Strong Environment-Genotype Interactions Determine the Fitness Costs of Antibiotic Resistance In Vitro and in an Insect Model of Infection

Abstract

The acquisition of antibiotic resistance commonly imposes fitness costs, a reduction in the fitness of bacteria in the absence of drugs. These costs have been primarily quantified using in vitro experiments and a small number of in vivo studies in mice, and it is commonly assumed that these diverse methods are consistent. Here, we used an insect model of infection to compare the fitness costs of antibiotic resistance in vivo relative to in vitro conditions. Experiments explored diverse mechanisms of resistance in a Gram-positive pathogen, Bacillus thuringiensis, and a Gram-negative intestinal symbiont, Enterobacter cloacae. Rifampicin resistance in B. thuringiensis showed fitness costs that were typically elevated in vivo, although these were modulated by genotype-environment interactions. In contrast, resistance to cefotaxime via de-repression of AmpC β-lactamase in E. cloacae resulted in undetectable costs in vivo or in vitro, while spontaneous resistance to nalidixic acid, and carriage of the IncP plasmid RP4, imposed costs that increased in vivo. Overall, fitness costs in vitro were a poor predictor of fitness costs in vivo because of strong genotype environment interactions throughout this study. Insect infections provide a cheap and accessible means of assessing fitness consequences of resistance mutations, data that is important to understand the evolution and spread of resistance. This study emphasizes that the fitness costs imposed by particular mutations or different modes of resistance are extremely variable, and that only a subset of these mutations are likely to be prevalent outside of the laboratory.

Filling knowledge gaps related to AmpC-dependent β-lactam resistance in Enterobacter cloacae

“…Finally, in contrast with other species 12 , 14 , 16 , the interplay between chromosomal AmpC-dependent resistance, its peptidoglycan metabolism-related regulation, and the potentially associated fitness/virulence costs is an almost unexplored field in Enterobacteriaceae . Only some specific amino acid variants in AmpR have been characterized in this regard, suggesting insignificant associated costs 38 . Conversely, it is still unknown whether AmpC β-lactamase hyper-production per se, and/or achieved through typical mutational pathways could dampen virulence, and/or whether the alteration of peptidoglycan recycling itself could enhance this outcome, as happens in P. aeruginosa 14 , 16 , 39 .…”

Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions

“…Resistance-associated genes and mutations impose bacterial fitness costs [ 87 ]. However, microbial competition studies reveal that resistance costs for one antibiotic depend on alleles conferring resistance to other antibiotics [ 89 , 90 ]. Trindade et al [ 53 ] found that positive epistasis in combined therapies could induce double resistance in microorganisms, specifically via point mutations.…”

Resistance-resistant antibacterial treatment strategies

“…Furthermore, most of our understanding of bacterial responses to antibiotics is founded on in vitro experiments. In the host, antibiotic concentrations fluctuate between doses, and bacteria face additional selective pressures that have unknown consequences for their fitness and evolution (Yang et al, 2017;Manktelow et al, 2020). Altogether, these variables emphasize the fact that collateral effects are not guaranteed and must be considered probabilistic events that complicate the predictability of evolutionary trajectories (Nichol et al, 2019;Burmeister et al, 2020).…”