Comparative Respiratory Tract Microbiome Between Carbapenem-Resistant Acinetobacter baumannii Colonization and Ventilator Associated Pneumonia

Tingting Xiao; Qian Guo; Yanzi Zhou; Ping Shen; Yuan Wang; Qiang Fang; Mo Li; Shuntian Zhang; Lihua Guo; Xiao Yu; Yulin Liao; Chunhui Wang; Xiaohui Chi; Xiaoyang Kong; Kai Zhou; Beiwen Zheng; Qixia Luo; Yunbo Chen; Huaiqiu Zhu; Yonghong Xiao

doi:10.3389/fmicb.2022.782210

Comparative Respiratory Tract Microbiome Between Carbapenem-Resistant Acinetobacter baumannii Colonization and Ventilator Associated Pneumonia

Front Microbiol. 2022 Mar 4:13:782210. doi: 10.3389/fmicb.2022.782210. eCollection 2022.

Authors

Tingting Xiao¹, Qian Guo², Yanzi Zhou¹, Ping Shen¹, Yuan Wang¹, Qiang Fang³, Mo Li², Shuntian Zhang¹, Lihua Guo¹, Xiao Yu¹, Yulin Liao², Chunhui Wang², Xiaohui Chi¹, Xiaoyang Kong¹, Kai Zhou⁴, Beiwen Zheng¹, Qixia Luo¹, Yunbo Chen¹, Huaiqiu Zhu², Yonghong Xiao¹

Affiliations

¹ State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
² State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Future Technology and Center for Quantitative Biology, Peking University, Beijing, China.
³ Department of Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
⁴ Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.

Abstract

Background: 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. 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.

Methods: A 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.

Results: Fifty-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.

Conclusion: Lower respiratory tract microbiota dysbiosis including elevated relative abundance of Acinetobacter and reduced bacterial interactions, and virulence enrichment may lead to CRAB VAP.

Keywords: carbapenem-resistant Acinetobacter baumannii (CRAB); microbiome; multi-genomics analysis; ventilator-associated pneumonia (VAP); virulence gene.