阮陟，生物信息学博士，副研究员。浙江大学医学院临床检验诊断学硕士研究生导师，浙江省杰出青年科学基金项目获得者，浙江省优秀硕士学位论文指导教师。现任中华医学会检验医学分会青年教师科研创新联盟委员、中国环境诱变剂学会致突变专业委员会委员、浙江省医学创新学科——个体化检验诊断学后备学科带头人、浙江大学医学院附属邵逸夫医院卓越人才培养工程第二层次入选者。常年从事微生物基因组学与生物信息学交叉研究，关注以鲍曼不动杆菌、肺炎克雷伯菌为代表的临床重要病原菌基因组流行病学特征、耐药与传播机制，围绕细菌基因组分型、溯源与暴发流行前瞻性预警开发了一系列生物信息学工具与数据库，代表性成果主要包括病原菌基因组分型与溯源一站式数据分析平台BacWGSTdb、临床宏基因组测序（mNGS）病原菌亚种分型工具MIST等。近年在Lancet Infectious Diseases、Nucleic Acids Research、Briefings in Bioinformatics与Drug Resistance Updates等学术期刊发表SCI论文70余篇（包括2篇ESI高被引论文），授权国家发明专利1项，登记国家计算机软件著作权6项，研究成果获2018年浙江省科学技术进步奖一等奖、2016年浙江省医药卫生科技奖一等奖。主持国家自然科学基金、浙江省自然科学基金等科研项目8项。现任Travel Medicine and Infectious Disease、BMC Genomics、New Microbes and New Infections、Frontiers in Microbiology、Frontiers in Genetics、Antibiotics、Scientific Reports、PLoS ONE等SCI期刊编委，担任Emerging Microbes & Infections、Journal of Antimicrobial Chemotherapy、Microbiology Spectrum、Microbial Genomics、Journal of Environmental Management、Frontiers in Microbiology、BMC Genomics、Infection and Drug Resistance、Microbial Drug Resistance、Infection, Genetics and Evolution等多个SCI期刊审稿人。担任国家自然科学基金、浙江省自然科学基金、广东省自然科学基金、浙江省医药卫生科技计划通讯评审专家。

 

1. 2007/09 - 2013/12，浙江大学，医学院，生物信息学，博士；
2. 2003/09 - 2007/06，中国计量学院，生命科学学院，生物工程，学士。

 

1. 2025/01 - 至今，浙江大学，医学院附属邵逸夫医院，研究员；
2. 2020/01 - 2024/12，浙江大学，医学院附属邵逸夫医院，副研究员；
3. 2014/01 - 2019/12，浙江大学，医学院附属邵逸夫医院，助理研究员。

 

授权国家发明专利：

阮陟、陈欢、冯晔、单杲，一种病原微生物基因组快速分析方法及系统，2018.12.21，中国，ZL201510932914.6

登记国家计算机软件著作权：

阮陟，临床病原菌基因组分型与溯源一站式数据分析系统，2021.01.28，2021SR0159382

阮陟，基于基因组测序技术的感染性疾病病原体快速检测系统，2019.03.21，2019SR0269877

阮陟，基于实时全基因组测序的医院感染暴发预警与智能决策辅助系统，2018.06.11，2018SR434924

阮陟，基于基因组测序数据的病原微生物快速药敏预测系统，2017.06.09，2017SR249834

阮陟，病原微生物多位点序列分型数据分析与可视化系统，2016.05.31，2016SR126532

阮陟，细菌基因组分型与溯源系统，2016.04.19，2016SR079830

 

中华医学会检验医学分会青年教师科研创新联盟委员、中国环境诱变剂学会致突变专业委员会委员、浙江省药学会微生物耐药与控制专委会青委副主任委员、浙江省生物信息学学会精准医学专业委员会委员、浙江省医学创新学科——个体化检验诊断学后备学科带头人、浙江大学医学院临床检验诊断学研究生教育委员会秘书。

 

主持国家自然科学基金面上项目、国家重点研发计划项目子课题、浙江省领雁研发攻关计划项目子课题、浙江省自然科学基金等科研项目10余项。

 

