De novo acquisition of antibiotic resistance in six species of bacteria

Bacteria can become resistant to antibiotics in two ways, by acquiring resistance genes through horizontal gene transfer and by de novo development of resistance upon exposure to non-lethal concentrations. The importance of the second process, de novo build-up, has not been investigated systematically over a range of species and may be underestimated as a result. To investigate the DNA mutation patterns accompanying the de novo antibiotic resistance acquisition process, six bacterial species encountered in the food chain were exposed to step-wise increasing sublethal concentrations of six antibiotics to develop high levels of resistance. Phenotypic and mutational landscapes were constructed based on whole genome sequencing (WGS) sequencing at two time points of the evolutionary trajectory. In this study, we found: 1) all of the six strains can develop high levels of resistance against most antibiotics. 2) increased resistance is accompanied by different mutations for each bacterium-antibiotic combination. 3) the number of mutations varies widely, with Y. enterocolitica having by far the most. 4) in the case of fluoroquinolone resistance, a mutational pattern of gyrA combined with parC is conserved in five of six species. 5) mutations in genes coding for efflux pumps are widely encountered in gram-negative species. The overall conclusion is that very similar phenotypic outcomes are instigated by very different genetic changes. IMPORTANCEThe significance of this study lies in the comparison of how six species of distinct genomic background under uniform conditions develop high levels of antibiotic resistance against six antibiotics. The mutational patterns in these six species of bacteria identify common target mutations and reveal how they acquire mutations from various pathways to survive and grow when exposed to sub-lethal levels of antibiotics. In addition to providing insights in microbial genetics, outcome of this study will assist policymakers when formulating practical strategies to prevent development of antimicrobial resistance in human and veterinary health care.