Publications by authors named "Edze R Westra"

58 Publications

Immune lag is a major cost of prokaryotic adaptive immunity during viral outbreaks.

Proc Biol Sci 2021 Oct 20;288(1961):20211555. Epub 2021 Oct 20.

Department of Biological Sciences-Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA.

Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptive immune systems enable bacteria and archaea to efficiently respond to viral pathogens by creating a genomic record of previous encounters. These systems are broadly distributed across prokaryotic taxa, yet are surprisingly absent in a majority of organisms, suggesting that the benefits of adaptive immunity frequently do not outweigh the costs. Here, combining experiments and models, we show that a delayed immune response which allows viruses to transiently redirect cellular resources to reproduction, which we call 'immune lag', is extremely costly during viral outbreaks, even to completely immune hosts. Critically, the costs of lag are only revealed by examining the early, transient dynamics of a host-virus system occurring immediately after viral challenge. Lag is a basic parameter of microbial defence, relevant to all intracellular, post-infection antiviral defence systems, that has to-date been largely ignored by theoretical and experimental treatments of host-phage systems.
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http://dx.doi.org/10.1098/rspb.2021.1555DOI Listing
October 2021

Individual bacteria in structured environments rely on phenotypic resistance to phage.

PLoS Biol 2021 Oct 12;19(10):e3001406. Epub 2021 Oct 12.

Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom.

Bacteriophages represent an avenue to overcome the current antibiotic resistance crisis, but evolution of genetic resistance to phages remains a concern. In vitro, bacteria evolve genetic resistance, preventing phage adsorption or degrading phage DNA. In natural environments, evolved resistance is lower possibly because the spatial heterogeneity within biofilms, microcolonies, or wall populations favours phenotypic survival to lytic phages. However, it is also possible that the persistence of genetically sensitive bacteria is due to less efficient phage amplification in natural environments, the existence of refuges where bacteria can hide, and a reduced spread of resistant genotypes. Here, we monitor the interactions between individual planktonic bacteria in isolation in ephemeral refuges and bacteriophage by tracking the survival of individual cells. We find that in these transient spatial refuges, phenotypic resistance due to reduced expression of the phage receptor is a key determinant of bacterial survival. This survival strategy is in contrast with the emergence of genetic resistance in the absence of ephemeral refuges in well-mixed environments. Predictions generated via a mathematical modelling framework to track bacterial response to phages reveal that the presence of spatial refuges leads to fundamentally different population dynamics that should be considered in order to predict and manipulate the evolutionary and ecological dynamics of bacteria-phage interactions in naturally structured environments.
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http://dx.doi.org/10.1371/journal.pbio.3001406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8509860PMC
October 2021

Regulation of prophage induction and lysogenization by phage communication systems.

Curr Biol 2021 Sep 22. Epub 2021 Sep 22.

CEFE, CNRS, Univ Montpellier, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France. Electronic address:

Many viruses cause both lytic infections, where they release viral particles, and dormant infections, where they await future opportunities to reactivate. The benefits of each transmission mode depend on the density of susceptible hosts in the environment. Some viruses infecting bacteria use molecular signaling to respond plastically to changes in host availability. These viruses produce a signal during lytic infection and regulate, based on the signal concentration in the environment, the probability with which they switch to causing dormant infections. We present an analytical framework to examine the adaptive significance of plasticity in viral life-history traits in fluctuating environments. Our model generalizes and extends previous theory and predicts that host density fluctuations should select for plasticity in entering lysogeny as well as virus reactivation once signal concentrations decline. Using Bacillus subtilis and its phage phi3T, we experimentally confirm the prediction that phages use signal to make informed decisions over prophage induction. We also demonstrate that lysogens produce signaling molecules and that signal is degraded by hosts in a density-dependent manner. Declining signal concentrations therefore potentially indicate the presence of uninfected hosts and trigger prophage induction. Finally, we find that conflict over the responses of lysogenization and reactivation to signal is resolved through the evolution of different response thresholds for each trait. Collectively, these findings deepen our understanding of the ways viruses use molecular communication to regulate their infection strategies, which can be leveraged to manipulate host and phage population dynamics in natural environments.
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http://dx.doi.org/10.1016/j.cub.2021.08.073DOI Listing
September 2021

Interactions between bacterial and phage communities in natural environments.

Nat Rev Microbiol 2021 Aug 9. Epub 2021 Aug 9.

Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK.

We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.
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http://dx.doi.org/10.1038/s41579-021-00602-yDOI Listing
August 2021

Coevolution between bacterial CRISPR-Cas systems and their bacteriophages.

Cell Host Microbe 2021 05;29(5):715-725

ESI, Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9FE, UK. Electronic address:

CRISPR-Cas systems provide bacteria and archaea with adaptive, heritable immunity against their viruses (bacteriophages and phages) and other parasitic genetic elements. CRISPR-Cas systems are highly diverse, and we are only beginning to understand their relative importance in phage defense. In this review, we will discuss when and why CRISPR-Cas immunity against phages evolves, and how this, in turn, selects for the evolution of immune evasion by phages. Finally, we will discuss our current understanding of if, and when, we observe coevolution between CRISPR-Cas systems and phages, and how this may be influenced by the mechanism of CRISPR-Cas immunity.
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http://dx.doi.org/10.1016/j.chom.2021.03.018DOI Listing
May 2021

The effect of Quorum sensing inhibitors on the evolution of CRISPR-based phage immunity in Pseudomonas aeruginosa.

ISME J 2021 08 10;15(8):2465-2473. Epub 2021 Mar 10.

Biosciences, Environment and Sustainability Institute, University of Exeter, Penryn, UK.

Quorum sensing controls the expression of a wide range of important traits in the opportunistic pathogen Pseudomonas aeruginosa, including the expression of virulence genes and its CRISPR-cas immune system, which protects from bacteriophage (phage) infection. This finding has led to the speculation that synthetic quorum sensing inhibitors could be used to limit the evolution of CRISPR immunity during phage therapy. Here we use experimental evolution to explore if and how a quorum sensing inhibitor influences the population and evolutionary dynamics of P. aeruginosa upon phage DMS3vir infection. We find that chemical inhibition of quorum sensing decreases phage adsorption rates due to downregulation of the Type IV pilus, which causes delayed lysis of bacterial cultures and favours the evolution of CRISPR immunity. Our data therefore suggest that inhibiting quorum sensing may reduce rather than improve the therapeutic efficacy of pilus-specific phage, and this is likely a general feature when phage receptors are positively regulated by quorum sensing.
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http://dx.doi.org/10.1038/s41396-021-00946-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8319334PMC
August 2021

It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements.

Proc Natl Acad Sci U S A 2020 11 29;117(45):27777-27785. Epub 2020 Oct 29.

Department of Biology, Emory University, Atlanta, GA 30307

Articles on CRISPR commonly open with some variant of the phrase "these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements." There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.
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http://dx.doi.org/10.1073/pnas.1915966117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668106PMC
November 2020

Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems.

Curr Biol 2020 10;30(19):R1189-R1202

Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK. Electronic address:

Like many organisms, bacteria and archaea have both innate and adaptive immune systems to defend against infection by viruses and other parasites. Innate immunity most commonly relies on the endonuclease-mediated cleavage of any incoming DNA that lacks a specific epigenetic modification, through a system known as restriction-modification. CRISPR-Cas-mediated adaptive immunity relies on the insertion of short DNA sequences from parasite genomes into CRISPR arrays on the host genome to provide sequence-specific protection. The discovery of each of these systems has revolutionised our ability to carry out genetic manipulations, and, as a consequence, the enzymes involved have been characterised in exquisite detail. In comparison, much less is known about the importance of these two arms of the defence for the ecology and evolution of prokaryotes and their parasites. Here, we review our current ecological and evolutionary understanding of these systems in isolation, and discuss the need to study how innate and adaptive immune responses are integrated when they coexist in the same cell.
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http://dx.doi.org/10.1016/j.cub.2020.08.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116224PMC
October 2020

Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity.

ISME J 2021 02 3;15(2):534-544. Epub 2020 Oct 3.

Biosciences, University of Exeter, Exeter, TR10 9EZ, UK.

