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.

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

“…While this diversity can be representative of certain clinical samples [79][80][81], other environments with relevance to public health, such as the human gut, soil and livestock, can have 100-1000s of species [82][83][84][85]. In addition, MGEs such as GIs and plasmids are known to recombine, producing closely related variants [86][87][88] that could further complicate assembly from a metagenomic sample. Polymorphic MGEs were not explicitly introduced in our simulated metagenome.…”

The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling

“…This enhances the potential for plasmid spread and maintenance dramatically, even when it was reported to be very low for a specific plasmid-host-combination. This finding is of particular importance considering that recent bioinformatic analysis revealed that more than 60% of the plasmids of the global prokaryotic plasmidome were reported to be able to colonize species from different phyla [58] . Plasmids coding for antibiotic resistance could therefore initially acquire cost-compensating mutations in co-evolution with a particular common host and later spread as optimized vectors to other less common but potentially more harmful species.…”

COPLA, a taxonomic classifier of plasmids

“…Plasmid clustering algorithm (sHSBM). The PTU definition algorithm was based on a DNA homology network constructed from the pairwise comparison of all RefSeq84 plasmids (NCBI, dataset from September 2017), using Average Nucleotide Identity (ANI), as detailed in (2). An edge was drawn between two plasmid nodes if homology was detected over 50% of the shorter genome length.…”

“…Only clusters with at least four members were considered representative enough to be included in the next step. A home-made algorithm was added in (2) to join the previously divided clusters into a single PTU if two biological specifications were met:…”