High-throughput paired scRNA sequencing reveals crosstalk between zinc starvation and zinc toxicity in macrophage antibacterial defense

Mechanisms by which macrophages deploy antibacterial zinc toxicity are poorly understood. To gain insight into this antimicrobial pathway, we developed high-throughput bacterial-paired single-cell RNA sequencing of human monocyte-derived macrophages (HMDM) infected with an E. coli zinc-stress reporter strain. Here, the 10X Genomics Chromium platform and feature barcoding was utilized, to capture feature barcode sequences in reporter genes of an E. coli strain to allow for transcript capture and enrichment during the 10X Genomics workflow. These genes report on zinc stress, and were used to track E. coli zinc stress during infection in human monocyte-derived macrophages. Utilising this approach, we identified HMDM sub-populations harbouring zinc-stressed E. coli and corresponding mammalian genes predicted to be associated with either zinc toxicity or survival of zinc-stressed bacteria.