CRISPR-Cas immune systems are widespread in bacteria and archaea, but not ubiquitous. Previous work has demonstrated that CRISPR immunity is associated with an infection-induced fitness cost, which may help explain the patchy distribution observed. However, the mechanistic basis of this cost has remained unclear. Using Pseudomonas aeruginosa PA14 and its phage DMS3vir as a model, we perform a 30-day evolution experiment under phage mediated selection. We demonstrate that although CRISPR is initially selected for, bacteria carrying mutations in the phage receptor rapidly invade the population following subsequent reinfections. We then test three potential mechanisms for the observed cost of CRISPR: (1) autoimmunity from the acquisition of self-targeting spacers, (2) immunopathology or energetic costs from increased cas gene expression and (3) toxicity caused by phage gene expression prior to CRISPR-mediated cleavage. We find that phages can express genes before the immune system clears the infection and that expression of these genes can have a negative effect on host fitness. While infection does not lead to increased expression of cas genes, it does cause differential expression of multiple other host processes that may further contribute to the cost of CRISPR immunity. In contrast, we found little support for infection-induced autoimmunological and immunopathological effects. Phage gene expression prior to cleavage of the genome by the CRISPR-Cas immune system is therefore the most parsimonious explanation for the observed phage-induced fitness cost.
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http://dx.doi.org/10.1038/s41396-020-00794-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027618PMC
February 2021

Avoidance of Self during CRISPR Immunization.

Trends Microbiol 2020 07 10;28(7):543-553. Epub 2020 Apr 10.

Department of Biology, University of Maryland, College Park, MD, USA. Electronic address:

The battle between microbes and their viruses is ancient and ongoing. Clustered regularly interspaced short palindromic repeat (CRISPR) immunity, the first and, to date, only form of adaptive immunity found in prokaryotes, represents a flexible mechanism to recall past infections while also adapting to a changing pathogenic environment. Critical to the role of CRISPR as an adaptive immune mechanism is its capacity for self versus non-self recognition when acquiring novel immune memories. Yet, CRISPR systems vary widely in both how and to what degree they can distinguish foreign from self-derived genetic material. We document known and hypothesized mechanisms that bias the acquisition of immune memory towards non-self targets. We demonstrate that diversity is the rule, with many widespread but no universal mechanisms for self versus non-self recognition.
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http://dx.doi.org/10.1016/j.tim.2020.02.005DOI Listing
July 2020

Diversity in CRISPR-based immunity protects susceptible genotypes by restricting phage spread and evolution.

J Evol Biol 2020 May 8. Epub 2020 May 8.

ESI and CEC, Biosciences, University of Exeter, Penryn, UK.

Diversity in host resistance often associates with reduced pathogen spread. This may result from ecological and evolutionary processes, likely with feedback between them. Theory and experiments on bacteria-phage interactions have shown that genetic diversity of the bacterial adaptive immune system can limit phage evolution to overcome resistance. Using the CRISPR-Cas bacterial immune system and lytic phage, we engineered a host-pathogen system where each bacterial host genotype could be infected by only one phage genotype. With this model system, we explored how CRISPR diversity impacts the spread of phage when they can overcome a resistance allele, how immune diversity affects the evolution of the phage to increase its host range and if there was feedback between these processes. We show that increasing CRISPR diversity benefits susceptible bacteria via a dilution effect, which limits the spread of the phage. We suggest that this ecological effect impacts the evolution of novel phage genotypes, which then feeds back into phage population dynamics.
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http://dx.doi.org/10.1111/jeb.13638DOI Listing
May 2020

Publisher Correction: Targeting of temperate phages drives loss of type I CRISPR-Cas systems.

Nature 2020 03;579(7799):E10

ESI, Biosciences, University of Exeter, Penryn, UK.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41586-020-2089-zDOI Listing
March 2020

Targeting of temperate phages drives loss of type I CRISPR-Cas systems.

Nature 2020 02 22;578(7793):149-153. Epub 2020 Jan 22.

ESI, Biosciences, University of Exeter, Penryn, UK.

On infection of their host, temperate viruses that infect bacteria (bacteriophages; hereafter referred to as phages) enter either a lytic or a lysogenic cycle. The former results in lysis of bacterial cells and phage release (resulting in horizontal transmission), whereas lysogeny is characterized by the integration of the phage into the host genome, and dormancy (resulting in vertical transmission). Previous co-culture experiments using bacteria and mutants of temperate phages that are locked in the lytic cycle have shown that CRISPR-Cas systems can efficiently eliminate the invading phages. Here we show that, when challenged with wild-type temperate phages (which can become lysogenic), type I CRISPR-Cas immune systems cannot eliminate the phages from the bacterial population. Furthermore, our data suggest that, in this context, CRISPR-Cas immune systems are maladaptive to the host, owing to the severe immunopathological effects that are brought about by imperfect matching of spacers to the integrated phage sequences (prophages). These fitness costs drive the loss of CRISPR-Cas from bacterial populations, unless the phage carries anti-CRISPR (acr) genes that suppress the immune system of the host. Using bioinformatics, we show that this imperfect targeting is likely to occur frequently in nature. These findings help to explain the patchy distribution of CRISPR-Cas immune systems within and between bacterial species, and highlight the strong selective benefits of phage-encoded acr genes for both the phage and the host under these circumstances.
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http://dx.doi.org/10.1038/s41586-020-1936-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007301PMC
February 2020

Exploitation of the Cooperative Behaviors of Anti-CRISPR Phages.

