Internet-based sequence-typing databases for bacterial molecular epidemiology.
As the use of nucleotide sequence-based typing has become more widespread in the investigation of microbial epidemiology, there has been a natural requirement for curated Internet-based databases that can act as central authorities for nomenclature and type definitions. These facilitate the sharing and comparison of data between laboratories without the need for reference samples. Here, the use of the most common multilocus sequence typing (MLST) and antigen sequence databases are described. In particular, for MLST, the steps required for allele sequence and profile identification are explained along with a detailed overview of searching and matching isolate records. BLAST searching of antigen sequence databases is also described.
Jolley
Keith A
KA
Department of Zoology and Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford, UK.
D000483:Alleles; D000942:Antigens, Bacterial / Q000235:genetics; D001419:Bacteria / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification; D015373:Bacterial Typing Techniques / Q000706:statistics & numerical data; D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D017720:Molecular Epidemiology / Q000706:statistics & numerical data*
D000942:Antigens, Bacterial