Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

<jats:p><jats:bold>Background</jats:bold>. Empirical gonorrhoea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance.</jats:p> <jats:p><jats:bold>Methods</jats:bold>. We investigated if Nanopore sequencing can detect sufficient <jats:italic>N. gonorrhoeae</jats:italic> DNA to reconstruct whole genomes directly from urine samples. We used <jats:italic>N. gonorrhoeae</jats:italic> spiked urine samples and samples from gonorrhoea infections to determine optimal DNA extraction methods that maximize the amount of <jats:italic>N. gonorrhoeae</jats:italic> DNA sequenced whilst minimizing contaminating host DNA.</jats:p> <jats:p><jats:bold>Results</jats:bold>. In simulated infections the Qiagen UCP Pathogen Mini kit provided the highest ratio <jats:italic>N. gonorrhoeae</jats:italic> to human DNA and the most consistent results. Depletion of human DNA with saponin increased <jats:italic>N. gonorrhoeae</jats:italic> yields in simulated infections, but decreased yields in clinical samples. In ten urine samples from men with symptomatic urethral gonorrhoea, ≥92.8% coverage of an <jats:italic>N. gonorrhoeae</jats:italic> reference genome was achieved in all samples, with ≥93.8% coverage breath at ≥10-fold depth in 7 (70%) samples. In simulated infections if ≥10<jats:sup>4</jats:sup> CFU/ml of <jats:italic>N. gonorrhoeae</jats:italic> was present, sequencing of the large majority of the genome was frequently achieved. <jats:italic>N. gonorrhoeae</jats:italic> could also be detected from urine in cobas PCR Media tubes and from urethral swabs, and in the presence of simulated <jats:italic>Chlamydia</jats:italic> co-infection.</jats:p> <jats:p><jats:bold>Conclusion</jats:bold>. Using Nanopore sequencing of urine samples from men with urethral gonorrhoea sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture.</jats:p>

Original publication




Journal article


Journal of Clinical Microbiology


American Society for Microbiology

Publication Date