Core-Genome Multilocus Sequence Typing Service

Core genome is the set of genes that exist across all strains of a species, which typically includes housekeeping genes for cell envelope or regulatory functions. And core genome multilocus sequence typing (cgMLST) can be managed whereby the blooming technology of whole genome sequencing (WGS)-based subtyping, which provides great value to the study of microbial surveillance, outbreak detection, source tracking, ect. A glance at figure 1 reveals the discrimination level of different sequencing schemes, which significantly indicates that cgMLST is an extraordinary typing approach that identify the strains in clone level, with the capability of providing solutions for study the evolution, phylogeny, spread of the organisms.

Figure 1: Discrimination level of different sequencing schemes (Maiden, 2013)

Application & Advantages

cgMLST is an extended method of MLST but much more than that. Based on WGS and using the core genome of a large number of strains as the sequence typing marker, cgMLST is a competent tool with high resolution, yet much more efficient than traditional molecular typing methods. This scheme could contribute a lot to the early detection of nosocomial infection, the traceability of drug-resistant strains and the confirmation of transmission routes, which shows great applicability in the study of strain evolution and epidemiological traceability. A study carried out by Enteric Diseases Laboratory Branch (Centers for Disease Control and Prevention, the USA) on the diversity of serotypes and lineages in Listeria monocytogenes whereby schemes of wgMLST and cgMLST, which showed that 4,804 unique loci were identified by wgMLST, while 1,748 by cgMLST. With high concordance in the phylogenetic tree reconstruction regarding both distance and clustering, the two schemes provide equally reliable results. However, cgMLST targets at well-defined set of species-wide conserved genes. Thus, a precisely calibrated cgMLST is particularly stable for especially routine epidemiology research, while wgMLST may not be able to provide with such high stability.

Figure 2. Phylogenic trees with the 208 L. monocytogenes based on genomic MLST scheme (Henri, 2017)

What we can offer

As a premier research-assist institution, Creative Biogene offers you professional and comprehensive cgMLST services. We present you with cgMLST data analysis service as follows:

1) Original data processing: reads with low sequencing quality value were filtered and high-quality reads were retained for data quality control;

2) Sample assembly: algorithm was used for genome assembly to obtain a sequence data that could reflect the basic situation of the sample genome, and the assembly result was evaluated; 

3) Allele ID acquisition: the allele ID number of gene loci in the genome was obtained;

4) Annotation: functional annotation and pathogenic and drug resistance analysis of different databases for coding gene sequences;

5) Evolutionary analysis: the cgMLST data were used to construct high-resolution species typing results, to explain the outbreak of infectious diseases, and to analyze the population structure and evolutionary process of target strains, which is extremely helpful with routine epidemiology research;

6) Genome visual analysis: basic research results of genome are presented by combining the results of genome component analysis and functional annotation.

With professional scientist and powerful automated allele curation tools, we make it possible to analyze thousands of loci for your target strains. Simply let us know your research requirement, and we will help you propose the best strategy for you.

References
1. Henri C.; et al. An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes. Frontiers in Microbiology, 2017, 8: 2351.
2. Maiden M. C.; et al. A nomenclature for discussing the genetic relatedness of bacteria. Nature Reviews Microbiology, 2013, 11: 728–736.

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