Biology subjects

Turner, P. E.

Publications and source records attributed to Turner, P. E..

12 recordsLinked to original sources

bioRxiv2026

Bacteriophage susceptibility varies within chronic Pseudomonas aeruginosa lung infections

Phage therapy is receiving renewed interest in the face of rising rates of antibiotic resistance. One drawback of phages as antibiotic agents is their high host specificity: phages can often only kill a subset of strains within a bacteria species. Phage specificity may be especially problematic for chronic infections, which tend to be genetically diverse, suggesting they may contain variation in phage susceptibility. Such within-population variation in phage susceptibility could make phage treatment less effective, however the extent of this variation in chronic bacterial infections has not been thoroughly studied. To address this gap, we investigated variation in phage susceptibility in four populations of Pa derived from chronic lung infections in people with cystic fibrosis. We first measured the lytic efficiency of 12 virulent phages across 40 isolates from each patient, which revealed substantial variation in susceptibility to four LPS-targeting phages in two of four lung-derived populations. Genomic analysis suggested that within-population variation in phage susceptibility was not explained by the acquisition or loss of phage defense systems, as phage defense system carriage did not strongly vary within lung-derived populations. Conversely, phylogenetic analysis of isolates from one lung-derived population revealed that some evolutionary transitions in phage susceptibility coincided with mutations in genes involved in LPS biosynthesis. This association suggested that within-patient diversification in cell-surface features may have been responsible for variation in phage susceptibility in this population. Finally, phenotypic characterization of lung-derived isolates revealed favorable clinical associations between phage susceptibility and antibiotic resistance in one population. However, associations were largely absent in other populations, suggesting the potential to use phages to drive favorable phenotypic shifts is limited in bacterial infections with existing variation in phage susceptibility. Collectively, this work shows that phage susceptibility can vary within Pa chronic infections in the lungs of people with cystic fibrosis, possibly as a consequence of standing variation in cell-surface features. This variation poses a challenge for phage therapy, necessitating new approaches to ensure high efficacy in the face of extreme within-patient heterogeneity.

evolutionary biology↗

bioRxiv2026

Community diversity favors coexistence between bacteria and parasitic bacteriophages

Microbial communities often contain diverse bacteria and their specific viruses (bacteriophages). Lytic phages frequently select for host bacteria to evolve resistance, in-turn threatening phage extinction. However, in nature phage-bacteria interactions do not occur in isolation, but within complex communities containing other species. To test how community context can alter resistance evolution and phage persistence, we experimentally evolved Pseudomonas aeruginosa bacteria and a Pseudomonas-targeting phage with and without a community representing a cystic fibrosis disease pulmonary infection. Phages selected for rapid evolution of receptor-mediated resistance, regardless of community context. However, susceptible bacteria often persisted due to resistance-growth trade-offs. A diverse community favored increased frequencies of susceptibility, fueling higher phage densities and fewer phage extinctions. Our findings show that community complexity can constrain the evolution of phage resistance in bacteria, promoting host-parasite coexistence and fostering microbial diversity.

microbiology↗

bioRxiv2026

Prophage activity shapes the thermal ecology and evolution of a marine bacterial host

Predicting the response of populations to thermal change is challenging due to temperature-dependent interspecific interactions, such as those between bacteria and their integrated viruses (prophages). Temperature is known to modulate prophage activity, raising the question of whether and how prophages alter host responses to temperature. In this work, we explored how prophage infection shapes host thermal ecology and evolution in a novel marine bacterial isolate carrying a spontaneously inducing prophage. We first characterized the effect of temperature on bacteria and phage population dynamics, finding that high temperatures led to bacterial population crashes and reduced yield, with abundant phage production across all temperatures. To then determine the causal impacts of this phage, we infected a conspecific susceptible strain and found that performance in the novel lysogen was reduced across all temperatures and indistinguishable from the naturally infected strain. Further, we found that evolutionary rescue mutants of the naturally infected strain with an expanded upper thermal limit gained high temperature adaptation through a reduction in prophage activity. Overall, we found that intraspecific variation in thermal ecology was explained by prophage infection, and that adaptation to nonpermissive temperature occurred through modifications to prophage dynamics. This work demonstrates a critical link between viral mobile genetic elements and bacterial thermal responses, and emphasizes the importance of ecological interactions in thermal ecology and evolution.

ecology↗

bioRxiv2026

Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa

Microbial populations strongly shape their environment, which can re-route adaptation toward organism-generated fitness optima. However, the conditions that promote these eco-evolutionary feedbacks are unclear. Here, we used experimental evolution to test whether high population density, by strengthening niche construction, drives eco-evolutionary feedbacks in the bacterial pathogen Pseudomonas aeruginosa MPAO1. We then tested for adaptation to organism-modified environments by measuring the relative performance of ancestral and endpoint populations in filtrate generated by each evolutionary line sampled across generations. Contrary to expectations, we found that endpoint populations had higher performance than the ancestral strain in filtrate across nearly all evolutionary lines regardless of population density. This was caused by the emergence of hyperactive filamentous bacterio(phage) mutants during experimental passaging that inhibited the ancestral strain but not endpoint populations in modified media. Hyperactive phages emerged from one of two avirulent prophages in MPAO1s genome (Pf4 or Pf6). Hyperactive phages drove the evolution of phage resistance in bacterial populations via mutations in the type IV pilus (TIVP), the phages binding receptor. In a follow-up experiment, we showed that these TIVP mutations pleiotropically reduced motility and decreased susceptibility to a TIVP-targeting virulent phage, both of which are important traits for P. aeruginosa infection and treatment. Overall, this work suggests that filamentous phage evolution can act as a driver of eco-evolutionary feedbacks in bacterial populations, causing phenotypic and genetic changes that would not be anticipated from adaptation to the extrinsic environment alone.

