全基因组测序提高了对南非克鲁格国家公园南部边境菌株的鉴别能力。
Whole genome sequencing improves the discrimination between strains on the southern border of Kruger National Park, South Africa.
作者信息
Roos Eduard O, Loubser Johannes, Kerr Tanya J, Dippenaar Anzaan, Streicher Elizma, Olea-Popelka Francisco, Robbe-Austerman Suelee, Stuber Tod, Buss Peter, de Klerk-Lorist Lin-Mari, Warren Robin M, van Helden Paul D, Parsons Sven D C, Miller Michele A
机构信息
Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa.
Department of Pathology and Laboratory Medicine, Schulich Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada.
出版信息
One Health. 2023 Nov 12;17:100654. doi: 10.1016/j.onehlt.2023.100654. eCollection 2023 Dec.
BACKGROUND
forms part of the complex and has an extensive host range and zoonotic potential. Various genotyping methods (e.g., spoligotyping) have been used to describe the molecular epidemiology of Advances in whole genome sequencing (WGS) have increased resolution to enable detection of genomic variants to the level of single nucleotide polymorphisms. This is especially relevant to One Health research on tuberculosis which benefits by being able to use WGS to identify epidemiologically linked cases, especially recent transmission. The use of WGS in molecular epidemiology has been extensively used in humans and cattle but is limited in wildlife. This approach appears to overcome the limitations of conventional genotyping methods due to lack of genetic diversity in .
METHODS
This pilot study investigated the spoligotype and WGS of isolates ( = 7) from wildlife in Marloth Park (MP) and compared these with WGS data from other South African isolates. In addition, the greater resolution of WGS was used to explore the phylogenetic relatedness of isolates in neighbouring wildlife populations.
RESULTS
The phylogenetic analyses showed the closest relatives to the seven isolates from MP were isolates from wildlife in Kruger National Park (KNP), which shares a border with MP. However, WGS data indicated that the KNP and MP isolates formed two distinct clades, even though they had similar spoligotypes and identical in silico genetic regions of difference profiles.
CONCLUSIONS
isolates from MP were hypothesized to be directly linked to KNP wildlife, based on spoligotyping. However, WGS indicated more complex epidemiology. The presence of two distinct clades which were genetically distinct (SNP distance of 19-47) and suggested multiple transmission events. Therefore, WGS provided new insight into the molecular epidemiology of the isolates from MP and their relationship to isolates from KNP. This approach will facilitate greater understanding of transmission at wildlife-livestock-human interfaces and advances One Health research on tuberculosis, especially across different host species.
背景
是复合体的一部分，具有广泛的宿主范围和人畜共患病潜力。已使用各种基因分型方法（如间隔寡核苷酸分型）来描述的分子流行病学。全基因组测序（WGS）的进展提高了分辨率，能够检测到单核苷酸多态性水平的基因组变异。这对于结核病的“同一个健康”研究尤为重要，因为能够利用WGS识别具有流行病学关联的病例，尤其是近期传播病例。WGS在分子流行病学中的应用已在人类和牛中广泛使用，但在野生动物中有限。由于缺乏遗传多样性，这种方法似乎克服了传统基因分型方法的局限性。
方法
本试点研究调查了来自马洛思公园（MP）野生动物的分离株（n = 7）的间隔寡核苷酸分型和WGS，并将其与其他南非分离株的WGS数据进行比较。此外，利用WGS更高的分辨率来探索相邻野生动物种群中分离株的系统发育相关性。
结果
系统发育分析表明，与来自MP的7株分离株亲缘关系最近的是来自与MP接壤的克鲁格国家公园（KNP）野生动物的分离株。然而，WGS数据表明，KNP和MP分离株形成了两个不同分支，尽管它们具有相似的间隔寡核苷酸分型和相同的虚拟遗传差异图谱。
结论
基于间隔寡核苷酸分型，推测来自MP的分离株与KNP野生动物直接相关。然而，WGS表明流行病学更为复杂。存在两个遗传上不同的不同分支（单核苷酸多态性距离为19 - 47），提示存在多次传播事件。因此，WGS为来自MP的分离株的分子流行病学及其与来自KNP的分离株的关系提供了新的见解。这种方法将有助于更好地理解野生动物 - 家畜 - 人类界面的传播情况，并推动结核病的“同一个健康”研究，特别是跨不同宿主物种的研究。
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