Document Detail


Selection of optimal loci combinations by a computer program Optimal Combination Finder from a group of variable number tandem repeat loci for Staphylococcus aureus food poisoning case investigations.
MedLine Citation:
PMID:  22267543     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Staphylococcus aureus is a pathogen causing nosocomial infection, community-acquired diseases, and food borne outbreak diseases. A number of variable number tandem repeat loci have been reported by various groups for epidemiological studies and outbreak investigations. The aims of this study were (1) to systematically evaluate a total of 18 commonly used loci with the same S. aureus population for the first time so that the properties of each locus would be comparable and useful for typing; and (2) to develop a computer program enabling calculation of the Simpson Index (SI) of all possible loci combinations so that an optimal loci combination could be identified for multi-locus variable-tandem-repeat analysis (MLVA) typing. A collection of 160 S. aureus isolates from sporadic food borne illness patients and skin infections of pet animals such as canine, feline, and equine were used to assess the MLVA loci. The newly developed computer program Optimal Combination Finder (OCF) was used for the analysis and it was found that the minimal number of 8 loci combination of SIRU05, SIRU07, SIRU13, SIRU15, SIRU21, fnbB, sdrD, and clfB produced the same Simpson Index (0.999528) as that of the 18 loci combined. This suggested that the 8 loci optimal combination could be used for future S. aureus routine outbreak investigations and surveillance, instead of using all 18 loci. In addition, the software OCF would be a useful tool for development of typing schemes for other organisms.
Authors:
Xian Wang; Bixing Huang; Barry Blair; Sofroni Eglezos; John Bates
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-1-19
Journal Detail:
Title:  Journal of medical microbiology     Volume:  -     ISSN:  1473-5644     ISO Abbreviation:  -     Publication Date:  2012 Jan 
Date Detail:
Created Date:  2012-1-23     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0224131     Medline TA:  J Med Microbiol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
1 Shijiazhuang Center for Disease Control and Prevention, China;
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