The whole genome sequencing of Acinetobacter-calcoaceticus-baumannii complex strains involved in suspected outbreak in an Intensive Care Unit of a pediatric hospital

Abstract

Background: To analyze the genetic characteristics of Acinetobacter-calcoaceticus-baumannii complex strains isolated in suspected outbreak in a Intensive Care Unit of a pediatric hospital in order to promptly stop the dissemination of this dangerous strain.Methods: This study described the use of whole genome obtained by Next Generation Sequencing to define the clonality of 13 Acinetobacter-calcoaceticus-baumannii complex strains and to study their Resistoma. This was required because Acinetobacter baumannii is known to be resistant to desiccation and to disinfectants and is difficult to treat and eradicate. Thus, this microorganism is a major problem that demands a rigorous outbreak monitoring program to prevent and control the spread of the dangerous strain.Results: The first result of our analysis has been to describe precisely the characteristics of isolates involved in the nosocomial infection, reduce the dimension of the more problematic isolates sustaining the outbreak and promptly facilitate the control of the strains diffusion. Indeed, our study indicated that among the 13 Acinetobacter baumannii-calcoacteticus complex strains, identified by biochemical and mass-spectrometry assays, 7 were Acinetobacter baumannii, 5 were Acinetobacter calcoaceticus, and one was Acinetobacter haemolyticus. The analysis of clonality of Acinetobacter baumannii indicated that three strains of ST744 were identical for > 99.8% among them and thus have sustained an outbreak in Intensive Care Unit. All personnel and possible environment samples were also monitored and all the procedures aimed to the prevention and control of Hospital Acquired Infections (HAI), have been strictly enforced by the Hospital Infection Control Committee. This gave the possibility to trace a strain from an environmental contamination characterized by high degree of clonality with the one isolated from a patient. On the contrary Acinetobacter calcoaceticus strains were different from each other and thus they were not responsible for any outbreak. The Resistoma analysis indicated a correspondence between phenotypic and genotypic characteristics of analyzed strains.Conclusions: Next Generation Sequencing is an appropriate technique to trace the circulation of dangerous strains sustaining nosocomial infections. The combination of the high resolution genotyping together with the definition of the antibiotic genetic determinants and the precise species identification make this technique a useful tool employed as standard practice to control HAI.