Phylogenomics and Outbreak Typing
One-Sentence Definition
Phylogenomics uses genome-wide variation to infer relatedness among isolates; outbreak typing applies those relationships to infection-control questions (“same chain of transmission?”).
Simple Explanation
Compare whole genomes like barcodes — closer genomes are more likely linked in an outbreak (with epidemiology).
Detailed Scientific Explanation
| Method | Signal | Use |
|---|---|---|
| MLST / cgMLST / wgMLST | Allelic profiles | Standardized hospital networks |
| SNP phylogeny | Reference-mapped SNPs | High-resolution clusters |
| Mash / ANI | Whole-genome distances | Species/strain screening |
| Plasmid typing | Inc groups, mobility | AMR gene epidemiology ≠ clone |
Always interpret with epidemiologic data — genomes don’t prove direction of transmission alone. HGT can move AMR across unrelated clones (Horizontal Gene Transfer).
Mechanism
Align or hash genomes → distance matrix / tree (IQ-TREE, RAxML, FastTree) or allelic hierarchical clustering → define SNP/allele thresholds carefully (organism-specific).
Clinical Importance
- Confirm/refute ward outbreaks; link foodborne clusters; track CRE clones vs plasmids
Research Importance
- Population structure; vaccine serotype replacement; One Health reservoirs
Diagnostic Relevance
- Public-health and hospital epi more than routine individual Rx
- Built on WGS Bioinformatics Pipeline
AMR Relevance
- Separates clonal expansion vs plasmid outbreak narratives — critical for Klebsiella pneumoniae / Escherichia coli CRE
Related Methods
Related MOCs
- MOC - Bioinformatics in Microbiology · MOC - Antimicrobial Resistance (AMR) · MOC - Clinical Microbiology
Active Recall Questions
- Why might two patients share blaNDM but sit far apart on a core-genome tree?
- cgMLST vs SNP tree — when each?
- Why include epi timelines with genomic clusters?