GEM-SEE-Achro · GEM-SEE-Achro: Genomic Exploration—Mapping the Spread, Evolution, and Adaptation of an Emerging bacterial pathogen—Achromobacter

Achromobacter species are rapidly emerging Gram-negative opportunistic bacteria intrinsically resistant to several antibiotics and are often the cause of healthcare-associated infections, especially in individuals with compromised immune systems or underlying conditions. Following years of misclassification of Achromobacter spp. isolates combined with complicated species typing, the understanding of the ecology of Achromobacter spp. and their clinical significance is lacking. GEM-SEE-Achro aims to answer the questions regarding the population structure, evolution, adaptation, antibiotic resistance development, and genetic variability of Achromobacter spp. both globally and locally, providing crucial insights into the factors contributing to their prevalence, antimicrobial resistance patterns and potential novel therapy approaches. Analysis of whole genome sequencing (WGS) data allows to disentangle these questions. Therefore, I propose the largest Achromobacter spp. study to date including over 800 WGS encompassing its global diversity sampled from both the environment and infected patients. Employment of a number of bioinformatics analysis methodsgene content difference analysis; single nucleotide variant and mobile genomic element identification and association with population structure; evolutionary and migration rates analysis using Bayesian phylogenetics; and resistance phenotype association with genomic differenceswill help to answer the fundamental questions of how these bacteria evolve and adapt to their environment, what are the main differences in genetic composition between the environmental and clinical samples, and how these differences can inform us about the population structure and antibiotic resistance development in Achromobacter spp. The gained knowledge could be generalised and applied to studies of other less studied bacterial pathogens.