Biology subjects

Drabinska, J.

Publications and source records attributed to Drabinska, J..

5 recordsLinked to original sources

bioRxiv2026

OrthoGather: a local platform for orthology-based proteome and proteomics comparisons and Gene Ontology enrichment

MotivationComparative proteomic analysis may reveal common and unique pathways regulated by the same stimulus across species using data from differential protein expression studies or curated protein sets. Functional annotations are key but vary in quality, as many proteins, particularly in prokaryotes and non-model eukaryotes, are poorly or inconsistently annotated, complicating comparative studies. Orthology inference provides a robust framework to address this, but existing tools require technical expertise, command-line use, and manual processing of complex outputs, creating barriers for researchers without computational training. ResultsWe developed OrthoGather, a locally hosted web application that streamlines comparative proteomic analysis by integrating homologous protein groups across species and Gene Ontology (GO) enrichment. It leverages functional annotations from any orthogroup member to enable functional inference even when individual species lack comprehensive annotation. Its flexible design supports cross-species exploration of conserved and unique orthogroups across proteomes or user-defined protein sets, revealing functional patterns through orthogroup relationships. OrthoGather generates publication-ready, easy-to-interpret outputs including downloadable graphs and data files, lowering barriers for researchers without computational expertise. Availability and implementationSource code, documentation and tutorials are available at Zenodo (https://doi.org/10.5281/zenodo.18603238) and GitHub (https://github.com/CarlosVivasR/OrthoGather). Supplementary materials, including the example dataset analysis are available online at Bioinformatics.

systems biology↗

bioRxiv2025

From colonisation to chronicity: adaptation of Mycobacterium abscessus in the cystic fibrosis lung environment

Chronic infection by opportunistic pathogens is a major contributor to mortality in people with cystic fibrosis (CF). These infections are caused by antimicrobial resistant (AMR) pathogens such as the emerging pathogen, Mycobacterium abscessus, a nontuberculous mycobacteria (NTM) which causes recalcitrant infections with high resistance to antibiotics. M. abscessus adapts over time of colonisation to the conditions in the CF lung, hampering effective treatment. The mechanisms underlying this pathoadaptation are poorly understood and are critical for the development of future therapies. Sequential isolate pairs of M. abscessus from three people with CF were examined for adaptive changes over time of infection. Genomic analysis confirmed that these isolate pairs were clonal. The late infection isolates showed increased host cell attachment to CF bronchial epithelial cells and increased intracellular survival in macrophages, indicative of adaptation to the CF lung environment. Late isolates also showed changes in their proteomes, including changes in abundance of proteins with roles in intracellular survival and antibiotic resistance. Overall, it is clear that M. abscessus can adapt to the CF lung environment and improve its ability to interact with host cells. Impact StatementChronic infection by antimicrobial resistant bacteria impacts both the quality of life and mortality in people with CF. We explored the process of adaptation in the emerging pathogen, Mycobacterium abscessus, over the course of a chronic infection in the CF lung. While this process has been well-documented in other opportunistic pathogens which colonise the CF lung, limited data exist on this process in M. abscessus. Phenotype and proteome changes were assessed in sequential longitudinal clinical isolates of M. abscessus obtained from Saint Vincents University Hospital (SVUH), Dublin, Ireland. Significant changes in the interactions with human cells were observed in late infection isolates after as little as 33 days. Understanding these processes may reveal new avenues for clinical exploitation and this study reveals some novel adaptations which could be exploited to aid current therapies.

microbiology↗

bioRxiv2025

Adaptation of Burkholderia cenocepacia to low oxygen drives changes consistent with adaptation to chronic infection

BackgroundCystic fibrosis (CF) is characterised by chronic respiratory infections, involving opportunistic pathogens, including Burkholderia cenocepacia. The CF lung comprises hypoxic niches that drives bacterial adaptation and the adaptability of pathogens to this environment is key to their successful colonisation. We previously identified several proteins encoded on a low-oxygen activated (Lxa) locus that were significantly increased in abundance in late chronic infection B. cenocepacia isolates. However, the impact of long-term hypoxia exposure on B. cenocepacia adaptation remains unclear. ResultsTo investigate the role of hypoxia in driving traits associated with chronic infection, we exposed an early infection B. cenocepacia isolate to low (6% O2) or atmospheric oxygen (21% O2) over 22 days. By day 22, 364 proteins were significantly increased in abundance in hypoxia-adapted cultures relative to the ancestral strain. Overall, 1066 individual proteins were significantly increased in abundance in the hypoxia-adapted cultures relative to normoxia-adapted cultures, across four different timepoints from day 1 to day 22. Comparative proteome analysis identified 81 proteins with consistent changes in abundance both in hypoxia-adapted cultures and the respective late infection isolate relative to the ancestral strain (the early infection isolate), including lxa-encoded proteins and the FixK transcriptional regulator. Proteins associated with shikimate pathways were also significantly changed in abundance. Importantly, hypoxia-adapted cultures showed increased survival in CF macrophages, increased attachment to CF lung cells, elevated protease activity, greater resistance to ceftazidime and ciprofloxacin, all of which are consistent with adaptations observed in late chronic infection isolates. Hypoxia-adapted cultures also displayed enhanced virulence in Galleria mellonella larvae, as did the late infection isolate. ConclusionsThe changes in phenotype and proteome of B. cenocepacia observed after long-term hypoxia suggest that hypoxia may drive the adaptation to chronic infection, promoting survival in macrophages, host-cell attachment, antibiotic resistance and protease activity. Therapeutic strategies that modulate oxygen availability or target hypoxia-sensing may hold promise in preventing or mitigating chronic infection in CF.

microbiology↗

bioRxiv2025

Proteomic characterisation of three independent series of sequential cystic fibrosis strains in an international Pseudomonas aeruginosa reference panel indicates positive selection in late infection strains.

