RT Journal Article SR Electronic T1 High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.02.07.939322 DO 10.1101/2020.02.07.939322 A1 Nicholas D Sanderson A1 Jeremy Swann A1 Leanne Barker A1 James Kavanagh A1 Sarah Hoosdally A1 Derrick Crook A1 the GonFast Investigators Group A1 Teresa L Street A1 David W Eyre YR 2020 UL http://biorxiv.org/content/early/2020/02/09/2020.02.07.939322.abstract AB The rise of antimicrobial resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhoea can recover near-complete N. gonorrhoeae genomes. However, disentangling the N. gonorrhoeae genome from metagenomic samples and robustly identifying antimicrobial resistance determinants from error-prone Nanopore sequencing is a substantial bioinformatics challenge.Here we demonstrate an N. gonorrhoeae diagnostic workflow for analysis of metagenomic sequencing data obtained from clinical samples using R9.4.1 Nanopore sequencing. We compared results from simulated and clinical infections with data from known reference strains and Illumina sequencing of isolates cultured from the same patients. We evaluated three Nanopore variant callers and developed a random forest classifier to filter called SNPs. Clair was the most suitable variant caller after SNP filtering. A minimum depth of 20x reads was required to confidently identify resistant determinants over the entire genome. Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic information in N. gonorrhoeae infection.