Biology subjects

Duggan, N.

Publications and source records attributed to Duggan, N..

3 recordsLinked to original sources

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↗

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↗