(1) Xinyang Li, Yuye Wu, Tian Jiang, Bin Chen, Rui Feng, Jun Zhang, Xinyou Xie, Zhi Ruan^*. China's plan to combat antimicrobial resistance. Science. 2024, 383(6690): 1424-1425. (IF: 56.9)

(2) Yuye Wu, Chenghao Wu, Danni Bao, Huiqiong Jia, Mohamed Draz, Fang He, Zhi Ruan^*. Global evolution and geographic diversity of hypervirulent carbapenem-resistant Klebsiella pneumoniae. The Lancet Infectious Diseases. 2022, 22(6): 761-762. (IF: 71.421)

(3) Jo?o Pedro Rueda Furlan^*, Sergio Schenkman, Fábio Parra Sellera, Shuangshuang Li, Yilu Zhuang, Zhi Ruan^*.
Ex-situ trans-Gram transfer of clinically relevant antimicrobial
resistance genes from a genomic perspective: natural or
contamination-related events? The Lancet Microbe. 2025. (IF: 38.2)

(4) Yuye Wu, Yilu Zhuang, Chenghao Wu, Huiqiong Jia, Fang He, Zhi Ruan^*. Global emergence of gram-negative bacteria carrying the mobilised RND efflux pump gene cluster tmexCD-toprJ variants. The Lancet Microbe. 2024, 5(2): e105. (IF: 38.2)

(5)
Huiqiong Jia, Qingchao Tong, Le Wang, Yuye Wu, Xinyang Li, Shuangshuang
Li, Yingying Kong, Yingying Zhang, Jo?o Pedro Rueda Furlan, Nwai Oo
Khine, Patrick Butaye^*, Jun Zhang^*, Qing Yang^*, Zhi Ruan^*. Silent circulation of plasmid-borne tet(X6) and bla_OXA-58 genes in a community-acquired Acinetobacter baumannii strain. Drug Resistance Updates. 2025, 79: 101194. (IF: 24.3)

(6) Yuye Wu, Tian Jiang, Danni Bao, Meina Yue, Huiqiong Jia, Jianyong Wu, Zhi Ruan^*. Global population structure and genomic surveillance framework of carbapenem-resistant Salmonella enterica. Drug Resistance Updates. 2023, 68: 100953. (IF: 24.3)

(7) Ye Feng, Shengmei Zou, Hangfei Chen, Yunsong Yu^*, Zhi Ruan^*.
BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome
sequence typing and source tracking, Nucleic Acids Research. 2021,
49(D1): D644-D650. (IF: 19.160，ESI高被引论文)

(8) Zhi Ruan,
Ye Feng^*. BacWGSTdb, a database for genotyping and source tracking
bacterial pathogens. Nucleic Acids Research. 2016, 44(D1): D682-D687. (IF: 19.160，ESI高被引论文)

(9)
Yuye Wu, Tian Jiang, Xianhong He, Jiayu Shao, Chenghao Wu, Weifang Mao,
Huiqiong Jia, Fang He, Yingying Kong, Jianyong Wu, Qingyang Sun, Long
Sun, Mohamed Draz, Xinyou Xie^*, Jun Zhang^*, Zhi Ruan^*. Global phylogeography and genomic epidemiology of carbapenem-resistant bla_OXA-232-carrying Klebsiella pneumoniae ST15 lineage. Emerging Infectious Diseases. 2023, 29(11): 2246-2256. (IF: 16.126)

(10) Yilu Zhuang, Shuangshuang Li, Danni Bao, Jo?o Pedro Rueda Furlan^*, Zhi Ruan^*. Genomic integrity in Bordetella pertussis:
avoiding contaminant-derived misinterpretations of acquired
antimicrobial resistance. Journal of Infection. 2024, 89(6): 106356. (IF: 14.3)

