National Center for Biotechnology, Nur Sultan, Kazakhstan.
S. Seifullin Kazakh Agrotechnical University, Nur Sultan, Kazakhstan.
PLoS Negl Trop Dis. 2021 May 17;15(5):e0009419. doi: 10.1371/journal.pntd.0009419. eCollection 2021 May.
Tularemia is a highly dangerous zoonotic infection due to the bacteria Francisella tularensis. Low genetic diversity promoted the use of polymorphic tandem repeats (MLVA) as first-line assay for genetic description. Whole genome sequencing (WGS) is becoming increasingly accessible, opening the perspective of a time when WGS might become the universal genotyping assay. The main goal of this study was to describe F. tularensis strains circulating in Kazakhstan based on WGS data and develop a MLVA assay compatible with in vitro and in silico analysis. In vitro MLVA genotyping and WGS were performed for the vaccine strain and for 38 strains isolated in Kazakhstan from natural water bodies, ticks, rodents, carnivores, and from one migratory bird, an Isabellina wheatear captured in a rodent burrow. The two genotyping approaches were congruent and allowed to attribute all strains to two F. tularensis holarctica lineages, B.4 and B.12. The seven tandem repeats polymorphic in the investigated strain collection could be typed in a single multiplex PCR assay. Identical MLVA genotypes were produced by in vitro and in silico analysis, demonstrating full compatibility between the two approaches. The strains from Kazakhstan were compared to all publicly available WGS data of worldwide origin by whole genome SNP (wgSNP) analysis. Genotypes differing at a single SNP position were collected within a time interval of more than fifty years, from locations separated from each other by more than one thousand kilometers, supporting a role for migratory birds in the worldwide spread of the bacteria.
兔热病是由弗朗西斯菌引起的一种高度危险的人畜共患病感染。由于低遗传多样性，多态串联重复（MLVA）被用作遗传描述的一线检测方法。全基因组测序（WGS）越来越普及，为 WGS 可能成为通用基因分型检测方法的时代开辟了前景。本研究的主要目的是根据 WGS 数据描述哈萨克斯坦流行的弗朗西斯菌菌株，并开发一种与体外和计算机分析兼容的 MLVA 检测方法。对疫苗株和从哈萨克斯坦天然水体、蜱、啮齿动物、食肉动物以及从一只候鸟（在啮齿动物洞穴中捕获的 Isabellina wheatear）中分离的 38 株分离株进行体外 MLVA 基因分型和 WGS。两种基因分型方法一致，可将所有菌株归因于两个弗朗西斯菌全北极株系 B.4 和 B.12。在研究菌株集中可在单个多重 PCR 检测中对七个串联重复进行分型。体外和计算机分析产生了相同的 MLVA 基因型，证明了两种方法之间的完全兼容性。通过全基因组单核苷酸多态性（wgSNP）分析，将哈萨克斯坦的菌株与所有公开的全球来源的 WGS 数据进行比较。在超过五十多年的时间间隔内，从相隔一千多公里的地方收集到仅在一个 SNP 位置存在差异的基因型，支持候鸟在细菌的全球传播中发挥作用。
