Hiểu và vượt qua những cạm bẫy và thiên kiến của các phương pháp giải trình tự thế hệ mới (NGS) để sử dụng trong phòng thí nghiệm chẩn đoán vi sinh học lâm sàng thường quy

Stefan A. Boers1, Ruud Jansen2, John P. Hays1
1Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre Rotterdam (Erasmus MC), Rotterdam, The Netherlands
2Department of Molecular Biology, Regional Laboratory of Public Health Kennemerland, Haarlem, The Netherlands

Tóm tắt

Những tiến bộ gần đây trong lĩnh vực giải trình tự thế hệ mới (NGS) đã cung cấp nền tảng cho các nghiên cứu hiện đại về thành phần của cộng đồng vi sinh vật. Việc sử dụng các phương pháp NGS này cho phép phát hiện và xác định các vi sinh vật ('khó nuôi cấy') thông qua một chiến lược độc lập với văn hóa. Tuy nhiên, trong lĩnh vực chẩn đoán lâm sàng thường quy, việc áp dụng NGS hiện tại bị giới hạn chỉ ở việc phân loại chủng vi sinh vật cho mục đích dịch tễ học, mặc dù việc triển khai NGS cho phân tích cộng đồng vi sinh vật có thể mang lại thông tin quan trọng về lâm sàng. Sự thiếu sót trong việc thực hiện NGS là do nhiều yếu tố khác nhau, bao gồm những vấn đề liên quan đến tiêu chuẩn hóa phương pháp NGS và khả năng tái lập kết quả. Trong bài viết tổng quan này, các tác giả cung cấp một giới thiệu chung về các phương pháp NGS phổ biến nhất hiện nay (tức là, giải trình tự vùng mục tiêu và metagenomics shotgun) và các điểm mạnh cũng như yếu của từng phương pháp được thảo luận. Từ đó, nội dung bài viết chuyển sang các phương pháp NGS gien 16S rRNA, hiện là các phương pháp NGS tiết kiệm chi phí và được sử dụng rộng rãi nhất cho mục đích nghiên cứu, và do đó có khả năng được triển khai thành công vào chẩn đoán lâm sàng thường quy trong thời gian ngắn. Trong bối cảnh này, các cạm bẫy thực nghiệm và thiên kiến được tạo ra ở mỗi bước trong quy trình NGS gien 16S rRNA được giải thích, cũng như các giải pháp tiềm năng của chúng. Cuối cùng, một nền tảng chẩn đoán phân loại vi khuẩn mới (‘MYcrobiota’) được giới thiệu, đã được các tác giả phát triển bằng cách xem xét những cạm bẫy, thiên kiến, và giải pháp được giải thích trong bài viết này. Việc phát triển MYcrobiota và các phương pháp NGS tương lai sẽ góp phần mở đường cho việc triển khai thành công các phương pháp NGS vào chẩn đoán lâm sàng thường quy.

Từ khóa

#Giải trình tự thế hệ mới #NGS #chẩn đoán lâm sàng #vi sinh vật #thiểu số vi sinh.

Tài liệu tham khảo

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