OBJECTIVES Pathogen identification is crucial for the diagnosis and management of periprosthetic joint infection (PJI). Although culturing methods are the foundation of pathogen detection in PJI, false negative results often occur. Oxford nanopore sequencing (ONS) is a promising alternative to detect pathogens and provide information on their antimicrobial resistance (AMR) profiles without culturing. METHODS To evaluate the capability of metagenomic ONS (mONS) in detecting pathogens from PJI samples, both metagenomic next-generation sequencing (mNGS) and mONS were performed in 15 osteoarticular samples from 9 consecutive PJI patients according to the modified Musculoskeletal Infection Society (MSIS) criteria. The sequencing data generated from both platforms were then analysed for pathogen identification and AMR detection using an in-house-developed bioinformatics pipeline. RESULTS Our results showed that mONS could be applied for detecting the causative pathogen and characterizing its AMR features in fresh PJI samples. By real-time sequencing and analysis, pathogen identification and AMR detection from the initiation of sequencing were accelerated. CONCLUSION We showed proof of concept that mONS can function as a rapid, accurate tool in PJI diagnostic microbiology. Despite efforts to reduce host DNA, the high proportion of host DNA was still a limitation of this method that prevented full genome analysis.

中文翻译：

---

基于纳米孔的宏基因组测序在假体关节感染诊断中的初步评估

目的 病原体鉴定对于假体周围关节感染 (PJI) 的诊断和管理至关重要。虽然培养方法是 PJI 病原体检测的基础，但经常出现假阴性结果。牛津纳米孔测序 (ONS) 是检测病原体并提供有关其抗菌素耐药性 (AMR) 概况的信息而无需培养的有前途的替代方案。方法 为了评估宏基因组 ONS (mONS) 从 PJI 样本中检测病原体的能力，根据改良的肌肉骨骼感染协会 (MSIS)，对来自 9 名连续 PJI 患者的 15 个骨关节样本进行了宏基因组下一代测序 (mNGS) 和 mONS标准。然后使用内部开发的生物信息学管道分析从两个平台生成的测序数据以进行病原体鉴定和 AMR 检测。结果 我们的结果表明，mONS 可用于检测病原体并表征其在新鲜 PJI 样品中的 AMR 特征。通过实时测序和分析，加快了从测序开始的病原体鉴定和AMR检测。结论 我们证明了 mONS 可以作为 PJI 诊断微生物学中快速、准确的工具的概念证明。尽管努力减少宿主 DNA，但宿主 DNA 的高比例仍然是这种方法的一个限制，它阻止了全基因组分析。结果 我们的结果表明，mONS 可用于检测病原体并表征其在新鲜 PJI 样品中的 AMR 特征。通过实时测序和分析，加快了从测序开始的病原体鉴定和AMR检测。结论 我们证明了 mONS 可以作为 PJI 诊断微生物学中快速、准确的工具的概念证明。尽管努力减少宿主 DNA，但宿主 DNA 的高比例仍然是这种方法的一个限制，它阻止了全基因组分析。结果 我们的结果表明，mONS 可用于检测病原体并表征其在新鲜 PJI 样品中的 AMR 特征。通过实时测序和分析，加快了从测序开始的病原体鉴定和AMR检测。结论 我们证明了 mONS 可以作为 PJI 诊断微生物学中快速、准确的工具的概念证明。尽管努力减少宿主 DNA，但宿主 DNA 的高比例仍然是这种方法的一个限制，它阻止了全基因组分析。