Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK

Abstract Background We aimed to estimate the prevalence of different Achromobacter species among UK Cystic Fibrosis (CF) patients. Methods nrdA sequence clustering was used to identify 147 Achromobacter isolates from 96 patients from 27 hospitals to species level. Potential cross-infection was investigated by MLST, pulsed-field gel electrophoresis and whole genome sequencing (WGS). Results Achromobacter xylosoxidans was the most prevalent species affecting 59 of 96 (61%) patients, followed by Achromobacter insuavis and Achromobacter dolens (12.4% and 8%, respectively). Three novel nrdA clusters were identified. One was further characterised by sequencing the intrinsic bla OXA gene, revealing novel variants. WGS of A. insuavis 2a isolates from four patients attending the same paediatric unit revealed that three were ST144, but differed from one another by a minimum of 385 SNPs, suggesting cross-infection was unlikely. Conclusions nrdA sequence clustering permitted an estimation of UK Achromobacter species prevalence, highlighted additional novel species, and aided cross-infection investigations.