Biology subjects

Read, A. F.

Publications and source records attributed to Read, A. F..

15 recordsLinked to original sources

bioRxiv2026

Population genetic structure of disease-causing vancomycin-resistant Enterococcus faecium in a hospital closely reflects the dynamics of colonizing populations in patients

Vancomycin-resistant Enterococcus faecium (VREfm) is a common nosocomial pathogen that can lead to severe and difficult-to-treat infections. VREfm effectively exploits healthcare environments because transmission chains are difficult to prevent and eradicate. VREfm also readily acquires antimicrobial resistance (AMR), strongly reducing the likelihood of treatment success. Here we compare the genetic population structure and antimicrobial resistance load of VREfm strains that are typically associated with patient colonization, and those found to cause disease. We use two separate but contemporaneous collections of clinical bacterial isolates in a tertiary care medical center: one consisting of Enterococcus from blood samples, and a second originating from a hospital wide surveillance strategy screening for VREfm in perirectal swabs of incoming patients. Using whole-genome sequencing and analysis of 2061 VREfm clones, we found that the genetic structure of colonizing and disease-causing VREfm closely resemble each other, and that sequence type 117 (ST117) played an important role in shaping these populations. The population structures of strains acquired at the hospital and those present on arrival are also remarkably similar. We further observed a high likelihood that the colonizing clone genetically resembles the disease-causing strain in patients who are both colonized and infected. Finally, the AMR gene load and distribution did not vary significantly between the blood isolates and the gut-associated strains. Altogether, our results highlight the similarities between colonizing and infectious VREfm populations and further emphasize the need to focus infection prevention strategies to minimize gut colonization. Author SummaryVancomycin-resistant Enterococcus faecium (VREfm) often lives harmlessly in the human gut but can cause life-threatening infections when it enters the bloodstream. Hospitals struggle with is pathogen because it spreads easily and tends to resist many antibiotics. We compared bacteria collected from patients guts and from their blood to ask whether the strains that cause infection are different from those that only colonize. Studying more than 2,000 bacterial genomes, we found that the two groups look remarkably similar: the same genetic types dominate in both, patients are usually infected by the same strain already living in their gut, an both groups also carried similar sets of resistance genes. Overall, this is important because it suggests that preventing colonization--not just treating infection--may therefore be the most effective way to reduce VREfm disease in hospitals.

microbiology↗

bioRxiv2024

Reversion to sensitivity explains limited transmission of resistance in a hospital pathogen

1Bacterial pathogens that are successful in hospital environments must survive times of intense antibiotic exposure and times of no antibiotic exposure. When these organisms are closely associated with human hosts, they must also transmit from one patient to another for the resistance to spread. The resulting evolutionary dynamics have, in some settings, led to rising levels of resistance in hospitals. Here, we focus on an important but understudied aspect of this dynamic: the loss of resistance when the resistant organisms evolve in environments where the antibiotic pressure is removed. Based on prior data, we hypothesize that resistance arising in the context of strong selection may carry a high cost and revert to sensitivity quickly once the selective pressure is removed. Conversely, resistant isolates that persist through times of no antibiotic pressure should carry a lower cost and revert less quickly. To test this hypothesis, we utilize a genetically diverse set of patient-derived, daptomycin-resistant Enterococcus faecium isolates that include cases of both de novo emergence of resistance within patients and putatively transmitted resistance. Both of these sets of strains have survived periods of antibiotic exposure, but only putatively transmitted resistant strains have survived extended periods without antibiotic exposure. These strains were then allowed to evolve in antibiotic free laboratory conditions. We find that putatively transmitted resistant strains tended to have lower level resistance but that evolution in antibiotic-free conditions resulted in minimal loss of resistance. In contrast, resistance that arose de novo within patients was higher level but exhibited greater declines in resistance in vitro. Sequencing of the experimentally evolved isolates revealed that reversal of high level resistance resulted from evolutionary pathways that were frequently genetically associated with the unique resistance mutations of that strain. Thus, the rapid reversal of high-level resistance was associated with accessible evolutionary pathways where an increase in fitness is associated with decreased resistance. We describe how this rapid loss of resistance may limit the spread of resistance within the hospital and shape the diversity of resistance phenotypes across patients.

microbiology↗

bioRxiv2023

Deep Whole-Genome Resequencing of Marek's Disease Virus Strains Reveals Intrastrain Variation

