gcPathogen: a comprehensive genomic resource of human pathogens for public health

Author:

Guo Chongye12,Chen Qi12,Fan Guomei12,Sun Yan12,Nie Jingyi12,Shen Zhihong3,Meng Zhen3,Zhou Yuanchun3,Li Shiwen12,Wang Shuai12,Ma Juncai124,Sun Qinglan12,Wu Linhuan124ORCID

Affiliation:

1. Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences , Beijing  100101 , China

2. Chinese National Microbiology Data Center (NMDC) , Beijing  100101 , China

3. Computer Network Information Center, Chinese Academy of Sciences , Beijing  100190 , China

4. State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing  100101 , China

Abstract

Abstract Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration and monitoring of antibiotic resistance features and virulence factors. The catalogue seamlessly integrates and analyzes genomic data and associated metadata for human pathogens isolated from infected patients, animal hosts, food and the environment. The pathogen list is supported by evidence from medical or government pathogenic lists and publications. The current version of gcPathogen boasts an impressive collection of 1 164 974 assemblies comprising 986 044 strains from 497 bacterial taxa, 4794 assemblies encompassing 4319 strains from 265 fungal taxa, 89 965 assemblies featuring 13 687 strains from 222 viral taxa, and 646 assemblies including 387 strains from 159 parasitic taxa. Through this database, researchers gain access to a comprehensive ‘one-stop shop’ that facilitates global, long-term public health surveillance while enabling in-depth analysis of genomes, sequence types, antibiotic resistance genes, virulence factors and mobile genetic elements across different countries, diseases and hosts. To access and explore the data and statistics, an interactive web interface has been developed, which can be accessed at https://nmdc.cn/gcpathogen/. This user-friendly platform allows seamless querying and exploration of the extensive information housed within the gcPathogen database.

Funder

National key Research Program of China

Chinese Academy of Sciences

14th Five-year Informatization Plan of Chinese Academy of Sciences

Key Research Program of the Chinese Academy of Sciences

National Science Foundation for International Cooperation

Publisher

Oxford University Press (OUP)

Subject

Genetics

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