In short
- Bacteria often become resistant by acquiring existing resistance genes through mobile genetic elements, rather than through new mutations.
- Insertion sequences, transposons and integrons move genes within and between DNA molecules. Plasmids and integrative conjugative elements move them between cells.
- A resistance gene on a transferable plasmid carries a higher risk of spread than the same gene in the chromosome.
- Plasmids are hard to reconstruct from short reads. In one benchmark, PlasmidFinder had 99% specificity but 50% sensitivity for plasmid contigs, while MOB-suite had 95% sensitivity and 88% specificity.
How resistance genes move
Both Gram-negative and Gram-positive bacteria often become resistant by acquiring resistance genes that already exist in the wider bacterial gene pool. This happens through mobile genetic elements. Some move within or between DNA molecules in the same cell, while others transfer between cells. Together they drive horizontal gene exchange and the spread of resistance [1].
| Element | How it moves | Role in resistance |
|---|---|---|
| Insertion sequence (IS) | Within and between DNA molecules in a cell | Can disrupt genes or switch on neighbouring genes; often flanks resistance genes |
| Transposon | Within and between DNA molecules | Carries resistance genes between the chromosome and plasmids |
| Integron and gene cassettes | Captures and rearranges cassettes | Collects several resistance genes in one array |
| Plasmid | Between cells, by conjugation or mobilisation | Moves whole sets of resistance genes between strains and species |
| Integrative conjugative element (ICE) | Sits in the chromosome but transfers between cells | Behaves like a plasmid that hides in the chromosome |
Why location matters
- Risk of spread: a gene on a conjugative plasmid can reach other bacteria, including other species.
- Probiotic and food safety: acquired, transferable resistance is a key concern in a genome-based safety assessment.
- Surveillance: the same plasmid in isolates from different hosts or sites points to plasmid spread rather than spread of a single strain.
- Stability: plasmids can be lost in culture, so a plasmid-borne trait may disappear during production or passaging.
Finding plasmids in a draft genome
Plasmids share repeats and mobile elements with the chromosome, so short-read assemblies often break them into pieces that can't be clearly assigned. PlasmidFinder identifies plasmids by their replicon sequences, the regions that control plasmid replication [2]. It is very specific, but a plasmid with an unknown or missing replicon goes undetected.
MOB-suite tackles the reconstruction problem. On a set of closed genomes with matching Illumina data, it identified plasmid-derived contigs with 95% sensitivity and 88% specificity, compared with 99% specificity and 50% sensitivity for PlasmidFinder. Of 377 known plasmids, MOB-recon correctly reconstructed 207, compared with 102 for plasmidSPAdes [3].
Other elements need their own tools. MobileElementFinder detects mobile elements and their genetic context using a database of 4,452 known elements. Applied to 1,725 Salmonella enterica isolates, it found that mobile elements were largely conserved by sequence type and identified putative mobile units carrying aminoglycoside, sulphonamide and tetracycline resistance genes [4].
When you need long reads
If the exact structure of a plasmid matters, for example which resistance genes share a plasmid or whether a gene sits on a plasmid or the chromosome, a short-read draft can only give a probable answer. Long-read or hybrid sequencing resolves each plasmid as a complete circular sequence. See choosing an assembly strategy.
Plasmid and MGE analysis in BacSeq reports
The Standard and Premium packages include plasmid analysis and mapping of mobile genetic elements, such as transposons, integrons and insertion sequences. Reports flag resistance genes found on plasmid-associated contigs or next to mobile elements, alongside the AMR results, and state how confident the assignment is given the data.
References
- Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev. 2018;31(4):e00088-17. doi:10.1128/CMR.00088-17
- Carattoli A, Zankari E, García-Fernández A, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58:3895–3903. doi:10.1128/AAC.02412-14
- Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom. 2018;4(8):e000206. doi:10.1099/mgen.0.000206
- Johansson MHK, Bortolaia V, Tansirichaiya S, et al. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother. 2021;76:101–109. doi:10.1093/jac/dkaa390