Biology subjects

Collins, A. J.

Publications and source records attributed to Collins, A. J..

8 recordsLinked to original sources

bioRxiv2026

Epidemiology of Legionella: Genome-bAsed Typing (el_gato) - a new bioinformatic tool for identifying sequence-based types of Legionella pneumophila from whole genome sequencing data

Sequence-based typing (SBT) via Sanger sequencing has been the standard for describing Legionella pneumophila relationships for two decades. SBT involves sequencing seven loci, identifying alleles using the United Kingdom Health Security Agency (UKHSA) database, and inferring the corresponding sequence type (ST). While similar SBT approaches for other organisms can be easily adapted to whole genome sequencing (WGS), L. pneumophila presents two known challenges for this adaptation: multiple copies of one locus (mompS) and extensive heterogeneity in a second locus (neuA/neuAh). Although several computational methods have been proposed to address these issues, a WGS-based replacement with equal resolution to traditional SBT has been elusive. To address this gap, we developed el_gato (Epidemiology of Legionella: Genome-bAsed Typing; https://github.com/CDCgov/el_gato), which offers several advantages over existing methods: (1) a novel approach for resolving multiple mompS alleles identified in the same isolate, (2) the ability to capture diverse neuA/neuAh alleles, (3) fast runtime with an average of 27.7 seconds per sample, (4) easy installation via Bioconda or Docker and (5) an updated database as of March 2025. el_gato works with either paired-end short reads or genome assemblies, performing more accurately with paired-end short reads at least 250 base pairs (bp) in length. We compared el_gato against two other in silico SBT tools ("mompS", hereafter referred to as mompS tool and "legsta") using a dataset of 441 isolates with sequence types (STs) previously determined by Sanger-based sequencing. el_gato correctly identified the ST for 98.9% of the test isolates, compared to 95.2% for the mompS tool and 42.2% for legsta, demonstrating a significant improvement compared to the mompS tool (adjusted p = 1.06e-3) and legsta (adjusted p = 4.24e-55) in ST identification. Furthermore, el_gatos determination of ST was not significantly different from Sanger sequencing (adjusted p = 0.442). In summary, el_gato significantly improves in silico SBT and given its growing adoption, is poised to support the public health community.

bioinformatics↗

bioRxiv2026

Within-host population structure, migration, and parallel adaptive evolution of Pseudomonas aeruginosa in cystic fibrosis lung disease

Pseudomonas aeruginosa infections in adults with cystic fibrosis (CF) are comprised of heterogeneous populations, most often tracing ancestry back to a single recent common ancestor. What is not clear is the physical spatial structure within the lung infection population, its stability over time and whether this physical structure leads to different evolutionary trajectories in different adaptive environments. To compare the P. aeruginosa populations across a single lung, we performed whole genome sequence analyses of 450 isolates recovered from lavage samples of the three different lobes of the right lung from a person with mild-to-moderate CF lung disease at three time points over the course of [~]1.5 years. We found that isolates fell into five distinct phylogenetic lineages with evidence for repeated translocation of isolates from different lineages across lobes and loss-of-function mutations in lasR and mucA were present in all 450 isolates. The well-resolved phylogenetic analyses revealed a structured population in which we find the coexistence of a slowly evolving lineage and more rapidly evolving lineages. There is also support for numerous migration events. Further, strong evidence for parallel adaptive mutations in multiple genes revealed distinct evolutionary paths affecting mucoid phenotypes and genetic variation in antibiotic resistance-associated pathways across coexisting populations within a single individual over time. These results provide an example of within-host evolution leading to microheterogeneity that may be useful to consider in future study of infection metapopulations dynamics over the course of chronic infection. IMPORTANCEIndividuals with cystic fibrosis (CF) commonly have chronic lung infections that contain clonally derived Pseudomonas aeruginosa populations with genotypic and phenotypic diversity. This study describes a substantial dataset containing 450 isolates from different lobes of the right lung across three timepoints from an individual with mild-to-moderate CF lung disease. Some regional enrichment for specific lineages with parallel mutations among individual lobes of the lung was observed, but longitudinal analysis also demonstrated that compartmentalization is not strictly maintained and that isolates migrate between lobes of the lung over time. Perspectives on within lung evolution will be important for understanding the pathogen populations in chronic respiratory infections in CF and other diseases.

microbiology↗

bioRxiv2025

Activation of the Spx redox sensor counters cysteine-driven Fe(II) depletion under disulfide stress

