Within-patient gene transfer between transiently and chronically infecting bacteria causes extreme antibiotic resistance during lung infections

Antibiotic resistance arising during infections is generally thought to be due to mutations in pathogen genomes. Here we studied Pseudomonas aeruginosa and Achromobacter collected from people with cystic fibrosis and non-cystic fibrosis bronchiectasis that suddenly developed 10,000-fold increases in tobramycin resistance after tobramycin treatment was initiated. Genomic analysis showed that resistance did not arise from mutation accumulation or strain displacement. Instead, it occurred because plasmid-borne resistance genes were transferred to the previously sensitive pathogens inside patients' lungs. In some cases, we identified the bacteria that carried plasmids into patients' lungs and they were species capable of environmental growth like Pseudomonas putida. The most commonly transferred gene was an aac(3) aminoglycoside N-acetyltransferase (aac(3)-IIId), not previously associated with clinical resistance. Further analysis suggested that this gene was mobilized from environmental bacteria by a transposon and incorporated into transmissible plasmids. This work shows that gene transfer between transiently and chronically infecting bacteria can produce sudden and large increases in antibiotic resistance during human infections.