Genomic and phylogenetic study of emerging strains of Acinetobacter baumannii belonging to Intenational Clone 2 during the COVID-19 pandemic period

Abstract

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a pathogen of great importance in healthcare-associated infections (HAI), associated with high mortality rates. Different resistance mechanisms are associated with CRAB, such as those related to chromosomal genes, mobile genetic elements and mutations. The distribution of CRAB in the world is limited to a few strains, known as high-risk clones. Isolates belonging to Clonal Complex (CC) 2 (also called International Clone 2, IC2) are highly prevalent in Europe, Australia, Asia and North America, while in Latin America, they are seldom reported. During the COVID-19 pandemic, health services faced unprecedented challenges, and HAI rates increased. For A. baumannii it was no different; due to the pathophysiology of COVID-19, the use of mechanical ventilation was frequent during the pandemic, which seems to have contributed to the increase in ventilator-associated pneumonia (VAP) caused by CRAB. In August 2020, a CRAB isolate belonging to IC2 was identified in our service, followed by a major outbreak at the index hospital. Subsequently, other CRAB IC2 isolates were identified in other hospitals, which motivated the development of this study. Thus, our objective is to investigate the spread and to evaluate the mechanisms associated with antimicrobial resistance in clinical isolates of A. baumannii belonging to IC2, from different hospitals in the state of São Paulo. Therefore, the isolates will be submitted to antimicrobial susceptibility tests (disk diffusion and broth microdilution) and genome sequencing (Illumina) to characterize clonality in fine scale (SNPs analysis) and to detect resistance and virulence genetic determinants. We will also sequence representative isolates by long read technology (MinIon) in order to identify and characterize the genetic environment of resistance genes, present in plasmids or not. A short-term internship at the University of Cologne, Germany, under the supervision of Dr Paul Higgins, is planned to improve genomic analyses.