Cell Host Microbe 2020 Feb 31;27(2):189-198.e6. Epub 2019 Dec 31.

ESI, Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK. Electronic address:

Bacteriophages encoding anti-CRISPR proteins (Acrs) must cooperate to overcome phage resistance mediated by the bacterial immune system CRISPR-Cas, where the first phage blocks CRISPR-Cas immunity in order to allow a second Acr phage to successfully replicate. However, in nature, bacteria are frequently not pre-immunized, and phage populations are often not clonal, exhibiting variations in Acr presence and strength. We explored how interactions between Acr phages and initially sensitive bacteria evolve, both in the presence and absence of competing phages lacking Acrs. We find that Acr phages benefit "Acr-negative" phages by limiting the evolution of CRISPR-based resistance and helping Acr-negative phages to replicate on resistant host sub-populations. These benefits depend on the strength of CRISPR-Cas inhibitors and result in strong Acrs providing smaller fitness advantages than weaker ones when Acr phages compete with Acr-negative phages. These results indicate that different Acr types shape the evolutionary dynamics and social interactions of phage populations in natural communities.
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http://dx.doi.org/10.1016/j.chom.2019.12.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7013381PMC
February 2020

The effect of phage genetic diversity on bacterial resistance evolution.

ISME J 2020 03 2;14(3):828-836. Epub 2020 Jan 2.

Biosciences, Environment and Sustainability Institute, University of Exeter, Penryn, TR10 9FE, UK.

CRISPR-Cas adaptive immune systems are found in bacteria and archaea and provide defence against phage by inserting phage-derived sequences into CRISPR loci on the host genome to provide sequence specific immunological memory against re-infection. Under laboratory conditions the bacterium Pseudomonas aeruginosa readily evolves the high levels of CRISPR-based immunity against clonal populations of its phage DMS3vir, which in turn causes rapid extinction of the phage. However, in nature phage populations are likely to be more genetically diverse, which could theoretically impact the frequency at which CRISPR-based immunity evolves which in turn can alter phage persistence over time. Here we experimentally test these ideas and found that a smaller proportion of infected bacterial populations evolved CRISPR-based immunity against more genetically diverse phage populations, with the majority of the population evolving a sm preventing phage adsorption and providing generalised defence against a broader range of phage genotypes. However, those cells that do evolve CRISPR-based immunity in response to infection with more genetically diverse phage acquire greater numbers of CRISPR memory sequences in order to resist a wider range of phage genotypes. Despite differences in bacterial resistance evolution, the rates of phage extinction were similar in the context of clonal and diverse phage infections suggesting selection for CRISPR-based immunity or sm-based resistance plays a relatively minor role in the ecological dynamics in this study. Collectively, these data help to understand the drivers of CRISPR-based immunity and their consequences for bacteria-phage coexistence, and, more broadly, when generalised defences will be favoured over more specific defences.
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http://dx.doi.org/10.1038/s41396-019-0577-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7031251PMC
March 2020

Type I-F CRISPR-Cas resistance against virulent phages results in abortive infection and provides population-level immunity.

Nat Commun 2019 12 4;10(1):5526. Epub 2019 Dec 4.

Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand.

Type I CRISPR-Cas systems are abundant and widespread adaptive immune systems in bacteria and can greatly enhance bacterial survival in the face of phage infection. Upon phage infection, some CRISPR-Cas immune responses result in bacterial dormancy or slowed growth, which suggests the outcomes for infected cells may vary between systems. Here we demonstrate that type I CRISPR immunity of Pectobacterium atrosepticum leads to suppression of two unrelated virulent phages, ɸTE and ɸM1. Immunity results in an abortive infection response, where infected cells do not survive, but viral propagation is severely decreased, resulting in population protection due to the reduced phage epidemic. Our findings challenge the view of CRISPR-Cas as a system that protects the individual cell and supports growing evidence of abortive infection by some types of CRISPR-Cas systems.
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http://dx.doi.org/10.1038/s41467-019-13445-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892833PMC
December 2019

Bacterial biodiversity drives the evolution of CRISPR-based phage resistance.

