Think about the last time you or a loved one had a bacterial infection and needed antibiotics. What if the antibiotics hadn’t worked? Unfortunately, this is becoming increasingly common around the world, causing at least 700,000 deaths per year (O’Neill, 2016). Resistance to antimicrobial treatments, also known as AMR, evolves rapidly, often over the course of a single infection. It occurs either by bacteria exchanging with one another the genes that confer resistance, or by an individual bacterium becoming resistant through mutations in its own genes. Resistant bacteria are more likely to survive antimicrobial treatments and go on to spread the infection to other people.
During infections, bacteria tend to grow on surfaces in communities called biofilms (Koo et al., 2017). Biofilms promote communication and cooperation, and physically shield bacteria from antimicrobials and the host immune system. These properties make biofilm infections hard to treat, even in the absence of AMR. It has been suggested that bacteria growing in biofilms may evolve AMR more rapidly, making treatment outcomes harder to predict. However, few studies have explored how different modes of growth influence the ability of bacteria to evolve (Steenackers et al., 2016).
Now, in eLife, Vaughn Cooper and colleagues at the University of Pittsburg — including Alfonso Santos-Lopez and Christopher Marshall as joint first authors — report how 'bacterial lifestyle' affects the evolution of resistance to an antibiotic called ciprofloxacin (CIP) in the pathogen Acinetobacter baumannii (Santos-Lopez et al., 2019). To do this, they compared bacteria that had been floating in liquid culture as they grew to bacteria that had been growing as biofilms. The bacteria growing in liquid culture were experimentally evolved by transferring small amounts of culture to a new container with fresh growth medium every day (Figure 1A). Biofilms were evolved by growing A. baumannii on plastic beads submerged in liquid culture, and transferring these biofilm-coated beads to a new container with fresh medium and a clean bead each day (Figure 1B). At the start of the experiment, cells were exposed to a very low dose of CIP, and the CIP dose was then doubled every 72 hours as resistance evolved over a 12 day period.
To understand how bacterial lifestyle influences the evolution antimicrobial resistance, strains of the bacterium A.baumannii were experimentally evolved either in liquid culture (A) or as biolfims …
Samples of bacteria were collected from each culture at various times during the experiment and also at the end of the experiment. Whole genome sequencing of these samples revealed that liquid-grown and biofilm-grown A. baumannii take different, but repeatable, paths during experimental evolution. For the bacteria grown in liquid culture, Santos-Lopez et al. found that the most resistant CIP lineage outcompetes the other bacterial lineages, allowing its offspring to rapidly take over the population (Figure 1C). However, for the bacteria grown in biofilms, the researchers found that there was less competition between lineages – presumably because they are not as free to move as the liquid-grown bacteria – and that multiple co-existing lineages were able to emerge (Figure 1D).
Further experiments showed that liquid-grown and biofilm-grown bacteria had evolved unique strategies to resist CIP, resulting in different degrees of CIP resistance. Liquid-grown bacteria evolved low-level CIP resistance via mutations that increased the number of pump proteins that transport CIP out of cells. These resistant cells took over rapidly and then gained additional mutations that prevented CIP from binding to its target proteins. Bacteria with both types of mutations could resist doses of CIP that were far higher than those used during the evolution experiment. Biofilm-grown bacteria also evolved low-level CIP resistance through increased pump protein production but used different pumps than their liquid-evolved counterparts. However, biofilm-grown bacteria failed to evolve high-level resistance through additional mutations. The selective pressures imposed by the different lifestyles seem to interact with the pressure of CIP exposure and limit the evolutionary pathways, and thus outcomes, available to each lifestyle.
Santos-Lopez et al. found that in the absence of CIP, liquid-evolved CIP resistant bacteria were less fit than the ancestor strain and could be easily outcompeted. Notably, similar fitness trade-offs have been reported before and reduced fitness is thought to slow the spread of AMR bacteria. Disturbingly, biofilm-evolved CIP-resistant strains were at least as fit as their ancestor when grown without CIP. Whilst the liquid-evolved strain frequently became resistant to additional antimicrobials, biofilm-grown bacteria usually evolved increased sensitivity to at least one other antimicrobial treatment. This means that although biofilm-evolved strains may be fitter and more likely to spread to new patients, they also may be easier to kill with other antimicrobials.
