Affinity molecular assay for detecting Candida albicans using chitin affinity and RPA-CRISPR/Cas12a

Nat Commun. 2024 Oct 28;15(1):9304. doi: 10.1038/s41467-024-53693-5.

Shimei Shen ^# ¹ ² ³ ⁴ ⁵, Wen Wang ^# ¹ ² ⁶, Yuanyan Ma ^# ¹ ⁴, Shilei Wang ^# ³, Shaocheng Zhang ^# ⁶ ⁷, Xuefei Cai ⁴, Liang Chen ⁸, Jin Zhang ¹ ⁴, Yalan Li ¹ ⁴, Xiaoli Wu ¹ ⁴, Jie Wei ⁹, Yanan Zhao ¹⁰, Ailong Huang ¹¹, Siqiang Niu ¹², Deqiang Wang ¹³ ¹⁴ ¹⁵

Affiliations

1 Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China.
2 Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
3 Department of Dermatology and Cosmetology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China.
4 The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
5 Department of Clinical Laboratory Medicine, Chongqing Red Cross Hospital (Jiangbei District People's Hospital), Chongqing, China.
6 Department of Laboratory Medicine, The Second Affiliated Hospital of Chengdu Medical College (Nuclear Industry 416 Hospital), Chengdu, China.
7 School of Clinical Medicine, Chengdu Medical College, Chengdu, China.
8 Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA.
9 Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China.
10 Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA. yananzh@buffalo.edu.
11 The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China. ahuang@cqmu.edu.cn.
12 Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China. siqiangniu@cqmu.edu.cn.
13 Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China. wangdq333@cqmu.edu.cn.
14 The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China. wangdq333@cqmu.edu.cn.
15 Western (Chongqing) Collaborative Innovation Center for Intelligent Diagnostics and Digital Medicine, Chongqing National Biomedicine Industry Park, Chongqing, China. wangdq333@cqmu.edu.cn.
# Contributed equally.

PMID: 39468064 DOI: 10.1038/s41467-024-53693-5

Abstract

Invasive Fungal infections (IFIs) pose a significant threat to immunocompromised individuals, leading to considerable morbidity and mortality. Prompt and accurate diagnosis is essential for effective treatment. Here we develop a rapid molecular diagnostic method that involves three steps: Fungal enrichment using affinity-magnetic separation (AMS), genomic DNA extraction with silicon hydroxyl Magnetic Beads, and detection through a one-pot system. This method, optimized to detect 30 CFU/mL of C. albicans in blood and bronchoalveolar lavage (BAL) samples within 2.5 h, is approximately 100 times more sensitive than microscopy-based staining. Initial validation using clinical samples showed 93.93% sensitivity, 100% specificity, and high predictive values, while simulated tests demonstrated 95% sensitivity and 100% specificity. This cost-effective, highly sensitive technique offers potential for use in resource-limited clinical settings and can be easily adapted to differentiate between Fungal species and detect drug resistance.

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