High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection
High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection
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DOI：
10.1038/s41598-020-60992-6
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发表时间：
2020-03-03
影响因子：
4.6
通讯作者：
Shi, Mang
中科院分区：
文献类型：
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作者：
Li, Ci-Xiu;Li, Wei;Shi, Mang
与急性呼吸道感染(ARI)相关的病原体的多样性使诊断具有挑战性。传统的病原体筛查试验检测范围有限，提供的额外信息很少。我们使用总RNA测序(“元转录组学”)来揭示与儿科ARI相关的微生物的全谱。采集48例ARI患儿和7例健康儿童的咽拭子。对样本进行元转录组学分析，以确定病毒、细菌和真核病原体的存在和丰度，并揭示混合感染、病原体基因/亚型、进化起源、流行病史和抗菌素耐药性。我们鉴定出11种RNA病毒、4种DNA病毒、4种细菌和1种真菌。虽然大多数已知会导致ARI，但其他病毒，如Echo病毒6，很少与呼吸道疾病有关。病毒和细菌的混合感染和多种病毒的混合感染很常见(9/48)，一名患者携带5种不同的病原体，基因组序列数据显示出很大的种内多样性。对8种抗生素均表现出抗性，其中MLS、Bla、Tet、Phe的耐药率较高。综上所述，我们使用了一种简单的总RNA测序方法来揭示ARI中复杂的多菌感染体。这为了解呼吸系统疾病提供了全面的临床信息。
The diversity of pathogens associated with acute respiratory infection (ARI) makes diagnosis challenging. Traditional pathogen screening tests have a limited detection range and provide little additional information. We used total RNA sequencing ("meta-transcriptomics") to reveal the full spectrum of microbes associated with paediatric ARI. Throat swabs were collected from 48 paediatric ARI patients and 7 healthy controls. Samples were subjected to meta-transcriptomics to determine the presence and abundance of viral, bacterial, and eukaryotic pathogens, and to reveal mixed infections, pathogen genotypes/subtypes, evolutionary origins, epidemiological history, and antimicrobial resistance. We identified 11 RNA viruses, 4 DNA viruses, 4 species of bacteria, and 1 fungus. While most are known to cause ARIs, others, such as echovirus 6, are rarely associated with respiratory disease. Co-infection of viruses and bacteria and of multiple viruses were commonplace (9/48), with one patient harboring 5 different pathogens, and genome sequence data revealed large intra-species diversity. Expressed resistance against eight classes of antibiotic was detected, with those for MLS, Bla, Tet, Phe at relatively high abundance. In summary, we used a simple total RNA sequencing approach to reveal the complex polymicrobial infectome in ARI. This provided comprehensive and clinically informative information relevant to understanding respiratory disease.