evolutionary biology↗

bioRxiv2026

Evaluating Synergy of Clinically Utilized Phage OMKO1 with Five Antibiotics from Different Classes against Pseudomonas aeruginosa

Decades of antibiotic overuse and misuse have placed us at the precipice of a post-antibiotic era. This rise in multidrug-resistant and pandrug-resistant bacteria poses a serious risk to public health, warranting urgent exploration of alternative treatment options for bacterial infections. One emerging method displaying promise in the field is phage-antibiotic combination therapy: the use of bacteriophages, viruses that exclusively infect bacteria, as adjuvants to antibiotics. This study investigated the synergistic effects of phage OMKO1, previously utilized in compassionate-use cases, with five antibiotics of diverse drug classes against Pseudomonas aeruginosa. Modified checkerboard assays were performed to test phage-antibiotic combination treatments across several antibiotic concentrations and phage multiplicities of infection. Synergy was achieved by four of the five phage-antibiotic pairings at sub-minimum inhibitory antibiotic concentrations. All combination treatments reduced the antibiotic minimum inhibitory concentration (MIC) by [≥] 2-fold and resulted in a reduction in resistant regrowth. These findings highlight the potential of phages to lower effective antibiotic concentrations and prolong their utility by slowing the rise of antimicrobial resistance.

microbiology↗

bioRxiv2025

Evolutionary consequences of bacterial resistance to a flagellotropic phage

Bacteria can evolve resistance to bacteriophage attack via mutations that alter phage receptors on the cell surface. Flagellotropic phages bind to motility-enabling flagella, creating an evolutionary trade-off, since losing flagellar function reduces fitness in many environments. We experimentally evolved Escherichia coli populations under selection by flagellotropic phage (chi), on soft-agar swim plates which favor motility. Whole genome sequencing revealed early emergence of non-motile mutants with disrupted motility-genes, followed by motile mutants with flagellin gene mutations. Swim-plate assays and single-cell tracking showed variable motility effects among resistant mutants, with some faster and others slower than ancestors. Increased tumble bias suggested altered flagellar rotation. Kinase-response in the upstream chemotaxis pathway was also remodeled in -resistant mutants. Our findings demonstrate that evolved phage-resistance can cause motility to trade-off or trade-up, revealing diverse evolutionary outcomes under combined selection pressures. TeaserEvolution redesigns bacterial swimming and navigation to escape viruses while maintaining motility in complex environments.

evolutionary biology↗

bioRxiv2024

Genetic shifts in viral populations: how sudden vs gradual changes in host species composition affect the stability and dynamics of genetic variability in viral populations

Sudden and gradual changes in host species composition --transitioning from more permissive to less permissive hosts-- have been shown to influence viral fitness, virulence, and rates of molecular evolution. In this study, we analyzed the roles of stochasticity and selection using previously published time-series data from evolving populations of Sindbis virus under different rates of host replacement. First, an approximate Markov model within the Wright-Fisher diffusion framework revealed a reduction in effective population size by approximately half in scenarios involving sudden host changes. These scenarios were also associated with fewer and generally weaker beneficial mutations. Second, genetic distance analysis between populations at consecutive time points indicated that populations undergoing gradual host changes evolved steadily until the original host was no longer present. Distances to the ancestral sequence in these cases exhibited occasional leapfrog phenomena, where the rise of certain haplotypes is not predictable based solely on their relatedness to previously dominant ones. In contrast, populations exposed to sudden host changes displayed less stable compositions and diverged from the ancestral sequence at a more constant rate. Third, we observed that allele frequencies distribution followed a power law consistent with Taylors law. Both treatments exhibited high levels of allele aggregation with significant fluctuations, where neutral, beneficial, and deleterious alleles could be distinguished by their general behavior and their position on Taylors plot. Finally, we found evidence that the host replacement regime influences the temporal distribution of mutations across the genome.

evolutionary biology↗

bioRxiv2024

Microscopic Phage Adsorption Assay: High-throughput quantification of virus particle attachment to host bacterial cells

