Rapid Identification of <i>Brucella</i> Genus and Species In Silico and On-Site Using Novel Probes with CRISPR/Cas12a

Yan Zhang; Yufei Lyu; Dongshu Wang; Meijie Feng; Sicheng Shen; Li Zhu; Chao Pan; Xiaodong Zai; Shuyi Wang; Yan Guo; Shujuan Yu; Xiaowei Gong; Qiwei Chen; Hengliang Wang; Yuanzhi Wang; Xiankai Liu

doi:10.3390/microorganisms12051018

Microorganisms (May 2024)

Rapid Identification of <i>Brucella</i> Genus and Species In Silico and On-Site Using Novel Probes with CRISPR/Cas12a

Yan Zhang,
Yufei Lyu,
Dongshu Wang,
Meijie Feng,
Sicheng Shen,
Li Zhu,
Chao Pan,
Xiaodong Zai,
Shuyi Wang,
Yan Guo,
Shujuan Yu,
Xiaowei Gong,
Qiwei Chen,
Hengliang Wang,
Yuanzhi Wang,
Xiankai Liu

Affiliations

Yan Zhang: College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Lingang New City, Shanghai 201306, China
Yufei Lyu: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Dongshu Wang: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Meijie Feng: College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Lingang New City, Shanghai 201306, China
Sicheng Shen: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Li Zhu: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Chao Pan: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Xiaodong Zai: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Shuyi Wang: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Yan Guo: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Shujuan Yu: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
Xiaowei Gong: State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chengguan District, Lanzhou 730046, China
Qiwei Chen: State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chengguan District, Lanzhou 730046, China
Hengliang Wang: College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Lingang New City, Shanghai 201306, China
Yuanzhi Wang: School of Medicine, Shihezi University, Xinjiang Uygur Autonomous Region, Shihezi 832002, China
Xiankai Liu: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China

DOI: https://doi.org/10.3390/microorganisms12051018
Journal volume & issue: Vol. 12, no. 5
p. 1018

Abstract

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Human brucellosis caused by Brucella is a widespread zoonosis that is prevalent in many countries globally. The high homology between members of the Brucella genus and Ochrobactrum spp. often complicates the determination of disease etiology in patients. The efficient and reliable identification and distinction of Brucella are of primary interest for both medical surveillance and outbreak purposes. A large amount of genomic data for the Brucella genus was analyzed to uncover novel probes containing single-nucleotide polymorphisms (SNPs). GAMOSCE v1.0 software was developed based on the above novel eProbes. In conjunction with clinical requirements, an RPA-Cas12a detection method was developed for the on-site determination of B. abortus and B. melitensis by fluorescence and lateral flow dipsticks (LFDs). We demonstrated the potential of these probes for rapid and accurate detection of the Brucella genus and five significant Brucella species in silico using GAMOSCE. GAMOSCE was validated on different Brucella datasets and correctly identified all Brucella strains, demonstrating a strong discrimination ability. The RPA-Cas12a detection method showed good performance in detection in clinical blood samples and veterinary isolates. We provide both in silico and on-site methods that are convenient and reliable for use in local hospitals and public health programs for the detection of brucellosis.

Published in Microorganisms

ISSN: 2076-2607 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Biology (General)
Website: https://www.mdpi.com/journal/microorganisms

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