Current strategies to understand the molecular basis of Mareks disease virus (MDV) virulence primarily consist of cataloguing divergent nucleotides between strains with different phenotypes. However, each MDV strain is typically represented by a single consensus genome despite the confirmed existence of mixed viral populations. To assess the reliability of single-consensus interstrain genomic comparisons, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform 3-way comparisons between consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). In contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Phylogenomic analyses showed all three Md5 consensus genomes clustered closely together, while also showing that CVI988GenBank.BAC diverged from CVI988Pirbright.lab and CVI988USDA.PA.field. Comparison of CVI988 consensus genomes revealed 19 SNPs in the unique regions of CVI988GenBank.BAC that were not present in either CVI988Pirbright.lab or CVI988USDA.PA.field. Finally, we evaluated the genomic heterogeneity of CVI988 and Md5 populations by identifying positions with >2% read support for alternative alleles in two ultra-deeply sequenced samples. We were able to confirm that both populations of CVI988 and Md5 were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. We did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988GenBank.BAC. Taken together, our findings confirm that consensus genomes of the same strain of MDV can vary and suggest that multiple consensus genomes per strain are needed in order to maximize the accuracy of interstrain genomic comparisons.

microbiology↗

bioRxiv2023

Rising daptomycin resistance in Enterococcus faecium across a hospital system occurred via rampant recurrent evolution and occasional transmission between patients.

The rise of antibiotic resistance in a population involves two distinct processes: the origin of resistance and its spread. Here we study the contribution of both processes to the increase in daptomycin resistance in Enterococcus faecium in a hospital system. This case-control genomic study includes whole-genome sequencing of 82 isolates obtained from 24 case patients with clinically determined daptomycin-resistance and 24 controls. Among the case patients, the first isolate was resistant in 15 patients (R patients) while in the remaining nine the first isolate was susceptible but was followed by one or more resistant isolates (SR patients). Mutations in a set of candidate daptomycin resistance genes were compared within and between all patients. Additionally, among closely related isolates, mutations were identified across the entire assembled genome. Daptomycin resistance evolved separately multiple times and there was no phylogenetic clustering of the R or the SR groups. Six of the nine SR pairs gained mutations in previously identified candidate loci for daptomycin resistance, with the major cardiolipin synthase (clsA) being mutated most frequently. The hospital-wide increases in daptomycin resistance in E. faecium was the result of recurrent evolution taking multiple evolutionary pathways and occasional transmission of resistant isolates between patients. ImportanceAntimicrobial resistance in healthcare settings presents an important challenge, because infections with resistant organisms are associated with higher cost, longer hospital stays and worse outcomes for patients. However, it can be difficult to identify the factors driving the increase in resistance, specifically the relative contribution of resistance arising anew through mutation versus the transmission of resistant organisms from patient to patient. We study a hospital where resistance to daptomycin was increasing among Enterococcus faecium, an important hospital pathogen. We find the increase in resistance was the results of resistance arising many times independently. We also identify occasional transmission of daptomycin resistant organisms. Thus, control of daptomycin resistance in E. faecium may require interventions that both slow the emergence of resistance within patients and slow its spread. This work sheds light on the complex population dynamics leading to antibiotic resistance in hospitals.

evolutionary biology↗

bioRxiv2022

Ion exchange biomaterials to capture daptomycin and prevent resistance evolution in off-target bacterial populations

Daptomycin (DAP), a cyclic anionic lipopeptide antibiotic, is among the last resorts to treat multidrug resistant (vancomycin resistant Enterococcus faecium or methicillin resistant Staphylococcus aureus) Gram-positive bacterial infections. DAP is administered intravenously and biliary excretion results in the introduction of DAP ([~]5-10 % of the intravenous DAP dose) arriving in the gastrointestinal (GI) tract where it drives resistance evolution in off-target populations of Enterococcus faecium bacteria. Previously, we have shown that the oral administration of cholestyramine, an ion exchange biomaterial (IXB) sorbent, prevents DAP treatment from enriching DAP-resistance in populations of E. faecium shed from mice. Here, we engineer the biomaterial-DAP interfacial interactions to uncover the antibiotic removal mechanisms. The IXB-mediated DAP capture from aqueous media was measured in both controlled pH/electrolyte solutions and in simulated intestinal fluid (SIF) to uncover the molecular and colloidal mechanisms of DAP removal from the GI tract. Our findings show that the IXB electrostatically adsorbs the anionic antibiotic via a time-dependent diffusion-controlled process. Unsteady-state diffusion-adsorption mass balance describes the dynamics of adsorption well, and the maximum removal capacity is beyond the electric charge stoichiometric ratio because of DAP self-assembly. This study may open new opportunities for optimizing cholestyramine adjuvant therapy to prevent DAP resistance, as well as designing novel biomaterials to remove off-target antibiotics from the GI tract. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/495716v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@ec034eorg.highwire.dtl.DTLVardef@cd1106org.highwire.dtl.DTLVardef@118dbcborg.highwire.dtl.DTLVardef@106287c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility

