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Updated: Jan 9, 2026

Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow
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Publicly Available Neisseria Gonorrhoeae Genomes Predominantly Represent In Vitro-Derived Nonpiliated Variants.

Iryna Boiko1, Selma Metaane1, H Steven Seifert1

  • 1Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

The Journal of Infectious Diseases
|December 3, 2025
PubMed
Summary
This summary is machine-generated.

Most Neisseria gonorrhoeae strains analyzed had non-functional pilE genes, suggesting they are derived from nonpiliated variants. This pilin variation impacts gonococcal population diversity and immune evasion strategies.

Keywords:
Neisseria gonorrhoeaepilEpilSantigenic variationphase variation

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Area of Science:

  • Microbiology
  • Genomics
  • Bacterial Pathogenesis

Background:

  • Neisseria gonorrhoeae utilizes the pilE gene, encoding the Type IV pilus major subunit, for colonization and virulence.
  • High-frequency diversification of pilE via gene conversion from pilS copies aids immune evasion and population diversity.
  • Limited data exists on the diversity of pilE and pilS genes in clinical isolates.

Purpose of the Study:

  • To characterize the diversity of pilE and pilS genes in Neisseria gonorrhoeae.
  • To investigate the prevalence of functional pilE genes in clinical isolates.

Main Methods:

  • Analysis of 15,186 Neisseria gonorrhoeae genomes from the PubMLST database.
  • Inclusion of both finished (n=65) and draft (n=15,121) genome sequences.

Main Results:

  • While pilS loci were common (1-9 per genome), only 52.13% of sequences contained a pilE gene.
  • When present, pilE genes largely preserved conserved sequences, but many predicted PilE proteins had premature stop codons.
  • Premature stop codons were also observed in silent pilS copies.

Conclusions:

  • All strains possess the genetic machinery for pilin AV.
  • Most analyzed genomic sequences represent nonpiliated variants, likely due to in vitro culture-induced pilus phase variation and pilE gene deletion.
  • This suggests a significant proportion of N. gonorrhoeae may exist as nonpiliated forms.