Epidemiology and population structure of Acinetobacter baumannii outbreak in a COVID-19 concentration center

Coronavirus disease caused by the SARS-CoV-2 has become one of the most significant global health challenges. The coinfections in patients with COVID-19 are considered an important risk factor. The Instituto Nacional de Enfermedades Respiratorias (INER) was the main COVID-19 reference centre in Mexico and reported the first patient infected with SARS-CoV-2 coinfected with A. baumannii. A total of 179 Acinetobacter spp. clinical isolates were collected during pandemic period with the goal of determining the genetic (screening to carbapenemases and PFGE analysis) and antimicrobial resistance profile. In addition, biofilm formation and genomic analysis were performed. We observed that coinfections were caused by distinct A. baumannii clones, and most of them exhibited a multidrug-resistant phenotype primarily associated with the bla_OXA-23 gene (76.4%). A subset of A. baumannii isolates were sequenced and subjected to genome analyses. We identified that the predominant sequence types were ST2057/ST473 (60%) and ST1837/ST367 (36.6%). The phylogenetic analysis showed that the population structured followed a ST clustering and did not follow a dispersion according to the collection year, virulome, resistome or if it was isolated from a COVID-19 or non-COVID-19 patient. Similarly, when comparing the genome content between A. baumannii from COVID-19 or non-COVID-19 patients no distinction was observed in its accessory genome suggesting that A. baumannii does not require a specific array of genes to coinfect patients; any strain circulating in the hospital environment can cause outbreaks, particularly in patients undergoing invasive procedures like mechanical ventilation. The outbreak control measures effectively contained A. baumannii at the main COVID-19 concentration centre. This study highlights the importance of monitoring opportunistic pathogens like A. baumannii during global health emergencies.