Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments

For the swine industry, the post-weaning period is critical and for many years, antimicrobials have been the most effective strategy to control and treat post-weaning related infections. In this study, 210 piglets were transferred from a farm with recurrent cases of PWD to an experimental farm and divided into six treatment groups: trimethoprim/sulfamethoxazole, colistin, oral commercial vaccine, gentamicin, control with water acidification, and untreated control. An extra group remained at the farm of origin following the implemented amoxicillin routine treatment. Fecal samples were collected from pigs at four different sampling times: before weaning-treatment, and two days, two weeks, and four weeks post-treatment. A total of 280 samples were selected, considering ten animals per group and sampling time, and shotgun metagenomics was performed for group comparison and longitudinal analyses.