Francis I. Proctor Foundation, University of California San Francisco, CA.
Casey Eye Institute, Oregon Health & Science University, OR; and.
Cornea. 2022 Jan 1;41(1):39-44. doi: 10.1097/ICO.0000000000002766.
The purpose of this article was to evaluate the impact of sample collection order on the diagnostic yield of metagenomic deep sequencing (MDS) for determining the causative pathogen in infectious keratitis.
We performed a cross-sectional diagnostic test evaluation among subjects with infectious keratitis at Aravind Eye Hospital in Madurai, India. All subjects underwent corneal scrapings of the affected eye to obtain potassium hydroxide smear, Gram stain, bacterial culture, and fungal culture, in this order. The order of MDS specimen collection relative to smear and culture samples was randomized and served as the primary predictor. Outcomes included the normalized copy number of pathogenic RNA detected by MDS, the proportion of MDS samples that were diagnostic, and the agreement of MDS results with cultures.
MDS samples from 46 subjects with corneal ulcers were evaluated. MDS was positive in 33 subjects (76%) and had 74% overall agreement with culture results. There was no association between order of MDS sample collection and normalized copy number of genetic material detected (P = 0.62) or the likelihood of MDS positivity (P = 0.46). However, the likelihood of agreement between MDS and cultures decreased when MDS corneal swabs were collected after other diagnostic corneal scrapings (P = 0.05).
The overall yield of MDS for detecting the cause of infectious keratitis was not affected by sample collection order. However, diagnostic agreement between MDS and cultures decreased when MDS samples were collected after other specimens. Additional investigation is warranted to determine whether this represents increased sensitivity of MDS compared with cultures or higher susceptibility to contaminants.
本文旨在评估样本采集顺序对宏基因组深度测序（MDS）确定感染性角膜炎病原体的诊断效果的影响。
我们在印度马杜赖的 Aravind 眼科医院进行了一项横断面诊断测试评估，纳入了感染性角膜炎患者。所有患者均接受了受影响眼睛的角膜刮片，以获得氢氧化钾涂片、革兰氏染色、细菌培养和真菌培养，顺序如下。MDS 标本采集相对于涂片和培养样本的顺序是随机的，作为主要预测因子。结果包括通过 MDS 检测到的致病性 RNA 的标准化拷贝数、MDS 样本的诊断比例以及 MDS 结果与培养结果的一致性。
评估了 46 例角膜溃疡患者的 MDS 样本。33 例（76%）MDS 阳性，与培养结果总体一致率为 74%。MDS 样本采集顺序与检测到的遗传物质的标准化拷贝数之间（P=0.62）或 MDS 阳性的可能性（P=0.46）均无关联。然而，当 MDS 角膜拭子在其他诊断性角膜刮片后采集时，MDS 与培养之间的一致性可能性降低（P=0.05）。
MDS 检测感染性角膜炎病因的总体效果不受样本采集顺序的影响。然而，当 MDS 样本在其他样本后采集时，MDS 与培养之间的诊断一致性降低。需要进一步研究以确定这是否代表 MDS 与培养相比具有更高的敏感性，还是更容易受到污染物的影响。
