AbstractUpon host cell infection, the obligate intracellular bacteriumC. burnetiiresides and multiplies within theCoxiella–ContainingVacuole (CCV). The nascent CCV progresses through the endosomal maturation pathway into a phagolysosome, acquiring lysosomal markers as well as acidic pH and active proteases and hydrolases. Approximately 24-48 hours post infection, heterotypic fusion between the CCV and host endosomes/lysosomes leads to CCV expansion and subsequent bacterial replication in the mature CCV. Initial CCV acidification is required to activateC. burnetiimetabolism and the Type 4B Secretion System (T4BSS), which secretes effector proteins required for CCV maturation. However, we recently found that the mature CCV is less acidic (pH~5.2) than lysosomes (pH~4.8). Further, CCV acidification to pH~4.8 causesC. burnetiilysis, suggestingC. burnetiiactively regulates CCV pH. Because heterotypic fusion with host endosomes/lysosomes may influence CCV pH, we investigated endosomal maturation in cells infected with wildtype (WT) or T4BSS mutant (ΔdotA)C. burnetii. We observed significantly fewer LAMP1-positive lysosomes, along with less acidic “mature” endosomes (pH~5.8), in WT-infected cells, compared to mock or ΔdotA-infected cells. Further, while endosomes progressively acidified from the periphery (pH~5.5) to the perinuclear area (pH~4.7) in both mock and ΔdotA-infected cells, endosomes did not acidify beyond pH~5.2 in WT-infected cells, indicating that theC. burnetiiT4BSS inhibits endosomal maturation. Finally, increasing the number of acidic lysosomes by overexpressing the transcription factor EB inhibitedC. burnetiigrowth, indicating lysosomes are detrimental toC. burnetii. Overall, our data suggest thatC. burnetiiregulates CCV pH, possibly by reducing the number of host lysosomes available for heterotypic fusion.Author summaryThe obligate intracellular bacteriumCoxiella burnetiicauses human Q fever, which manifests as a flu-like illness but can develop into a life-threatening and difficult to treat endocarditis.C. burnetii,in contrast to many other intracellular bacteria, thrives within a lysosome-like vacuole in host cells. However, we previously found that theC. burnetiivacuole is not as acidic as lysosomes and increased acidification kills the bacteria, suggesting thatC. burnetiiregulates the pH of its vacuole. Here, we discovered thatC. burnetiiblocks endosomal maturation and acidification during host cell infection, resulting in fewer lysosomes in the host cell. Moreover, increasing lysosomes in the host cells blockedC. burnetiigrowth. Together, our study suggests thatC. burnetiiregulates vacuole acidity and blocks endosomal acidification in order to produce a permissive intracellular niche.