Bacteriocin-mediated competition in cystic fibrosis lung infections

Abstract

Bacteriocins are toxins produced by bacteria to kill competitors of the same species. Theory and laboratory experiments suggest that bacteriocin production and immunity play a key role in the competitive dynamics of bacterial strains. The extent to which this is the case in natural populations,especially human pathogens, remains to be tested. We examined the role of bacteriocins in competition using Pseudomonas aeruginosa strains infecting lungs of humans with cystic fibrosis (CF). We assessed the ability of different strains to kill each other using phenotypic assays, and sequenced their genomes to determine what bacteriocins (pyocins) they carry. We found that(i) isolates from later infection stages inhibited earlier infecting strains less,but were more inhibited by pyocins produced by earlier infecting strains and carried fewer pyocin types; (ii) this difference between early and late infections appears to be caused by a difference in pyocin diversity between competing genotypes and not by loss of pyocin genes within a lineage overtime; (iii) pyocin inhibition does not explain why certain strains outcompete others within lung infections; (iv) strains frequently carry the pyocin-killing gene, but not the immunity gene, suggesting resistance occurs via other unknown mechanisms. Our results show that, in contrast to patterns observed in experimental studies, pyocin production does not appear to have a major influence on strain competition during CF lung infections.

Figure 1.

Proportion of supernatants inhibiting and lawns inhibited. Strains that were isolated from later-stage infections were both (a) less likely to inhibit and (b) more likely to be inhibited by other strains. The error bars indicate ±95% CI bars around mean values.

Figure 2.

Pyocin diversity across different stages of infection. Isolates from later-stage infections carry fewer pyocin types than isolates from early infections and non-lung environments. Circles represent isolates and squares represent the means of number of pyocin types for each isolate category. The error bars indicate ±95% CI bars around mean values.

Figure 3.

Within patient competitive dynamics. Considering the eight patients where we were able to follow strain dynamics over time, five were infected by multiple strains. These patients contained 14 distinct genotypes, and none of the patients were infected with the same genotype. In only three of these five patients at least one of the strains was able to inhibit another strain in the infection. Squares represent genotypes that are not inhibited nor cause any inhibition; triangles are genotypes that inhibit the susceptible circle genotypes. In two out of these three patients (P36F2 and P96F4), the inhibiting genotype (triangle) persisted longer in the infection, consistent with a role of bacteriocin-mediated competition. In the other patient (P41M3), the inhibited genotype (circle) persisted longer in the infection, contrary to the prediction from bacteriocin dynamics.

Figure 4.

Soluble pyocin killing and immunity genes. Killing and immunity genes are found together (51%), or either the killing gene (35%) or the immunity gene (14%) alone. The error bars indicate ±95% CIs.

Figure 5.

Protection from S pyocins by unknown resistance mechanisms. Considering cases where one strain does not carry a pyocin type carried by another (403 strain pairs), resistance via some other mechanism is much more common (81%) than resistance likely due to the immunity gene (19%). The error bars indicate ±95% CIs with correction for continuity around proportion values.