Journal Article

Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle

Snyder, Daniel J, Cooper, Vaughn S, Santos-Lopez, Alfonso, Marshall, Christopher W, Scribner, Michelle R

2019

Overview

Bacterial populations vary in their stress tolerance and population structure depending upon whether growth occurs in well-mixed or structured environments. We hypothesized that evolution in biofilms would generate greater genetic diversity than well-mixed environments and lead to different pathways of antibiotic resistance. We used experimental evolution and whole genome sequencing to test how the biofilm lifestyle influenced the rate, genetic mechanisms, and pleiotropic effects of resistance to ciprofloxacin in Acinetobacter baumannii populations. Both evolutionary dynamics and the identities of mutations differed between lifestyle. Planktonic populations experienced selective sweeps of mutations including the primary topoisomerase drug targets, whereas biofilm-adapted populations acquired mutations in regulators of efflux pumps. An overall trade-off between fitness and resistance level emerged, wherein biofilm-adapted clones were less resistant than planktonic but more fit in the absence of drug. However, biofilm populations developed collateral sensitivity to cephalosporins, demonstrating the clinical relevance of lifestyle on the evolution of resistance. A bacterium known as Acinetobacter baumannii causes serious lung infections in people with weakened immune systems. These illnesses are becoming more common largely because A. baumannii is increasingly developing resistance to antibiotics. Inside the airways, individual A. baumannii cells can stick together and coat themselves in a slimy substance to form a structure called biofilm, which physically protects bacteria from antibiotics. This may be one of the reasons why it is often harder to treat bacterial infections associated with biofilms. Another possibility is that bacteria may evolve differently in biofilms compared with cells living independently. For example, A. baumannii may colonize several regions of the lungs during an infection, leading to distinct groups of bacteria that experience different conditions and evolve separately. Each population may therefore respond differently to an antibiotic. In contrast, bacteria living independently in a well-mixed population – such as in the bloodstream of their host – would be more likely to all evolve in the same way. Santos-Lopez, Marshall et al. tested this theory by exposing populations of A. baumannii that lived either independently or in biofilms to increasing levels of an antibiotic called ciprofloxacin. The genetic information of these cells was examined as the populations were evolving, and the bacteria were also put in contact with other types of antibiotics. The analyses revealed that bacteria in well-mixed populations shared the same limited number of mutations: these gave the bacteria high levels of resistance to the antibiotic’s primary target, an enzyme involved in DNA processes. The bacteria had also become resistant to other classes of antibiotics. In contrast, the bacteria in biofilm populations evolved to be more genetically diverse, exhibiting different types of mutations that helped the cells to pump out the drug. These bacteria were less resistant to ciprofloxacin and more sensitive to other types of antibiotics. Further experiments looked into the fitness of the bacteria – their ability to survive, reproduce and compete with each other. High levels of antibiotic resistance came with lower fitness: biofilm bacteria had evolved to become being fitter than those from well-mixed population. Even in the absence of drugs, these populations were in fact fitter than the original cells. Overall, understanding how the lifestyles of bacteria affect the way they respond to drugs may help researchers to develop new approaches that limit the spread of antibiotic resistance and improve treatment.

• Publisher: eLife Science Publications, Ltd,eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Acinetobacter baumannii / Acinetobacter baumannii - drug effects / Acinetobacter baumannii - genetics / Acinetobacter baumannii - growth & development / Adaptation / Adaptation, Biological / Anti-Bacterial Agents - pharmacology / Antibiotic resistance / Antibiotics / Antimicrobial agents / antimicrobial resistance / Bacteria / Bacterial genetics / Bacterial infections / Biodiversity / biofilm / Biofilms / Biofilms - drug effects / Biofilms - growth & development / Biological Evolution / Cephalosporins / Ciprofloxacin / Ciprofloxacin - pharmacology / Cloning / Data processing / Disease susceptibility / DNA sequencing / Drug resistance / Drug Resistance, Bacterial / Environmental Exposure / Evolution / Evolutionary Biology / Experiments / Genetic diversity / Genetics, Population / Genomes / Genomics / Lifestyles / Lung diseases / Medicine / Microbial drug resistance / Microbiological research / Microbiology and Infectious Disease / Mutation / Population / population genetics / Population structure / Selection, Genetic / Software / Whole Genome Sequencing