The organism is different from other rickettsias in its ability to survive outside host cells by forming a resistant spore like body which resist drying, heating up to 63C for 30 minutes and chemical disinfectant such as phenol and formaline, and its ability to undergo phase variation and give phase I and phase II antigens. The phase I is weakly antigenic.
Genetically phase II is missing a 26 kb region of the chromosome, which is what renders it avirulent. In addition there is another Coxiella genotype possible, and is the C. burneii Nine Mile Crazy, which is missing a 32 kb region in the same area of the chromosome. To differentiate between phase I and phase II, I would design PCR or qPCR primers to target this area. If you get a product then it is phase I if no product then phase II. See http://jb.asm.org/content/188/7/2309.long for more details on the deleted regions.
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