The inter-continental population dynamics of Neisseria gonorrhoeae

Osnes, M. N.; Brynildsrud, O. B.; Alfsnes, K.; van Dorp, L.; McKeand, S. A.; Ross, J.; Town, K.; De Korne-Elenbaas, J.; van Dam, A.; Bruisten, S.; de Blasio, B. F.; Caugant, D. A.; Grad, Y. H.; Williamson, D. A.; Balloux, F.; Didelot, X.; Eldholm, V.

doi:10.1101/2023.08.02.551601

bioRxiv · 10.1101/2023.08.02.551601

The inter-continental population dynamics of Neisseria gonorrhoeae

Osnes, M. N.·Brynildsrud, O. B.·Alfsnes, K.·van Dorp, L.·McKeand, S. A.·Ross, J.·Town, K.·De Korne-Elenbaas, J.·van Dam, A.·Bruisten, S.·de Blasio, B. F.·Caugant, D. A.·Grad, Y. H.·Williamson, D. A.·Balloux, F.·Didelot, X.·Eldholm, V.

View original source ↗Export metadata ↓

Abstract

Neisseria gonorrhoeae is a globally distributed sexually transmitted bacterial pathogen. Recent studies have revealed that its evolution has been shaped by antibiotic use, while molecular surveillance efforts have demonstrated large changes in lineage composition over relatively short time-spans. However, the global population dynamics of N. gonorrhoeae remain unsatisfyingly characterized. To reconstruct recent large-scale population dynamics, we generated a dated phylogeny from 9,732 N. gonorrhoeae genomes and found the effective population size of the species to have expanded gradually over the past two centuries. While the effective population size of clades with reduced susceptibility to extended-spectrum cephalosporins started declining around 2010, a major clade containing a mosaic mtr operon associated with cephalosporin susceptibility and decreased azithromycin did not display any reduction in population size. Using ancestral trait reconstruction analyses, we delineated transmission lineages, defined as groups of sequences in which all the samples can be traced back to the same import event to a given location. Import, export and local transmission dynamics across two densely sampled locations (Norway and Victoria, Australia) were investigated in detail. Norway exhibited substantially higher rates of strain import and export compared to Victoria, where incidence was to a larger extent fuelled by locally transmitted lineages. Taken together, our work highlights the power of large-scale phylogenomic analyses to uncover the complex dynamics of lineage transmission in N. gonorrhoeae.

Explore related subjects

microbiology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Osnes, M. N., Brynildsrud, O. B., Alfsnes, K., van Dorp, L., McKeand, S. A., Ross, J., Town, K., De Korne-Elenbaas, J., van Dam, A., Bruisten, S., de Blasio, B. F., Caugant, D. A., Grad, Y. H., Williamson, D. A., Balloux, F., Didelot, X., Eldholm, V.. 2023-08-02. The inter-continental population dynamics of Neisseria gonorrhoeae. https://doi.org/10.1101/2023.08.02.551601

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Cell cycle progression and stalked cell morphogenesis in Caulobacter crescentus are regulated independently by the flagellum

Bacteria colonize surfaces and form biofilms to survive in stressful environmental conditions. Many bacteria use an appendage called the flagellum to sense surface contact, and responding to these mechanical cues triggers rapid physiological changes to promote downstream attachment. Bacteria are known to secrete adhesins and alter their motility behavior to facilitate surface colonization, but these changes alone are insufficient to explain the breadth of adaptations observed in surface-attached cells. Disrupting flagellar assembly in the bacterium Caulobacter crescentus constitutively activates the surface sensing pathway, and this gain-of-function phenotype was previously used to identify a suite of flagellar signaling suppressor (fss) genes that promotes surface adhesion downstream of the flagellum. We show herein that a subset of fss genes also regulates the C. crescentus developmental program. Live-cell microscopy analysis of fss mutants identified independent sub-pathways that target stalked cell morphogenesis and cell cycle progression. We identify the predicted chemotaxis genes fssD and fssE as novel regulators of stalked cell morphogenesis and show that these genes act to stimulate the diguanylate cyclase PleD in flagellar assembly mutants. A separate pathway that includes the stator protein MotB and the recently characterized dNTPase FssC regulates entry into S phase downstream of the flagellum. We show that motB regulates cell cycle progression specifically in response to surface cues, and that stator-dependent cell cycle control occurs independently of c-di-GMP and CtrA. This work clarifies the downstream targets of the surface sensing network and establishes a comprehensive model for how surface sensing influences the C. crescentus developmental program.

microbiology↗

bioRxiv2026

Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota

Phylum Actinomycetota (syn. Actinobacteriota or Actinobacteria), one of the largest well-studied bacterial phyla, is renowned for complex morphology, non-motility, ecological versatility, and secondary metabolite production. Chemosensory systems (CSS) are among the most sophisticated prokaryotic signal transduction architectures, yet their evolutionary distribution in this phylum remains poorly understood. Here, a comparative genomic analysis of 693 high-quality genomes spanning the phylum resolves the diversity, distribution, and evolutionary trajectories of CSS. Despite extensive genomic complexity and ecological versatility, only 6.9% of genomes encode complete CSS clusters, confined to a subset of lineages within a few classes, indicating lineage-specific retention or loss. In contrast, two-component systems (TCS) are ubiquitously abundant, with hybrid kinases enriched in CSS-deficient classes, suggesting functional compensation for the absence of dedicated chemosensory pathways. Basal lineages retain simplified CSS (F1 or F5), whereas Actinomycetes show lineage-specific expansion into multiple classes (F5, F8, F9, and ACF), often co-occurring, indicative of enhanced sensory complexity. The phylogeny of CheA homologs shows a polyphyletic distribution, supporting a mosaic evolutionary history shaped by multiple independent acquisitions, diversification, and gene loss. Collectively, our findings show that, unlike motile bacteria, members of Actinomycetota rely predominantly on TCS-driven regulatory networks, with CSS retained only in select lineages where ecological demands require enhanced environmental sensing. This work provides a phylum-wide evolutionary framework for the emergence, diversification, and functional specialization of CSS in non-motile bacteria.

microbiology↗

bioRxiv2026

Seasonal H1N1 influenza A virus preferentially infects a pre-existing ciliogenesis-primed secretory cell state

Influenza A viruses (IAV) infect secretory and ciliated cells of the human airway epithelium , but whether all cells within one cell type are equally susceptible to infection remains unresolved. Here, single-cell RNA sequencing analysis of primary human bronchial epithelial cultures from three donors identified preferential infection of a transcriptionally distinct subpopulation of secretory cells by seasonal H1N1 IAV A/Hawaii/70/2019 . Genes upregulated in this subpopulation showed enrichment for cilium-related gene ontology terms. In an ex post facto approach, this enrichment persisted after excluding genes differentially expressed between infected and mock-treated samples, including those identified in secretory cell-specific comparisons. Single-cell analysis further revealed no significant increase in ciliogenesis scores in infected secretory cells compared to mock infected cells at 6 hours post-infection , arguing against infection-induced activation of the canonical ciliogenesis programme during the initial viral replication cycle . Collectively, these results support preferential infection of ciliogenesis-primed secretory cells and refine IAV tropism beyond cell type to encompass epithelial differentiation state.

microbiology↗