In many low G+C Gram-positive bacteria, the global regulator Spx helps maintain thiol homeostasis during disulfide stress, when protein thiols form aberrant disulfide bonds that can lead to misfolding and oxidative damage. Spx-dependent gene expression is triggered when an intramolecular disulfide bond forms between two cysteines in its redox switch. Surprisingly, some Spx functions persist even in the absence of an active redox switch, highlighting the need to better understand the physiological significance of maintaining this regulatory feature. Here, we utilize a spxC10A mutant that encodes a redox-insensitive Spx variant to study the role of the Spx redox switch in Staphylococcus aureus. We show that the spxC10A mutant is hypersensitive to diamide-induced disulfide stress and exhibits widespread transcriptional dysregulation of genes that contribute to thiol maintenance and disulfide repair. Remarkably, the spxC10A mutant rapidly adapts to disulfide stress by increasing its intracellular pool of L-cysteine (L-Cys) through enhanced uptake, which helps restore a reduced intracellular environment. However, during this process increased L-Cys inadvertently depletes cytosolic Fe(II), leading to growth inhibition of the spxC10A mutant. Finally, we show that the Spx-dependent control of intracellular L-Cys is critical for S. aureus survival when it encounters human neutrophils. Overall, these findings suggest that staphylococcal adaptation to disulfide stress through intracellular L-Cys accumulation imposes significant fitness costs that S. aureus overcomes by rapid regulatory control of thiol homeostasis through a functional Spx redox switch. SignificanceAll cells have a pool of low molecular weight thiols, such as cysteine, glutathione, bacillithiol, and coenzyme A, to maintain redox balance under oxidative and disulfide stress. Among these, cysteine is a very effective thiol but is highly reactive, and its intracellular concentration must be tightly regulated. In S. aureus, we found that cysteine accumulates intracellularly during disulfide stress and if left unchecked, can inadvertently deplete cytosolic Fe(II), leading to growth inhibition. To prevent cysteine toxicity, S. aureus activates the global regulator Spx, which rapidly induces genes that restore thiol homeostasis and limits cysteine accumulation.

microbiology↗

bioRxiv2025

Fluidic Programmable Gravi-maze Array for High Throughput Multiorgan Drug Testing

The high attrition rate of drug candidates in clinical trials underscores the urgent need for more predictive preclinical models that accurately replicate human physiology. Traditional 2D cell cultures and animal models often fail to predict human responses due to their limited physiological relevance, particularly for biologics and immunotherapies involving complex multicellular and cross-organ interactions. This highlights the need for modeling and measurements of multiorgan interactions at higher throughput, prompting the development of multiorgan-on-a-plate platforms. Here, we present OrganRX, a modular, gravity-driven recirculation-based platform designed to imitate human organ function, physiological flow, immune cells circulation, and inter-organ communication in vitro. The Fluidic Programmable Gravi-maze Array (FPGA) technology integrates multiple organ models, including gut, liver, kidney, brain, tumor, and vascular compartments, within a microfluidic architecture designed to reproduce physiologically relevant shear stresses and gravity-driven recirculating flow that facilitates inter-organ communication. Using computational fluid dynamics (CFD) simulations and impedance-based flow validation, we confirmed accurate shear control across organ compartments. Organ-specific and multiorgan models were constructed using 3D extracellular matrix hydrogels and assessed for metabolism, toxicity, and senescence. Liver-kidney co-cultures demonstrated metabolic interplay via differential albumin and urea production. In addition, the platform was evaluated for biologics testing using immune-oncology models incorporating tumor spheroids, endothelial barriers, and circulating immune cells. Antigen-specific T-cells, checkpoint inhibitors, bispecific antibody and antibody-drug conjugate (ADC) studies demonstrated the ability to measure on-target tumor killing, off-target toxicity, cytokine release, and bystander effects across interconnected tissue compartments under dynamic recirculating conditions. The system enabled longitudinal evaluation of immune-mediated cytotoxicity, tissue-selective responses, and cross-organ signaling not readily captured in conventional static assays. Overall, the OrganRX platform offers a physiologically relevant, scalable, and automation-compatible platform for preclinical drug evaluation, biologics safety assessment, and disease modeling. Its ability to capture complex, dynamic inter-organ effects position it as a powerful tool for advancing translational research, mechanistic toxicology, and precision medicine.

bioengineering↗

bioRxiv2022

CRISPR comparison toolkit (CCTK): Rapid identification, visualization, and analysis of CRISPR array diversity