Nature 2019 10 23;574(7779):549-552. Epub 2019 Oct 23.

Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn Campus, Penryn, UK.

About half of all bacteria carry genes for CRISPR-Cas adaptive immune systems, which provide immunological memory by inserting short DNA sequences from phage and other parasitic DNA elements into CRISPR loci on the host genome. Whereas CRISPR loci evolve rapidly in natural environments, bacterial species typically evolve phage resistance by the mutation or loss of phage receptors under laboratory conditions. Here we report how this discrepancy may in part be explained by differences in the biotic complexity of in vitro and natural environments. Specifically, by using the opportunistic pathogen Pseudomonas aeruginosa and its phage DMS3vir, we show that coexistence with other human pathogens amplifies the fitness trade-offs associated with the mutation of phage receptors, and therefore tips the balance in favour of the evolution of CRISPR-based resistance. We also demonstrate that this has important knock-on effects for the virulence of P. aeruginosa, which became attenuated only if the bacteria evolved surface-based resistance. Our data reveal that the biotic complexity of microbial communities in natural environments is an important driver of the evolution of CRISPR-Cas adaptive immunity, with key implications for bacterial fitness and virulence.
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http://dx.doi.org/10.1038/s41586-019-1662-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6837874PMC
October 2019

Transposition: A CRISPR Way to Get Around.

Curr Biol 2019 09;29(18):R886-R889

Environment and Sustainability Institute, Biosciences, University of Exeter, Cornwall Campus, Penryn, Cornwall TR10 9FE, UK. Electronic address:

CRISPR-Cas systems provide sequence-specific immunity against selfish genetic elements in prokaryotes. Now, two studies show that transposon-encoded variants can guide sequence-specific transposition. These findings have important practical implications but also raise questions of why and how this strategy would benefit transposons.
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http://dx.doi.org/10.1016/j.cub.2019.08.010DOI Listing
September 2019

The ecology and evolution of microbial CRISPR-Cas adaptive immune systems.

Philos Trans R Soc Lond B Biol Sci 2019 05;374(1772):20190101

3 Department of Microbiology, University of Illinois , Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, IL 61801 , USA.

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http://dx.doi.org/10.1098/rstb.2019.0101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452260PMC
May 2019

The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity.

Philos Trans R Soc Lond B Biol Sci 2019 05;374(1772):20180094

ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9EZ , UK.

CRISPR-Cas immune systems are present in around half of bacterial genomes. Given the specificity and adaptability of this immune mechanism, it is perhaps surprising that they are not more widespread. Recent insights into the requirement for specific host factors for the function of some CRISPR-Cas subtypes, as well as the negative epistasis between CRISPR-Cas and other host genes, have shed light on potential reasons for the partial distribution of this immune strategy in bacteria. In this study, we examined how mutations in the bacterial mismatch repair system, which are frequently observed in natural and clinical isolates and cause elevated host mutation rates, influence the evolution of CRISPR-Cas-mediated immunity. We found that hosts with a high mutation rate very rarely evolved CRISPR-based immunity to phage compared to wild-type hosts. We explored the reason for this effect and found that the higher frequency at which surface mutants pre-exist in the mutator host background causes them to rapidly become the dominant phenotype under phage infection. These findings suggest that natural variation in bacterial mutation rates may, therefore, influence the distribution of CRISPR-Cas adaptive immune systems. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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http://dx.doi.org/10.1098/rstb.2018.0094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452272PMC
May 2019

CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage.

Philos Trans R Soc Lond B Biol Sci 2019 05;374(1772):20180098

ESI and CEC, Biosciences, University of Exeter , Cornwall Campus, Penryn TR10 9EZ , UK.