(11)
Xinyang Li, Yilu Zhuang, Yawen Yu, Huiqiong Jia, Yingying Kong, Jun
Zhang, Xinyou Xie, Eliana Stehling, Jo?o Pedro Furlan, Zhemin Zhou, Zhi
Ruan^*. Interplay of multiple carbapenemases and tigecycline resistance in Acinetobacter species: a serious combined threat. Clinical Microbiology and Infection. 2025, 31(1): 128-133. (IF: 13.310)

(12) Zhi Ruan, Shengmei Zou, Zeyu Wang, Luhan Zhang, Hangfei Chen, Yuye Wu, Huiqiong Jia, Mohamed Draz, Ye Feng^*.
Toward accurate diagnosis and surveillance of bacterial infections
using enhanced strain-level metagenomic next-generation sequencing of
infected body fluids. Briefings in Bioinformatics. 2022, 23(2): bbac004. (IF: 13.994)

(13) Zhi Ruan, Yunsong Yu^*, Ye Feng^*.
The global dissemination of bacterial infections necessitates the study
of reverse genomic epidemiology. Briefings in Bioinformatics. 2020,
21(2): 741-750. (IF: 13.994)

(14) Qixia Luo, Yuye Wu, Danni Bao, Linna Xu, Hangfei Chen, Meina Yue, Mohamed S. Draz, Yingying Kong, Zhi Ruan^*. Genomic epidemiology of mcr carrying multidrug-resistant ST34 Salmonella enterica
serovar Typhimurium in a One Health context: the evolution of a global
menace. Science of The Total Environment. 2023, 896: 165203. (IF: 10.754)

(15)
Yuye Wu, Weifang Mao, Jiayu Shao, Xianhong He, Danni Bao, Meina Yue,
Jinyue Wang, Weiwei Shen, Xinhua Qiang, Huiqiong Jia, Fang He, Zhi Ruan^*.  Monitoring the long-term spatiotemporal transmission dynamics and ecological surveillance of multidrug-resistant Salmonella enterica serovar Goldcoast: a multicenter genomic epidemiology study. Science of The Total Environment. 2024, 912: 169116. (IF: 10.754)

(16) Yilu Zhuang, Xinyang Li, Yuye Wu, Huiqiong Jia, Xinyou Xie^*, Zhi Ruan^*. Colistin resistance landscape: insights into the global spread of mcr-carrying Gram-negative bacteria. International Journal of Antimicrobial Agents. 2024, 64(2): 107207. (IF: 10.8)

(17) Yawen Yu, Xinyang Li, Yuye Wu, Ningjie Lou, Huiqiong Jia, Ning Liu, Jun Zhang^*, Xinyou Xie^*, Zhi Ruan^*.  Global prevalence of fosfomycin resistance genes, fosA and fosB in multidrug-resistant bacteria. International Journal of Antimicrobial Agents. 2024, 64(3): 107272. (IF: 10.8)

(18) Fábio Parra Sellera, Yilu Zhuang, Nilton Lincopan, Eliana Guedes Stehling, Sergio Schenkman, Zhi Ruan^*, Jo?o Pedro Rueda Furlan^*. Genomic tracking the coexistence of mcr and
carbapenemase genes in Gram-negative bacteria: a global perspective.
International Journal of Antimicrobial Agents. 2024, 64(5): 107350. (IF: 10.8)

(19) Yuye Wu, Dheerendranath Battalapalli, Mohammed Hakeem, Venkatarao Selamneni, Pengfei Zhang^*, Mohamed Draz^*, Zhi Ruan^*.
Engineered CRISPR-Cas systems for the detection and control of
antibiotic-resistant infections. Journal of Nanobiotechnology. 2021,
19(1): 401. (IF: 10.435)

(20) Zhi Ruan, Qingyang Sun, Huiqiong Jia, Chenyun Huang, Weili Zhou, Xinyou Xie^*, Jun Zhang^*. Emergence of a ST2570 Klebsiella pneumoniae isolate carrying mcr-1 and bla_CTX-M-14 recovered from a bloodstream infection in China. Clinical Microbiology and Infection. 2019, 25(7): 927-929. (IF: 13.310)

