While classical MLST is based on sequencing each of 6 to 10 housekeeping genes separately whereby approaches such as Sanger technology, wgMLST is built upon the advent of next-generation sequencing, providing much richer information for differentiating bacterial strains than the predecessor MLST, which makes it possible to consider many more loci (typically 1500 - 4000) at the same time in a fast and cost-effective way. Based on the concept that allelic variation - recombinations and deletions or insertions of multiple positions are regarded as single evolutionary events, wgMLST is biologically more relevant than approaches that only take point mutations into account.
Application & Advantages
wgMLST is extremely powerful and has provided better resolution compared to classical MLST. A number of studies have demonstrated the advantages of using whole genome sequencing analysis for microbial surveillance, outbreak detection and source tracking. For example, a study carried out by Leal C on whole-genome sequencing of numerous isolates has revealed that the single MLST lineage ST283 of Streptococcus agalactiae screened from Brazil showed loci variations ranging from 71 to 256 out of 3,539 loci between each other; van Hoek showed the gene differences among stx2f-carrying E. coli by the approach of wgMLST. With the large quantity of information that standard MLST could not provide, wgMLST has the capability of providing solutions for study the evolution, spread of the organisms, ect.
Figure 1. A wgMSLT scheme in building phylogenetic tree of 218 stx2f-carrying E. coli. (van Hoek et al. 2019)
With the rapid evolution of pathogens and large variations among drug-resistance genes, classical typing methods, in most cases, could not keep up the pace with disease outbreak. The typing approach based on next-generation sequencing, wgMLST, has met the needs for typing with high accuracy and reliability. Furthermore, with the decreasing cost of second-generation sequencing, typing methods based on it are gradually replacing traditional molecular typing methods, becoming the new standard of epidemiological strain typing.
What we can offer
As a premier research-assist institution, Creative Biogene offers you professional and comprehensive wgMLST services. We have years of experience to meet your specific project needs in using the wgMLST technology to add value to your research project.
We present you with wgMLST 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: the Velvet 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: based on the Assembly-Based and Assembly-Free algorithms, 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 wgMLST 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, so as to provide fundamental data for disease prevention and control;
6) Genome visual analysis: basic research results of genome are presented by combining the results of genome component analysis and functional annotation.
Available wgMLST schemes for organisms include:
• Acinetobacter baumannii
• Bacillus cereus
• Bacillus subtilis
• Burkholderia cepacia complex
• Brucella spp.
• Campylobacter coli - C. jejuni
• Citrobacter spp.
• Clostridium difficile
• Cronobacter spp.
• Enterobacter cloacae
• Enterococcus faecalis
• Enterococcus faecium
• Enterococcus raffinosus
• Escherichia coli / Shigella
• Francisella tularensis
• Klebsiella aerogenes
• Klebsiella oxytoca
• Klebsiella pneumoniae
• Legionella pneumophila
• Listeria monocytogenes
• Micrococcus spp.
• Mycobacterium bovis
• Mycobacterium leprae
• Mycobacterium tuberculosis
• Neisseria gonorrhoeae
• Pseudomonas aeruginosa
• Salmonella enterica
• Serratia marcescens
• Staphylococcus aureus
• Staphylococcus epidermidis
• Staphylococcus pseudointermedius
• Streptococcus pyogenes
With professional scientist and powerful automated allele curation tools, we make it possible to analyze thousands of loci for your target trains. Simply let us know your research requirement. We will provide support for each step in your workflow and propose the best strategy for you.
1. van Hoek AHAM, et al. Comparative genomics reveals a lack of evidence for pigeons as a main source of stx2f-carrying Escherichia coli causing disease in humans and the common existence of hybrid Shiga toxin-producing and enteropathogenic E. coli pathotypes. BMC Genomics. 2019;20(1):271.
2. Leal CAG, et al. Streptococcus agalactiae Sequence Type 283 in Farmed Fish, Brazil. Emerg Infect Dis.2019;25(4): 776-779.