1. 国家自然科学基金委员会，面上项目，82570013，环状DNA介导的基因扩增致肺炎克雷伯菌在下呼吸道感染中发生异质性耐药的分子机制研究，2026-01至2029-12，49万元，在研，主持

2. 北京市卫生健康委员会，首都卫生发展科研专项公共卫生研究方向重点攻关项目，首发2024-1G-43，基于病原直报的传染病实验室监测预警技术研究，2024-01至2026-12，326.46万元，在研，参加

3. 中华人民共和国科学技术部，国家重点研发计划，2020YFC0840900，2019-nCoV基因组变异规律和流行趋势预测研究，2020-01至2021-12，240万元，已结题，参加

4. 国家自然科学基金委员会，青年科学基金项目，81702038，T4SS C型分泌系统在肺炎链球菌形成新耐药岛中的机制研究，2018-01至2020-12，20万元，已结题，主持

1. 重点研究方向和成绩

1) 细菌进化、耐药和致病机制研究：阐明病原菌传播和变异特征、耐药和致病新机制，支持临床感染防控和诊疗

    长期关注细菌耐药问题，聚焦于高毒力多耐药肺炎克雷伯菌的耐药、毒力和传播，开展表型—基因型—临床感染和致病特征的关联研究和机制研究。带领团队持续产出高水平研究成果：通过临床监测识别出多种新型多耐药、高毒力肺炎克雷伯菌亚型，阐明其出现的分子机制（Lancet Infectious Diseases，2017 [IF=31]；Lancet Microbe，2023 [IF=20.4]；Nature Communications，2025[IF=15.7]）；首次发现插入序列IS26导致耐药基因blaSHV-12发生串联重复、拷贝数增加是新型抗菌药物头孢地尔、头孢他啶/阿维巴坦等异质性耐药的新机制（Drug Resistance Updates，2024 [IF=21.7]；Emerging Microbes &Infections，2024 [IF=7.5]）；通过对全球肺炎克雷伯菌基因组大数据的深入挖掘，发现了新冠疫情期间高毒力菌株在全球范围内的高流行及新型高毒力多耐药菌株的出现机制（Drug Resistance Updates，2024 [IF=21.7]）。为临床耐药菌防控和感染诊疗提供了重要依据，研究课题获国家自然科学基金面上项目支持，研究成果被北京市科学技术协会评选为首都前沿学术成果。

2) 基于组学和生物信息学的感染性疾病分子诊断新技术研究和新发突发传染病防控快速响应：高通量病原检测、实时识别和快速溯源

    开展基于基因组学和生物信息学的病原体进化、传播机制研究和新发突发传染病防控相关技术研究。作为研究骨干骨干参与人感染H7N9禽流感、人感染猪链球菌等疫情的防控和调查研究（Emerging Microbes & Infections，2013 [IF=7.5]；Emerging Infectious Diseases，2017 [IF=6.6]；Eurosurveillance，2019 [IF=7.8]），相关研究成果“序列 7 型猪链球菌在中国的显现、暴发和应对研究”获中华预防医学会科学技术奖一等奖、中华医学科技奖二等奖（排名第8）。在新冠疫情中，与北京大学、中国疾病预防控制中心病毒病预防控制所等单位合作，及时建立了病毒基因组快速测序方法MINERVA（Molecular Cell，2020 [IF=16.6]）；明确了疫情早期北京地区不同来源病例的病毒基因组特征和传播特征，支持了口岸隔离防控等措施的必要性（Nature Communications，2020 [IF=15.7]）；阐明了病毒在患者体内的异质性和宿主内变异特征和机制（Clinical Infectious Diseases，2021 [IF=7.3]；Cell Reports，2021，[IF=6.9]）。基于最新的国产纳米孔测序平台，研发了宏基因组病原检测试剂盒、多重靶向检测试剂盒、实时病原检测报告软件等产品，形成了“样本进——结果出”的整体解决方案，将高通量测序病原检测全流程从16小时极大缩短至4-5小时，获得发明专利两项，有效满足疾控和临床对感染性疾病快速精准诊断、新发突发传染病防控关口前移的迫切需求。