CRISPR-Cas is an adaptive prokaryotic immune system that prevents phage infection. By incorporating phage-derived 'spacer' sequences into CRISPR loci on the host genome, future infections from the same phage genotype can be recognized and the phage genome cleaved. However, the phage can escape CRISPR degradation by mutating the sequence targeted by the spacer, allowing them to re-infect previously CRISPR-immune hosts, and theoretically leading to coevolution. Previous studies have shown that phage can persist over long periods in populations of Streptococcus thermophilus that can acquire CRISPR-Cas immunity, but it has remained less clear whether this coexistence was owing to coevolution, and if so, what type of coevolutionary dynamics were involved. In this study, we performed highly replicated serial transfer experiments over 30 days with S. thermophilus and a lytic phage. Using a combination of phenotypic and genotypic data, we show that CRISPR-mediated resistance and phage infectivity coevolved over time following an arms race dynamic, and that asymmetry between phage infectivity and host resistance within this system eventually causes phage extinction. This work provides further insight into the way CRISPR-Cas systems shape the population and coevolutionary dynamics of bacteria-phage interactions. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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http://dx.doi.org/10.1098/rstb.2018.0098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452269PMC
May 2019

Variability in the durability of CRISPR-Cas immunity.

Philos Trans R Soc Lond B Biol Sci 2019 05;374(1772):20180097

1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France.

The durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) alleles of the bacteria Streptococcus thermophilus against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be because of variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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http://dx.doi.org/10.1098/rstb.2018.0097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452261PMC
May 2019

Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci.

Nat Microbiol 2019 06 18;4(6):956-963. Epub 2019 Mar 18.

Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.

CRISPR (clustered regularly interspaced short palindromic repeats) loci and their associated (cas) genes encode an adaptive immune system that protects prokaryotes from viral and plasmid invaders. Following viral (phage) infection, a small fraction of the prokaryotic cells are able to integrate a small sequence of the invader's genome into the CRISPR array. These sequences, known as spacers, are transcribed and processed into small CRISPR RNA guides that associate with Cas nucleases to specify a viral target for destruction. Although CRISPR-cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizontal gene transfer, the drivers of CRISPR dissemination remain unclear. Here, we show that spacers can recombine with phage target sequences to mediate a form of specialized transduction of CRISPR elements. Phage targets in phage 85, ΦNM1, ΦNM4 and Φ12 can recombine with spacers in either chromosomal or plasmid-borne CRISPR loci in Staphylococcus, leading to either the transfer of CRISPR-adjacent genes or the propagation of acquired immunity to other bacteria in the population, respectively. Our data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer.
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http://dx.doi.org/10.1038/s41564-019-0400-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533911PMC
June 2019

Addiction systems antagonize bacterial adaptive immunity.

FEMS Microbiol Lett 2019 03;366(5)

Environment and Sustainability Institute, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK.

CRISPR-Cas systems provide adaptive immunity against mobile genetic elements, but employment of this resistance mechanism is often reported with a fitness cost for the host. Whether or not CRISPR-Cas systems are important barriers for the horizontal spread of conjugative plasmids, which play a crucial role in the spread of antibiotic resistance, will depend on the fitness costs of employing CRISPR-based defences and the benefits of resisting conjugative plasmids. To estimate these costs and benefits we measured bacterial fitness associated with plasmid immunity using Escherichia coli and the conjugative plasmid pOX38-Cm. We find that CRISPR-mediated immunity fails to confer a fitness benefit in the absence of antibiotics, despite the large fitness cost associated with carrying the plasmid in this context. Similar to many other conjugative plasmids, pOX38-Cm carries a CcdAB toxin-anti-toxin (TA) addiction system. These addiction systems encode long-lived toxins and short-lived anti-toxins, resulting in toxic effects following the loss of the TA genes from the bacterial host. Our data suggest that the lack of a fitness benefit associated with CRISPR-mediated defence is due to expression of the TA system before plasmid detection and degradation. As most antibiotic resistance plasmids encode TA systems this could have important consequences for the role of CRISPR-Cas systems in limiting the spread of antibiotic resistance.
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http://dx.doi.org/10.1093/femsle/fnz047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478593PMC
March 2019

CRISPR evolution and bacteriophage persistence in the context of population bottlenecks.

RNA Biol 2019 04 17;16(4):588-594. Epub 2019 Feb 17.

a ESI, Biosciences , University of Exeter , Penryn , UK.

