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Background   Coxiella burnetii  is the etiologic agent of Q fever, a zoonotic disease causing influenza-like illness, pregnancy loss, cardiovascular disease and chronic fatigue syndrome in people.  C. burnetii  is considered to be enzootic in ruminants, but clinical signs of infection do not always manifest. National studies have documented the presence of  C. burnetii  in dairy herds in Indiana. This represents an opportunity to better characterize the distribution and prevalence of  C. burnetii  infection at the state scale, allowing evaluation of the need for surveillance and response planning to occur at this level. A cross-sectional study was conducted to estimate the herd prevalence of  C. burnetii  in commercial cattle dairies in Indiana and characterize the strains of  C. burnetii  within these dairies.    Results  Bulk tank milk samples were collected between June and August of 2011 by the Indiana State Board of Animal Health (ISBOAH). A total of 316 of these samples were tested for the  IS1111  transposon of  C. burnetii  using quantitative real time polymerase chain reaction (PCR). Single nucleotide polymorphism (SNP) genotyping was used to identify the multispacer sequence genotypes (ST) present in samples where the  IS1111  transposon was identified. The geographic distribution of dairies testing positive for  C. burnetii  DNA and the identified STs were also evaluated. The estimated overall herd prevalence for  C. burnetii  DNA was 61.1 % (95 % CI 55.6–66.3 %). The highest estimated regional prevalence was 70.2 % in the Central region of Indiana. An ST was identifiable in 74 of the positive 178 samples (41.6 %) and none of the 10 negative samples tested. Of these samples, 71 (95.9 %) were identified as  ST20 , 2 (2.7 %) as  ST8  and a combination of  ST20  and  ST8  was identified in a single sample.    Conclusions   C. burnetii  is present in dairy herds throughout Indiana. Indiana follows national trends with  ST20  most commonly identified. The presence of multiple STs in a single bulk tank sample indicates that multiple strains of  C. burnetii  can circulate within a herd. This supports potential transmission of  C. burnetii  between goats and cattle, presenting the potential for a switch in the dominant genotype found in a given species.    Electronic supplementary material  The online version of this article (doi:10.1186/s12917-015-0517-3) contains supplementary material, which is available to authorized users.

Estimated herd prevalence and sequence types of Coxiella burnetii in bulk tank milk samples from commercial dairies in Indiana