Efficient transmission of pathogens by an arthropod vector is influenced by the ability of the pathogen to replicate and develop infectiousness within the arthropod host. While the basic life cycle of development within and transmission from the arthropod vector are known for many bacterial and protozoan pathogens, the determinants of transmission efficiency are largely unknown and represent a significant gap in our knowledge. The St. Maries strain of Anaplasma marginale is a high-transmission-efficiency strain that replicates to a high titer in the tick salivary gland and can be transmitted by <10 ticks. In contrast, A. marginale subsp. centrale (Israel vaccine strain) has an identical life cycle but replicates to a significantly lower level in the salivary gland, with transmission requiring >30-fold more ticks. We hypothesized that strain-specific genes expressed in the tick salivary gland at the time of transmission are linked to the differences in the transmission efficiency phenotype. Using both annotation-dependent and -independent analyses of the complete genome sequences, we identified 58 strain-specific genes. These genes most likely represent divergence from common ancestral genes in one or both strains based on analysis of synteny and lack of statistical support for acquisition as islands by lateral gene transfer. Twenty of the St. Maries strain-specific genes and 16 of the strain-specific genes in the Israel strain were transcribed in the tick salivary gland at the time of transmission. Although associated with the transmission phenotype, the expression levels of strain-specific genes were equal to or less than the expression levels in infected erythrocytes in the mammalian host, suggesting that function is not limited to salivary gland colonization.Transmission efficiency is a primary determinant of pathogen prevalence. Strain-specific differences in transmission efficiency underlie the strain structure in the host population and the patterns of infection and disease. For example, cholera pandemics are associated with a limited diversity of related, highly transmissible Vibrio cholerae strains (4). For vectorborne pathogens, efficient transmission is also dictated by infection and replication within the arthropod host (10,15,25,26). While the basic cycle of development within the arthropod vector has been identified for many important pathogens, including Anaplasma, Borrelia, Plasmodium, Rickettsia, and Trypanosoma, the critical microbial determinants of transmission efficiency in the vector remain unknown for most bacterial and protozoan pathogens.Transmission of Anaplasma spp. is initiated when ixodid ticks ingest an infected blood meal during acquisition feeding on a bacteremic mammalian host (25, 26). The organisms then replicate within the midgut epithelium, invade the salivary gland, and, concomitant with attachment and feeding on a naïve host, undergo a second round of replication and are released into the saliva for transmission (13,25,26). Importantly, the efficiencies of this developmental...