(21) Yingying Kong, Chao Li, Gangfeng Li, Ting Yang, Mohamed Draz, Xinyou Xie^*, Jun Zhang^*, Zhi Ruan^*. In vitro activity of delafloxacin and finafloxacin against Mycoplasma hominis and Ureaplasma species. Microbiology Spectrum. 2022, 10(3): e00099-22. (IF: 9.043)

(22) Wenwen Liu, Ting Yang, Yingying Kong, Xinyou Xie^*, Zhi Ruan^*. Ureaplasma infections:
update on epidemiology, antimicrobial resistance, and pathogenesis.
Critical Reviews in Microbiology. 2024. doi:
10.1080/1040841X.2024.2349556. (IF: 6.5)

(23) Xinyang Li, Tian Jiang, Chenghao Wu, Yingying Kong, Yilei Ma, Jianyong Wu, Xinyou Xie^*, Jun Zhang^*, Zhi Ruan^*. Molecular epidemiology and genomic characterization of a plasmid-mediated mcr-10 and bla_NDM-1 co-harboring multidrug-resistant Enterobacter asburiae. Computational and Structural Biotechnology Journal. 2023, 21: 3885-3893. (IF: 6.0)

(24) Fen Wan, Mohamed Draz, Mengjie Gu, Wei Yu, Zhi Ruan^*, Qixia Luo^*.
Novel strategy to combat antibiotic resistance: a sight into the
combination of CRISPR/Cas9 and nanoparticles. Pharmaceutics. 2021,
13(3): 352. (IF: 6.525)

(25)  Zhi Ruan, Huiqiong Jia, Hangfei Chen, Jianyong Wu, Fang He, Ye Feng^*. Co-existence of plasmid-mediated tigecycline and colistin-resistant genes tet(X4) and mcr-1 in a community-acquired Escherichia coli isolate in China. Journal of Antimicrobial Chemotherapy. 2020, 75(11): 3400-3402. (IF: 5.758)

(26)
Huiqiong Jia, Xinyang Li, Yilu Zhuang, Yuye Wu, Shasha Shi, Qingyang
Sun, Fang He, Shanyan Liang, Jianfeng Wang, Mohamed Draz, Xinyou Xie,
Jun Zhang^*, Qing Yang^*, Zhi Ruan^*. Neural network-based predictions of antimicrobial resistance phenotypes in multidrug-resistant Acinetobacter baumannii from whole genome sequencing and gene expression. Antimicrobial Agents and Chemotherapy. 2024, 68(12): e01446-24. (IF: 5.938)

(27) Xueying Zhang, Yongying Bai, Long Zhang, Mohamed Draz, Zhi Ruan^*, Yuning Zhu^*. Antimicrobial susceptibility and clonality of vaginally derived multidrug-resistant Mobiluncus isolates in China. Antimicrobial Agents and Chemotherapy. 2020, 64(8): e00780-20. (IF: 5.938)

(28) Yingying Kong, Qingyang Sun, Hangfei Chen, Mohamed Draz, Xinyou Xie^*, Jun Zhang^*, Zhi Ruan^*. Transmission dynamics of carbapenem-resistant Klebsiella pneumoniae sequence type 11 strains carrying capsular loci KL64 and rmpA/rmpA2 genes. Frontiers in Microbiology. 2021, 12: 736896. (IF: 5.2)

(29) Yingying Kong, Chao Li, Hangfei Chen, Wei Zheng, Qingyang Sun, Xinyou Xie^*, Jun Zhang^*, Zhi Ruan^*. In vivo emergence of colistin resistance in carbapenem-resistant Klebsiella pneumoniae mediated by premature termination of the mgrB gene regulator. Frontiers in Microbiology. 2021, 12: 656610. (IF: 5.2)

(30) Zhi Ruan,
Yan Chen, Yan Jiang, Hua Zhou, Zhihui Zhou, Ying Fu, Haiping Wang,
Yanfei Wang, Yunsong Yu^*. Wide distribution of CC92 carbapenem-resistant
and OXA-23-producing Acinetobacter baumannii in multiple provinces of China. International Journal of Antimicrobial Agents. 2013, 42(4): 322-328. (IF: 15.441)

(31) Hangfei Chen, Dheerendranath Battalapalli, Mohamed Draz, Pengfei Zhang^*, Zhi Ruan^*. The application of cell-penetrating-peptides in antibacterial agents. Current Medicinal Chemistry. 2021, 28(29):5896-5925.

