Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland.
Division of Pulmonology, University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland.
Eur J Clin Microbiol Infect Dis. 2019 Oct;38(10):1873-1881. doi: 10.1007/s10096-019-03621-z. Epub 2019 Jul 16.
The diagnosis of mycobacterial infections has been dramatically improved by the introduction of molecular methods aimed to reduce the time to diagnosis as compared with culture. The broad range pan-mycobacterial PCR can detect all the mycobacterial species directly from clinical specimens. We aimed to evaluate its usefulness and its clinical added value for the diagnosis of nontuberculous mycobacterial (NTM) infections. We performed a retrospective study (2003-2013) including 952 samples taken from 639 patients with clinical suspicion of NTM infection. The performance of smear microscopy, PCR and culture was established using clinical data to investigate discrepant results. We also compared the time to microbial diagnosis between the direct PCR and culture. The sensitivity, specificity, positive and negative predictive values of the PCR were 61.6% (53.5-69.1), 99.1% (98.2-99.6), 92.8% (85.8-96.5) and 93.4% (91.6-94.9), respectively, when considering all specimens. When considering smear-positive specimens and smear-negative specimens, the sensitivity was 81.6% and 40%, respectively. The sensitivity for pulmonary and extra-pulmonary smear-positive specimens was 85.2% versus 72.7%. The median time to identification at species level was 35 days (SD, 17.67) for culture and 6 days (SD, 2.67) for the PCR (when positive), which represents a 29-day shorter time to results (p < 0.0001). The 16S rRNA gene pan-mycobacterial PCR displays a substantial benefit in terms of time to diagnose NTM infections when compared with culture. Despite an excellent specificity, its sensitivity is yet limited in particular for smear-negative specimens, which might be improved by relying onto real-time PCRs.
分枝杆菌感染的诊断因引入分子方法而得到显著改善，与培养相比，这些方法可以缩短诊断时间。广泛的分枝杆菌 pan-PCR 可以直接从临床标本中检测到所有分枝杆菌物种。我们旨在评估其对非结核分枝杆菌（NTM）感染的诊断的有用性及其临床附加值。我们进行了一项回顾性研究（2003-2013 年），包括 639 例临床疑似 NTM 感染患者的 952 份样本。使用临床数据建立了涂片镜检、PCR 和培养的性能，以研究不一致的结果。我们还比较了直接 PCR 和培养之间微生物诊断的时间。考虑所有标本时，PCR 的灵敏度、特异性、阳性预测值和阴性预测值分别为 61.6%（53.5-69.1）、99.1%（98.2-99.6）、92.8%（85.8-96.5）和 93.4%（91.6-94.9）。考虑到涂片阳性标本和涂片阴性标本时，灵敏度分别为 81.6%和 40%。肺和肺外涂片阳性标本的灵敏度分别为 85.2%和 72.7%。培养鉴定种水平的中位时间为 35 天（标准差，17.67），PCR（阳性时）为 6 天（标准差，2.67），结果时间缩短了 29 天（p<0.0001）。与培养相比，16S rRNA 基因 pan-PCR 在诊断 NTM 感染方面具有显著的优势，可缩短诊断时间。尽管特异性很好，但它的灵敏度在特定情况下（例如涂片阴性标本）仍然有限，这可以通过依赖实时 PCR 来提高。
