你原来的翻译弄得太复杂了.
当一研究用两个系统分别鉴定相同菌株时,我们计算其鉴定率时取该两系统鉴定率的平均值:
In identifying the same bacterial strain by means of two systems in a research,the average (value) of (proportions from) the two system is taken when calculating the proportion (鉴定率?).
【注】不懂你句子中术语,但结构应该如上.