Genomic characterization of carbapenem-resistant Acinetobacter baumannii in mechanically ventilated COVID-19 patients and role of IPC measures in reducing its circulation during the second wave of SARS-CoV-2 pandemic in Milan, Italy
Background COVID-19 has significantly affected hospitals infection prevention and control practices (IPC), especially in intensive care units (ICUs). This frequently caused the dissemination of multidrug resistant organisms (MDROs), including carbapenem-resistant Acinetobacter baumannii (CRAB). Here we report the management of a CRAB outbreak in a large ICU COVID-19 hub Hospital in Italy, together with retrospective genotypic analysis by whole genome sequencing (WGS).  Methods Bacterial strains obtained from severe COVID-19, mechanically-ventilated (median PaO2:FiO2 ratio on admission of 112 [92-158]) patients diagnosed with CRAB infection or colonization between October 2020-May 2021 were sequenced by WGS, to assess antimicrobial resistance and virulence genes, alongside mobile genetic elements. Phylogenetic analysis in combination with epidemiological data was  used to identify putative transmission chains. Results CRAB infections and colonizations were diagnosed in 14/40 (35%) and 26/40 (65%) cases, respectively, with diagnosis occurring within 48h from admission in 7 cases (17.5%).. All CRAB strains belonged to sequence type 2 and presented blaOXA-23 gene-carrying Tn2006 transposons. Phylogenetic analysis revealed the existence of three transmission chains inside and among ICU units, made of 3, 15 and 9 strains each, circulating mainly between November and December 2020. After the rapid implementation of an IPC strategy, composed by a 5-point bundle, including ICU modules temporary conversion to CRAB-ICU units and dynamic re-opening, no CRAB transmission chains were detected.  Conclusions Our study underlies the potentiality of integrating classical epidemiological studies with genomic investigation, to identify transmission routes during outbreaks, which could represent a valuable tool to ensure IPC strategies and prevent MDROs spread.