To characterize the ongoing evolution of myxoma virus in Australian rabbits we used experimental infections of laboratory rabbits to determine the virulence and disease phenotypes of recent virus isolates. The viruses, collected between 2012-2015, fell into three lineages, one of which, lineage c, experienced a punctuated increase in evolutionary rate. All viruses were capable of causing acute death with aspects of neutropenic septicaemia, characterized by minimal signs of myxomatosis, the occurrence of pulmonary oedema and bacteria invasions throughout internal organs, but with no inflammatory response. For the viruses of highest virulence all rabbits usually died at this point. In more attenuated viruses some rabbits died acutely while others developed an amyxomatous phenotype. Rabbits that survived for longer periods developed greatly swollen cutaneous tissues with very high virus titres. This was particularly true of lineage c viruses. Unexpectedly, we identified a line of laboratory rabbits with some innate resistance to myxomatosis and used these in direct comparisons with the fully susceptible rabbit line. Importantly, the same disease phenotype occurred in both susceptible and resistant rabbits, although virulence was shifted towards more attenuated grades in resistant animals. We propose that selection against inflammation at cutaneous sites prolongs virus replication and enhances transmission, leading to the amyxomatous phenotype. In some virus backgrounds this creates an immunosuppressive state that predisposes to high virulence and acute death. The alterations in disease pathogenesis, particularly the overwhelming bacterial invasions that characterize the modern viruses, suggest that their virulence grades are not directly comparable with earlier studies. IMPORTANCEThe evolution of the myxoma virus (MYXV) following its release as a biological control for European rabbits in Australia is the textbook example of the co-evolution of virus virulence and host resistance. However, most of our knowledge of MYXV evolution only covers the first few decades of its spread in Australia and often with little direct connection between how changes in virus phenotype relate to those in the underlying virus genotype. By conducting detailed experimental infections of recent isolates of MYXV in different lines of laboratory rabbits we examined the ongoing evolution of MYXV disease phenotypes. Our results reveal a wide range of phenotypes, including an amyxomatous type as well as the impact of invasive bacteria, that in part depended on the level of rabbit host resistance. These results provide a unique insight into the complex virus and host factors that combine to shape disease phenotype and viral evolution.

microbiology↗

bioRxiv2022

Oral cholestyramine prevents enrichment of diverse daptomycin-resistance mutations in intestinal Enterococcus faecium

Background and ObjectivesPreviously, we showed proof-of-concept in a mouse model that oral administration of cholestyramine prevented enrichment of daptomycin-resistant Enterococcus faecium in the gastrointestinal (GI) tract during daptomycin therapy. Cholestyramine binds daptomycin in the gut, which removes daptomycin selection pressure and so prevents the enrichment of resistant clones. Here, we investigated two open questions related to this approach: 1) can cholestyramine prevent the enrichment of diverse daptomycin mutations emerging de novo in the gut? 2) how does the timing of cholestyramine administration impact its ability to suppress resistance? MethodologyMice with GI E. faecium were treated with daptomycin with or without cholestyramine, and E. faecium was cultured from feces to measure changes in daptomycin susceptibility. A subset of clones was sequenced to investigate the genomic basis of daptomycin resistance. ResultsCholestyramine prevented the enrichment of diverse resistance mutations that emerged de novo in daptomycin-treated mice. Whole-genome sequencing revealed that resistance emerged through multiple genetic pathways, with most candidate resistance mutations observed in the clsA gene. Additionally, we observed that cholestyramine was most effective when administration started prior to the first dose of daptomycin. However, beginning cholestyramine after the first daptomycin dose reduced the frequency of resistant E. faecium compared to not using cholestyramine at all. Conclusions and ImplicationsCholestyramine prevented the enrichment of diverse daptomycin-resistance mutations in intestinal E. faecium populations during daptomycin treatment, and it is a promising tool for managing transmission of daptomycin-resistant E. faecium.

microbiology↗

bioRxiv2021

Genetic determinants of antibiotic resistance and the evolution of trade-offs during adaptation in a single patient

