Allen, V. | bioRxiv Science

bioRxiv2025

Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system

Moraxella catarrhalis is an important cause of infectious exacerbations of chronic obstructive pulmonary disease and otitis media. Previously, seroresistant (SR) and serosensitive (SS) lineages that differed in virulence potential were described, which raised questions about their evolutionary relationship and species classification. To investigate the population structure of M. catarrhalis, we developed a core-genome multilocus sequence typing (cgMLST) scheme using 1,319 core genes, and a life identification number (LIN) barcode classification system. Whole-genome analyses of nearly 2,000 genomes confirmed two divergent SR and SS M. catarrhalis lineages with distinct evolutionary trajectories. SR genomes were more conserved, while SS genomes exhibited greater genetic variability. Virulence gene analyses revealed lineage-specific variations in ubiquitous surface proteins (UspA1 and UspA2) and lipooligosaccharide (LOS) types, and SR genomes had more diverse LOS variants. The bro {beta}-lactamase gene, and the mcb bacteriocin cluster, were more common in SR, which suggested different selective pressures and ecological adaptation. This cgMLST scheme and LIN code system provides a robust method for characterising M. catarrhalis, distinguishes between SR and SS lineages, and offers a unified framework for population structure analyses. Implemented within PubMLST, this open-access resource facilitates high-resolution genomic studies and supports the scientific community in understanding the evolutionary complexity of M. catarrhalis.

genomics↗

bioRxiv2024

Phenotypic diversity and shared genomic determinants among isolates causing a large incidence of disseminated gonococcal infections in Canada

The incidence of disseminated gonococcal infection (DGI) has remained low since the advent of antibiotics, however recent surge in DGI have inexplicably emerged within several regions during the past decade. In an effort to understand whether Neisseria gonorrhoeae that cause disseminated disease can be differentiated from non-invasive strains, we have performed a phenotypic and genotypic analysis on a selection of isolates obtained from invasive and uncomplicated infections in Canada. Phenotypic analysis of a matched subset of 19 isolates obtained since 2013 found that these varied in their capacity to aggregate in suspension and in their association with serum complement proteins, however these interactions did not discriminate between the invasive and mucosal isolates. Sequence typing of 360 Canadian isolates revealed that two porB alleles are significantly associated with the DGI strains, one of these being present throughout the past decade whereas the other became associated more recently. A PopNet-based population dynamics analysis, which instead establishes relationships based upon variance among discrete chromosomal segments, found that DGI isolates were restricted in their phylogenetic distribution. While this implies a genetically-linked potential to cause invasive disease, it cannot distinguish between an inherent difference in the phenotype of these populations or the horizontal exchange of some virulence factor among closely related strains. Regardless, a large number of genetic determinants are enriched in the DGI strains, making these enticing candidates for future work to understand how they might either promote the gonococcal capacity to cause systemic infection or reduce the presentation of clinical symptoms from localized infection so that it remains untreated. AUTHOR SUMMARYNeisseria gonorrhoeae is a sexually transmitted bacteria that causes over 82 million cases of gonorrhea each year. With its re-emergence, rising incidence rates and the prevalence of multidrug resistant strains increasing, the bacteria is considered to be a high burden threat to global public health. While disseminated gonococcal disease arising from untreated infections are uncommon, there have recently been regions with high incidence invasive disease. Here, we take advantage of the active ongoing collection of gonococcal isolates in Canada to perform a combined phenotypic and genotypic analysis that aims to understand whether certain strains are more often linked to invasive infections. We found that all disseminated isolates bound to the complement regulatory factors factor H and/or C4 binding protein to facilitate their resistance to the bactericidal activity of serum, but this was not sufficient to explain the heightened instance of invasive disease. While classical genome-based phylogenetic analysis displayed little association between invasive strains, PopNet-based analysis revealed that invasive isolates fell within defined sub-populations and indicated variant alleles enriched among the disseminating bacteria, and a broader pan-genome approach revealed genes more likely to be present in invasive strains. Our study thereby provides support for a genetic contribution to the invasive potential of gonococcal isolates and provides candidate drivers of this virulent outcome.

microbiology↗

bioRxiv2017

Automated analysis of internally programmed grooming behavior in Drosophila using a k-nearest neighbors classifier

Despite being pervasive, the control of programmed grooming is poorly understood. We have addressed this gap in knowledge by developing a high-throughput platform that allows long-term detection of grooming in the fruit fly Drosophila melanogaster. Automatic classification of daily behavior shows flies spend 30% of their active time grooming. We show that a large proportion of this behavior is driven by two major internal programs. One of these programs is the circadian clock that modulates rhythms in daily grooming. The second program depends on cycle and clock and regulates the amount of time flies spend grooming. This emerging dual control model of programmed grooming in which one regulator controls the timing and another controls the duration, resembles the well-established two-process regulatory model of fly sleep. Together, our quantitative approach in Drosophila has revealed that grooming is an important internally driven behavior under the control of two regulatory programs.

bioinformatics↗