enteroaggregative Escherichia coli and Shiga toxin-producing Escherichia coli in chickens and humans in southern Vietnam