Frequently asked questions
Browse through these FAQs to find answers to commonly asked questions.
The bacterial typing and source tracking based on whole-genome sequencing primarily includes two strategies: SNP (sequence-based) and cgMLST (allele-based).
The SNP approach involves comparing single nucleotide differences among isolates to a reference genome, which can be utilized to investigate the relationships between highly similar or clonal group isolates.
The cgMLST approach is an extension of traditional multilocus sequence typing (MLST), expanding the scope of genes analyzed to the whole-genome level. It is often employed as a means to unravel the middle- to long-term evolutionary history of bacterial pathogens.
The phylogenetic grouping scheme for species is generally defined based on the evolutionary relationships and genetic similarities among organisms. In TracePatho, the implementation of this scheme specifically follows these steps:
Firstly, strains from previously published articles with established groupings are utilized as benchmarks, along with existing phylogenetic tree topologies as references. Secondly, based on these reference information, a thorough analysis of the current strains is conducted by constructing new phylogenetic trees or using additional analysis methods (including species identification). Finally, according to the analysis results, the strains are classified into different evolutionary lineages or branches, reflecting their evolutionary histories and genetic similarities.
References for the phylogenetic grouping schemes of individual species can be obtained on the “SourceTrace” page.
Please refer to the PubMLST database for further nformation. It is noted that Acinetobacter baumannii, Vibrioc olerae, and Escherichia coli have more than one public MLSTsc eme. Here in TracePatho, the Pasteur MLST scheme for Acinetobacterbau annii and the Achtman MLST scheme for Escherichia coli are used.