Quantitative three-dimensional imaging of Coxiella burnetii infection by focused ion beam-scanning electron microscopy.

Coxiella burnetii is a highly virulent intracellular pathogen and the causative agent of acute and chronic Q fever in humans. Central to its pathogenicity is the Dot/Icm type IV secretion system, which translocates more than 100 effector proteins into host cells to drive the biogenesis of Coxiella-containing vacuoles (CCVs), which are specialized, lysosome-derived compartments that support bacterial replication. During intracellular growth, C. burnetii undergoes a distinctive biphasic developmental cycle, transitioning between the infectious, dormant small cell variant and the replicative large cell variant. Although this developmental transition is tightly linked to CCV biogenesis, the underlying mechanisms remain poorly understood. Here, we combine advanced focused ion beam-scanning electron microscopy (FIB-SEM) with machine learning-based data analysis to visualize C. burnetii-infected host cells in three dimensions. This approach reveals striking pleiomorphism in both bacterial morphology and CCV architecture. Moreover, we demonstrate that FIB-SEM-based quantitative analysis can sensitively detect CCV biogenesis defects in C. burnetii mutants that fail to generate the large vacuoles characteristic of wild-type infection. Specifically, analysis of HeLa cells infected with a cig2::Tn mutant confirms that this strain forms smaller CCVs with pronounced defects in homotypic fusion. Our study provides unprecedented three-dimensional insights into the complex intracellular lifestyle of C. burnetii and establishes FIB-SEM as a powerful platform for dissecting CCV biogenesis, bacterial development, and mutant phenotypes in infected host cells.