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

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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

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)1. 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 phages2,3. 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.

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

About half of all bacteria carry genes for CRISPR-Cas adaptive immune systems1, which provide immunological memory by inserting short DNA sequences from phage and other parasitic DNA elements into CRISPR loci on the host genome2. Whereas CRISPR loci evolve rapidly in natural environments3,4, bacterial species typically evolve phage resistance by the mutation or loss of phage receptors under laboratory conditions5,6. Here we report how this discrepancy may in part be explained by differences in the biotic complexity of in vitro and natural environments7,8. 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.

Selection by a panel of clinicians and family representatives of important early morbidities associated with paediatric cardiac surgery suitable for routine monitoring using the nominal group technique and a robust voting process.

OBJECTIVE: With survival following paediatric cardiac surgery improving, the attention of quality assurance and improvement initiatives is shifting to long-term outcomes and early surgical morbidities. We wanted to involve family representatives and a range of clinicians in selecting the morbidities to be measured in a major UK study. SETTING: Paediatric cardiac surgery services in the UK. PARTICIPANTS: We convened a panel comprising family representatives, paediatricians from referring centres, and surgeons and other clinicians from surgical centres. PRIMARY AND SECONDARY OUTCOME MEASURES: Using the nominal group technique augmented by a robust voting process to identify group preferences, suggestions for candidate morbidities were elicited, discussed, ranked and then shortlisted. The shortlist was passed to a clinical group that provided a view on the feasibility of monitoring each shortlisted morbidity in routine practice. The panel then met again to select a prioritised list of morbidities for further study, with the list finalised by the clinical group and chief investigators. RESULTS: At the first panel meeting, 66 initial suggestions were made, with this reduced to a shortlist of 24 after two rounds of discussion, consolidation and voting. At the second meeting, this shortlist was reduced to 10 candidate morbidities. Two were dropped on grounds of feasibility and replaced by another the panel considered important. The final list of nine morbidities included indicators of organ damage, acute events and feeding problems. Family representatives and clinicians from outside tertiary centres brought some issues to greater prominence than if the panel had consisted solely of tertiary clinicians or study investigators. CONCLUSION: The inclusion of patient and family perspectives in identifying metrics for use in monitoring a specialised clinical service is challenging but feasible and can broaden notions of quality and how to measure it.