Transmission and Antibiotic Resistance of in Cystic Fibrosis.

species are increasingly being detected in patients with cystic fibrosis (CF), and this emerging pathogen is associated with antibiotic resistance and more-severe disease outcomes. Nonetheless, little is known about the extent of transmission and antibiotic resistance development in infections. We sequenced the genomes of 101 clinical isolates (identified as based on matrix-assister laser desorption ionization-time of flight [MALDI-TOF] or API N20 typing) collected from 51 patients with CF-the largest longitudinal data set to date. We performed phylogenetic analysis on the genomes and combined this with epidemiological and antibiotic resistance data to identify patient-to-patient transmission and the development of antibiotic resistance. We confirmed that the MALDI-TOF or API N20 method was not sufficient for species-level typing and that the population of isolates was composed of five different species, among which accounted for 52% of infections. Most patients were infected by unique clone types; nonetheless, suspected patient-to-patient transmission cases identified by shared clone types were observed in 35% ( = 18) of patients. In 15 of 16 cases, the suspected transmissions were further supported by genome- or clinic visit-based epidemiological analysis. Finally, we found that resistance developed over time. We show that whole-genome sequencing (WGS) is essential for species typing and identification of patient-to-patient transmission, which was revealed for , , and, for the first time, Furthermore, we show that the development of antibiotic resistance is associated with chronic infections. Our findings emphasize that transmission and antibiotic resistance should be considered in future treatment strategies.