Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids
Abstract
Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I-VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier.
Domains
Life Sciences [q-bio] Microbiology and Parasitology Bacteriology Life Sciences [q-bio] Genetics Populations and Evolution [q-bio.PE] Life Sciences [q-bio] Quantitative Methods [q-bio.QM] Life Sciences [q-bio] Biochemistry, Molecular Biology Genomics [q-bio.GN] Life Sciences [q-bio] Biodiversity Populations and Evolution [q-bio.PE] Computer Science [cs] Bioinformatics [q-bio.QM]
Origin : Publication funded by an institution
