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Targeted versus Shotgun Metagenomic Sequencing-Based Detection of Microorganisms in Sonicate Fluid for Periprosthetic Joint Infection Diagnosis
Clinical Infectious Diseases ( IF 11.8 ) Pub Date : 2022-08-09 , DOI: 10.1093/cid/ciac646
Hyo-Lim Hong 1, 2 , Laure Flurin 1, 3 , Matthew J Thoendel 4 , Matthew J Wolf 1 , Matthew P Abdel 5 , Kerryl E Greenwood-Quaintance 1 , Robin Patel 1, 4
Affiliation  

Background Next-generation sequencing (NGS) is increasingly used for periprosthetic joint infection (PJI) diagnosis, but its clinical utility is poorly defined. Shotgun metagenomic sequencing (sNGS) has been reported to identify PJI pathogens undetected by culture in sonicate fluid. However, sNGS is complex and costly. Here, 16S ribosomal RNA (rRNA) gene-based targeted metagenomic sequencing (tNGS) was compared to sNGS of sonicate fluid for microbial detection and identification in patients with total hip arthroplasty (THA) and total knee arthroplasty (TKA) failure. Methods A convenience sample of sonicate fluids derived from patients who had undergone THA or TKA removal, enriched with culture negative PJI cases, was tested. Samples had been previously tested by sNGS. For tNGS, samples were extracted, amplified by PCR targeting the V1 to V3 regions of the 16S rRNA gene, and sequenced on an Illumina MiSeq. Results A total of 395 sonicate fluids, including 208 from subjects with PJI, were studied. Compared to sonicate fluid culture, tNGS had higher positive percent agreement (72.1 versus 52.9%, P < 0.001), detecting potential pathogens in 48.0% of culture-negative PJIs. Compared to sNGS, tNGS showed concordant results in 83.6% of culture-positive, and 77.6% of culture-negative PJIs. There was no difference between the positive percent agreement of tNGS (72.1%) and sNGS (73.1%, P = 0.83). Conclusions 16S rRNA gene-based tNGS is a potential diagnostic tool for PJI pathogen identification in sonicate fluid from failed THAs and TKAs in culture-negative cases, with similar performance characteristics to sNGS.

中文翻译:

基于靶向与鸟枪法宏基因组测序的超声液中微生物检测用于假体周围感染诊断

背景 下一代测序(NGS)越来越多地用于假体周围关节感染(PJI)诊断,但其临床效用尚不清楚。据报道,鸟枪法宏基因组测序 (sNGS) 可识别超声液体培养中未检测到的 PJI 病原体。然而,sNGS 复杂且昂贵。在此,将基于 16S 核糖体 RNA (rRNA) 基因的靶向宏基因组测序 (tNGS) 与超声流体的 sNGS 进行比较,以用于全髋关节置换术 (THA) 和全膝关节置换术 (TKA) 失败患者的微生物检测和鉴定。方法 对取自接受过 THA 或 TKA 切除术的患者的超声处理液的方便样本进行测试,其中富含培养物阴性的 PJI 病例。样本之前已经过 sNGS 测试。对于 tNGS,提取样品,通过针对 16S rRNA 基因的 V1 至 V3 区域的 PCR 进行扩增,并在 Illumina MiSeq 上进行测序。结果 总共研究了 395 份超声处理液,其中 208 份来自 PJI 受试者。与超声液体培养相比,tNGS 具有更高的阳性一致性百分比(72.1 比 52.9%,P < 0.001),在 48.0% 的培养阴性 PJI 中检测到潜在病原体。与 sNGS 相比,tNGS 在 83.6% 的培养阳性 PJI 和 77.6% 的培养阴性 PJI 中显示出一致的结果。tNGS (72.1%) 和 sNGS (73.1%, P = 0.83) 的阳性一致性百分比没有差异。结论 基于 16S rRNA 基因的 tNGS 是一种潜在的诊断工具,可用于鉴定培养阴性病例中失败的 THA 和 TKA 超声液中的 PJI 病原体,与 sNGS 具有相似的性能特征。
更新日期:2022-08-09
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