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Achromobacterspecies 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 inAchromobacterinfections.We sequenced the genomes of 101 clinical isolates ofAchromobacter(A. xylosoxidansbased on MALDI-TOF/API N20 typing) collected from 51 patients with CF—the largest longitudinal dataset 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 development of antibiotic resistance.We found that MALDI-TOF/API N20 was not sufficient forAchromobacterspecies-level typing, and that the population ofAchromobacterisolates was composed of five different species whereA. xylosoxidansaccounted for 52% of infections. Most patients were infected by uniqueAchromobacterclone types; nonetheless, suspected patient-to-patient transmission cases identified by shared clone types were observed in 35% (N=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 forAchromobacterspecies typing and patient-to-patient transmission identification which was identified inA. ruhlandii, A. xylosoxidansand, for the first time,A. insuavis. Furthermore, we show that the development of antibiotic resistance is associated with chronicAchromobacterinfections. Our findings emphasize that transmission and antibiotic resistance should be considered in future treatment strategies. |
