Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome
Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome
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DOI：
10.3389/fmed.2016.00022
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发表时间：
2016-06-13
影响因子：
3.9
通讯作者：
Poss, Mary
中科院分区：
文献类型：
--
作者：
Schiff, Steven J.;Kiwanuka, Julius;Poss, Mary
新生儿败血症（NS）是全球每年超过100万人死亡的原因。在发展中国家，NS通常在没有确定的微生物病原体的情况下进行治疗。细菌16S rRNA基因的扩增子测序可用于鉴定常规微生物学方法难以检测的微生物。然而，污染细菌在医院环境和研究试剂中无处不在，必须考虑到这些数据的有效利用。在这项研究中，我们测序的细菌16S rRNA基因从血液和脑脊液（CSF）的80名新生儿提出NS在乌干达姆巴拉拉地区医院。假设背景污染的模式将独立于病原微生物DNA，我们应用了一种新的定量方法，使用主正交分解从测序数据中的潜在病原体分离背景污染。我们设计了对比血液、CSF和对照标本的定量方法，并采用各种统计随机矩阵自助假设来估计统计学显著性。这些分析表明，钩端螺旋体似乎存在于一些婴儿在出生后48小时内，在子宫内感染，并长达28天的年龄，表明环境暴露。这种微生物不能在常规细菌学环境中培养，并且在经常生活在乌干达西部农村居民附近的牛中流行。我们的研究结果表明，统计方法，以消除背景生物常见的16S序列数据可以揭示推定的病原体在小体积的生物样本从新生儿。因此，这种计算分析揭示了一个重要的医学发现，有可能改变重症人群的治疗和预防工作。
Neonatal sepsis (NS) is responsible for over 1 million yearly deaths worldwide. In the developing world, NS is often treated without an identified microbial pathogen. Amplicon sequencing of the bacterial 16S rRNA gene can be used to identify organisms that are difficult to detect by routine microbiological methods. However, contaminating bacteria are ubiquitous in both hospital settings and research reagents and must be accounted for to make effective use of these data. In this study, we sequenced the bacterial 16S rRNA gene obtained from blood and cerebrospinal fluid (CSF) of 80 neonates presenting with NS to the Mbarara Regional Hospital in Uganda. Assuming that patterns of background contamination would be independent of pathogenic microorganism DNA, we applied a novel quantitative approach using principal orthogonal decomposition to separate background contamination from potential pathogens in sequencing data. We designed our quantitative approach contrasting blood, CSF, and control specimens and employed a variety of statistical random matrix bootstrap hypotheses to estimate statistical significance. These analyses demonstrate that Leptospira appears present in some infants presenting within 48 h of birth, indicative of infection in utero, and up to 28 days of age, suggesting environmental exposure. This organism cannot be cultured in routine bacteriological settings and is enzootic in the cattle that often live in close proximity to the rural peoples of western Uganda. Our findings demonstrate that statistical approaches to remove background organisms common in 16S sequence data can reveal putative pathogens in small volume biological samples from newborns. This computational analysis thus reveals an important medical finding that has the potential to alter therapy and prevention efforts in a critically ill population.