Birmingham-group IncP-1α plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates

TL;DR

This paper confirms that three plasmids, RP1, RP4, and RK2, are identical and finds evidence of their remnants in environmental bacteria, suggesting a possible lab-to-environment leak.

Contribution

The study provides nucleotide-level confirmation that RP1, RP4, and RK2 are identical and identifies a fusion gene and environmental remnants of these plasmids.

Findings

RP1, RP4, and RK2 plasmids are identical at the nucleotide level despite decades of use in different labs.

A fusion gene called pecM-orf2 was identified in the plasmid sequence.

Remnants of the plasmids were found in environmental bacterial isolates, suggesting a possible leak from laboratory settings.

Abstract

RP4, RP1, RK2 and R68 were isolated from the multidrug-resistant bacterial wound isolates in 1969 in the Birmingham Accident Hospital, Birmingham, England, and collectively called Birmingham-group IncP-1α plasmids. These plasmids have been widely used as models to study different aspects of plasmid biology, develop genetic delivery systems and design plasmid vectors. Early studies showed that these plasmids conferred the same antibiotic resistance profile, had a similar size and were undistinguishable from each other using DNA heteroduplex electron microscopy and restriction endonuclease analyses. These observations have led to the widely held assumption that they are identical, although there has been no conclusive supporting evidence. In this work, we sequenced the plasmids RP1 and RP4 from our laboratory strain collection and compared these new sequences with the plasmids RP4 and RK2 assembled from a publicly available sequencing database, showing that the RP1, RP4 and RK2 plasmids are 60 095 bp in length and identical at the nucleotide resolution. Noteworthily, the plasmid sequence is highly conserved despite having been distributed to different labs over 50 years and propagated in different bacterial hosts, strengthening the previous observation that the bacterial host adapts to the RP4/RP1/RK2 plasmid rather than the opposite. In the updated RP4/RP1/RK2 sequence, we found a fusion gene, called pecM-orf2, that was formed putatively by a genetic deletion event. By searching for pecM-orf2 in the National Center for Biotechnology Information database, we detected remnants of the RP4/RP1/RK2 plasmid that carry features of laboratory-engineered vectors in bacterial environmental isolates, either in their chromosome or as a plasmid. This suggests a leak of these plasmids from the laboratory into the environment, which may subsequently impact bacterial evolution and raises concerns about the biocontainment of engineered plasmids when being handled in laboratory settings.

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