摘要
出身背景
宏基因组下一代测序（mNGS）由于能够一次无条件地检测样本中的所有微生物遗传信息，并且不依赖于传统培养，因此得到了广泛的研究。然而，mNGS在临床病原体诊断中的应用仍然具有挑战性。
方法
从2019年12月到2021年3月，在秦皇岛市第一医院连续采集了134份样本，包括支气管肺泡灌洗液（BAFL）、血液、痰、脑脊液（CSF）、胆汁、胸膜液、脓液，将其回顾性诊断分为传染病（128，95.5%）和非传染病（6，4.5%）。将mNGS的病原体检测性能与常规微生物检测（CMT）和培养方法进行比较。此外，还分析了常见耐药鲍曼不动杆菌的抗生素抗性基因（ARGs）及其进化关系。
后果
与CMT和培养方法相比，mNGS在病原体检测方面表现出更高的灵敏度（分别为74.2%和57.8%；P<0.001和66.3%和31.7%；P<0.001）。重要的是，对于仅mNGS阳性的病例，18例（35%）导致诊断改变，7例（23%）证实了临床诊断。在17例在mNGS和培养物中均检测到鲍曼不动杆菌的病例中，ade基因是最常检测到的ARGs（来自13例），其次是sul2和APH（3“）-Ib（均来自12例）。在这些ARG和相关表型之间观察到高度一致性（ade基因为100%，sul2和APH（3“）-Ib为91.6%）。鲍曼不动杆菌菌株被分为三组，大多数菌株都很好地聚集在一起。这表明这些菌株可能是流行菌株。
结论
在我们的研究中，mNGS比CMT和培养方法具有更高的灵敏度。鲍曼不动杆菌ARGs频率和聚类分析结果对抗感染治疗具有重要意义。
Abstract
Background
Metagenomic next-generation sequencing (mNGS) has been widely studied, due to its ability of detecting all the microbial genetic information unbiasedly in a sample at one time and not relying on traditional culture. However, the application of mNGS in the diagnosis of clinical pathogens remains challenging.

Methods
From December 2019 to March 2021, 134 specimens including Broncho alveolar lavage fluid (BAFL), blood, sputum, cerebrospinal fluid (CSF), bile, pleural fluid, pus, were continuously collected in The First Hospital of Qinhuangdao, and their retrospective diagnoses were classified into infectious disease (128, 95.5%) and noninfectious disease (6, 4.5%). The pathogen-detection performance of mNGS was compared with conventional microbiological tests (CMT) and culture method. In addition, the antibiotic resistance genes (ARGs) and evolutionary relationship of common drug-resistant A. baumannii were also analyzed.

Results
Compared with CMT and culture methods, mNGS showed higher sensitivity in pathogen detection (74.2% vs 57.8%; P < 0.001 and 66.3% vs 31.7%; P < 0.001, respectively). Importantly, for cases that mNGS-positive only, 18 (35%) cases result in diagnosis modification, and 7 (23%) cases confirmed the clinical diagnosis. In 17 cases that A. baumannii were both detected in mNGS and culture, ade genes were the most frequently detected ARGs (from 13 cases), followed by sul2 and APH(3”)-Ib (both from 12 cases). High consistency was observed among these ARGs and the related phenotype (100% for ade genes, 91.6% for sul2 and APH(3”)-Ib). A. baumannii strains were classified into three groups, and most were well-clustered. It suggested those strains may be the epidemic strains.

Conclusion
In our study, mNGS had a higher sensitivity than CMT and culture method. And the result of ARGs frequency and cluster analysis of A. baumannii was of great significance to the anti-infective therapy.

https://www.tandfonline.com/doi/full/10.2147/IDR.S370964