Recombination in Bacterial Phylogenies
One-Sentence Definition
Recombination in bacteria imports DNA tracts that violate a single vertical tree; recombination-aware methods detect and mask or model these tracts so outbreak phylogenies reflect clonal descent more accurately.
Simple Explanation
If you build a family tree while some relatives swapped large DNA chunks with neighbors, the tree lies. Recombination-aware tools find those swapped chunks and correct the picture.
Detailed Scientific Explanation
Consequences of ignoring recombination:
- Inflated branch lengths and wrong topology
- False outbreak clustering
- Biased molecular clocks (Phylodynamics)
| Tool / class | Approach |
|---|---|
| Gubbins | Iteratively identifies high-SNP-density tracts on a starting tree |
| ClonalFrameML | Statistical model of import on ML trees |
| BRAT NextGen / similar | Spatial recombination detection |
| Gene-by-gene (cgMLST) | Sidesteps full SNP tree for typing (MLST and cgMLST) |
Species with high recombination (S. pneumoniae, Neisseria, Helicobacter) need this more than clonal M. tuberculosis.
Mechanism
Detect regions with excess homoplasy or SNP density relative to clonal frame → mask or model imports → rebuild tree from clonal signal → use for epi inference (Phylogenomics and Outbreak Typing).
Clinical Importance
- Prevents over-splitting or false linking of hospital outbreak isolates.
- Essential for vaccine-escape and serotype-switch analyses in pneumococcus.
Research Importance
- Separates vertical evolution from HGT tracts for selection scans and dating.
Diagnostic Relevance
- Reference pipelines for pneumococcus/meningococcus incorporate recombination handling before reporting relatedness.
AMR Relevance
Recombined tracts often carry resistance/virulence; detecting them explains sudden phenotype jumps without whole-clone replacement.
Related Methods
Related MOCs
Active Recall Questions
- What artifact appears if recombination is ignored?
- When is cgMLST preferred over SNP trees?
- Name a tool that masks recombinant regions.