2. 重要学术论文

1) Yunfei Tang#,Pengcheng Du#*,Chunjing Du, Ping Yang, Ning Shen*, Thomas A. Russo*, andChao Liu#*.Genomically defined hypervirulent Klebsiellapneumoniae contributed to early-onset increased mortality. Nat Commun,2025, 16(1): 2096. (IF=15.7，中科院1区)

2) Chao Liu#∗,Pengcheng Du#∗, Ping Yang#, Yunfei Tang, Juan Yi, Qiaojun Wang,Chunjing Du, Ming Lu, Ruichao Li∗,Ning Shen∗. Long-distance transmission of tmexCD1-toprJ1positive Klebsiella pneumoniae between humans and food animals. IntJ Antimicrob Agents， 2025, 66(5):107566. (IF=4.6)

3) Chao Liu#，Juan Yi#，Ping Yang，Chunjing Du，Fan Jiang，Ming Lu，Pengcheng Du*，and Ning Shen*. Overexpression of blaSHV-12 causedby tandem amplification contributed to ceftazidime/avibactam resistance inhypervirulent and carbapenem-resistant Klebsiellapneumoniae. Emerg Microbes Infec, 2024, 13(1):2426481. (IF=7.5)

4) Pengcheng Du#, Jiarui Li#,Mingxi Hua, Liuluan Zhu, Chen Chen*, and Hui Zeng*.Potential contributions of human endogenous retroviruses in innate immunememory. J Immunol, 2024, 213: 1-9. (IF=3.4)

5) Chao Liu#,Jun Guo#, Shuaihua Fan,Wei Guo, Huaiqing Qi, Stephen Baker, PengchengDu*, and Bin Cao*. An increased prevalenceof carbapenem resistance hypervirulent Klebsiellapneumoniae associated with the COVID-19 pandemic. DrugResist Updat, 2024, 77: 101124. (IF=21.7，中科院1区)

6) Chao Liu#,Juan Yi#, Ming Lu#, Ping Yang, Chunjing Du,Fan Jiang, Pengcheng Du*,and Ning Shen*. Dynamic within-host cefiderocol heteroresistancecaused by blaSHV-12amplification in pandrug-resistant and hypervirulent Klebsiella pneumoniae sequence type 11. Drug Resist Updat, 2024,73: 101038. (IF=21.7，中科院1区)

7) Chao Liu, Jun Guo, Ming Lu, Ning Shen*, and Pengcheng Du*. Disseminationof the mobilised RND efflux pump gene cluster tmexCD-toprJ among Klebsiellapneumoniae. The Lancet Microbe, 2023, 4(3): e135. (IF=20.4，中科院1区)

8) Yanyun Gao#,Pengcheng Du#, Pei Zhang,Juan Wang, Ziyi Liu, S´eamus Fanning, Zhiqiang Wang, Ruichao Li*, and Li Bai*. Dynamic evolution andtransmission of a blaNDM-1-bearingfusion plasmid in a clinical Escherichiacoli. Microbiol Res, 2023, 275:127450. (IF=6.9)

9) Pengcheng Du#, Xiaobin Liu#, Yue Liu#, Ruichao Li, Xin Lu,Shenghui Cui, Yongning Wu, Séamus Fanning, and Li Bai*. Dynamics ofAntimicrobial Resistance and Genomic Epidemiology of Multidrug-Resistant Salmonella enterica Serovar Indiana ST17from 2006 to 2017 in China. mSystems, 2022, 7(4):e0025322. (IF=4.6)

10) Yujiao Mu#,Ruichao Li#, Pengcheng Du#, Pei Zhang,Yan Li, Shenghui Cui, Séamus Fanning, and Li Bai*. GenomicEpidemiology of ST34 Monophasic Salmonellaenterica Serovar Typhimurium from Clinical Patients from 2008 to 2017 inHenan, China. Engineering, 2022, 15: 34-44. (IF=11.6)

11) Pengcheng Du#, Chao Liu#, Shuaihua Fan, StephenBaker, and Jun Guo*. The Role of Plasmid and Resistance GeneAcquisition in the Emergence of ST23 Multi-Drug Resistant, Hypervirulent Klebsiella pneumoniae. MicrobiolSpectr, 2022, 10(2):e0192921. (IF=3.8)

