More evolvable bacteriophages better suppress their host - PubMed (original) (raw)
. 2024 Jul 4;17(7):e13742.
doi: 10.1111/eva.13742. eCollection 2024 Jul.
Affiliations
- PMID: 38975285
- PMCID: PMC11224127
- DOI: 10.1111/eva.13742
More evolvable bacteriophages better suppress their host
Elijah K Horwitz et al. Evol Appl. 2024.
Abstract
The number of multidrug-resistant strains of bacteria is increasing rapidly, while the number of new antibiotic discoveries has stagnated. This trend has caused a surge in interest in bacteriophages as anti-bacterial therapeutics, in part because there is near limitless diversity of phages to harness. While this diversity provides an opportunity, it also creates the dilemma of having to decide which criteria to use to select phages. Here we test whether a phage's ability to coevolve with its host (evolvability) should be considered and how this property compares to two previously proposed criteria: fast reproduction and thermostability. To do this, we compared the suppressiveness of three phages that vary by a single amino acid yet differ in these traits such that each strain maximized two of three characteristics. Our studies revealed that both evolvability and reproductive rate are independently important. The phage most able to suppress bacterial populations was the strain with high evolvability and reproductive rate, yet this phage was unstable. Phages varied due to differences in the types of resistance evolved against them and their ability to counteract resistance. When conditions were shifted to exaggerate the importance of thermostability, one of the stable phages was most suppressive in the short-term, but not over the long-term. Our results demonstrate the utility of biological therapeutics' capacities to evolve and adjust in action to resolve complications like resistance evolution. Furthermore, evolvability is a property that can be engineered into phage therapeutics to enhance their effectiveness.
Keywords: antimicrobial resistance; bacteriophage; evolvability; phage therapy.
© 2024 The Author(s). Evolutionary Applications published by John Wiley & Sons Ltd.
Conflict of interest statement
The authors declare that there are no conflicts of interest.
Figures
FIGURE 1
A trio of closely related phage genotypes demonstrate a three‐way tradeoff between stability, reproduction, and evolvability. Panel a: AlphaFold prediction of the domain of the λ receptor binding protein that determines host range. The three λ genotypes in this study were identical except for a single amino acid difference in this domain. Insets show the wild type amino acid and three variant amino acids. Panel b: Three‐dimensional plot of phage trait values. Stability is measured by decay rate, the rate at which phage lose infectivity in an environment lacking hosts. Reproduction is measured by reproductive rate, the rate at which phage replicate on their host bacteria, adjusted to account for the phage lost to decay. Evolutionary path length is the number of mutations required to infect through the non‐native receptor. It is the inverse of evolvability because a genotype requiring fewer mutations to achieve a new function is more evolvable. The position on the graph corresponding to optimality of all three traits is indicated by the star in the lower back corner. No phage was able to optimize all three traits.
FIGURE 2
λ suppression of bacteria monitored daily for 10 days. Each line corresponds to the bacterial titer in a single replicate flask population. Six replicate flasks were initiated for each phage genotype. Across all genotypes, the same bacterial strain was used to initiate the flask and approximately the same ratio of phage and bacteria were added. Panel a: All three phage genotypes are shown together. Median lines for bacterial population replicates suppressed by a given genotype are shown in bold, and individual populations are shown by translucent lines. Panel b–d: pairs of genotypes are shown for ease of visualizing differences. Statistical differences are present on days 2–6 between the fast‐evolvable replicates and fast‐stable replicates, days 2, 4, 5, and 6 between the fast‐evolvable replicates and stable‐evolvable replicates, and statistical differences were not detected between the fast‐stable replicates and stable‐evolvable treatments at any time (Table S2). A Wilcoxon rank‐sum test was used to test statistical significance between levels of suppression between two phage genotypes. **p < 0.01.
FIGURE 3
Escherichia coli resistance evolution. (a–c) Plaque forming units (PFU) of each phage genotype on bacteria that was cocultured with the phage. The dashed line indicates the PFU measured on the bacterial strain used in the suppression experiments (REL606). A single isolate from each replicate was studied for each day of the experiment through the third day. PFU values lower than the dotted line indicates a gain of resistance, values on the _x_‐axis were cases of complete resistance where no plaques were observed. (d) Frequency of colonies with morphologies in line with possessing resistant mutations in genes malT and manYZ. All six replicates per treatment were sampled on day two of the experiment.
FIGURE 4
Bacterial population dynamics exposed to two λ genotypes differing only in their reproductive rates. Both genotypes were engineered to contain a key mutation that conferred activity on the OmpF receptor, allowing infection of bacteria that are resistant to OmpF− phage. Six replicate flask populations were initiated for each phage genotype, with the same bacterial strain. Median lines for bacterial population replicates of a given genotype are shown in bold, and individual populations are shown by translucent lines. Each translucent line corresponds to the bacterial titer in a single replicate flask population. The stable, slow reproducing phage (green) poorly suppressed the bacteria and the phages passed below our limit of detection after the first day. The stable‐evolved replicates were discontinued after 3 days of no phage detection. Statistical differences between replicate populations are present on days 1, 2, and 3 (Table S2). A Wilcoxon rank‐sum test was used to test statistical significance between levels of suppression between the two phage genotypes. **p < 0.01.
FIGURE 5
Environmental contingency of bacterial suppression dynamics. The conditions of this experiment were identical to those of Figure 2, except that the available glucose was reduced by 10‐fold, limiting the maximum potential bacterial carrying capacity throughout the duration of the experiment. Panel a: All three phage genotypes are shown together. Median lines for bacterial population replicates suppressed by a given genotype are shown in bold, and individual populations are shown by translucent lines. Panels b–d: pairs of genotypes are shown for ease of visualizing differences. Statistical differences are present on days 1, 4, and 6 between the fast‐evolvable replicates and fast‐stable replicates, day 6 between the fast‐evolvable replicates and stable‐evolvable replicates, and days 1 and 6 between the fast‐stable replicates and stable‐evolvable replicates (Table S2). A Wilcoxon rank‐sum test was used to test statistical significance between levels of suppression between two phage genotypes. **p < 0.01.
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