The effects of antibiotic combination treatments on Pseudomonas aeruginosa tolerance evolution and coexistence with Stenotrophomonas maltophilia

<p><em>Pseudomonas aeruginosa</em> bacterium is a common pathogen of Cystic Fibrosis (CF) patients due to its ability to evolve resistance to antibiotics during treatments. While <em>P. aeruginosa</em> resistance evolution is well characterised in monocultures, it is less well understood in polymicrobial CF infections. Here, we investigated how exposure to ciprofloxacin, colistin, or tobramycin antibiotics, administered at sub-MIC doses alone and in combination, shaped the tolerance evolution of <em>P. aeruginosa</em> (PAO1 lab and clinical CF LESB58 strains) in the absence and presence of a commonly co-occurring species, <em>Stenotrophomonas maltophilia</em>. Increases in antibiotic tolerances were primarily driven by the presence of that antibiotic in the treatment. We observed a reciprocal cross-tolerance between ciprofloxacin and tobramycin, and when combined these antibiotics selected increased MICs for all antibiotics. Though the presence of <em>S. maltophilia</em> did not affect the tolerance or the MIC evolution, it drove <em>P. aeruginosa</em> into extinction more frequently in the presence of tobramycin due to its relatively greater innate tobramycin tolerance. In contrast, <em>P. aeruginosa</em> dominated and drove <em>S. maltophilia</em> extinct in most other treatments. Together, our findings suggest that besides driving high-level antibiotic tolerance evolution, sub-MIC antibiotic exposure can alter competitive bacterial interactions, leading to target pathogen extinctions in multi-species communities.</p>