Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.

中文翻译：

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逃离西西弗斯的命运：评估抗微生物抗性基因捕获的抗性杂交诱饵

寻找、表征和监测抗菌素耐药性 (AMR) 的宿主对于保护公众健康至关重要。杂交捕获诱饵是一种准确、灵敏且具有成本效益的技术，用于丰富和表征复杂环境样本中的目标 DNA 序列，包括抗菌素耐药基因 (ARG)。我们展示了从综合抗生素耐药性数据库 (CARD)v1.1.2 和致病性岛数据库 (PAIDB)v2.0 设计的一组 19933 个杂交捕获诱饵的持续效用，针对 3565 个赋予耐药性的独特核苷酸序列。我们在定制的抗性模拟社区和复杂的环境样本上展示了我们的诱饵集的效率，以将目标读取的比例提高 200 倍以上。然而，在研究 AMR 时，与新发现的 ARG 保持同步是一项挑战，因为新的 ARG 会不断被识别，并且不会包含在发现之前设计的诱饵组中。我们提供了关于我们的诱饵集如何针对 CARDv3.3.1 执行的必要信息，以及确定何时以及如何更新杂交捕获诱饵集的通用方法。这项研究概括了诱饵的整个生命周期，用于杂交捕获从设计和验证的抗性组（两者 以及决定何时以及如何更新杂交捕获诱饵集的通用方法。这项研究概括了诱饵的整个生命周期，用于杂交捕获从设计和验证的抗性组（两者 以及决定何时以及如何更新杂交捕获诱饵集的通用方法。这项研究概括了诱饵的整个生命周期，用于杂交捕获从设计和验证的抗性组（两者在计算机和体外）到利用和预测更新和退休。