title: Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK.
abstract: We aimed to estimate the prevalence of different Achromobacter species among UK Cystic Fibrosis (CF) patients.
  
  
  
  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).
  
  
  
  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 blaOXA 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.
  
  
  
  nrdA sequence clustering permitted an estimation of UK Achromobacter species prevalence, highlighted additional novel species, and aided cross-infection investigations.
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
authors.forename: Amy
authors.initials: A
authors.lastname: Coward
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom. Electronic address: dervla.kenna@phe.gov.uk.
authors.forename: Dervla T D
authors.initials: DT
authors.lastname: Kenna
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
authors.forename: Claire
authors.initials: C
authors.lastname: Perry
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
authors.forename: Kate
authors.initials: K
authors.lastname: Martin
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; Bioinformatics Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
authors.forename: Michel
authors.initials: M
authors.lastname: Doumith
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
authors.forename: Jane F
authors.initials: JF
authors.lastname: Turton
mesh_terms: D042402:Achromobacter / Q000145:classification*; D042441:Achromobacter denitrificans / Q000235:genetics / Q000302:isolation & purification; D015373:Bacterial Typing Techniques / Q000379:methods*; D003428:Cross Infection / Q000175:diagnosis / Q000453:epidemiology / Q000382:microbiology; D003550:Cystic Fibrosis / Q000175:diagnosis / Q000453:epidemiology / Q000382:microbiology; D004269:DNA, Bacterial / Q000032:analysis*; D016521:Electrophoresis, Gel, Pulsed-Field / Q000379:methods; D016905:Gram-Negative Bacterial Infections / Q000175:diagnosis / Q000453:epidemiology / Q000382:microbiology; D006801:Humans; D005810:Multigene Family; D058885:Multilocus Sequence Typing / Q000379:methods*; D015995:Prevalence; D006113:United Kingdom / Q000453:epidemiology; D000073336:Whole Genome Sequencing / Q000379:methods
chemical_list: D004269:DNA, Bacterial
keywords: Achromobacter species; CF; bla(OXA) genes; nrdA