Design and evaluation of probe-capture sequencing for clinical Neisseria gonorrhoeae specimens

Custom probe-capture sequencing for Neisseria gonorrhoeae achieved 94.6% nucleotide coverage of FA 1090 and enabled large fold increases in pathogen reads from clinical urine.

• Why it matters: Culture-independent diagnostics detect N. gonorrhoeae rapidly, but genomic surveillance still needs methods that align with these workflows to study epidemiology and evolution from hard-to-culture specimens.
• What they did: Biotinylated oligonucleotide baits were designed from 2,877 representative genomes selected from 32,574 assemblies using core genome clustering and resistance genotype/phenotype representation, then tested on 12 urine specimens.
• The result: In complex urine, probe capture increased N. gonorrhoeae read abundance by 226–2046-fold, supporting substantial genome coverage, high-quality assemblies, and detection of resistance-associated genotypes.

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