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Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq

Abstract : Streptococcus pneumoniae is an opportunistic human pathogen that causes invasive diseases, including pneumonia, with greater health risks upon influenza A virus (IAV) co-infection. To facilitate pathogenesis studies in vivo, we developed an inducible CRISPR interference system that enables genome-wide fitness testing in one sequencing step (CRISPRi-seq). We applied CRISPRi-seq to assess bottlenecks and identify pneumococcal genes important in a murine pneumonia model. A critical bottleneck occurs at 48 h with few bacteria causing systemic infection. This bottleneck is not present during IAV superinfection, facilitating identification of pneumococcal pathogenesis-related genes. Top in vivo essential genes included purA, encoding adenylsuccinate synthetase, and the cps operon required for capsule production. Surprisingly, CRISPRi-seq indicated no fitness-related role for pneumolysin during superinfection. Interestingly, although metK (encoding S-adenosylmethionine synthetase) was essential in vitro, it was dispensable in vivo. This highlights advantages of CRISPRi-seq over transposon-based genetic screens, as all genes, including essential genes, can be tested for pathogenesis potential.
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https://www.hal.inserm.fr/inserm-03299441
Contributor : Jean-Claude Sirard Connect in order to contact the contributor
Submitted on : Monday, July 26, 2021 - 2:28:36 PM
Last modification on : Tuesday, July 27, 2021 - 2:40:15 PM

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Xue Liu, Jacqueline Kimmey, Vincent de Bakker, Victor Nizet, Jan-Willem Veening. Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq. Cell Host & Microbe, 2021, 29 (1), pp.107-120.e6. ⟨10.1016/j.chom.2020.10.001⟩. ⟨inserm-03299441⟩

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