cgMLST - Genome-wide gene by gene microbial typing
Figure 1. MLST of 6 genes versus genome-wide cgMLST. Shown are the six N. meningitidis MLST loci and red dots across the genome that represent symbolically the cgMLST loci.
"Bacterial epidemiological typing generates isolate-specific geno- or phenotypic characters that can be used to elucidate the sources and routes of spread of bacteria. Typing may also be used to identify emerging pathogenic strains or clones within a species, including potential agents of bioterrorism" (cited from: CMI 2007, 13:Suppl 3:1 [PubMed]).
With fast and affordable microbial whole genome shotgun sequencing (WGS) and automatized software analysis (Fig. 1), microbiologists can use genome-wide gene-by-gene allele calling of hundreds/thousands of genes (core genome MLST [cgMLST]) for genotyping. cgMLST schemes consist of a fixed set of conserved genome-wide genes. Alleles are used instead of single nucleotide polymorphisms (SNP) or concatenated sequences to mitigate the effects of recombination and to enable for a global and public nomenclature (cgMLST.org Nomenclature Server). The high discriminatory power of cgMLST, coupled with rapid and simple WGS workflow, makes this complete solution ideal for everyday usage in a routine laboratory, e.g., for prospective surveillance of multi- drug resistant bacteria in a hospital (JCM 54: 2874, 2016). That is, one disruptive, accurate, and highly reproducible technology (JCM 55: 908, 2017) that fits any bacteria, any research topic, and any lab is finally within reach for every microbiologist.
The figure below illustrates how in future a hierarchical microbial WGS typing pyramid from bottom to top with increasing discriminatory power might look like. The species-specific multi locus sequence typing (MLST) will remain the basis for backwards compatibility reasons (PNAS 1998, 95:3140 [PubMed]). MLST sequence types (ST) can be easily extracted from NGS data. With appropriate software the ribosomal MLST with one pan-bacterial scheme might play in future a more prominent role (Microbiology 2012 158:1005 [PubMed]). Genome-wide gene by gene bacterial typing, i.e. cgMLST is an obvious extension of the traditional MLST concept (e.g., PLoS One 2011, 6:e22751 [PubMed] and Nature Rev. Microbiol. 2013, 11:728 [PubMed]). All three methods can be standardized in contrast to lineage-specific schemes based on explorative single nucleotide polymorphisms (SNPs; e.g., NEJM 2012, 366:2267 [PubMed]) or accessory gene alleles of the species reference genome or the species pan-genome (whole genome MLST [wgMLST]). Lineage-specific SNP or accessory gene allele approaches can be always layered on top of the standardized cgMLST schemes for 'ad hoc' analysis to gain even more discriminatory power.