Neisseria meningitidis is a leading cause of bacterial meningitis and sepsis worldwide and an occasional cause of meningococcal urethritis. When isolates are unavailable for surveillance or outbreak investigations, molecular characterization of pathogens needs to be performed directly from clinical specimens, such as cerebrospinal fluid (CSF), blood, or urine. However, genome sequencing of specimens is challenging because of low bacterial and high human DNA abundances. We developed selective whole-genome amplification (SWGA), an isothermal multiple-displacement amplification-based method, to efficiently enrich, sequence, and de novo assemble N. meningitidis DNA from clinical specimens with low bacterial loads. SWGA was validated with 12 CSF specimens from invasive meningococcal disease cases and 12 urine specimens from meningococcal urethritis cases. SWGA increased the mean proportion of N. meningitidis reads by 2 to 3 orders of magnitude, enabling identification of at least 90% of the 1,605 N. meningitidis core genome loci for 50% of the specimens. The validated method was used to investigate two meningitis outbreaks recently reported in Togo and Burkina Faso. Twenty-seven specimens with low bacterial loads were processed by SWGA before sequencing, and 12 of 27 were successfully assembled to obtain the full molecular typing and vaccine antigen profile of the N. meningitidis pathogen, thus enabling thorough characterization of outbreaks. This method is particularly important for enhancing molecular surveillance in regions with low culture rates. SWGA produces enough reads for phylogenetic and allelic analysis at a low cost. More importantly, the procedure can be extended to enrich other important human bacterial pathogens.

中文翻译：

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直接从临床标本中对脑膜炎奈瑟菌进行全面分子分型，用于疫情调查。

脑膜炎奈瑟菌是全世界细菌性脑膜炎和败血症的主要原因，也是脑膜炎球菌性尿道炎的偶然原因。当分离株无法用于监测或疫情调查时，需要直接从临床样本（例如脑脊液 (CSF)、血液或尿液）中进行病原体的分子表征。然而，由于细菌 DNA 丰度低而人类 DNA 丰度高，样本基因组测序具有挑战性。我们开发了选择性全基因组扩增 (SWGA)，这是一种基于等温多重置换扩增的方法，可从低细菌负荷的临床标本中高效富集、测序和从头组装脑膜炎奈瑟氏菌DNA。SWGA 通过 12 份侵袭性脑膜炎球菌病病例的脑脊液样本和 12 份脑膜炎球菌性尿道炎病例的尿液样本进行了验证。SWGA 将脑膜炎奈瑟氏菌读数的平均比例提高了2 至 3 个数量级，从而能够识别 50% 样本的 1,605 个脑膜炎奈瑟氏菌核心基因组位点中的至少 90%。经过验证的方法用于调查最近在多哥和布基纳法索报告的两起脑膜炎疫情。27 个低细菌载量样本在测序前经过 SWGA 处理，27 个样本中的 12 个成功组装，以获得脑膜炎奈瑟氏球菌病原体的完整分子分型和疫苗抗原谱，从而能够全面表征疫情。该方法对于加强培养率低的地区的分子监测特别重要。SWGA 以低成本生成足够的读数用于系统发育和等位基因分析。更重要的是，该程序可以扩展以富集其他重要的人类细菌病原体。