The processes by which pathogens evolve within single hosts dictate the efficacy of treatment strategies designed to slow antibiotic resistance evolution and influence the population-wide resistance levels. The aim of this study is to describe the underlying genetic and phenotypic changes leading to antibiotic resistance within a single patient who died as resistance evolved to available antibiotics. We assess whether robust patterns of collateral sensitivity and response to combinations exist that might have been leveraged to improve therapy. Whole-genome sequencing was completed for nine isolates taken from this patient over 279 days of chronic infection with Enterobacter hormaechei, along with systematic measurements of changes in resistance against five of the most relevant drugs considered for treatment. The entirety of the genetic change is consistent with de novo mutations and plasmid loss events, without the acquisition of foreign genetic material via horizontal gene transfer. The isolates formed three genetically distinct lineages, with early evolutionary trajectories being supplanted by previously unobserved multi-step evolutionary trajectories. Importantly, no single isolate evolved resistance to all of the antibiotics considered for treatment against E. hormaechei (i.e., none was pan-resistant). Patterns of collateral sensitivity and response to combination therapy revealed contrasting patterns across this diversifying population. Translating antibiotic resistance management strategies from theoretical and laboratory data to clinical situations, such as this, may require managing diverse populations with unpredictable resistance trajectories.

evolutionary biology↗

bioRxiv2020

Modifying adaptive therapy to enhance competitive suppression

Adaptive therapy is a promising new approach to cancer treatment. It is designed to leverage competition between drug-sensitive and drug-resistant cells in order to suppress resistance and maintain tumor control for longer. Prompted by encouraging results from a recent pilot clinical trial, we evaluate the design of this initial test of adaptive therapy and identify three simple modifications that should improve performance. These modifications are designed to increase competition and are easy to implement. Using the mathematical model that supported the recent adaptive therapy trial, we show that the suggested modifications further delay time to tumor progression and also increase the range of patients who can benefit from adaptive therapy.

cancer biology↗

bioRxiv2020

An adjunctive therapy approach prevents antibiotic resistance emergence in opportunistic pathogens colonizing the gut

A key challenge in antibiotic stewardship is figuring out how to use antibiotics therapeutically without promoting the evolution of antibiotic resistance. Here, we demonstrate proof of concept for an adjunctive therapy that allows intravenous antibiotic treatment without driving the evolution and onward transmission of resistance. We repurposed the FDA-approved bile sequestrant cholestyramine, which we show binds the antibiotic daptomycin, as an anti-antibiotic to disable systemically-administered daptomycin reaching the gut. We hypothesized that adjunctive cholestyramine could enable therapeutic daptomycin treatment in the bloodstream, while preventing transmissible resistance emergence in opportunistic pathogens colonizing the gastrointestinal tract. We tested this idea in a mouse model of Enterococcus faecium gastrointestinal tract colonization. In mice treated with daptomycin, adjunctive cholestyramine therapy reduced the fecal shedding of daptomycin-resistant E. faecium by up to 80-fold. These results provide proof of concept for an approach that could reduce the spread of antibiotic resistance for important hospital pathogens.

evolutionary biology↗

bioRxiv2020

The effect of drug dose and timing of treatment on the emergence of drug resistance in vivo in a malaria model

Background and objectivesThere is significant interest in identifying clinically effective drug treatment regimens that minimize the de novo evolution of antimicrobial resistance in pathogen populations. However, in vivo studies that vary treatment regimens and directly measure drug resistance evolution are rare. Here, we experimentally investigate the role of drug dose and treatment timing on resistance evolution in an animal model. MethodologyIn a series of experiments, we measured the emergence of atovaquone-resistant mutants of Plasmodium chabaudi in laboratory mice, as a function of dose and timing of treatment with the antimalarial drug atovaquone. ResultsIncreasing the concentration of atovaquone increased the likelihood of high-level resistance emergence. Treating very early or late in infection reduced the risk of resistance, likely as a result of population size at time of treatment, but we were not able to exclude influence of the immune response in the latter. When we varied starting inoculum, resistance was more likely at intermediate inoculum sizes, but this did not correlate directly with population sizes at time of treatment. Conclusions and implications(i) Higher doses do not always minimize resistance emergence and can result in competitive release of parasites with high-level resistance. (ii) Altering treatment timing affects the risk of resistance emergence, but not as a simple function of population size at the time of treatment. (iii) Finding the right dose and right time to maximize clinical gains and limit resistance emergence can vary depending on biological context and was non-trivial even in our simplified experiments.

evolutionary biology↗

bioRxiv2019

Breaking down defenses: Quantitative analysis of malaria infection dynamics reveals distinct immune defense strategies

