Selection of optimal combinations of loci by the Optimal Combination Finder computer program from a group of variable number tandem repeat loci for use in Staphylococcus aureus food poisoning case investigations

Staphylococcus aureus is a pathogen that can be the cause of nosocomial infections, community-acquired diseases and food-borne disease outbreaks. A number of variable number tandem repeat loci have been reported by various groups for use in epidemiological studies and outbreak investigations. The aim of this study was to systematically evaluate a total of 18 commonly used loci with the same S. aureus population so that the properties of each locus could be compared and used for typing, and to develop a computer program enabling calculation of the Simpson index (SI) of all possible loci combinations so that an optimal combination of loci could be identified for multilocus variable-number tandem-repeat analysis (MLVA) typing. A collection of 160 S. aureus isolates from patients with sporadic food-borne illnesses, and pet animals, such as canine, feline and equine pets, with skin infections were used to assess the MLVA loci. The newly developed Optimal Combination Finder (OCF) computer program was used for the analysis and it was found that the minimal number of loci combinations that produced the same SI (0.999528) as that of the 18 loci combined was eight; SIRU05, SIRU07, SIRU13, SIRU15, SIRU21, fnbB, sdrD and clfB. This suggested that the optimal combination of eight loci could be used for the routine investigation and surveillance of future S. aureus outbreaks instead of using all 18 loci. In addition, the OCF software could be a useful tool for the development of typing schemes for other organisms.