Biology subjects

Alfsnes, K.

Publications and source records attributed to Alfsnes, K..

7 recordsLinked to original sources

bioRxiv2025

Biased enrichment of DNA uptake enhancing sequences in Pasteurellaceae and Neisseriaceae

Some naturally transformable bacteria can selectively take up homologous DNA through short conserved motifs termed DNA Uptake Enhancing Sequences (DUES), comprising DNA Uptake Sequences (DUS) in Neisseriaceae and Uptake Signal Sequences (USS) in Pasteurellaceae. Using 177 complete genomes, this study provides the most extensive comparative analysis of DUES distribution, composition, and functional associations to date. Three novel DUS dialects were identified in Neisseria animalis and Vitreoscilla spp., extending the known diversity of the transformation system. Approximately half of all DUES and more than 90% of inverted repeat DUES occurred within predicted transcriptional terminators, and DUES inside coding-sequences were biased toward reading frames minimizing bioenergetic cost, indicating both structural and metabolic selection pressures. Gene Ontology and KEGG analyses revealed extensive but asymmetric functional enrichment: both families showed bias toward genome maintenance processes, yet Neisseriaceae displayed stronger enrichment for DNA repair, replication, and the UvrABC complex, whereas Pasteurellaceae were more associated with homologous recombination and the RecBCD complex. These patterns indicate that while DUES enrichment is broadly conserved, its functional integration diverges between families, reflecting distinct evolutionary adaptations that couple DNA uptake specificity to genome stability and cellular maintenance.

evolutionary biology↗

bioRxiv2025

HCVTyper: A Nextflow pipeline for hepatitis C virus genome assembly, genotyping and antiviral resistance detection

MotivationHigh-throughput sequencing is increasingly used for the characterization of hepatitis C virus (HCV), enabling genotyping, detection of mixed infections, and identification of resistance-associated variants (RAVs). However, the bioinformatics analysis of capture-based or metagenomic HCV datasets remains challenging due to high genome diversity, co-infections, and the need for reproducible workflows. ResultsWe present HCVTyper, a reproducible bioinformatics pipeline for HCV genome analysis implemented in Nextflow. HCVTyper integrates quality control, taxonomic classification, two-step reference-based mapping, consensus generation, de novo assembly, and antiviral resistance annotation. Benchmarking with simulated mixtures and real-world datasets demonstrated robust identification of both major and minor genotypes across a wide abundance range, with user-adjustable thresholds for co-infection detection. Integration with HCV-GLUE enables sensitive detection of RAVs from mapping files, including low-frequency variants. The pipeline is fully containerized (Docker) and produces comprehensive reports to facilitate interpretation. Availability and implementationHCVTyper is open-source and available at: https://github.com/folkehelseinstituttet/hcvtyper Contactjon.brate@fhi.no

bioinformatics↗

bioRxiv2025

Type IV minor pilin ComN predicted the USS-receptor in Pasteurellaceae

The Uptake Signal Sequence (USS) receptor, facilitating acquisition of homologous DNA by natural transformation in Haemophilus influenzae and other Pasteurellaceae, remains unknown. Assuming extracellular USS-binding in accordance with experimental data and existing models of the transformation process, discriminating functional gene ontology assessment, cellular localization predictions and deep-learning structural modeling of protein-DNA complexes, a prepilin peptidase-dependent protein A (PpdA), was identified as the strongest USS receptor candidate in different Pasteurellaceae family members with divergent USS specificities. PpdA was the only orthogroup to be modeled to form specific protein-USS complexes significantly better than complexes with sequence-scrambled versions of USS by AlphaFold3. Further analyses of PpdA complexes, from ten different Pasteurellaceae with divergent USS-type enrichment, using geometric deep learning protein-DNA sequence specificity predictions and coevolution analyses were found to further support this USS receptor candidacy. PpdA was found to share overall structural domains with the non-sequence specific DNA receptor FimT in Legionella pneumophila and a particular {beta}-sheet transversing disulfide-bridge with ComP, the DNA uptake sequence receptor of the Neisseriaceae. In compliance with a previously given gene name, we propose ComN to be used for these PpdA orthologs which structurally and evolutionary were here predicted to be the USS-receptors in Pasteurellaceae.

