Jutzeler Kathrin S, Platt Roy N, Li Xue, Morales Madison, Diaz Robbie, LE Clec'h Winka, Chevalier Frédéric D, Anderson Timothy J C
Texas Biomedical Research Institute.
Res Sq. 2024 Sep 16:rs.3.rs-4869982. doi: 10.21203/rs.3.rs-4869982/v1.
Genomic analysis has revealed extensive contamination among laboratory-maintained microbes including malaria parasites, and spp. Here, we provide direct evidence for recent contamination of a laboratory schistosome parasite population, and we investigate its genomic consequences. The Brazilian 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.
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.
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 (=~ 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.
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.
基因组分析揭示了实验室保存的微生物（包括疟原虫和其他物种）中存在广泛的污染。在此，我们提供了实验室血吸虫寄生虫种群近期受到污染的直接证据，并研究了其基因组后果。巴西血吸虫种群SmBRE具有几种独特的表型，表现为感染力差、子孢子数量减少、尾蚴逸出水平低以及在中间螺宿主中毒力低，在脊椎动物啮齿动物宿主中虫负荷低且繁殖力低。2021年，我们观察到SmBRE寄生虫表型发生了快速变化，尾蚴产量增加了约10倍，虫负荷增加了约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年寄生虫保存期间收集的SmBRE成虫样本进行了测序。我们还对与SmBRE一起保存且无表型变化的另一个寄生虫种群（SmLE）进行了测序。
虽然SmLE等位基因频率在八年期间保持稳定，但我们观察到2021年7月至2023年2月期间SmBRE基因组中的等位基因频率突然变化，这与实验室污染的预期一致。（i）2021年9月至10月期间，SmBRE种群中SmLE特异性等位基因在全基因组中的比例从0上升到41 - 46%，记录了污染事件的时间和程度。（ii）污染后，强烈的选择（约为0.23）促使适应性低的SmBRE被适应性高的SmLE等位基因取代。（iii）除了4号染色体上的一个区域SmBRE等位基因仍保持高频外，全基因组的等位基因频率迅速变化。
我们能够在这种情况下检测到污染是因为SmBRE表现出独特的表型。然而，如果是表型相似的寄生虫，这种污染可能很容易被忽略。这些结果警示了追踪寄生虫种群身份的重要性，但也展示了一种简单的方法，即通过对混合种群样本进行分子分析以表征固定的单核苷酸多态性来监测种群内的变化。我们还表明，即使在没有污染的情况下，遗传漂变也会导致持续变化，使保存在不同实验室（或在不同时间从同一实验室采样）的寄生虫产生差异。
