Whole-genome sequencing as an improved means of investigating Neisseria gonorrhoeae treatment failures
Cameron Buckley A , Scott A. Beatson B C D , Athena Limnios E , Monica M. Lahra E F , David M. Whiley A B G and Brian M. Forde B C D H
+ Author Affiliations
- Author Affiliations
A Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Herston, Qld 4029, Australia.
B Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Qld 4072, Australia.
C Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld 4072, Australia.
D School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia.
E WHO Collaborating Centre for STI and AMR, Microbiology Department, New South Wales Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia.
F School of Medical Sciences, UNSW, Sydney, NSW 2052, Australia.
G Pathology Queensland, Microbiology Department, Herston, Qld 4029, Australia.
H Corresponding author: Email: b.forde@uq.edu.au
Sexual Health 16(5) 500-507 https://doi.org/10.1071/SH19012
Submitted: 24 January 2019 Accepted: 22 August 2019 Published: 4 September 2019
Journal Compilation © CSIRO 2019 Open Access CC BY-NC-ND
Abstract
Background: Although rare, Neisseria gonorrhoeae treatment failures associated with ceftriaxone have been reported. The World Health Organization (WHO) recommends standardised protocols to verify these cases. Two cases from Australia were previously investigated using N. gonorrhoeae multiantigen sequence typing (NG-MAST), which has been used extensively to assess treatment failures. Case 1 pharyngeal isolates were indistinguishable, whereas Case 2 pharyngeal isolates were distinguished based on an 18-bp deletion in the major outer membrane porin encoded by the porB gene, questioning the reliability of NG-MAST results. Here we used whole-genome sequencing (WGS) to reinvestigate Cases 1 and 2, with a view to examining WGS to assess treatment failures. Methods: Pre- and post-treatment isolates for each case underwent Illumina sequencing, and the two post-treatment isolates underwent additional long-read sequencing using Pacific Biosciences. Sequence data were interrogated to identify differences at single nucleotide resolution. Results: WGS identified variation in the pilin subunit encoded by the pilE locus for both cases and the specific 18-bp porB deletion in Case 2 was confirmed, but otherwise the isolates in each case were indistinguishable. Conclusions: The WHO recommends standardised protocols for verifying N. gonorrhoeae treatment failures. Case 2 highlights the enhanced resolution of WGS over NG-MAST and emphasises the immediate effect that WGS can have in a direct clinical application for N. gonorrhoeae. Assessing the whole genome compared with two highly variable regions also provides a more confident predictor for determining treatment failure. Furthermore, WGS facilitates rapid comparisons of these cases in the future.
Additional keywords: antimicrobial resistance, public health, surveillance.
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