microbiology↗

bioRxiv2024

The conserved ComP structure with two distinct DNA binding modes - systematic modeling with AlphaFold3, RoseTTAFold2NA, Chai-1 and re-docking in HADDOCK

The competence protein ComP is a Type IV minor pilin and the extracellular DNA binding protein involved in natural transformation in the human pathogens Neisseria gonorrhoeae, Neisseria meningitidis, Eikenella corrodens and related Neisseriaceae bacteria. Details of the DNA binding mode of ComP is enigmatic, and the 3D structure of the DNA :: protein complex remains unresolved. Here we characterize the ComP orthologs in a set of Neisseriaceae family members, model their common structural domains and their interaction with different preferred 12 base pair long DNA binding motifs, DNA Uptake Sequences (DUS) and scrambled versions of these. Through systematic in silico modeling using AlphaFold 3, RoseTTAFold2NA, and Chai-1 and model comparisons, we bring a new understanding of the interactions between DNA and ComP. We report six distinct binding modes of which two, here named Epsilon and Gamma, were robustly modeled across platforms and different ComPs. The characteristics and robustness of the predicted models and DNA binding modes from each tool are assessed and discussed. This work expands the knowledge on the ComP :: DUS interaction and guides further wet- and dry-lab systematic and experimental characterization of these complexes through which molecular and clinical interventions may be developed.

microbiology↗

bioRxiv2023

The inter-continental population dynamics of Neisseria gonorrhoeae

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.

microbiology↗

bioRxiv2020

The sudden emergence of a Neisseria gonorrhoeae strain with reduced susceptibility to extended-spectrum cephalosporins, Norway

The Neisseria gonorrhoeae multilocus sequence type (ST) 7827 emerged in dramatic fashion in Norway in the period 2016-2018. Here, we aim to determine what enabled it to establish and spread so quickly. In Norway, ST-7827 isolates were almost exclusively isolated from men. Phylogeographic analyses demonstrated an Asian origin of the ST with multiple importation events to Europe. The ST was uniformly resistant to fluoroquinolones and associated with reduced susceptibility to both azithromycin and the extended-spectrum cephalosporins (ESC) cefixime and ceftriaxone. We identified additional independent events of acquisition of penA and porB alleles in Europe, associated with further reduction in cefixime and ceftriaxone susceptibility, respectively. Transmission of the ST was largely curbed in Norway in 2019, but our results indicate the existence of a reservoir in Europe. The worrisome drug resistance profile and rapid emergence of ST-7827 calls for close monitoring of the situation.

genomics↗

bioRxiv2017

Genome-based transmission modeling separates imported tuberculosis from recent transmission within an immigrant population

BackgroundIn many countries tuberculosis incidence is low and largely shaped by immigrant populations from high-burden countries. This is the case in Norway, where more than 80 per cent of TB cases are found among immigrants from high-incidence countries. A variable latent period, low rates of evolution and structured social networks make separating import from within-border transmission a major conundrum to TB-control efforts in many low-incidence countries.\n\nMethodsClinical Mycobacterium tuberculosis isolates belonging to an unusually large genotype cluster associated with people born in the Horn of Africa, have been identified in Norway over the last two decades. We applied modeled transmission based on whole-genome sequence data to estimate infection times for individual patients. By contrasting these estimates with time of arrival in Norway, we estimate on a case-by-case basis whether patients were likely to have been infected before or after arrival.\n\nResultsIndependent import was responsible for the majority of cases, but we estimate that about a quarter of the patients had contracted TB in Norway.\n\nConclusionsThis study illuminates the transmission dynamics within an immigrant community. Our approach is broadly applicable to many settings where TB control programs can benefit from understanding when and where patients acquired tuberculosis.

epidemiology↗