Hosts defend themselves against pathogens by mounting an immune response. Fully understanding the immune response as a driver of host disease and pathogen evolution requires a quantitative account of its impact on parasite population dynamics. Here, we use a data-driven modeling approach to quantify the birth and death processes underlying the dynamics of infections of the rodent malaria parasite, Plasmodium chabaudi, and the red blood cells (RBCs) it targets. We decompose the immune response into three components, each with a distinct effect on parasite and RBC vital rates, and quantify the relative contribution of each component to host disease and parasite density. Our analysis suggests that these components are deployed in a coordinated fashion to realize distinct resource-directed defense strategies that complement the killing of parasitized cells. Early in the infection, the host deploys a strategy reminiscent of siege and scorched-earth tactics, in which it both restricts the supply of RBCs and destroys them. Late in the infection, a juvenilization strategy, in which turnover of RBCs is accelerated, allows the host to recover from anemia while holding parasite proliferation at bay. By quantifying the impact of immunity on both parasite fitness and host disease, we reveal that phenomena often interpreted as immunopathology may in fact be beneficial to the host. Finally, we show that, across mice, the components of the host response are consistently related to each other, even when infections take qualitatively different trajectories. This suggests the existence of simple rules that govern the immune systems deployment.

ecology↗

bioRxiv2019

Sensitive cells extend antibiotic-driven containment of drug-resistant bacterial populations

Standard infectious disease practice calls for aggressive drug treatment that rapidly eliminates the pathogen population before resistance can emerge. When resistance is absent, this elimination strategy can lead to complete cure. However, it also removes drug-sensitive cells as quickly as possible, removing competitive barriers that may slow the growth of resistant cells. In contrast to the elimination strategy, the containment strategy aims to maintain the maximum tolerable number of pathogens, exploiting competitive suppression to achieve chronic control. Here we combine in vitro experiments in computer-controlled bioreactors with mathematical modeling to investigate whether containment strategies can delay failure of antibiotic treatment regimens. To do so, we measured the \"escape time\" required for drug-resistant E. coli populations to eclipse a threshold density maintained by adaptive antibiotic dosing. Populations containing only resistant cells rapidly escape containment, but we found that matched populations with the maximum possible number of sensitive cells could be contained for significantly longer. The increase in escape time occurs only when the threshold density-the acceptable bacterial burden-is sufficiently high, an effect that mathematical models attribute to increased competition. The findings provide decisive experimental confirmation that maintaining the maximum number of sensitive cells can be used to contain resistance when the size of the population is sufficiently large.

microbiology↗

bioRxiv2018

Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia

Myxoma virus (MYXV) has been evolving in a novel host species - European rabbits - in Australia since 1950. Previous studies of viruses sampled from 1950 to 1999 revealed a remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 2008 and 2017 we show that MYXV evolution in Australia can be characterized by three lineages, one of which exhibited a greatly elevated rate of evolutionary change and a dramatic break-down of temporal structure. Phylogenetic analysis revealed that this apparently punctuated evolutionary event occurred between 1996 and 2012. The branch leading to the rapidly evolving lineage contained a relatively high number of non-synonymous substitutions, and viruses in this lineage reversed a mutation found in the progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the reading frame of the M005L/R gene. Analysis of genes encoding proteins involved in DNA synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. Although there was some evidence for recombination across the MYXV phylogeny, this was not associated with the increase in evolutionary rate. The period from 1996 to 2012 saw significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic disease and prolonged drought in south-eastern Australia, followed by the partial recovery of populations. We therefore suggest that a rapidly changing environment for virus transmission changed the selection pressures faced by MYXV and altered the course of virus evolution.\n\nIMPORTANCEThe co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural experiments in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a break-down in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple non-synonymous and indel mutations. We suggest that this punctuated evolutionary event likely reflects a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.

evolutionary biology↗

bioRxiv2017

Modeling Marek’s disease virus transmission: a framework for evaluating the impact of farming practices and evolution on disease

Mareks disease virus (MDV) is a pathogen of chickens whose control has twice been un-dermined by pathogen evolution. Disease ecology is believed to be the main driver of this evolution, yet mathematical models of MDV disease ecology have never been confronted with data to test their reliability. Here, we develop a suite of MDV models that differ in the ecological mechanisms they include. We fit these models with maximum likelihood in pomp to data on MDV concentration in dust collected from two commercial broiler farms. Using AIC to compare the models, we find that virus dynamics are influenced by between-flock variation in host susceptibility to virus, shedding rate from infected birds, and cleanout efficiency. We also find evidence that virus is reintroduced to farms approximately once per month, but we do not find evidence that virus sanitization rates vary between flocks. Of the models that survive model selection, we find agreement between parameter estimates and previous experimental data, as well as agreement between field data and the predictions of these models, suggesting robustness of model predictions. Using the set of surviving models, we explore how changes to farming practices are predicted to influence MDV costs, should pathogen evolution undermine existing control measures. By quantitatively capturing the mechanisms of disease ecology, we have laid the groundwork to explore the future trajectory of virus evolution.

ecology↗