CRISPR-Cas systems provide immunity against mobile genetic elements (MGEs) through sequence-specific targeting by spacer sequences encoded in CRISPR arrays. Spacers are highly variable between microbial strains and can be acquired rapidly, making them well suited for use in strain typing of closely related organisms. However, the historical record of spacer acquisitions and deletions represented by arrays has not previously been used to reconstruct strain histories. We therefore developed the CRISPR Comparison Toolkit (CCTK) to enable analyses of array relationships. CCTK includes tools to identify arrays, analyze relationships between arrays using CRISPRdiff and CRISPRtree, and predict targets of spacers. CRISPRdiff visualizes arrays and highlights the similarities between them. CRISPRtree infers a phylogenetic tree from array relationships and presents a hypothesis of the evolutionary history of the arrays. CCTK unifies several CRISPR analysis tools into a single command line application, including the first tool to infer phylogenies from array relationships.

bioinformatics↗

bioRxiv2022

Evaluation of P. aeruginosa attachment on mineralized collagen scaffolds and addition of manuka honey to increase mesenchymal stem cell osteogenesis

The design of biomaterials to regenerate bone is likely to increasingly require modifications that reduce bacterial attachment and biofilm formation as infection during wound regeneration can significantly impede tissue repair and typically requires surgical intervention to restart the healing process. Here, we investigate the ability of a mineralized collagen biomaterial to natively resist infection as well as how the addition of manuka honey affects bacterial colonization and mesenchymal stem cell osteogenesis. We incorporate manuka honey into these scaffolds via either direct fabrication into the scaffold microarchitecture or via soaking the scaffold in a solution of Manuka honey after fabrication. Direct incorporation results in a change in the surface characteristics and porosity of mineralized collagen scaffolds. Soaking scaffolds in honey concentrations greater than 10% had significant negative effects on mesenchymal stem cell metabolic activity but soaking or incorporating 5% honey had no impact on endothelial cell tube formation. Soaking and incorporating 5% honey into scaffolds reduced metabolic activity of mesenchymal stem cells, however, soaking 5% honey into scaffolds increased calcium and phosphorous mineral formation, osteoprotegerin release, and alkaline phosphatase activity. The addition of manuka honey did not prevent P. aeruginosa attachment but may be able to limit attachment of other common wound-colonizing bacteria. Overall, our results demonstrate the potential for soaking mineralized collagen scaffolds in 5% manuka honey to increase osteogenesis of mesenchymal stem cells.

bioengineering↗

bioRxiv2021

Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species

The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one other, primarily via transformation and homologous recombination, and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from other prophages and MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus. IMPORTANCEDrug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus, and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) have been identified and characterized in Neisseria species. In this study, we identified a large number of candidate phages integrated within the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.

microbiology↗

bioRxiv2020

MapA, a second large RTX adhesin, contributes to biofilm formation by Pseudomonas fluorescens

Mechanisms by which cells attach to a surface and form a biofilm are diverse and differ greatly between organisms. The Gram-negative, Gammaproteobacterium Pseudomonas fluorescens attaches to a surface through the localization of the large type 1-secreted RTX adhesin LapA to the outer surface of the cell. LapA localization to the cell surface is controlled by the activities of a periplasmic protease, LapG and an inner-membrane spanning cyclic di-GMP responsive effector protein, LapD. A previous study identified a second, LapA-like protein encoded in the P. fluorescens Pf0-1 genome: Pfl01_1463. However, deletion of this gene had no discernible phenotype under our standard laboratory growth conditions. Here, we identified specific growth conditions wherein, Pfl01_1463, hereafter called MapA (Medium Adhesion Protein A) is a functional adhesin contributing to biofilm formation. This adhesin, like LapA, appears to be secreted through a Lap-related type 1 secretion machinery. We show MapA involvement in biofilm formation is also controlled by LapD and LapG, and that the differing roles of LapA and MapA in biofilm formation are achieved, at least in part, through the differences in the sequences of the two adhesins and their differential, cyclic di-GMP-dependent transcriptional regulation. This differential regulation appears to lead to different distributions of the expression of lapA and mapA within a biofilm. Our data indicate that the mechanisms by which a cell forms a biofilm and the components of a biofilm matrix can differ depending on growth conditions in the biofilm. ImportanceAdhesins are critical for the formation and maturation of bacterial biofilms. We identify a second adhesin in P. fluorescens, called MapA, which appears to play a role in biofilm maturation and whose regulation is distinct from the previously reported LapA adhesin, which is critical for biofilm initiation. Analysis of bacterial adhesins show that LapA-like and MapA-like adhesins are found broadly in Pseudomonads and related organisms, indicating that the utilization of different suites of adhesins may be broadly important in the Gammaproteobacteria.

microbiology↗