Một khung giám sát và công cụ định danh di truyền cho Klebsiella pneumoniae và các loài liên quan trong phức hợp

Nature Communications - Tập 12 Số 1
Margaret M. C. Lam1, Ryan R. Wick1, Stephen C. Watts2, Louise Cerdeira1, Kelly L. Wyres1, Kathryn E. Holt3
1Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
2Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
3London School of Hygiene & Tropical Medicine, London, UK

Tóm tắt

Tóm tắt

Klebsiella pneumoniae là nguyên nhân hàng đầu gây ra các nhiễm khuẩn kháng kháng sinh (AMR) liên quan đến chăm sóc sức khỏe, nhiễm trùng huyết ở trẻ sơ sinh và áp xe gan mắc phải trong cộng đồng, cũng như có liên quan đến các bệnh đường ruột mãn tính. Sự đa dạng và cấu trúc quần thể phức tạp của nó gây ra thách thức trong việc phân tích và diễn giải dữ liệu bộ gen K. pneumoniae. Trong nghiên cứu này, chúng tôi giới thiệu Kleborate, một công cụ nhằm phân tích bộ gen của K. pneumoniae và phức hợp các loài liên quan của nó, tập trung vào việc thẩm định các đặc điểm quan trọng có ý nghĩa lâm sàng chứng minh. Kleborate cung cấp một khung nền tảng hỗ trợ giám sát bộ gen và dịch tễ học trong các nghiên cứu, y tế lâm sàng và chăm sóc sức khoẻ cộng đồng. Để chứng minh tính hữu dụng của nó, chúng tôi áp dụng Kleborate để phân tích các bộ gen Klebsiella công khai, bao gồm các chủng phân lập lâm sàng từ một nghiên cứu toàn châu Âu về Klebsiella tạo carbapenemase, làm nổi bật các xu hướng toàn cầu trong AMR và độc lực như những ví dụ về những gì có thể đạt được khi áp dụng khung bộ gen này vào các nỗ lực giám sát hệ thống bộ gen có phương pháp hơn. Chúng tôi cũng chứng minh việc ứng dụng Kleborate để phát hiện và định danh K. pneumoniae từ những bộ gen metagenome của ruột.

Từ khóa

#Klebsiella pneumoniae #kháng kháng sinh #Kleborate #giám sát bộ gen #dịch tễ học #lây nhiễm đường ruột #bệnh mãn tính #cấu trúc quần thể #dữ liệu bộ gen #khung giám sát #dịch tễ y tế

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