Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.
Appl Environ Microbiol. 2021 Feb 26;87(6). doi: 10.1128/AEM.02275-20.
(syn. , ) is the causative agent of giardiasis, one of the most common diarrheal infections in humans. Evolutionary relationships among genotypes (or subtypes) of assemblage B, one of two genetic assemblages causing the majority of human infections, remain unclear due to poor phylogenetic resolution of current typing methods. In this study, we devised a methodology to identify new markers for a streamlined multilocus sequence typing (MLST) scheme based on comparisons of all core genes against the phylogeny of whole-genome sequences (WGS). Our analysis identified three markers with resolution comparable to that of WGS data. Using newly designed PCR primers for our novel MLST loci, we typed an additional 68 strains of assemblage B. Analyses of these strains and previously determined genome sequences showed that genomes of this assemblage can be assigned to 16 clonal complexes, each with unique gene content that is apparently tuned to differential virulence and ecology. Obtaining new genomes of spp. and other eukaryotic microbial pathogens remains challenging due to difficulties in culturing the parasites in the laboratory. Hence, the methods described here are expected to be widely applicable to other pathogens of interest and advance our understanding of their ecology and evolution. assemblage B is a major waterborne pathogen and the most commonly identified genotype causing human giardiasis worldwide. The lack of morphological characters for classification requires the use of molecular techniques for strain differentiation; however, the absence of scalable and affordable next-generation sequencing (NGS)-based typing methods has prevented meaningful advancements in high-resolution molecular typing for further understanding of the evolution and epidemiology of assemblage B. Prior studies have reported high sequence diversity but low phylogenetic resolution at standard loci in assemblage B, highlighting the necessity of identifying new markers for accurate and robust molecular typing. Data from comparative analyses of available genomes in this study identified three loci that together form a novel high-resolution typing scheme with high concordance to whole-genome-based phylogenomics and which should aid in future public health endeavors related to this parasite. In addition, data from newly characterized strains suggest evidence of biogeographic and ecologic endemism.
（同义词： ）是贾第虫病的病原体，是人类最常见的腹泻感染之一。由于当前分型方法的系统发育分辨率较差，因此两个引起大多数人类感染的遗传组合体之一的组合体 B 的 基因型（或亚型）之间的进化关系仍不清楚。在这项研究中，我们设计了一种方法，通过比较整个基因组序列（WGS）的系统发育和所有核心基因，为简化的多位点序列分型（MLST）方案确定新的标记。我们的分析确定了三个标记，其分辨率与 WGS 数据相当。使用针对我们新的 MLST 基因座设计的新 PCR 引物，我们对另外 68 株组合体 B 进行了分型。对这些菌株和先前确定的基因组序列的分析表明，该组合体的基因组可以分配到 16 个克隆复合物中，每个复合物都具有独特的基因组成，显然与差异毒力和生态有关。由于在实验室中培养寄生虫存在困难，因此获得新的 属和其他真核微生物病原体的基因组仍然具有挑战性。因此，这里描述的方法有望广泛应用于其他感兴趣的病原体，并增进我们对其生态和进化的理解。组合体 B 是一种主要的水传播病原体，也是全球最常见的鉴定基因型，可引起人类贾第虫病。由于缺乏分类的形态学特征，因此需要使用分子技术进行菌株分化；但是，缺乏可扩展且负担得起的基于下一代测序（NGS）的分型方法，阻碍了在组合体 B 的高分辨率分子分型方面取得有意义的进展，无法进一步了解其进化和流行病学。先前的研究报告称，组合体 B 中的标准基因座具有高序列多样性但低系统发育分辨率，这突出表明需要鉴定新的标记，以进行准确而稳健的分子分型。本研究中对现有基因组进行比较分析的数据确定了三个基因座，它们共同形成了一种新的高分辨率分型方案，与基于全基因组的系统发生学具有高度一致性，并且应该有助于未来与这种寄生虫有关的公共卫生工作。此外，新表征的菌株数据表明存在生物地理和生态特有现象的证据。