(32) Huiqiong Jia, Mohamed Draz, Zhi Ruan^*.
Functional nanomaterials for detection and control of bacterial
infections. Current Topics in Medicinal Chemistry. 2019, 19(27):
2449-2475.

(33) Huiqiong Jia, Yan Chen, Jianfeng Wang, Xinyou Xie, Zhi Ruan^*.
Emerging challenges of whole-genome-sequencing–powered epidemiological
surveillance of globally distributed clonal groups of bacterial
infections, giving Acinetobacter baumannii ST195 as an example. International Journal of Medical Microbiology. 2019, 309(7): 151339.

(34) Yafei Fan, Hangfei Chen, Ning Mu, Wengui Wang, Kongkai Zhu^*, Zhi Ruan^*, Shoufeng Wang^*.
Nosiheptide analogues as potential antibacterial agents via
dehydroalanine region modifications: Semi-synthesis, antimicrobial
activity and molecular docking study. Bioorganic & Medicinal
Chemistry. 2021, 31: 115970.

(35) Huiqiong Jia, Qingyang Sun, Zhi Ruan^*, Xinyou Xie. Characterization of a small plasmid carrying the carbapenem resistance gene bla_OXA-72 from community-acquired Acinetobacter baumannii sequence type 880 in China. Infection and Drug Resistance. 2019, 12: 1545-1553.

(36) Zhi Ruan, Jianyong Wu, Hangfei Chen, Mohamed Draz, Juan Xu, Fang He^*. Hybrid genome assembly and annotation of a pandrug-resistant Klebsiella pneumoniae strain using Nanopore and Illumina sequencing. Infection and Drug Resistance. 2020, 13: 199-206.

(37) Danni Bao, Linyao Huang, Jianxin Yan, Yexuzi Li, Zhi Ruan^*, Tian Jiang^*. First identification of a multidrug-resistant Pseudomonas putida
co-carrying five β-lactam resistance genes recovered from a urinary
tract infection in China. Infection and Drug Resistance. 2022, 15:
2229-2234.

(38) Fen Wan, Linna Xu, Zhi Ruan^*, Qixia Luo^*.
Genomic and transcriptomic analysis of colistin-susceptible and
colistin-resistant isolates identify two-component system EvgS/EvgA
associated with colistin resistance in Escherichia coli. Infection and Drug Resistance. 2021, 14: 2437-2447.

(39) Zhi Ruan, Yan Chen, Jianfeng Wang^*. Glimpse into the genome sequence of a multidrug-resistant Acinetobacter pittii ST950 clinical isolate carrying the bla_OXA-72 and bla_OXA-533 genes in China. Memórias do Instituto Oswaldo Cruz. 2017, 112 (10): 723-727.

(40) Zhi Ruan, Ting Yang, Xinyan Shi, Yingying Kong, Xinyou Xie^*, Jun Zhang^*. Clonality and distribution of clinical Ureaplasma isolates recovered from male patients and infertile couples in China. PLoS One, 2017, 12 (8): e0183947.

(41) Hangfei Chen, Tian Jiang, Jianyong Wu, Qingyang Sun, Qiuying Zha, Shurui Jin, Zhi Ruan^*.  Genomic and phylogenetic analysis of a multidrug-resistant mcr-1-carrying Klebsiella pneumoniae recovered from a urinary tract infection in China. Journal of Global Antimicrobial Resistance. 2021, 27:222-224.

(42) Wei Zheng, Meina Yue, Jun Zhang^*, Zhi Ruan^*. Coexistence of two bla_CTX-M-14 genes in a bla_NDM-5-carrying multidrug-resistant Escherichia coli strain recovered from a bloodstream infection in China. Journal of Global Antimicrobial Resistance. 2021, 26: 11-14.