Pseudomonas aeruginosa is a frequent cause of chronic opportunistic infections in people with cystic fibrosis (CF). It is a highly diverse and adaptable Gram-negative bacterium that thrives in many environments. It is well recognised that P. aeruginosa adapts over time of colonisation to facilitate chronic infection including loss of virulence factors, however proteomic analyses of the adaptation to chronic infection have been limited. We previously collated and characterised an international panel of P. aeruginosa strains from different clinical presentations and geographical regions. Within this panel were three series of sequential isolates from people with CF, comprising eight strains in total which present an excellent opportunity to seek potential conserved adaptations that may be involved in driving chronic colonisation in the CF lung. We compared the proteomes of all eight strains (early versus respective late) to examine whether there were any changes in the proteomes over time of colonisation that were common to the three series of chronic P. aeruginosa infection isolates from three different patients. We identified 11 proteins that showed increased abundance in late isolates from all three patient series, many of which are reported to be involved in virulence, regulation of virulence or response to hypoxia and include cystic fibrosis inhibitory factor repressor (CifR), WspR, two two-component response regulators (PA2572 and PA3702), and transcriptional regulator (PA2551). Moreover, we identified three proteins (PA2572, PA3819 and PA5028) that showed increased abundance in all five late isolates from three people with CF. The probability of this being a random event is 5.06 x 10-53 and consequently is very strong evidence of positive selection. The increased abundance of PA2573 and PA3819 appears to improve the fitness P. aeruginosa to antibiotics and oxidative stress. Overall, despite the diversity within this species, there appear to be common mechanisms of adaptation in the cystic fibrosis lung.

microbiology↗

bioRxiv2024

Long-term adaptation to hypoxia provides insight into mechanisms facilitating the switch of Pseudomonas aeruginosa to chronic lung infections

Opportunistic bacterial infections are an increasing threat, especially for immunocompromised individuals such as people with cystic fibrosis (CF), driving morbidity and mortality. Pseudomonas aeruginosa is a key pathogen associated with chronic lung infections, that has been extensively studied in this context, but the mechanism(s) driving its adaptation towards chronic colonisation in the lung are not fully understood. This work focuses on the adaptations of P. aeruginosa to long-term hypoxia, one of the important environmental pressures present in the CF lung, to investigate whether it drives the development of persistence in CF patients. We used an experimental evolution approach to investigate how an early CF strain adapted to 6% oxygen over 28 days. We focussed on the impact of long-term hypoxia on the proteome and investigated the emergence of stable changes in phenotype. Changes in the abundance of >140 proteins were observed compared to the ancestral strain, including proteins involved in antibiotic resistance, stress response, iron homeostasis, biofilm formation and those previously associated with chronic infection. Significant changes in the abundance of proteins regulating cellular c-di-GMP levels were also observed. We show that two distinct P. aeruginosa small colony variants (SCVs) emerged, one exclusively in hypoxia exposed cultures. Hypoxia-adapted cultures developed resistance to 8 out of 13 antibiotics tested; increased biofilm and exopolysaccharide production; and decreased pyocyanin production, consistent with the changes in the proteome. All hypoxia-adapted cultures showed decreased siderophore production. Overall, we demonstrate that long-term hypoxia exposure contributes to multiple changes in phenotype and proteome that are frequently observed in P. aeruginosa CF lung chronic infection isolates. This suggests that hypoxia is driving these adaptations, at least in part, and opens a new path to treatment. Author SummaryOpportunistic antibiotic-resistant bacterial infections are an increasing threat, particularly for immunocompromised individuals such as people with cystic fibrosis (CF). These infections increase disease severity, the number of deaths and healthcare costs. Pseudomonas aeruginosa is a major pathogen in this context, causing persistent infections, yet the mechanisms driving its adaptation towards chronic colonisation in the CF lung are not understood. We investigated the adaptations that P. aeruginosa exposed to low oxygen conditions (an important environmental pressure in the CF lung) for 28 days, to examine whether it drives adaptations that lead to chronic infection. We found that prolonged exposure to hypoxia induced stable changes in P. aeruginosa, which are distinct from those reported after short term exposure. We observed multiple adaptations in hypoxia adapted cultures, many of which were associated with important signalling networks linked to lifestyle shifts in bacteria and several were also observed in isolates that had adapted to chronic infection. Similar adaptive responses in other opportunistic environmental pathogens suggest that this process of adaptation could be targeted to create universal therapeutic approaches preventing antibiotic overuse and improving patient outcomes.

microbiology↗