12) Pengcheng Du#, Chuan Song#, Rui Li#, Yangzi Song#, Jiarui Li, Nan Ding, JuZhang, Rui Song, Junyan Han, Guiju Gao, Jinglin Yue, Ang Duan, Yanyi Huang,Jing An, Jianbin Wang*, Fujie Zhang*, Chen Chen*,and Hui Zeng*. Specific Redistribution of Severe Acute RespiratorySyndrome Coronavirus 2 Variants in the Respiratory System and Intestinal Tract.Clin Infect Dis, 2021, 73(9):e2814-e2817. (IF=7.3)

13) Jiarui Li#,Pengcheng Du#,Lijiang Yang#, Ju Zhang#, Chuan Song#, Danying Chen#, Yangzi Song, Nan Ding,Mingxi Hua, Kai Han, Rui Song, Wen Xie, Zhihai Chen, Xianbo Wang, Jingyuan Liu,Yanli Xu, Guiju Gao, Qi Wang, Lin Pu, Lin Di, Jie Li, Jinglin Yue, Junyan Han,Xuesen Zhao, Yonghong Yan, Fengting Yu, Angela R. Wu, Fujie Zhang*,Yi Qin Gao*, Yanyi Huang*, Jianbin Wang*, HuiZeng*, and Chen Chen*. Two-step fitness selection forintra-host variations in SARS-CoV-2. Cell Rep, 2021: 110205. (IF=6.9)

14) Mingxi Hua#,Jingyuan Liu#, PengchengDu#, Xinzhe Liu, MinLi, Huizhu Wang, Chen Chen, Xinmin Xu, Yu Jiang, Yajie Wang, Hui Zeng*, and AngLi*. The novel outer membrane protein from OprD/Occ family is associated withhypervirulence of carbapenem resistant Acinetobacterbaumannii ST2/KL22. Virulence, 2021, 12(1):1-11. (IF=5.4)

15) Ruichao Li#,Pengcheng Du#, Pei Zhang,Yan Li, Xiaorong Yang, Zhiqiang Wang, Juan Wang, and Li Bai*. ComprehensiveGenomic Investigation of Coevolution of mcr genes in Escherichia coli Strains via Nanopore Sequencing. GlobalChallenges, 2021, 5(3): 2000014. (IF=6.4)

16) Pengcheng Du#, Nan Ding#,Jiarui Li#, Fujie Zhang#, Qi Wang#, ZhihaiChen#, Chuan Song, Kai Han, Wen Xie, Jingyuan Liu, Linghang Wang,Lirong Wei, Shanfang Ma, Mingxi Hua, Fengting Yu, Lin Wang, Wei Wang, Kang An,Jianjun Chen, Haizhou Liu, Guiju Gao, Sa Wang, Yanyi Huang, Angela R. Wu,Jianbin Wang*, Di Liu*, Hui Zeng*, and ChenChen*. Genomic surveillance of COVID-19 cases in Beijing. Natcommun, 2020, 11(1): 1-9. (IF=15.7，中科院1区)

17) Chao Liu#,Pengcheng Du#, Nan Xiao, Fansen Ji, Thomas A. Russo*,and Jun Guo*. Hypervirulent Klebsiellapneumoniae is emerging as an increasingly prevalent K. pneumoniae pathotype responsible for nosocomial andhealthcare-associated infections in Beijing, China. Virulence, 2020, 11(1):1215-24. (IF=5.4)

18) Chen Chen#,Jizhou Li#, Lin Di#, Qiuyu Jing#, Pengcheng Du#, Chuan Song, Jiarui Li,Qiong Li, Yunlong Cao, X. Sunney Xie, Angela R. Wu*, Hui Zeng*,Yanyi Huang*, and Jianbin Wang*. MINERVA: A FacileStrategy for SARS-CoV-2 Whole-Genome Deep Sequencing of Clinical Samples. Mol Cell, 2020,80(6):1123-1134.e4. (IF=16.6)