(43) Huiqiong Jia, Yan Chen, Jianfeng Wang, Zhi Ruan^*. Genomic characterization of a clinical Acinetobacter baumannii ST1928 isolate carrying a new ampC allelic variant bla_ADC-196 gene from China. Journal of Global Antimicrobial Resistance. 2019, 19: 43-45.

(44) Huiqiong Jia, Hangfei Chen, Zhi Ruan^*. Unravelling the genome sequence of a pandrug-resistant Klebsiella pneumoniae
isolate with sequence type 11 and capsular serotype KL64 from China.
Journal of Global Antimicrobial Resistance. 2019, 19: 40-42.

(45) Tiejun Song, Jun Huang, Zhiwei Liu, Ying Zhang, Yingying Kong, Zhi Ruan^*. Antibiotic susceptibilities and genetic variations in macrolide resistance genes of Ureaplasma spp. isolated in China. New Microbiologica. 2019, 42(4): 225-227.

(46) Zhi Ruan, Fangwei Dai, Xu Fang, Huan Chen^*, Dongliang Yu^*. The complete mitochondrial genome of a rare human pathogen, Aspergillus ustus. Mitochondrial DNA Part A. 2016, 27(6): 3876-3877.

 

贾慧琼，浙江大学临床检验诊断学硕士生（2017级），获2020届浙江大学优秀毕业研究生、浙江省优秀硕士学位论文、美国微生物学会ASM Student and Postdoctoral Travel Award等荣誉称号，现就职于浙江大学医学院附属第一医院检验科，2021年获国家自然科学基金、浙江省自然科学基金项目各1项；

陈航飞，浙江大学临床检验诊断学硕士生（2019级），获2022届浙江省优秀毕业研究生荣誉称号，毕业后在浙江大学内科学（呼吸病学）专业继续攻读博士学位；

吴钰烨，浙江大学临床检验诊断学硕士生（2021级），获2023年硕士研究生国家奖学金，现硕转博；

刘雯雯，浙江大学临床检验诊断学硕士生（2021级），2024届浙江省优秀毕业研究生，现就职于浙江大学医学院附属邵逸夫医院检验科；

李欣阳，浙江大学临床检验诊断学直博生（2021级），预计于2026年6月毕业；

江天，浙江大学临床检验诊断学同等学力博士生（2020级），浙江省第十四届人民代表大会代表，现就职于温州医科大学附属温岭医院科研管理处，入选2020年度浙江省卫生高层次人才培养对象（医坛新秀）、2022年度台州市高层次人才特殊支持计划（卫生健康类）第三层次，目前在读；

孙青阳，浙江大学临床检验诊断学同等学力硕士生，2019年12月已获硕士学位，现就职于中国人民解放军联勤保障部队第903医院检验科；

岳美娜，浙江大学临床检验诊断学同等学力硕士生，2021年12月已获硕士学位，现就职于杭州市儿童医院检验科；

郑玮，浙江大学临床检验诊断学同等学力硕士生，2021年12月已获硕士学位，现就职于乐清市第三人民医院检验科；

包丹妮，浙江大学临床检验诊断学同等学力硕士生，2022年12月已获硕士学位，现就职于三门县人民医院检验科，入选2022年浙江省卫生高层次人才培养对象（医坛新秀）；

吴剑涌，浙江大学临床检验诊断学同等学力硕士生，2022年3月已获硕士学位，现就职于浙江大学医学院附属第四医院检验科;

邵嘉瑜，浙江大学临床检验诊断学同等学力硕士生，2024年6月已获硕士学位，现就职于杭州市萧山区第三人民医院检验科；

何献红，浙江大学临床检验诊断学同等学力硕士生，2024年6月已获硕士学位，现就职于杭州市萧山区第三人民医院检验科；

毛伟芳，浙江大学临床检验诊断学同等学力硕士生，2024年6月已获硕士学位，现就职于绍兴文理学院附属医院检验科；

何雪倩，浙江大学临床检验诊断学同等学力硕士生，现就职于浙江省人民医院检验科，目前在读。