Genomic Insights into Antibiotic-Resistant Bacteria Associated with Plants: A Meta-Analysis of Publicly Available Whole Genome Sequences

Abstract

This study aimed to investigate plant-associated antibiotic-resistant bacteria (ARB) using publicly available bacterial whole genome sequences (WGS) from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). A total of 1,058 WGS datasets were analyzed to identify bacterial genera, antibiotic resistance genes (ARGs), and plasmid mobility types. The dominant genera were Xanthomonas, Mesorhizobium, Streptomyces, Pseudomonas, and Erwinia, accounting for more than 65% of the isolates. Streptomyces and Pseudomonas exhibited the highest ARG abundances, averaging 0.6 and 0.3 ARGs per genome, respectively. ARG-carrying isolates were most frequent in peanut, sweet basil, bread wheat, sweet orange, and maize hosts. Ninety-three isolates (8.8%) harbored ARG-containing plasmids, among which 18% were conjugative, 25% mobilizable, and the remainder non-mobilizable. Conjugative and mobilizable plasmids were mainly found in Pseudomonas and Xanthomonas from tomato and kiwifruit hosts, while non-mobilizable plasmids predominated in Agrobacterium, Streptomyces, and Bacillus. The findings suggest that plant-associated bacteria, particularly Pseudomonas, Xanthomonas, and Streptomyces, constitute important ARG reservoirs and may facilitate resistance dissemination through conjugative and mobilizable plasmids in agricultural ecosystems.