Background: Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS).
Methods: A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis.
Results: A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥ 2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum  (C. striatum ) (11.76%, 51/434), Acinetobacter baumannii  (A. baumannii ) (11.52%, 50/434) and Enterococcus faecium  (E. faecium ) (8.99%, 39/434). ermX  conferred resistance to MSL_B and cmx  to phenicol were the only two ARGs detected in C. striatum ; in A. baumannii , most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB  conferred resistance to MSL_B and efmA  to multi-drug were the predominant ARGs in E. faecium . Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples.
Conclusion: High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum  resistant to MSL_B and/or phenicol, multi-drug resistance A. baumannii  and E. faecium  were the lead bacteria.
Keywords: intensive care units, pulmonary infection, antibiotic resistant bacteria, antibiotic resistance genes