Bacterial surface display enables lysis-independent joint host-pathogen single-cell profiling

Area of Science:

• Microbiology
• Immunology
• Genomics

Background:

• Host-pathogen interactions exhibit heterogeneity due to variations in both host and pathogen states.
• Current single-cell methods often analyze host and pathogen features separately, limited by technical mismatches.
• Existing techniques struggle with differences in cell wall structure, lysis requirements, and molecular abundance between host and pathogen.

Purpose of the Study:

• To develop a lysis-independent strategy for unified measurement of intracellular bacteria and host single-cell profiles.
• To enable joint profiling of host cell state and pathogen state simultaneously.
• To overcome technical limitations in current single-cell analysis of host-pathogen interactions.

Main Methods:

• Repurposed bacterial surface display to encode promoter activity and bacterial identity as antibody-detectable signals.
• Utilized antibody-based single-cell assays for unified measurement.
• Applied flow cytometry and droplet-based single-cell RNA sequencing for readout without pathogen-specific lysis.

Main Results:

• Demonstrated a lysis-independent strategy for joint host-pathogen single-cell measurements.
• Successfully linked heterogeneous bacterial uptake to heterogeneous host phagocytosis programs in macrophages.
• Showcased modularity across different bacterial species, including *Escherichia coli* and *Mycobacterium tuberculosis*.

Conclusions:

• The developed strategy enables scalable, joint host-pathogen single-cell measurements.
• Expanded the range of pathogens and states accessible to high-throughput single-cell analysis.
• Facilitates a deeper understanding of host-pathogen dynamics at the single-cell level.