MLST and cgMLST
One-Sentence Definition
MLST types bacteria by allele profiles of a few housekeeping genes; cgMLST/wgMLST extends the same allele logic to hundreds or thousands of core/whole-genome loci for high-resolution typing.
Simple Explanation
Give each version of a gene a number. A strain becomes a list of numbers — easy to compare between labs and countries.
Detailed Scientific Explanation
| Scheme | Loci | Resolution | Use |
|---|---|---|---|
| MLST | ~7 housekeeping genes | Low–moderate (sequence type, ST) | Global lineage naming (e.g., ST258 K. pneumoniae) |
| cgMLST | Hundreds–thousands core loci | High | Hospital/national outbreak surveillance |
| wgMLST | Core + accessory loci | Highest gene-level | Detailed investigation |
Advantages over raw SNPs: allele calls are portable (no shared reference needed) and nomenclature is centrally curated (PubMLST, EnteroBase, Ridom).
Limits: scheme availability varies by species; allele definition depends on assembly quality (Read QC and Preprocessing).
Mechanism
Assemble genome → extract loci → match to curated allele database → allele profile → cluster by allelic distance thresholds.
Clinical Importance
- Cluster thresholds trigger infection-control investigations
- Lineage names (STs, clonal complexes) carry known risk (e.g., high-risk MDR clones)
Research Importance
- Long-term population genomics, international comparability
Diagnostic Relevance
- Standard output of clinical/public health Whole-Genome Sequencing
AMR Relevance
- High-risk clones (Klebsiella pneumoniae, Escherichia coli ST131) tracked by ST + resistome
Related MOCs
- MOC - Bioinformatics in Microbiology · MOC - Antimicrobial Resistance (AMR) · MOC - Clinical Microbiology
Active Recall Questions
- Why is allele-based typing more portable than SNP distances?
- What is a sequence type (ST)?
- What can ruin allele calling?