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首页> 外文期刊>Journal of Medical Microbiology: An Official Journal of the Pathological Society of Great Britain and Ireland >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
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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

机译：通过最优组合查找器计算机程序从一组可变数目的串联重复基因座中选择最佳基因座组合，用于金黄色葡萄球菌食物中毒案例研究

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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.
机译：金黄色葡萄球菌是一种病原体，可以引起医院感染，社区获得性疾病和食源性疾病暴发。各个小组已经报告了许多可变数目的串联重复基因座，用于流行病学研究和暴发调查。这项研究的目的是系统地评估总共18个具有相同金黄色葡萄球菌种群的常用基因座，以便可以比较每个基因座的特性并将其用于打字，并开发一个计算机程序以计算辛普森指数（SI）所有可能的基因座组合，以便可以确定基因座的最佳组合，以进行多基因座可变数串联重复分析（MLVA）分型。从散发性食源性疾病的患者和宠物动物（如犬，猫和马的宠物）中感染皮肤的160株金黄色葡萄球菌分离株用于评估MLVA基因座。使用新开发的最佳组合查找程序（OCF）计算机程序进行分析，发现产生与18个位点组合相同的SI（0.999528）的最小位点组合数目为8; SIRU05，SIRU07，SIRU13，SIRU15，SIRU21，fnbB，sdrD和clfB。这表明可以将八个基因座的最佳组合用于常规调查和未来金黄色葡萄球菌暴发的监测，而不是全部使用18个基因座。另外，OCF软件可能是开发其他生物的打字方案的有用工具。

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