Decuypere Saskia, Meehan Conor J, Van Puyvelde Sandra, De Block Tessa, Maltha Jessica, Palpouguini Lompo, Tahita Marc, Tinto Halidou, Jacobs Jan, Deborggraeve Stijn
Telethon Kids Institute, University of Western Australia, Perth, Australia.
Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.
PLoS Negl Trop Dis. 2016 Feb 29;10(2):e0004470. doi: 10.1371/journal.pntd.0004470. eCollection 2016 Feb.
Bacterial bloodstream infection (bBSI) is one of the leading causes of death in critically ill patients and accurate diagnosis is therefore crucial. We here report a 16S metagenomics approach for diagnosing and understanding bBSI.
METHODOLOGY/PRINCIPAL FINDINGS: The proof-of-concept was delivered in 75 children (median age 15 months) with severe febrile illness in Burkina Faso. Standard blood culture and malaria testing were conducted at the time of hospital admission. 16S metagenomics testing was done retrospectively and in duplicate on the blood of all patients. Total DNA was extracted from the blood and the V3-V4 regions of the bacterial 16S rRNA genes were amplified by PCR and deep sequenced on an Illumina MiSeq sequencer. Paired reads were curated, taxonomically labeled, and filtered. Blood culture diagnosed bBSI in 12 patients, but this number increased to 22 patients when combining blood culture and 16S metagenomics results. In addition to superior sensitivity compared to standard blood culture, 16S metagenomics revealed important novel insights into the nature of bBSI. Patients with acute malaria or recovering from malaria had a 7-fold higher risk of presenting polymicrobial bloodstream infections compared to patients with no recent malaria diagnosis (p-value = 0.046). Malaria is known to affect epithelial gut function and may thus facilitate bacterial translocation from the intestinal lumen to the blood. Importantly, patients with such polymicrobial blood infections showed a 9-fold higher risk factor for not surviving their febrile illness (p-value = 0.030).
CONCLUSIONS/SIGNIFICANCE: Our data demonstrate that 16S metagenomics is a powerful approach for the diagnosis and understanding of bBSI. This proof-of-concept study also showed that appropriate control samples are crucial to detect background signals due to environmental contamination.
细菌血流感染（bBSI）是重症患者死亡的主要原因之一，因此准确诊断至关重要。我们在此报告一种用于诊断和了解bBSI的16S宏基因组学方法。
方法/主要发现：在布基纳法索的75名患有严重发热性疾病的儿童（中位年龄15个月）中进行了概念验证。入院时进行了标准血培养和疟疾检测。对所有患者的血液进行回顾性16S宏基因组学检测，一式两份。从血液中提取总DNA，通过PCR扩增细菌16S rRNA基因的V3-V4区域，并在Illumina MiSeq测序仪上进行深度测序。对配对读数进行整理、分类标记和过滤。血培养诊断出12例bBSI患者，但将血培养和16S宏基因组学结果相结合时，这一数字增加到22例。与标准血培养相比，16S宏基因组学不仅具有更高的灵敏度，还揭示了关于bBSI性质的重要新见解。与近期未诊断出疟疾的患者相比，急性疟疾患者或正在从疟疾中康复的患者发生多微生物血流感染的风险高7倍（p值 = 0.046）。已知疟疾会影响肠道上皮功能，因此可能促进细菌从肠腔转移到血液中。重要的是，患有这种多微生物血液感染的患者因发热性疾病而死亡的风险因素高9倍（p值 = 0.030）。
结论/意义：我们的数据表明，16S宏基因组学是诊断和了解bBSI的有力方法。这项概念验证研究还表明，适当的对照样本对于检测环境污染引起的背景信号至关重要。