Phages, viruses of bacteria, play a pivotal role in Earths biosphere and hold great promise as therapeutic and diagnostic tools in combating infectious diseases. Attachment of phages to bacterial cells is a crucial initial step of the interaction. The classic assay to quantify the dynamics of phage attachment involves co-culturing and enumeration of bacteria and phages, which is laborious, lengthy, hence low-throughput, and only provides ensemble estimates of model-based adsorption rate constants. Here, we utilized fluorescence microscopy and particle tracking to obtain trajectories of individual virus particles interacting with cells. The trajectory durations quantified the heterogeneity in dwell time, the time that each phage spends interacting with a bacterium. The average dwell time strongly correlated with the classically-measured adsorption rate constant. We successfully applied this technique to quantify host-attachment dynamics of several phages including those targeting key bacterial pathogens. This approach should benefit the field of phage biology by providing highly quantitative, model-free readouts at single-virus resolution, helping to uncover single-virus phenomena missed by traditional measurements. Owing to significant reduction in manual effort, our method should enable rapid, high-throughput screening of a phage library against a target bacterial strain for applications such as therapy or diagnosis.

microbiology↗

bioRxiv2024

Lytic bacteriophages interact with respiratory epithelial cells and induce the secretion of antiviral and proinflammatory cytokines

Phage therapy is a therapeutic approach to treat multidrug resistant infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. We determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.

microbiology↗

bioRxiv2019

Phage steering of antibiotic-resistance evolution in the bacterial pathogen Pseudomonas aeruginosa

Antimicrobial resistance is a growing global concern and has spurred increasing efforts to find alternative therapeutics. Bacteriophage therapy has seen near constant use in eastern Europe since its discovery over a century ago. One promising approach is to use phages that not only reduce bacterial pathogen loads, but also select for phage resistance mechanisms that trade-off with antibiotic resistance - so called phage steering. Recent work has shown that phage OMKO1 can interact with efflux pumps and in so doing select for both phage resistance and antibiotic sensitivity. We tested the robustness of this approach to three different antibiotics in vitro and one in vivo. We show that in vitro OMKO1 can reduce antibiotic resistance either in the absence or the presence of antibiotics. Our in vivo experiment showed that phage increased the survival times of wax moth larvae and increased bacterial sensitivity to erythromycin, both in the absence and presence of the antibiotic. We discuss the implications of our findings for future research on this promising therapeutic approach using OMKO1.

evolutionary biology↗

bioRxiv2019

Quantitative Models of Phage-Antibiotics Combination Therapy

The spread of multi-drug resistant (MDR) bacteria is a global public health crisis. Bacteriophage therapy (or \"phage therapy\") constitutes a potential alternative approach to treat MDR infections. However, the effective use of phage therapy may be limited when phage-resistant bacterial mutants evolve and proliferate during treatment. Here, we develop a nonlinear population dynamics model of combination therapy that accounts for the system-level interactions between bacteria, phage and antibiotics for in-vivo application given an immune response against bacteria. We simulate the combination therapy model for two strains of Pseudomonas aeruginosa, one which is phage-sensitive (and antibiotic resistant) and one which is antibiotic-sensitive (and phage-resistant). We find that combination therapy outperforms either phage or antibiotic alone, and that therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at sub-inhibitory concentrations of antibiotics, e.g., ciprofloxacin. These in-silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of innate immunity in shaping therapeutic outcomes.

microbiology↗

bioRxiv2018

Two lytic bacteriophages that depend on the Escherichia coli multi-drug efflux gene tolC and differentially affect bacterial growth and selection

Bacterial pathogens are increasingly evolving drug resistance under natural selection from antibiotics in medicine, agriculture, and nature. Meanwhile, bacteria ubiquitously encounter bacteriophages and can rapidly evolve phage resistance. However, the role of phages in interacting with drug-resistant and drug-sensitive bacteria remains unclear. To gain insight into such relationships, we screened for and characterized phages that rely on the multi-drug efflux pump gene tolC. First, we screened a collection of 33 environmental and commercial Escherichia coli phages for their ability to infect cells that lacked tolC. Our screen revealed two phages that had reduced efficiency of plating (EOP) on the tolC knockout compared to wild type. We further characterized these phages with bacterial growth curves, transmission electron microscopy, and analysis of phage-resistant mutants. Phage U136B is a curly-tailed virus in family Siphoviridae with no ability to infect a tolC knockout, suggesting TolC is the U136B receptor. Phage 132 is a contractile-tailed virus in family Myoviridae with reduced EOP on cells lacking ompF and its positive regulators tolC and ompR. U136B and 132 differentially effect bacterial growth and lysis, and U136B-resistant mutants contain mutations of the tolC gene. Together, these results show that the tolC gene involved in drug resistance can modify bacteria-phage interactions in multiple ways, altering bacterial lysis and selection. These new phages offer utility for studying evolution, tradeoffs, and infection mechanisms.\n\nImportanceBacteria face strong selection by antibiotics in medicine and agriculture, resulting in increasing levels of drug resistance among bacterial pathogens. Slowing this process will require an understanding of the environmental contexts in which drug resistance evolutionarily increases or decreases. In this study, we investigate two newly-isolated bacteriophages that rely on a bacterial antibiotic resistance gene. These bacteriophages vary in their interactions with drug-resistant bacteria, with one of the phages selecting for phage-resistant mutants that have mutations in the antibiotic resistance gene. Further study of these new phages will be useful to understanding evolutionary tradeoffs and how phages might be applied in natural settings to reverse the problem of drug resistance.

microbiology↗