In this work, Santos-Lopez et al. have focused on how biofilms affect competition and selection pressures during evolution. However, biofilms may alter evolution in other ways and bacterial lifestyle is only one of many factors that shape the evolution of AMR 'in the wild.' For example, many species of bacteria experience increased gene sharing and mutation rates when forming a biofilm, both of which could also drive the evolution of AMR (Steenackers et al., 2016). Additionally, AMR evolution may be driven by increases in mutation rate caused by antimicrobials (Cirz et al., 2005; Kohanski et al., 2010; Gutierrez et al., 2013; Pribis et al., 2019) and other stressors, such as starvation, encountered by bacteria during infection (Fitzgerald and Rosenberg, 2019).
These findings have important implications for treatment of A. baumannii, which is already resistant to multiple drugs and has been deemed a critical threat by both the World Health Organization and the Centers for Disease Control and Prevention in the United States. A better understanding of the variables shaping AMR evolution will improve predictions of evolutionary outcomes, antimicrobial stewardship efforts, and clinical outcomes for individual patients.
© 2019, Fitzgerald
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
Gene duplication drives evolution by providing raw material for proteins with novel functions. An influential hypothesis by Ohno (1970) posits that gene duplication helps genes tolerate new mutations and thus facilitates the evolution of new phenotypes. Competing hypotheses argue that deleterious mutations will usually inactivate gene duplicates too rapidly for Ohno’s hypothesis to work. We experimentally tested Ohno’s hypothesis by evolving one or exactly two copies of a gene encoding a fluorescent protein in Escherichia coli through several rounds of mutation and selection. We analyzed the genotypic and phenotypic evolutionary dynamics of the evolving populations through high-throughput DNA sequencing, biochemical assays, and engineering of selected variants. In support of Ohno’s hypothesis, populations carrying two gene copies displayed higher mutational robustness than those carrying a single gene copy. Consequently, the double-copy populations experienced relaxed purifying selection, evolved higher phenotypic and genetic diversity, carried more mutations and accumulated combinations of key beneficial mutations earlier. However, their phenotypic evolution was not accelerated, possibly because one gene copy rapidly became inactivated by deleterious mutations. Our work provides an experimental platform to test models of evolution by gene duplication, and it supports alternatives to Ohno’s hypothesis that point to the importance of gene dosage.
Life-history theory, central to our understanding of diversity in morphology, behaviour, and senescence, describes how traits evolve through the optimisation of trade-offs in investment. Despite considerable study, there is only minimal support for trade-offs within species between the two traits most closely linked to fitness – reproductive effort and survival – questioning the theory’s general validity. We used a meta-analysis to separate the effects of individual quality (positive survival/reproduction correlation) from the costs of reproduction (negative survival/reproduction correlation) using studies of reproductive effort and parental survival in birds. Experimental enlargement of brood size caused reduced parental survival. However, the effect size of brood size manipulation was small and opposite to the effect of phenotypic quality, as we found that individuals that naturally produced larger clutches also survived better. The opposite effects on parental survival in experimental and observational studies of reproductive effort provide the first meta-analytic evidence for theory suggesting that quality differences mask trade-offs. Fitness projections using the overall effect size revealed that reproduction presented negligible costs, except when reproductive effort was forced beyond the maximum level observed within species, to that seen between species. We conclude that there is little support for the most fundamental life-history trade-off, between reproductive effort and survival, operating within a population. We suggest that within species the fitness landscape of the reproduction–survival trade-off is flat until it reaches the boundaries of the between-species fast–slow life-history continuum. Our results provide a quantitative explanation as to why the costs of reproduction are not apparent and why variation in reproductive effort persists within species.