Comprehensive Surveillance and Sampling Reveal Carbapenem-Resistant Organism Spreading in Tertiary Hospitals in China

Yi Zhang,1,* Shenglei Yu,1,* Chen Chen,1,* Feng Sun,1,* Lei Zhou,1 Haijun Yao,2 Jin Hu,2 Shirong Li,3 Jingwen Ai,1 Ning Jiang,1 Jing Wang,1 Qihui Liu,1 Jialin Jin,1 Wenhong Zhang1,4,5 1Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China; 2Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China; 3Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, China; 4National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; 5Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China*These authors contributed equally to this workCorrespondence: Wenhong Zhang; Jialin Jin, Email wenhongzhang_hs@126.com; jinjialin@fudan.edu.cnPurpose: Carbapenem-resistant organisms (CROs) have posed a great threat to antibiotic use and induce multi-drug resistance. Contamination of the hospital environment and infection of healthcare workers (HCWs) are reported as sources of nosocomial infections. Here, we performed a comprehensive environment sampling and timely epidemiological investigation during outbreaks to investigate the role of the environment and HCWs in CRO transmission.Patients and Methods: We enrolled carbapenem-resistant organism outbreaks in ICU-1 of Huashan Hospital from January 2019 to March 2019, and ICU-2 located at west branch of Huashan Hospital from October 2019 to November 2019. Carbapenem-resistant Klebsiella pneumoniae (CRKP) and carbapenem-resistant Acinetobacter baumannii (CRAB) isolates were collected from the patients. We performed a real-time comprehensive environmental and HCW sampling in the two ICUs. Isolated strains from patients and the positive colonies from the screening were sent for whole-genome sequencing. Finally, phylogenetic trees were constructed.Results: CRAB and CRKP outbreaks simultaneously occurred in ICU-1; the outbreak involved 13 patients. Meanwhile, the CRKP outbreak in ICU-2 included 11 patients. Twelve out of 146 environment and HCWs samples in ICU-1 were carbapenem-resistant bacteria, including six CRKP and six CRAB strains. For ICU-2, hospital surfaces and HCWs were negative for CRKP. Phylogenetic analyses showed that CRKP strains in ICU-1 were classified into two clades: Clade 1 and Clade 2, sharing a high similarity of isolates from the environment and HCWs. The same phenomenon was observed in CRAB.Conclusion: A timely comprehensive sampling combined with genome-based investigation may aid in tracking the transmission route of and controlling the infections. The environment and HCWs could be contaminated during CRO transmission, which calls for strengthened prevention and control measures.Keywords: carbapenem-resistant, environment, whole-genome sequencing, prevention, control