Mosaic plasmids are abundant and unevenly distributed across prokaryotic taxa

Abstract

Mosaic plasmids, plasmids composed of genetic elements from distinct sources, are associated with the spread of antibiotic resistance genes. Transposons are considered the primary mechanism for mosaic plasmid formation, though other mechanisms have been observed in specific instances. The frequency with which mosaic plasmids have been described suggests they may play an important role in plasmid population dynamics. Our survey of the confirmed plasmid sequences available from complete and draft genomes in the RefSeq database shows that 46% of them fit a strict definition of mosaic. Mosaic plasmids are also not evenly distributed over the taxa represented in the database. Plasmids from some genera, including Piscirickettsia and Yersinia, are almost all mosaic, while plasmids from other genera, including Borrelia, are rarely mosaic. While some mosaic plasmids share identical regions with hundreds of others, the median mosaic plasmid only shares with 8 other plasmids.When considering only plasmids from finished genomes (51.6% of the total), mosaic plasmids have significantly higher proportions of transposases and antibiotic resistance genes. Conversely, only 56.6% of mosaic fragments (DNA fragments shared between mosaic plasmids) contain a recognizable transposase, and only 1.2% of mosaic fragments are flanked by inverted repeats. Mosaic fragments associated with the IS26 transposase are 3.8-fold more abundant than any other sequence shared between mosaic plasmids in the database, though this is at least partly due to overrepresentation of Enterobacteriaceae plasmids..

Structure and Evolution of Acinetobacter baumannii Plasmids

“…Acinetobacter baumannii plasmids belong to a limited number of plasmid lineages and their structure seem to be very stable, in contrast to the observations made in the so-called mosaic plasmids. Mosaic plasmids are composed of genetic elements from distinct sources and they are highly dynamic in acquisition and loss of genes (Pesesky et al, 2019).…”

Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids

“…These mobile genetic elements have a typical modular structure consisting of a conserved backbone region ensuring their survival or propagation and a variable accessory region that may encode host-beneficial traits (Garcillán-Barcia et al, 2011). The acquisition or deletion of adaptive modules from different phylogenetic origins begets enormous diversity among plasmids (de Toro et al, 2014;Pesesky et al, 2019). Plasmids are a keystone of horizontal gene transfer, facilitating the rapid evolution and adaptation of their hosts under changing environmental conditions.…”

Intracellular Competitions Reveal Determinants of Plasmid Evolutionary Success

“…Plasmid persistence in a host may depend on an interaction with co-residing plasmids (e.g., San Millan et al, 2009Silva et al, 2011;Dionisio et al, 2019;Jordt et al, 2020) or on their recombination and fusion with other plasmids. Recombination routes were shown to facilitate the formation of mosaic plasmids, a phenomenon often observed in different plasmids of the same host lineage (e.g., Chaconas and Norris, 2013;Pesesky et al, 2019). Recombination observed between sites in a single plasmid genome may indicate that plasmid recombinants form routinely when host recombination pathways are encoded in the host genome (e.g., Flores et al, 2000).…”