A genome-wide CRISPR screen identified host genes essential for intracellular survival.

is a zoonotic intracellular bacterium that poses threats to human health and economic security. Intracellular infection is a hallmark of the agent and a primary cause of distress, through which the bacterium regulates the host intracellular environment to promote its own colonization and replication, evading host immunity and pharmaceutical killing. Current studies of intracellular processes are typically premised on bacterial phenotype such as intracellular bacterial survival, followed by biochemical or molecular biological approaches to reveal detailed mechanisms. While such processes can deepen the understanding of -host interaction, the insights into host alterations in infection would be easily restricted to known pathways. In the current study, we applied CRISPR Cas9 screen to identify host genes that are most affected by infection on cell viability at the genomic level. As a result of CRISPR screening, we firstly identified that knockout of the negatively selected genes , , , and attenuate the viability of both the host cells and intracellular , suggesting these genes to be potential therapeutic targets for control. In particular, knockout of diminished intracellular survival by altering host cell autophagy. Conversely, knockout of positive screening genes promoted intracellular proliferation of . In summary, we screened host genes at the genomic level throughout infection, identified host genes that are previously not recognized to be involved in infection, and provided targets for intracellular infection control.IMPORTANCE is a Gram-negative bacterium that infects common mammals causing arthritis, myalgia, neuritis, orchitis, or miscarriage and is difficult to cure with antibiotics due to its intracellular parasitism. Therefore, unraveling the mechanism of -host interactions will help controlling infections. CRISPR-Cas9 is a gene editing technology that directs knockout of individual target genes by guided RNA, from which genome-wide gene-knockout cell libraries can be constructed. Upon infection with , the cell library would show differences in viability as a result of the knockout and specific genes could be revealed by genomic DNA sequencing. As a result, genes affecting cell viability during infection were identified. Further testing of gene function may reveal the mechanisms of -host interactions, thereby contributing to clinical therapy.