Bacterial biodiversity drives the evolution of CRISPR-based phage resistance in Pseudomonas aeruginosa

Abstract

evolution of virulence; biodiversity 19 20 21Approximately half of all bacterial species encode CRISPR-Cas adaptive immune 22 systems 1 , which provide immunological memory by inserting short DNA sequences 23 from phage and other parasitic DNA elements into CRISPR loci on the host genome 2 . 24Whereas CRISPR loci evolve rapidly in natural environments 3 , bacterial species 25 typically evolve phage resistance by the mutation or loss of phage receptors under 26 laboratory conditions 4,5 . Here, we report how this discrepancy may in part be explained 27 by differences in the biotic complexity of in vitro and natural environments 6,7 . 28 Specifically, using the opportunistic pathogen Pseudomonas aeruginosa and its phage 29DMS3vir, we show that coexistence with other human pathogens amplifies the fitness 30 trade-offs associated with phage receptor mutation, and therefore tips the balance in 31 favour of CRISPR-based resistance evolution. We also demonstrate that this has 32 important knock-on effects for P. aeruginosa virulence, which became attenuated only if 33 the bacteria evolved surface-based resistance. Our data reveal that the biotic complexity 34 of microbial communities in natural environments is an important driver of the 35 evolution of CRISPR-Cas adaptive immunity, with key implications for bacterial fitness 36 and virulence. 37 38Pseudomonas aeruginosa is a widespread opportunistic human pathogen that thrives in a 39 range of different environments, including hospitals, where it is a common source of 40 nosocomial infections. In particular, it frequently colonises the lungs of cystic fibrosis 41 patients, in whom it is the leading cause of morbidity and mortality 8 . In part fuelled by a 42 renewed interest in the therapeutic use of bacteriophages as antimicrobials (phage 43 therapy) 9,10 , many studies have examined if and how P. aeruginosa evolves resistance to 44 phage (reviewed in ref. 11). The clinical isolate P. aeruginosa strain PA14 has been reported 45 to predominantly evolve resistance against its phage DMS3vir by the modification or 46 complete loss of the phage surface receptor 12 when grown in nutrient-rich medium 4 despite 47

Coevolution between bacterial CRISPR-Cas systems and their bacteriophages

“…The magnitude of the fitness costs of CRISPR immunity and surface resistance depend on the ecological context beyond phage densities. For example, it was found that the cost of surface-based resistance relative to those of CRISPR immunity are amplified in the presence of a microbial community (Alseth et al, 2019). Moreover, these amplified costs manifested in the presence of some, but not other bacterial species.…”

Phage steering of antibiotic-resistance evolution in the bacterial pathogen Pseudomonas aeruginosa

“…Coevolution under different environmental pressures may shift dynamics between 'arms race' and 'fluctuating' with implications for phage resistance (41,42). Introducing other bacterial species that capture the multispecies nature of many infections may also change how resistance develops (43), shifting selection from the receptor target to other resistance mechanisms such as CRISPR-cas (43).…”

Steering Phages to Combat Bacterial Pathogens

“…Such costs (of bacterial defence) are of particular interest in the context of phage therapy since they could reduce the ability of the bacterial pathogen to respond to demanding environments, or to actively modify their environments. Recent work on community dynamics of phage therapy employing a virulent lysogenic phage in vitro has shown that the form of resistance could change depending on the local bacterial community [76].We discuss the impacts of phage steering on community dynamics in Box 3.…”

“…Chronic infections are often polymicrobial in nature and are receiving increasing attention [81]. Phage have been shown to affect the types of mutation that occur when bacteria compete in complex communities [76]. Surface factors that mediate interactions between the different species or with the environment are potential targets for phage steering.…”