Anti-influenza and anti-COVID-19 drugs promote bacterial antibiotic cross-resistance through drug-specific adaptive pathways.

The extensive use of antiviral drugs for COVID-19 and influenza has increased their release into clinical and environmental settings, yet their potential to promote bacterial antibiotic cross-resistance remains poorly understood. Here, we investigated the antibacterial off-target effects of four clinically used anti-IFV/COV drugs-baloxavir acid (BXA), favipiravir (FAV), nirmatrelvir/ritonavir (NMV/r), and oseltamivir phosphate (OSV)-and their potential to influence bacterial stress responses and antibiotic cross-resistance in Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa PAO1. BXA and NMV/r showed clear antibacterial off-target effects, while antiviral exposure induced rapid oxidative and metabolic stress in a drug- and species-dependent manner. Following high-dose single-drug selection, evolved populations developed distinct antibiotic cross-resistance profiles, with BXA producing the broadest effects and B. subtilis showing the most recurrent β-lactam-associated responses. Under chronic environmental mixture exposure, low-dose antivirals further promoted β-lactam resistance, again with the strongest response observed in B. subtilis, highlighting the potential risk of antiviral residues as environmental selective pressures for antibiotic resistance. Comparative transcriptomic analysis further revealed that cross-resistance did not arise from a universal resistance pathway, but from drug-specific adaptive remodeling, including transporter and metabolic responses under BXA, sporulation/biofilm-associated developmental responses under NMV/r, and a more limited response to OSV. Together, this study provides initial systematic evidence that clinically used anti-IFV/COV drugs can directly perturb bacterial physiology and promote antibiotic cross-resistance under both elevated and environmentally relevant exposure scenarios, identifying antiviral contamination as an underappreciated driver of antibiotic resistance evolution.