Biology subjects

Carruthers-Lay, D.

Publications and source records attributed to Carruthers-Lay, D..

3 recordsLinked to original sources

bioRxiv2026

Systematic Infectome-Phenome Profiling Reveals Cryptococcal Infection-Associated Proteins Driving Immune System Remodeling and Immunization Potential

Mortality and morbidity associated with invasive fungal infections continue to rise, driven by the emergence of new pathogens, increasing antifungal resistance, and expanding immunocompromised populations. Despite this growing threat, fungal biology lacks scalable, unbiased strategies to link infection-responsive fungal proteins to functional outcomes that drive virulence and immune modulation. Here, we present an integrated infectome-phenome discovery platform that combines high resolution mass spectrometry-based proteomics with systematic phenotypic profiling to globally interrogate Cryptococcus neoformans-macrophage interactions. This approach reveals coordinated host immune suppression alongside complementary fungal virulence programs and enables the unbiased prioritization of infection-associated fungal proteins. Systematic phenome fingerprinting of candidate mutant strains resolves two functional classes of putative therapeutic relevance: antifungal and antivirulence, with in vitro characterizations corroborated with a murine model of cryptococcosis. Prioritization of a conserved, previously uncharacterized virulence-associated protein, CipC, uncovers altered extracellular vesicle composition and enhanced antigenic properties. Immunization with CipC-derived vesicles elicits a robust and diversified host immune response, implicating fungal extracellular vesicles in immune remodeling and host priming. Together, these findings establish a broadly applicable framework for systematically identifying and functionally characterizing fungal drivers of infection for therapeutic and immunological target discovery with relevance across diverse human fungal pathogens.

microbiology↗

bioRxiv2025

Network-based population analysis of 31,595 gonococcal genomes reveals phase variability, genetic diversity and mobile element dynamics drive antimicrobial resistance and phenotypic diversity

With a highly plastic genome allowing the accumulation of antimicrobial resistance (AMR) determinants, Neisseria gonorrhoeae (Ngo) is an urgent public health threat. To better understand the spread of AMR in Ngo and its ability to persist in humans, we performed a systematic analysis of its global population structure. From 31,595 publicly available genomes, we curated a maximally diverse representative set of 485 gonococcal genomes, which were defined into 12 distinct clades on the basis of shared patterns of single nucleotide polymorphisms. Mapping AMR determinants and mobile elements onto these clades revealed significant correlation with gonococcal population structure. Notably, several variants associated with AMR were identified in genes not previously linked with resistance, suggesting roles as new determinants of resistance or compensatory mutations in resistant strains. Analysis of phase variable motifs, a significant mechanism driving regulation of expression in Ngo, identified 57 genes not previously identified as phase variable; in vivo and in vitro passaging validated our sequence-based definition of phase variability and revealed a strong association of phase variation of the surface proteins Opa and LgtG with improved colonization during infection. Together these findings highlight the ability of systematic comparative genomic analyses to shed new light on the drivers of Ngo population structure and identify new AMR determinants.

microbiology↗

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↗