bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2025.12.15.694340

The influence of heteroresistance, growth and antibiotic selection in shaping the invasion dynamics of colistin resistant Pseudomonas aeruginosa

Rios, A. C. A.·Pham, A. D.·Knibbe, C. A. J.·Rozen, D.·van Hasselt, J. G. C.·Aulin, L. B. S.
View original source ↗Export metadata ↓

Abstract

Heteroresistance, where a small subpopulation of phenotypically resistant cells coexists within an otherwise susceptible population, plays a critical role in bacterial survival during antibiotic exposure. Yet, its influence on the invasion success of genetically resistant strains remains poorly understood. In this study, we investigate the influence of bacterial heteroresistance, growth, and antibiotic selection on the outcome of an invasion experiment. We quantified the invasion dynamics of a bioluminescent colistin-resistant Pseudomonas aeruginosa strain across a colistin concentration gradient during co-culture with colistin-susceptible clinical P. aeruginosa isolates with varying levels of heteroresistance. The observed variation in heteroresistance and fitness of the clinical isolates allowed investigation of the impact of these factors on invasion dynamics. We hypothesized that fitter isolates would limit invasion through competitive exclusion, while heteroresistant isolates, despite their growth costs, may serve as reservoirs for resistance evolution under antibiotic selection. Our results show that in antibiotic-free conditions, faster-growing isolates competitively excluded the colistin resistant invader while isolates with high levels of heteroresistance failed to do so. This competitive landscape shifted with increasing colistin concentration, giving the invader a fitness advantage that peaked around 2-4xMIC of the clinical isolate. The shift in the landscape over the colistin gradient might further have been influenced by the presence of heteroresistance in the clinical isolates. These findings reveal how both heteroresistance and competitive exclusion shapes invasion dynamics. Understanding these interactions is critical for redesigning treatment strategies that minimize ecological opportunities for resistant strains to establish and expand.

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Rios, A. C. A., Pham, A. D., Knibbe, C. A. J., Rozen, D., van Hasselt, J. G. C., Aulin, L. B. S.. 2025-12-15. The influence of heteroresistance, growth and antibiotic selection in shaping the invasion dynamics of colistin resistant Pseudomonas aeruginosa. https://doi.org/10.64898/2025.12.15.694340

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗
bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗
bioRxiv2026

A microbiota-derived protease links phage susceptibility to host epithelial responses

Bacteriophages are major ecological drivers of gut microbial ecology, yet whether bacterial mechanisms that determine phage susceptibility have consequences for the mammalian host remains poorly understood. Here, we identify dipeptidyl peptidase 11 (Dpp11a), the predominant active serine protease of the prevalent gut commensal Phocaeicola vulgatus, as an unexpected bacterial defence factor. Dpp11a protects against environmental proteases and confers resistance to bacteriophage infection. Metatranscriptomic analyses further reveal increased expression of both dpp11a and P. vulgatus-associated phage transcripts in ulcerative colitis stool samples, indicating that both components of this interaction are transcriptionally active in disease-associated human microbiomes. Using the microfluidic gut-on-a-chip co-culture model HuMiX, we show that the absence of Dpp11 is accompanied by altered epithelial tight-junction remodelling during phage-bacterial infection. Together, our findings reveal that the consequences of bacterial phage defence can extend beyond phage-bacterium interactions to the mammalian epithelium.

microbiology↗