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

Abstract

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, and 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 their presence. This was because there were tradeoffs 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 coinfecting taxa can select against P. aeruginosa mutators, which may have potentially beneficial clinical consequences. MainInteractions with other species can be a key determinant of the rate of evolution 1-3 , as well as potentially imposing indirect selection for mechanisms that increase genetic variation, such as increased recombination rates 4,5 and, in the case of bacteria, increased mutation rates 6,7 . These findings are largely based on coevolutionary interactions between host-parasite pairs. It is unclear how being embedded in a multi-species microbial community affects selection for mutation rates in focal bacterial species. Fluctuations in the densities of community members, as well as coevolutionary changes, may result in continually changing selection pressures 1,2,8 , potentially selecting for bacteria with elevated mutation rates (mutators). Alternatively, mutators may be selected against if interspecific competitors constrain adaptation to other components of the environment, including other community members 6,9 . Furthermore, changes in population size of the focal species caused by interactions with other species could result in both selection for or against mutators 10,11 . Despite most mutations being deleterious or neutral, mutators can occur at high frequencies in natural populations of bacteria [12][13][14][15][16][17][18][19][20] . They can be found at particularly high frequencies in chronic infections [15][16][17][18][19][20] , where they are associated with treatment failure and patient morbidity [21][22][23][24][25][26][27] , especially in cystic fibrosis (CF) chronic lung infections by the opportunistic pathogen P.aeruginosa [24][25][26][27] . The success of mutators in this context is attributed to the ability of mutator alleles to generate, and hitchhike with, beneficial mutations that allow adapta...

Bacterial community structure and mucin drive Pseudomonas aeruginosa diversification and pathoadaptation

“…Mutations within pqsR were underrepresented in the presence of mucin and competition (Figure 3). These results support the recent findings of Luján et al, who demonstrated that pqsR-regulated QS system is retained in the presence of competing taxa and mucin, likely due to the fitness benefits of retaining the redox agent pyocyanin, an effective anti-competitor toxin 18 . Mutations in QS transcriptional regulators pqsR and vqsM are commonly observed during in vitro evolution of P. aeruginosa [17][18][19]38,48,49 , but mutations in these genes are rarely observed in chronic adapted strains isolated from CF sputum 5,50 .…”

“…These results support the recent findings of Luján et al, who demonstrated that pqsR-regulated QS system is retained in the presence of competing taxa and mucin, likely due to the fitness benefits of retaining the redox agent pyocyanin, an effective anti-competitor toxin 18 . Mutations in QS transcriptional regulators pqsR and vqsM are commonly observed during in vitro evolution of P. aeruginosa [17][18][19]38,48,49 , but mutations in these genes are rarely observed in chronic adapted strains isolated from CF sputum 5,50 . Our results suggest that mutations within these QS transcriptional regulators are dependent upon the interaction between the community composition and the physical environment, whereby intense competition coupled with the presence of mucin provide strong selection for the retention of these QS transcriptional regulators.…”

“…Many possible environmental drivers have been proposed to explain this diversification [12][13][14][15] (reviewed in 2,4,5 ), including the extensive use of antibiotics, the host immune system and nutrient availability in the lung. However, the role of interactions with surrounding microbes typical for polymicrobial CF lung infections 16 has received less attention even though they also likely shape the diversification of P. aeruginosa during CF lung infections [17][18][19][20] .…”

Recent advances in therapeutic targets identification and development of treatment strategies towards Pseudomonas aeruginosa infections

“…In the context of co-infecting pathogen communities, the augmented mutation rates (mutators) of P. aeruginosa bacteria infecting CF patients are found to be encouraged only in the absence of other species [ 42 ]. This illustrates the tremendous advantages that could be endorsed by polymicrobial infections in strategies aiming at P. aeruginosa eradication.…”

Testing for the fitness benefits of natural transformation during community-embedded evolution

“…This could be an important shortcoming, as for sex to remain selectively advantageous it is necessary for selection to be strong and dynamic (Charlesworth, 1993; Burt, 2000), and interspecific competitors could greatly influence both these requirements (Otto and Nuismer, 2004; Kawecki et al ., 2012). However, while interspecific competition can create fluctuating conditions, it can also constrain evolution (Luján et al ., 2022). Experimental evolution approaches have hitherto relied on evolving recombining clones in isolation.…”