High proportions of single-nucleotide variations associated with multidrug antibiotic resistance in gut microbial populations

Our study described microbiome response to environment change via antibiotics. We studied three treatment groups: non-antibiotic controls (C), chlortetracycline (CTC) treated, and tiamulin (TMY) treated. We collected fecal samples from each group and performed metagenomic sequencing for a time-series analysis of genetic variation and functions. We identified a subset of 11 MAGs with sustained detection and high sustained entropy (SDHSE). Entropy described genetic variation throughout the MAG. Our SDHSE MAGs were considered MDR as they were identified prior to, throughout, and after CTC and TMU treatments and in C swine. SDHSE MAGs were especially concerning as they harbored relatively high variation. Consistently high variation indicated these microbial populations may contain hypermutable elements which has been associated with increased chance of AMR and MDR acquisition. Altogether, our study provides comprehensive genetic support of MDR populations within the gut microbiome of swine, a major consumer of antibiotics globally.