The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild‐type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.

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从细菌基因组预测抗菌药物敏感性：一种健康耐药性监测的新范式

抗菌药物耐药性的实验室鉴定是传染病医学的基石。体外抗微生物药敏试验长期以来一直基于纯培养中生物体对特定浓度抗微生物剂的生长反应。通过将单个分离株与野生型易感性模式进行比较，可以识别具有获得性耐药性的菌株。获得性耐药也可以通过基因检测。经过数十年的研究，众所周知，抗菌素耐药性相关基因的清单包括几种致病菌属，包括沙门氏菌和弯曲杆菌等人畜共患肠道生物并继续为其他人大幅增长。随着大规模 DNA 测序成本的下降，现在可以使用全基因组测序来表征细菌，包括携带单个微生物和复杂生物样本中存在的抗性基因。通过基因组学，我们可以生成关于细菌、抗生素耐药性机制、其来源的线索以及耐药性传播的可移动 DNA 元件的性质的全面、详细的信息。这些发展为临床和公共卫生目的的抗菌素耐药性检测和跟踪指明了新的范式。