Based on the premise that similar isolates may share similar medical trait, a prima facie concern shared by the global medical community is: ‘Have we seen the particular pathogen before? Where, when and what kind of disease is it associated with?’ To address this concern, a variety of genotyping methods have been developed, of which multi-locus sequence typing (MLST) is considered the gold standard for many bacterial pathogens for over a decade.
Provides access to three typing databases about the Bacillus cereus. HyperCAT incorporates analysis tools combining genotyping data from multiple MultiLocus Sequence Typing (MLST) schemes, as provided in the SuperCAT database, but also from the altogether different approaches Amplified Fragment Length Polymorphism (AFLP) and MultiLocus Enzyme Electrophoresis (MLEE). The database also contains pages presenting various statistics relating to strain distribution, data content and overlap, as well as descriptions of the supertree and supercluster building procedures.
A genotype database of Kudoa septempunctata. We have developed an intraspecific genotyping method, using the sequence variation of mitochondrial genes. We collected olive flounder samples from foodborne disease outbreaks, domestic fish farms or quarantine offices and investigated whether K. septempunctata genotype is associated with pathogenicity or geographic origin. The 104 samples were classified into three genotypes, ST1, ST2 and ST3. Frequency of symptomatic cases differed by genotypes, but the association was not statistically significant. Whereas K. septempunctata detected from aquaculture-raised and natural fish from Japan were either ST1 or ST2, those from fish inspected at quarantine from Korea to Japan were ST3. Our method can be applied to phylogeographic analysis of K. septempunctata and contribute to containing the foodborne disease.
Assists users in the unambiguous characterization of pathogenic Escherichia coli. EcMLST is a multi-locus sequence typing (MLST) database system that comprises locus tables, profile tables, and an isolate table. The database can also be searched using customized queries, which allows users to combine all 27 searchable fields. It also includes data analysis tools in the system, such as scripts for sequence concatenation and allele frequencies calculation.
A bacterial whole genome sequence typing database which is designed for clinicians, clinical microbiologists and hospital epidemiologists. BacWGSTdb borrows the population structure from the current multi-locus sequence typing (MLST) scheme and adopts a hierarchical data structure: species, clonal complex and isolates. When users upload the pre-assembled genome sequences to BacWGSTdb, it offers the functionality of bacterial genotyping at both traditional MLST and whole-genome levels. More importantly, users are told which isolates in the public database are phylogenetically close to the query isolate, along with their clinical information such as host, isolation source, disease, collection time and geographical location. In this way, BacWGSTdb offers a rapid and convenient platform for worldwide users to address a variety of clinical microbiological issues such as source tracking bacterial pathogens.
A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic mobility of their gene products.
Hosts multi-locus sequence typing (MLST) data. PubMLST resources are hosted using the Bacterial Isolate Genome Sequence Database (BIGSdb) platform. A RESTful application programming interface (API) makes the curated and structured data on PubMLST accessible for programmatic access. Users may need to authenticate themselves, for instance to submit data for curation. Access to specific data resources can also be limited to registered users or project members.
Compiles and integrates multilocus sequence typing data from all five schemes for the B. cereus group often involved in food poisoning incidents. The isolates have been classified thank to the seven major phylogenetic clusters of the studied group. The SuperCAT database can be browsed by keywords, MLST scheme, or sequence similarity and according to various criteria such as species, isolate source, or genetic distance.