Bacterial biodiversity drives the evolution of CRISPR-based phage resistance

This is the author accepted manuscript. The final version is available from Springer Nature via the DOI in this record 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.European CommissionNatural Environment Research Council (NERC

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

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility: All code and raw data necessary to run models and generate figures are available at https://github.com/jlw-ecoevo/immunelagClustered 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.Simons FoundationEuropean Research Council (ERC)Biotechnology and Biological Sciences Research Council (BBSRC)Natural Environment Research Council (NERC

Polymicrobial infections can select against Pseudomonas aeruginosa mutators because of quorum-sensing trade-offs

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordData availability: All data used in this study are available on figshare at https://doi.org/10.6084/m9.figshare.13739452. Genome sequencing reads from P. aeruginosa populations from in vivo and in vitro experiments have been deposited under accession no. PRJEB35620. All other data used in this paper are available in the Supplementary Information. Source data are provided with this paper.Bacteria with increased mutation rates (mutators) are common in chronic infections and are associated with poorer clinical outcomes, especially in the case of Pseudomonas aeruginosa infecting cystic fibrosis (CF) patients. There is, however, considerable between-patient variation in both P. aeruginosa mutator frequency and the composition of co-infecting pathogen communities. We investigated whether community context might affect selection of mutators. Using an in vitro CF model community, we show that P. aeruginosa mutators were favoured in the absence of other species but not in their presence. This was because there were trade-offs between adaptation to the biotic and abiotic environments (for example, loss of quorum sensing and associated toxin production was beneficial in the latter but not the former in our in vitro model community) limiting the evolvability advantage of an elevated mutation rate. Consistent with a role of co-infecting pathogens selecting against P. aeruginosa mutators in vivo, we show that the mutation frequency of P. aeruginosa population was negatively correlated with the frequency and diversity of co-infecting bacteria in CF infections. Our results suggest that co-infecting taxa can select against P. aeruginosa mutators, which may have potentially beneficial clinical consequences.European Union FP7UKRIANPCyTNovo Nordisk FoundationRigshospitalets Rammebevilling 2015–17LundbeckfondenRegionH RammebevillingIndependent Research Fund Denmark/Medical and Health SciencesNatural Environment Research Council (NERC