Abstract
BackgroundCarbapenem-resistant Acinetobacter baumannii (CRAB) is a common cause of ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients, but its infection and colonization state are difficult to distinguish. If the judgment is wrong, it may aggravate the abuse of antibiotics and further accelerate the evolution of drug resistance. We sought to provide new clues for the diagnosis, pathogenesis and treatment of CRAB VAP based on lower respiratory tract (LRT) microbiota.MethodsA prospective study was conducted on patients with mechanical ventilation from July 2018 to December 2019 in a tertiary hospital. Multi-genomics studies (16S rRNA amplicon, metagenomics, and whole-genome sequencing [WGS]) of endotracheal deep aspirate (ETA) were performed.ResultsFifty-two ICU patients were enrolled, including 24 with CRAB VAP (CRAB-I), 22 with CRAB colonization (CRAB-C), and six CRAB-negative patients (infection-free) (CRAB-N). Diversity of pulmonary microbiota was significantly lower in CRAB-I than in CRAB-C or CRAB-N (mean Shannon index, 1.79 vs. 2.73 vs. 4.81, P < 0.05). Abundances of 11 key genera differed between the groups. Acinetobacter was most abundant in CRAB-I (76.19%), moderately abundant in CRAB-C (59.14%), and least abundant in CRAB-N (11.25%), but its interactions with other genera increased in turn. Metagenomics and WGS analysis showed that virulence genes were more abundant in CRAB-I than in CRAB-C. Multi-locus sequence typing (MLST) of 46 CRAB isolates revealed that the main types were ST208 (30.43%) and ST938 (15.22%), with no difference between CRAB-I and CRAB-C.ConclusionLower respiratory tract microbiota dysbiosis including elevated relative abundance of Acinetobacter and reduced bacterial interactions, and virulence enrichment may lead to CRAB VAP.
Highlights
Acinetobacter baumannii (AB) is a ubiquitous microorganism that can contaminate the surface of hospital equipment and colonize skin, wounds, and other parts of patients (Shamsizadeh et al, 2017)
Acinetobacter was most abundant in Carbapenem-resistant Acinetobacter baumannii (CRAB)-I (76.19%), moderately abundant in CRAB colonization (CRAB-C) (59.14%), and least abundant in CRAB-N (11.25%), but its interactions with other genera increased in turn
Lower respiratory tract microbiota dysbiosis including elevated relative abundance of Acinetobacter and reduced bacterial interactions, and virulence enrichment may lead to CRAB ventilator-associated pneumonia (VAP)
Summary
Acinetobacter baumannii (AB) is a ubiquitous microorganism that can contaminate the surface of hospital equipment and colonize skin, wounds, and other parts of patients (Shamsizadeh et al, 2017). Ventilator associated pneumonia (VAP) is a frequent complication in ICUs and is associated with prolonged mechanical ventilation, longer intensive care unit (ICU) stay, and poorer outcomes (Papazian et al, 2020). Acinetobacter baumannii is frequently isolated from the respiratory tract in patients with tracheal intubation, which is considered to be a high-risk factor for VAP (Consales et al, 2011; Huang et al, 2018). A survey of hospital-acquired pneumonia (HAP) and VAP conducted from 2007 to 2013 revealed that multidrug-resistant AB (MDRAB) increased yearly and ranked first in some ICU bacterial lists (Hu et al, 2016). Carbapenem-resistant Acinetobacter baumannii (CRAB) is a common cause of ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients, but its infection and colonization state are difficult to distinguish. We sought to provide new clues for the diagnosis, pathogenesis and treatment of CRAB VAP based on lower respiratory tract (LRT) microbiota
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