Genome sequencing and assembly from the Ab-One One Health Acinetobacter baumannii sampling program

Acinetobacter baumannii (Ab) is a bacterium responsible for a wide range of serious nosocomial infections. Ab is one of the most worrying infectious agents due to the constant worldwide increase in its multiresistance (including to antibiotics of last resort - e.g. carbapenems, colistin). The risk of Ab becoming a highly problematic pathogen in the coming years is all the higher because (i) it has a high dispersal capacity, (ii) it can evolve rapidly, in particular through high rates of horizontal gene transfer (HGT) and recombination, and (iii) because it can persist in healthcare institutions but also in other natural environments that are still only partially identified.The detection of Ab in livestock, animal and human medicine, as well as recent discoveries of environmental sources (animal and terrestrial) indicate that the integrated One Health approach is particularly relevant for this nosocomial pathogen. The Ab-One project aimed at capturing the diversity and dynamics of the Ab population with a local area by conducting a multisectorial sampling program. The sampling scheme involved exhaustive sampling of the hospital environment and patients of the city of Lyon, France. Sampling was conducted at a animal intensive-care unit, farms and soil within the Lyon region. All isolates were caracterized and their genome sequenced through a long-read approach.