基因组分析显示,包括疟疾寄生虫在内的实验室维持的微生物受到广泛污染,结核分枝杆菌和沙门氏菌。这里,我们提供了实验室血吸虫寄生虫种群最近受到污染的直接证据,我们研究了它的基因组后果。巴西曼氏血吸虫种群SmBRE具有几种独特的表型,传染性差,减少孢子囊数量,在中间蜗牛宿主中,低水平的子囊脱落和低毒力,脊椎动物啮齿动物宿主的蠕虫负担低,繁殖力低。2021年,我们观察到SmBRE寄生虫表型的快速变化,子囊的产量增加了10倍,蠕虫负担增加了4倍。
■为了确定这些变化的潜在基因组原因,我们对2015年至2023年期间寄生虫维持期间收集的SmBRE成虫池进行了测序。我们还对与SmBRE一起维持的另一个寄生虫种群(SmLE)进行了测序,没有表型变化。
■虽然SmLE等位基因频率在八年期间保持稳定,我们在2021年7月至2023年2月期间观察到SmBRE基因组中等位基因频率的突然变化,这与实验室污染的预期一致.(i)在2021年9月至10月之间,SmBRE群体中的SmLE特异性等位基因在整个基因组中从0上升到41-46%,记录了污染事件的时间和程度。(二)污染后,强选择(s=〜0.23)促使用高适合度SmLE等位基因替代低适合度SmBRE。(iii)等位基因频率在整个基因组中迅速变化,除了4号染色体上SmBRE等位基因保持高频率的区域。
■在这种情况下,我们能够检测到污染,因为SmBRE显示出独特的表型。然而,表型相似的寄生虫可能会错过这一点.这些结果为追踪寄生虫种群身份的重要性提供了警示,但也展示了一种简单的方法来监测人群内的变化,使用合并人群样本的分子谱分析来表征固定的单核苷酸多态性。我们还表明,即使在没有污染的情况下,遗传漂移也会导致连续变化,导致保存在不同实验室(或在不同时间从同一实验室取样)的寄生虫发散。
UNASSIGNED: Genomic analysis has revealed extensive contamination among laboratory-maintained microbes including malaria parasites, Mycobacterium tuberculosis and Salmonella spp. Here, we provide direct evidence for recent contamination of a laboratory schistosome
parasite population, and we investigate its genomic consequences. The Brazilian Schistosoma mansoni population SmBRE has several distinctive phenotypes, showing poor infectivity, reduced sporocysts number, low levels of cercarial shedding and low virulence in the intermediate snail host, and low worm burden and low fecundity in the vertebrate rodent host. In 2021 we observed a rapid change in SmBRE
parasite phenotypes, with a ~10x increase in cercarial production and ~4x increase in worm burden.
UNASSIGNED: To determine the underlying genomic cause of these changes, we sequenced pools of SmBRE adults collected during
parasite maintenance between 2015 and 2023. We also sequenced another
parasite population (SmLE) maintained alongside SmBRE without phenotypic changes.
UNASSIGNED: While SmLE allele frequencies remained stable over the eight-year period, we observed sudden changes in allele frequency across the genome in SmBRE between July 2021 and February 2023, consistent with expectations of laboratory contamination. (i) SmLE-specific alleles rose in the SmBRE population from 0 to 41-46% across the genome between September and October 2021, documenting the timing and magnitude of the contamination event. (ii) After contamination, strong selection (s = ~0.23) drove replacement of low fitness SmBRE with high fitness SmLE alleles. (iii) Allele frequency changed rapidly across the whole genome, except for a region on chromosome 4 where SmBRE alleles remained at high frequency.
UNASSIGNED: We were able to detect contamination in this case because SmBRE shows distinctive phenotypes. However, this would likely have been missed with phenotypically similar parasites. These results provide a cautionary tale about the importance of tracking the identity of
parasite populations, but also showcase a simple approach to monitor changes within populations using molecular profiling of pooled population samples to characterize fixed single nucleotide polymorphisms. We also show that genetic drift results in continuous change even in the absence of contamination, causing parasites maintained in different labs (or sampled from the same lab at different times) to diverge.