Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains
Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains
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古代结核病研究的并发症：人类考古遗迹中环境细菌的存在
DOI：
10.1016/j.jas.2016.03.002
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发表时间：
2016
影响因子：
2.8
通讯作者：
Müller R
中科院分区：
文献类型：
--
作者：
Müller R
有许多报告表明，来自结核分枝杆菌复合体(MTBC)细菌的古代DNA存在于骨骼中，无论是否有结核的骨学迹象。这些研究的一个可能的复杂情况是，提取液可能还含有正在分析其遗骸的个人微生物组的DNA和/或死后在骨骼上定居的环境细菌的DNA。这些污染物可能包括“结核病以外的分枝杆菌”(Mott)，它们在环境中很常见，但通常与结核病临床病例无关。在这篇文章中，我们证明了各种类型的Mott以及相关属的细菌，即使不是全部，也存在于大多数考古遗迹中。我们的结果强调了考古人类结核病的生物分子研究中固有的复杂性。不能假定任何针对MTBC的聚合酶链式反应的特异性，为了确认扩增是真实的，必须应用允许对PCR产物进行表征的测序策略。然后必须对照Mott和其他物种的序列数据检查参考MTBC序列的任何变异，以确保产物确实来自MTBC。我们的结果也说明了从古代DNA样本组装MTBC基因组序列时面临的挑战，因为将Mott序列错误识别为MTBC将导致组装中的错误。如果Mott DNA含量大于正品MTBC的DNA含量，识别此类错误将特别困难，如果不是不可能的话。许多Mott序列仍然没有特征，因此它们的序列特征未知，这加剧了识别和排除Mott序列的困难。
There are many reports of ancient DNA from bacteria of theMycobacterium tuberculosiscomplex (MTBC) being present in skeletons with and without osteological indications of tuberculosis. A possible complication in these studies is that extracts might also contain DNA from the microbiome of the individual whose remains are being analysed and/or from environmental bacteria that have colonised the skeleton after death. These contaminants might include ‘mycobacteria other than tuberculosis’ (MOTT), which are common in the environment, but which are not normally associated with clinical cases of tuberculosis. In this paper we show that MOTT of various types, as well as bacteria of related genera, are present in most if not all archaeological remains. Our results emphasise the complications inherent in the biomolecular study of archaeological human tuberculosis. The specificity of any polymerase chain reaction directed at the MTBC cannot be assumed and, to confirm that an amplification is authentic, a sequencing strategy must be applied that allows characterisation of the PCR product. Any variations from the reference MTBC sequence must then be checked against sequence data for MOTT and other species to ensure that the product does actually derive from MTBC. Our results also illustrate the challenges faced when assembling MTBC genome sequences from ancient DNA samples, as misidentification of MOTT sequence reads as MTBC would lead to errors in the assembly. Identifying such errors would be particularly difficult, if not impossible, if the MOTT DNA content is greater than that of the authentic MTBC. The difficulty in identifying and excluding MOTT sequences is exacerbated by the fact that many MOTT are still uncharacterized and hence their sequence features are unknown.
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