Du Rao, Feng Yu, Liu Li-Na, Liu Yan-Bin, Ye Hui, Lü Xiao-Ju, Wang Xiao-Hui, Zong Zhi-Yong
Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu 610041, China.
Center for Pathogen Microbiology, West China Hospital, Sichuan University, Chengdu 610041, China.
Sichuan Da Xue Xue Bao Yi Xue Ban. 2020 Mar;51(2):257-260. doi: 10.12182/20200360605.
This study is aimed to explore the value of metagenomic next-generation sequencing (mNGS) in diagnosing pathogen in fever patients. It is often a challenge to identify the pathogen that caused the infection in the HIV patients with fever. How could the mNGS be helpful for pathogen diagnosis is unclear. Here we reported a case of human immunodeficiency virus (HIV) patient with 2-month period of fever. After routine clinical laboratory tests including the conventional smear, culture, serological tests and pathological examinations, the causal pathogen still remained undiagnosed. Then the lymph node biopsy tissue was subjected to broad-range polymerase chain reaction (PCR) and the peripheral blood was subjected to mNGS. At the same time, peripheral blood culture was carried out with an extension of culture time to acquire the pathogen. Results from both broad-range PCR and mNGS revealed the pathogen was . The isolate recovered from the peripheral blood culture was subjected to the whole-genome sequencing. Whole genome sequencing revealed that the antimicrobial resistance gene 1 existed in this pathogen's genome, but mNGS did not detect the 1 gene. Phylogenetic analysis based on whole genome sequence revealed that this isolate was far from other clones published in NCBI database. Here we reported a case of infection diagnosed by mNGS, showing that mNGS is helpful in etiological diagnosis for HIV patients with unexplained fever. However, application of mNGS in antimicrobial resistant genes detection and pathogen tracing need to be well-studied in the future.
本研究旨在探讨宏基因组下一代测序（mNGS）在发热患者病原体诊断中的价值。对于发热的HIV患者，确定引起感染的病原体往往是一项挑战。mNGS如何有助于病原体诊断尚不清楚。在此，我们报告一例发热2个月的人类免疫缺陷病毒（HIV）患者。在进行包括传统涂片、培养、血清学检测和病理检查在内的常规临床实验室检查后，仍未确诊致病病原体。然后对淋巴结活检组织进行广谱聚合酶链反应（PCR），对外周血进行mNGS检测。同时，延长外周血培养时间以获取病原体。广谱PCR和mNGS的结果均显示病原体为 。从外周血培养物中分离出的菌株进行了全基因组测序。全基因组测序显示该病原体基因组中存在抗菌耐药基因1，但mNGS未检测到该基因。基于全基因组序列的系统发育分析表明，该分离株与NCBI数据库中公布的其他克隆株差异较大。在此，我们报告一例通过mNGS诊断的 感染病例，表明mNGS有助于不明原因发热的HIV患者的病因诊断。然而，mNGS在抗菌耐药基因检测和病原体溯源方面的应用在未来仍需深入研究。
