Calibrating public genome archives for AMR surveillance: four decades of redundancy-aware phylogenomics of pandemic Escherichia coli ST131

IF 22 1区医学 Q1 PHARMACOLOGY & PHARMACY

Drug Resistance Updates Pub Date : 2026-10-28 DOI:10.1016/j.drup.2026.101497

Rhys T. White, Patrick J. Biggs, Sara A. Burgess, Rose M. Collis, Adrian L. Cookson, Tim Downing, Juliet Elvy, Leo A. Featherstone, Nigel P. French, Isabelle Pattis, Erin P. Price, Derek S. Sarovich, Audrey Tiong, James E. Ussher, David J. Winter, Zuyu Yang, Kristin Dyet

引用次数: 0

Abstract

Escherichia coli sequence type (ST)131 is a globally disseminated multidrug-resistant pathogen, yet public genome collections are skewed by uneven sampling and repeated sequencing of genetically near-identical isolates. Rather than another reconstruction of ST131 evolution, we quantified redundancy, reassessed population structure, and tested how sampling bias affects estimates of phylogenetic diversity, clade-specific dating, and fluoroquinolone-resistance-associated diversification.

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校准AMR监测的公共基因组档案：大流行大肠杆菌ST131的四十年冗余意识系统基因组学

大肠杆菌序列型（ST）131是一种全球传播的多药耐药病原体，但由于采样不均匀和基因几乎相同的分离株的重复测序，公共基因组收集受到了影响。我们不再重建ST131进化，而是量化冗余，重新评估种群结构，并测试抽样偏差如何影响系统发育多样性、枝特异性定年和氟喹诺酮类药物耐药性相关多样性的估计。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Drug Resistance Updates 医学-药学

CiteScore

26.20

自引率

11.90%

发文量

审稿时长

29 days

期刊介绍： Drug Resistance Updates serves as a platform for publishing original research, commentary, and expert reviews on significant advancements in drug resistance related to infectious diseases and cancer. It encompasses diverse disciplines such as molecular biology, biochemistry, cell biology, pharmacology, microbiology, preclinical therapeutics, oncology, and clinical medicine. The journal addresses both basic research and clinical aspects of drug resistance, providing insights into novel drugs and strategies to overcome resistance. Original research articles are welcomed, and review articles are authored by leaders in the field by invitation. Articles are written by leaders in the field, in response to an invitation from the Editors, and are peer-reviewed prior to publication. Articles are clear, readable, and up-to-date, suitable for a multidisciplinary readership and include schematic diagrams and other illustrations conveying the major points of the article. The goal is to highlight recent areas of growth and put them in perspective. *Expert reviews in clinical and basic drug resistance research in oncology and infectious disease *Describes emerging technologies and therapies, particularly those that overcome drug resistance *Emphasises common themes in microbial and cancer research