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

This is the final version. Available from the publisher via the DOI in this record.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

Transient eco-evolutionary dynamics early in a phage epidemic have strong and lasting impact on the long-term evolution of bacterial defences

This is the final version. Available on open access from Public Library of Science (PLoS) via the DOI in this recordData Availability: Data and code are available online https://doi.org/10.5281/zenodo.8193506Organisms have evolved a range of constitutive (always active) and inducible (elicited by parasites) defence mechanisms, but we have limited understanding of what drives the evolution of these orthogonal defence strategies. Bacteria and their phages offer a tractable system to study this: Bacteria can acquire constitutive resistance by mutation of the phage receptor (surface mutation, sm) or induced resistance through their CRISPR-Cas adaptive immune system. Using a combination of theory and experiments, we demonstrate that the mechanism that establishes first has a strong advantage because it weakens selection for the alternative resistance mechanism. As a consequence, ecological factors that alter the relative frequencies at which the different resistances are acquired have a strong and lasting impact: High growth conditions promote the evolution of sm resistance by increasing the influx of receptor mutation events during the early stages of the epidemic, whereas a high infection risk during this stage of the epidemic promotes the evolution of CRISPR immunity, since it fuels the (infection-dependent) acquisition of CRISPR immunity. This work highlights the strong and lasting impact of the transient evolutionary dynamics during the early stages of an epidemic on the long-term evolution of constitutive and induced defences, which may be leveraged to manipulate phage resistance evolution in clinical and applied settings.Natural Environment Research Council (NERC)European Research Council (ERC)Biotechnology and Biological Sciences Research Council (BBSRC

Different genetic and morphological outcomes for phages targeted by single or multiple CRISPR-Cas spacers.

CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against genetic invaders, such as bacteriophages. The systems integrate short sequences from the phage genome into the bacterial CRISPR array. These 'spacers' provide sequence-specific immunity but drive natural selection of evolved phage mutants that escape the CRISPR-Cas defence. Spacer acquisition occurs by either naive or primed adaptation. Naive adaptation typically results in the incorporation of a single spacer. By contrast, priming is a positive feedback loop that often results in acquisition of multiple spacers, which occurs when a pre-existing spacer matches the invading phage. We predicted that single and multiple spacers, representative of naive and primed adaptation, respectively, would cause differing outcomes after phage infection. We investigated the response of two phages, ϕTE and ϕM1, to the Pectobacterium atrosepticum type I-F CRISPR-Cas system and observed that escape from single spacers typically occurred via point mutations. Alternatively, phages escaped multiple spacers through deletions, which can occur in genes encoding structural proteins. Cryo-EM analysis of the ϕTE structure revealed shortened tails in escape mutants with tape measure protein deletions. We conclude that CRISPR-Cas systems can drive phage genetic diversity, altering morphology and fitness, through selective pressures arising from naive and primed acquisition events. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.This work was supported by a Rutherford Discovery Fellow- ship from the Royal Society of New Zealand (RSNZ) (to P.C.F.), the Marsden Fund, RSNZ, the Bio-protection Research Centre (Tertiary Education Commission), a University of Otago Doctoral Scholarship (to B.N.J.W.), University of Otago Division of Health Sciences Career Development Post-doctoral Fellowship and a Veni grant (grant no. 016.Veni.171.047) from the The Netherlands Organization for Scienti- fic Research (to R.H.J.S.). G.P.C.S. was supported by the BBSRC, UK

Coevolution between bacterial CRISPR-Cas systems and their bacteriophages

This is the author accepted manuscript. The final version is available from Cell Press via the DOI in this record 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.VENIBiotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Counci

Evaluating Promotional Approaches for Citizen Science Biological Recording: Bumblebees as a Group Versus Harmonia axyridis as a Flagship for Ladybirds

Over the past decade, the number of biological records submitted by members of the public have increased dramatically. However, this may result in reduced record quality, depending on how species are promoted in the media. Here we examined the two main promotional approaches for citizen science recording schemes: flagship-species, using one charismatic species as an umbrella for the entire group (here, Harmonia axyridis (Pallas) for Coleoptera: Coccinellidae), and general-group, where the group is promoted as a whole and no particular prominence is given to any one species (here, bumblebees, genus Bombus (Hymenoptera: Apidae)). Of the two approaches, the general-group approach produced data that was not biased towards any one species, but far fewer records per year overall. In contrast, the flagship-species approach generated a much larger annual dataset, but heavily biased towards the flagship itself. Therefore, we recommend that the approach for species promotion is fitted to the result desired

Decolonizing drug-resistant E. coli with phage and probiotics: breaking the frequency-dependent dominance of residents (article)

This is the author accepted manuscript.The dataset associated with this article is available in ORE at: https://doi.org/10.24378/exe.4684Widespread antibiotic resistance in commensal bacteria creates a persistent challenge for human health. Resident drug-resistant microbes can prevent clinical interventions, colonize wounds post-surgery, pass resistance traits to pathogens or move to more harmful niches following routine interventions such as catheterization. Accelerating the removal of resistant bacteria or actively decolonizing particular lineages from hosts could therefore have a number of long-term benefits. However, removing resident bacteria via competition with probiotics, for example, poses a number of ecological challenges. Resident microbes are likely to have physiological and numerical advantages and competition based on bacteriocins or other secreted antagonists is expected to give advantages to the dominant partner, via positive frequency dependence. Since a narrow range of E. coli genotypes (primarily those belonging to the clonal group ST131) cause a significant proportion of multi-drug resistant infections, this group presents a promising target for decolonization with bacteriophage, as narrow host range viral predation could lead to selective removal of particular genotypes. In this study we tested how a combination of a ST131-specific phage and competition from the well-known probiotic E. coli Nissle strain could displace E. coli ST131 under aerobic and anaerobic growth conditions in vitro. We showed that the addition of phage could break the frequency-dependent advantage of a numerically dominant ST131 isolate. Moreover, the addition of competing E. coli Nissle could improve the ability of phage to suppress ST131 by two orders of magnitude. Low-cost phage resistance evolved readily in these experiments and was not inhibited by the presence of a probiotic competitor. Nevertheless, combinations of phage and probiotic produced stable long-term suppression of ST131 over multiple transfers and under both aerobic and anaerobic growth conditions. Combinations of phage and probiotic therefore have real potential for accelerating the removal of drug resistant commensal targets.Medical Research Council (MRC)Biotechnology and Biological Sciences Research Council (BBSRC)Lister Institute for Preventative MedicineEuropean Research Council (ERC

Clinical, histopathological and therapeutic considerations in a flock of sheep with facial staphylococcal-associated dermatitis

In a flock of 290 sheep, a total of 20 ewes (6.9%) with an age range of 1.5-4 years, developed a nonpruritic dermatitis characterized by alopecia/hypotrichosis, erythema, hyperpigmentation, crusting, superficial ulcers, exudation and thickening of the skin that was localized mainly to the peri-ocular area. Frequent and massive feeding of swarming sucking flies on the lesional sites was witnessed. In every instance (n = 6), Staphylococcus aureus was cultured from the exudate and the aseptically obtained skin biopsy samples from both recurrent and new cases. The main predisposing factor was the presence of small troughs, which forced the sheep to compete for food. Intramuscular administration of cefalexin for 7 days resulted in the resolution of lesions over a 2-week period. No further cases or recurrences were seen over the 16-month follow-up period. The main histopathological feature of this skin disease was a superficial and deep, perivascular to interstitial eosinophilic and mononuclear dermatitis