Plasmid Detection and Complete Plasmid DNA Sequencing

Bacterial plasmids

Bacterial plasmids are circular or linear double-stranded DNA molecules defined by their capability of autonomous replication in the hosts. They are critical sources for microbial evolution and genome innovation due to their ability to acquire foreign DNA sequences and transfer among bacteria and between distantly related organisms, like transferring from bacteria to eukaryotes via conjugation and mobilization. Bacterial plasmids undergo a higher frequency of genetic recombination than chromosomes. Plasmid genome, also known as the accessory or flexible genome, does not encode basic survival functions, but instead, it contributes to exploiting particular environmental niches, pathogenicity, degradation of aromatics, and antimicrobial resistance (AMR). Resistance to antibiotics has directly and sharply increased the number of multidrug-resistant bacteria. Thus, considerable effort has been made for plasmid detection and monitoring by using methods like complete plasmid DNA sequencing.

Methods for plasmid detection

There are several approaches for plasmid detection, based on PCR, gel electrophoresis, optical mapping or sequencing.

1. PCR-based replicon typing. This approach targets the conserved replicon sites of plasmid, and multiplex PCR can be expanded to simultaneously target many replicons. Although cheap and fast, this approach is hard to cover all novel plasmid groups.
2. Pulsed field gel electrophoresis (PFGE). This method separates digested DNA on a gel matrix by applying an electric field that periodically changes direction. However, it typically takes several days to reveal the size and number of plasmids in an isolate.

3. Optical mapping of plasmids. This method relying on the stretching of plasmid DNA can be used to depict the sequence of a plasmid. But optical mapping may not be suitable for the detection of short (

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