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

Amy Coward; Dervla T D Kenna; Claire Perry; Kate Martin; Michel Doumith; Jane F Turton

doi:10.1016/j.jcf.2015.09.005

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

J Cyst Fibros. 2016 Jul;15(4):479-85. doi: 10.1016/j.jcf.2015.09.005. Epub 2015 Sep 26.

Authors

Amy Coward¹, Dervla T D Kenna², Claire Perry¹, Kate Martin¹, Michel Doumith³, Jane F Turton¹

Affiliations

¹ Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
² 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.
³ 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.

PMID: 26412052
DOI: 10.1016/j.jcf.2015.09.005

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 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.

Conclusions: nrdA sequence clustering permitted an estimation of UK Achromobacter species prevalence, highlighted additional novel species, and aided cross-infection investigations.

Keywords: Achromobacter species; CF; bla(OXA) genes; nrdA.

MeSH terms

Achromobacter / classification*
Achromobacter denitrificans* / genetics
Achromobacter denitrificans* / isolation & purification
Bacterial Typing Techniques / methods*
Cross Infection / diagnosis
Cross Infection / epidemiology
Cross Infection / microbiology
Cystic Fibrosis* / diagnosis
Cystic Fibrosis* / epidemiology
Cystic Fibrosis* / microbiology
DNA, Bacterial / analysis*
Electrophoresis, Gel, Pulsed-Field / methods
Gram-Negative Bacterial Infections* / diagnosis
Gram-Negative Bacterial Infections* / epidemiology
Gram-Negative Bacterial Infections* / microbiology
Humans
Multigene Family
Multilocus Sequence Typing / methods*
Prevalence
United Kingdom / epidemiology
Whole Genome Sequencing / methods

Substances

DNA, Bacterial