The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach

Abstract

The evolution of antibiotic resistance carries a fitness cost, expressed in terms of reduced competitive ability in the absence of antibiotics. This cost plays a key role in the dynamics of resistance by generating selection against resistance when bacteria encounter an antibiotic-free environment. Previous work has shown that the cost of resistance is highly variable, but the underlying causes remain poorly understood. Here, we use a meta-analysis of the published resistance literature to determine how the genetic basis of resistance influences its cost. We find that on average chromosomal resistance mutations carry a larger cost than acquiring resistance via a plasmid. This may explain why resistance often evolves by plasmid acquisition. Second, we find that the cost of plasmid acquisition increases with the breadth of its resistance range. This suggests a potentially important limit on the evolution of extensive multidrug resistance via plasmids. We also find that epistasis can significantly alter the cost of mutational resistance. Overall, our study shows that the cost of antimicrobial resistance can be partially explained by its genetic basis. It also highlights both the danger associated with plasmidborne resistance and the need to understand why resistance plasmids carry a relatively low cost.

Keywords: adaptation; antibiotic resistance; antimicrobial resistance; fitness cost; microbes; mutation; plasmid.

Figure 1

Overview of the inclusion process.

Figure 2

(A): There is no significant difference between the cost of antimicrobial resistance measured in-vitro (grey bars, mean fitness ± SEM) or in a mouse (white bars, mean fitness ± SEM). Each pair of bars represents a separate published paper. 2(B): Fitness in a mouse correlates with fitness in-vitro. Each set of symbols represents a different paper, with each point an independent mutation.

Figure 3

(A): There is no significant difference between the cost of resistance measured by a proxy (such as growth rate, density at a set time, etc.) (grey bars, mean ± SEM) or by direct competition assays (white bars, mean ± SEM). Each pair of bars is a separate published paper. 3(B): Competitive fitness correlates with growth rate. Each set of symbols represents a different paper, with each point an independent mutation.

Figure 4

Evolving resistance by acquiring a plasmid has a smaller fitness cost than evolving resistance by mutation (bars show mean fitness ± SEM). The bars are the means of 78 mechanisms of mutational resistance, 49 plasmids, and 7 other mobile genetic elements, respectively.

Figure 5

(A): The fitness cost of acquiring a plasmid increases in proportion to the resistance range of a plasmid. The resistance range of a plasmid is defined as the number of antimicrobial families to which phenotypic resistance is gained upon acquiring the plasmid, as reported in the relevant paper. Symbols represent mean fitness (± SEM), with a sample size of 6, 6, 14, 7, 8, 5, 1, and 2 plasmids, from left to right, respectively. 5(B): The size of a plasmid (DNA KB) does not significantly correlate with its fitness cost. Each point represents the published fitness cost of acquiring a resistance plasmid.

Figure 6

Both plasmid factors and bacterial factors contribute the size of the cost of acquiring a plasmid. Bars show the mean coefficient of variation (± SEM) for papers which either measured the cost of several different plasmids on a single host, or measured the cost of a single plasmid in different bacterial hosts.

Figure 7

(A): The mechanistic basis of chromosomal resistance significantly affects the cost of resistance. Bars represent mean fitness (± SEM, if at least 2 published reports exist). 7(B): the metabolic pathway affected by target-site resistance significantly affects the cost of resistance. Bars represent the mean fitness cost of a single resistance mutation to either a DNA-topoisomerase inhibitor, a transcription inhibitor, or a translation inhibitor.

Figure 8

(A): The cost of stepwise resistance increases with each successive step. Bars show mean relative fitness (±SEM) from 13 papers which measured the stepwise evolution of resistance. 7 of these papers only compared strains with 1 or 2 resistance alleles or mutations. The remaining 6 then went on to study a third level of resistance, and 3 of these also reported the costs of acquiring a fourth and fifth resistance mutation. 8(B): There is significant negative epistasis between laboratory evolved alleles, but no significant epistasis between clinically evolved alleles. Bars represent the mean difference between no epistasis (where the cost of a second mutation is the same as the first), and what is actually observed from the 13 papers. A negative value indicates a greater than expected cost, and a positive result a smaller than expected cost.