Population bottlenecks often cause strong reductions in genetic diversity and alter population structure. In the context of host-parasite interactions, bottlenecks could in theory benefit either the host or the pathogen. We predicted that bottlenecking of bacterial populations that evolve CRISPR immunity against bacteriophages (phage) would benefit the pathogen, because CRISPR spacer diversity can rapidly drive phages extinct. To test this, we bottlenecked populations of bacteria and phage, tracking phage persistence and the evolution of bacterial resistance mechanisms. Contrary to our prediction, bottlenecking worked in the advantage of the host. With some possible exceptions, this effect was not caused by CRISPR immunity. This host benefit is consistent with a dilution effect disproportionately affecting phage. This study provides further insight into how bottlenecking influences bacteria-phage dynamics, the role of dilution in bacteria-phage interactions, and the evolution of host immune systems.
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http://dx.doi.org/10.1080/15476286.2019.1578608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546380PMC
April 2019

Evolutionary emergence of infectious diseases in heterogeneous host populations.

PLoS Biol 2018 09 24;16(9):e2006738. Epub 2018 Sep 24.

CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, Montpellier, France.

The emergence and re-emergence of pathogens remains a major public health concern. Unfortunately, when and where pathogens will (re-)emerge is notoriously difficult to predict, as the erratic nature of those events is reinforced by the stochastic nature of pathogen evolution during the early phase of an epidemic. For instance, mutations allowing pathogens to escape host resistance may boost pathogen spread and promote emergence. Yet, the ecological factors that govern such evolutionary emergence remain elusive because of the lack of ecological realism of current theoretical frameworks and the difficulty of experimentally testing their predictions. Here, we develop a theoretical model to explore the effects of the heterogeneity of the host population on the probability of pathogen emergence, with or without pathogen evolution. We show that evolutionary emergence and the spread of escape mutations in the pathogen population is more likely to occur when the host population contains an intermediate proportion of resistant hosts. We also show that the probability of pathogen emergence rapidly declines with the diversity of resistance in the host population. Experimental tests using lytic bacteriophages infecting their bacterial hosts containing Clustered Regularly Interspaced Short Palindromic Repeat and CRISPR-associated (CRISPR-Cas) immune defenses confirm these theoretical predictions. These results suggest effective strategies for cross-species spillover and for the management of emerging infectious diseases.
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http://dx.doi.org/10.1371/journal.pbio.2006738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6171948PMC
September 2018

Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity.

Cell 2018 08 19;174(4):908-916.e12. Epub 2018 Jul 19.

ESI and CEC, Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK. Electronic address:

Some phages encode anti-CRISPR (acr) genes, which antagonize bacterial CRISPR-Cas immune systems by binding components of its machinery, but it is less clear how deployment of these acr genes impacts phage replication and epidemiology. Here, we demonstrate that bacteria with CRISPR-Cas resistance are still partially immune to Acr-encoding phage. As a consequence, Acr-phages often need to cooperate in order to overcome CRISPR resistance, with a first phage blocking the host CRISPR-Cas immune system to allow a second Acr-phage to successfully replicate. This cooperation leads to epidemiological tipping points in which the initial density of Acr-phage tips the balance from phage extinction to a phage epidemic. Furthermore, both higher levels of CRISPR-Cas immunity and weaker Acr activities shift the tipping points toward higher initial phage densities. Collectively, these data help elucidate how interactions between phage-encoded immune suppressors and the CRISPR systems they target shape bacteria-phage population dynamics.
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http://dx.doi.org/10.1016/j.cell.2018.05.058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086933PMC
August 2018

CRISPR-Cas antimicrobials: Challenges and future prospects.

PLoS Pathog 2018 06 14;14(6):e1006990. Epub 2018 Jun 14.

Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1006990DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001953PMC
June 2018

Mechanisms and consequences of diversity-generating immune strategies.

Nat Rev Immunol 2017 Nov 7;17(11):719-728. Epub 2017 Aug 7.

Biosciences, University of Exeter, TR10 9EZ, UK.

Species from all five kingdoms of life have evolved sophisticated mechanisms to generate diversity in genes that are involved in host-pathogen interactions, conferring reduced levels of parasitism to both individuals and populations. Here, we highlight unifying concepts that underpin these evolutionarily unrelated diversity-generating mechanisms (DGMs). We discuss the mechanisms of and selective forces acting on these diversity-generating immune strategies, as well as their epidemiological and co-evolutionary consequences. We propose that DGMs can be broadly classified into two classes - targeted and untargeted DGMs - which generate different levels of diversity with important consequences for host-parasite co-evolution.
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http://dx.doi.org/10.1038/nri.2017.78DOI Listing
November 2017
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