IncQ plasmids facilitate the integration of antibiotic resistance genes in the chromosome.

Plasmids are self-replicating pieces of DNA that are particularly prominent in bacterial genomes. In addition to maintenance genes, plasmids typically carry cargo that allows cells to adapt to environmental challenges (such as exposure to antibiotics) or exploit new niches. The reason why these genes are kept in plasmids as opposed to integrating in the chromosome as not well understood, particularly considering the fitness cost of maintaining plasmids, a question known as "the plasmid paradox". Transient integration into the chromosome in the form of ICE (Integrative Conjugative Elements) appears to be part of the answer. Here we looked for other forms of plasmid integration. We collected 10,000+ complete genomes of E. coli from a NCBI. We identified MGEs associated with a plasmid origin of replication in the chromosome, with default parameters (95% id and 60% cov) and found 262 origins of replication in chromosomal sequence. Of these, 147 (56%) belonged to the IncQ incompatibility type and between 13 and 27 to IncF (5-10.3%). The high representation of IncQ origins of replication is remarkable. Unlike most plasmids, which replicate via a theta mode of replication, IncQ plasmids replicate by strand displacement, which includes replication initiation machinery for both strands, and limits plasmid size to less than 15 kb. We also found that, despite its size limitations, chromosome-integrated IncQ plasmids carry a significant load of antibiotic resistance genes. In the following cases: APH(3’)-Ia, sul2, APH(3’’)-lb, APH(6)-Id, catI, TEM-1, and CTX-M-1, integrated plasmids present between 5 and 7% of the total representation of the corresponding antibiotic resistance gene in the database. Thus, IncQ-mediated integration in the chromosome appears to facilitate the vertical transmission of a significant number of antibiotic resistance genes.