cgMLST

cgMLST, or core genome multilocus sequence typing, is a bacterial typing method that extends traditional MLST by analyzing a large set of conserved genes that define the core genome of a species. A cgMLST scheme specifies a curated list of core loci, typically hundreds to thousands, that are present in the vast majority of strains. For each isolate, sequences at these loci are compared to a reference allele database to assign an allele number for every locus. The combination of allele numbers across all loci forms an allelic profile that serves as a high-resolution genotype. Relatedness among isolates is inferred from allelic differences, with distance metrics and clustering approaches used to identify putative outbreak groups or lineages.

cgMLST provides standardized, portable data and offers higher discriminatory power than classical MLST while maintaining cross-laboratory comparability. It is distinct from whole-genome MLST (wgMLST), which includes a broader set of loci, including accessory genes; cgMLST focuses on the core genome to improve stability and reproducibility of typing results.

Applications of cgMLST include outbreak investigation, surveillance, and phylogenetic analyses in pathogens such as Salmonella, Listeria, Campylobacter, and other bacteria. Data and allele schemes are hosted in public databases and platforms such as PubMLST, EnteroBase, and BIGSdb, with software tools like Ridom SeqSphere+, chewBBACA, and in-house pipelines used to perform cgMLST typing.

Limitations include dependence on a well-defined core genome and high-quality sequences; missing data from incomplete assemblies can affect results; clustering thresholds can be context-dependent; ongoing curation of loci and allele databases is required to maintain accuracy.