Table 1.

Approaches to detect plasmid-based antimicrobial resistance (AMR) genes.

Approach	Sample types	Advantage	Limitation	References
Illumina-based WGS	Food/clinical samples	Fast, applicable for studying the genetic diversity evolutionary history of plasmid type and epidemiological tracking.	Challenge for plasmid detection in short read length.	Almeida et al., 2018
Oxford Nanopore Technology (ONT)	Food/clinical samples	Rapid tool Low instrument Cost and small footprint	Incomplete fragmentation of plasmid. High error rate. Performance often needs to be optimized with MiSeq reads.	Lemon et al., 2017
Pacific bioscience single-molecule real-time sequencing (SMRT)	Food/clinical samples	Generate long-read sequencing data that can lead to closed plasmid sequences.	The reads length of data relies on the individual polymerase.	Chen et al., 2019