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Background  Increasing bacterial resistance to antibiotics is a serious problem worldwide. We sought to record the acquisition of antibiotic-resistant  Escherichia coli  ( E. coli ) in healthy infants in Northern Thailand and investigated potential determinants.    Methods  Stool samples from 142 infants after birth, at ages 2wk, 2mo, 4 to 6mo, and 1y, and parent stool samples were screened for  E. coli  resistance to tetracycline, ampicillin, co-trimoxazole, and cefazoline by culture, and isolates were further investigated for multiresistance by disc diffusion method. Pulsed-field gel electrophoresis was performed to identify persistent and transmitted strains. Genetic comparison of resistant and transmitted strains was done by multilocus sequence typing (MLST) and strains were further investigated for extra- and intra-intestinal virulence factors by multiplex PCR.    Results  Forty-seven (33%) neonatal meconium samples contained resistant  E. coli.  Prevalence increased continuously: After 1y, resistance proportion (tetracycline 80%, ampicillin 72%, co-trimoxazole 66%, cefazoline 35%) almost matched those in parents. In 8 infants (6%), identical  E. coli  strains were found in at least 3 sampling time points (suggesting persistence). Transmission of resistant  E. coli  from parents to child was observed in only 8 families. MLST showed high diversity. We could not identify any virulence genes or factors associated with persistence, or transmission of resistant  E. coli . Full-term, vaginal birth and birth in rural hospital were identified as risk factors for early childhood colonization with resistant  E. coli .    Conclusion  One third of healthy Thai neonates harboured antibiotic-resistant  E. coli  in meconium. The proportion of resistant  E. coli  increased during the first year of life almost reaching the value in adults. We hypothesize that enhancement of infection control measures and cautious use of antibiotics may help to control further increase of resistance.    Electronic supplementary material  The online version of this article (10.1186/s13756-019-0522-6) contains supplementary material, which is available to authorized users.

“Enhanced acquisition of antibiotic-resistant intestinal E. coli during the first year of life assessed in a prospective cohort study”