HIV病毒感染不同阶段的合并感染病原体种类分析

Analysis of co-infected pathogens in HIV infected individuals at different stages

目的通过二代测序对HIV感染者血液标本进行宏基因组学分析,了解HIV感染者的微生物组,并检测在HIV病毒感染不同阶段的共感染病原体多样性的差异。方法将HIV感染者分为近期感染,长期感染,艾滋病发病期3个实验组和健康组(对照组)一同进行宏基因组测序分析,每组包括30个由血液中心和医院收集的血浆标本。在同一组中将10个样品作为1个单元混合后,提取各组的总DNA和总RNA,进行随机引物PCR、建库上机深度测序,利用Korna的方法分析宏基因组数据。并确定其中的微生物组,分析HIV不同感染阶段的合并感染病原体的差异。结果每个标本通过二代测序获得的5 GB数据,生物信息分析发现HIV长期感染患者中病原体的丰度和多样性明显高于其他3组,主要的合并感染病原体是假单胞菌属、伯克霍尔德菌属以及肠杆菌科等。HIV近期感染中具有威胁性的主要病原体包括假单胞菌属、埃希氏菌属,寡养单胞菌属、伯克霍尔德氏菌和依赖病毒属;长期感染阶段主要病原体有假单胞菌属、埃希氏菌属、沙雷氏菌属、伯克霍尔德菌属和依赖病毒属;埃希氏菌属、假单胞菌属、不动杆菌属、寡养单胞菌属及正肝病毒属则是AIDS患者实验组中丰度较高的合并感染病原体。结论在HIV感染的不同阶段,合并感染病原体的丰度和多样性随着感染过程的发展而增加。相较于HIV近期感染和长期感染阶段,艾滋病发病期患者体内合并感染病原体种类较少。本研究调查了不同的HIV感染阶段的合并感染状况,揭示了HIV感染者体内可能存在的病原体,有益于我国的艾滋病防控工作有效开展。

Objective To conduct metagenomics analysis on blood samples of HIV-infected patients through next generation sequencing and understand the microbiome, and then detect differences in co-infectious pathogen diversity in humans at different stages of HIV infection. Methods The HIV-infected patients were divided into recent infection group, long-term infection group, and AIDS group. Three experimental groups along with healthy group(control group), with 30 plasma samples per group collected by blood centers and hospitals, were subjected to metagenomic sequencing analysis. After mixing 10 samples as a unit in the same group, total DNA and total RNA was extracted and amplified with random primers PCR in order to construct library which would be sent to conduct deep sequencing using Illumina. Korna was used to analyze those assembled reads to illustrate the composition of microbiome as well as to detect differences in co-infectious pathogen diversity in humans at different stages of HIV infection.Results For 5 GB data obtained by next generation sequencing on each sample, bioinformatics analysis found that the abundance and diversity of pathogens in HIV long-term infection group were significantly higher than those of the other three groups. The main co-infected pathogens were Pseudomonas, Burkholderia and Enterobacteriaceae, etc. The major threatening pathogens in recent HIV infections include Pseudomonas, Escherichia, Stenotrophomonas, Burkholderia and Dependovirus;The principal pathogens in the long-term infection group were Pseudomonas, Escherichia, Serratia, Burkholderia and Dependovirus;Escherichia, Pseudomonas, Acinetobacter, Stenotrophomonas and Orthohepadnavirus are the chief co-infectious pathogens in AIDS patients. Conclusion At different stages of HIV infection, the abundance and multiplicity of co-infected pathogens increase with the development of the infection process, and co-infection pathogens exist at low diversity in AIDS patients as compared with those at recent and long-term HIV infection stages. Our study investigated the co-infection status at different stages of HIV infection and revealed the possible pathogens in HIV-infected patients, which is helpful contribution to comprehensive HIV control program in China.