Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages.
Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages.
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野外细菌进化的量化：弯曲杆菌谱系的一个生日问题。
DOI：
10.1371/journal.pgen.1009829
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发表时间：
2021-09
期刊：
影响因子：
4.5
通讯作者：
Sheppard SK
中科院分区：
文献类型：
--
作者：
Calland JK;Pascoe B;Bayliss SC;Mourkas E;Berthenet E;Thorpe HA;Hitchings MD;Feil EJ;Corander J;Blaser MJ;Falush D;Sheppard SK
测量细菌的分子进化通常需要估计核苷酸变化在不同时间取样的菌株中积累的速率，这些菌株具有共同的祖先。这种方法对于确定与重要谱系（如爆发菌株和专性人类病原体）出现同时发生的生态和进化事件的年代是有用的。然而，在多宿主（生态位）传播情况下，病原体本质上是一种机会性环境生物，采样通常是零星的，很少反映总体，特别是当集中在临床分离株时。这意味着假设最近的共同祖先的方法是不适用的。在这里，我们提出了一种新的方法来估计弯曲杆菌的分子时钟速率，该方法利用了被称为“生日问题”的流行概率难题。使用大型基因组数据集和比较基因组方法，我们使用具有最近共同祖先的分离对来估计人群的核苷酸变化率。通过鉴定基因组重组区域内外的同义和非同义核苷酸变化，我们量化了钟样多样化，以估计常见致病菌大肠弯曲杆菌（2.4 x 10 - 6 s/s/y）和空肠弯曲杆菌（3.4 x 10 - 6 s/s/y）的同义核苷酸变化率。最后，利用估计的核苷酸总变化率，我们推断出样本时间框架内有效谱系的数量——类似于一个共同的生日——并评估我们样本中谱系在短进化时间尺度内的周转率。这为校准环境细菌种群的速率提供了一种通用的方法，并表明维持了多个谱系，这意味着在这些物种中大规模克隆扫描可能需要数百年或更长时间。生物体的生长和繁殖需要DNA复制，但这一过程容易出错。随着水平基因转移带来的变异，它可以导致核苷酸序列的改变。这些核苷酸的变化随着时间的推移，在连续的几代人中以大约恒定的速率积累，称为分子钟。因此，如果这个比率是已知的，人们就可以估计出两个或更多血统分化的日期。在细菌中，这可以为了解致病菌株出现和传播的时间尺度提供信息。当祖先种群已知时，例如对于只感染人类的专性病原体，这种分析是可靠的。然而，当细菌寄生于多个宿主或生态位时，很难从一个菌株推断出另一个菌株的直接祖先，从而降低了分子钟估计的准确性。在这里，我们集中在一个这样的多宿主生物，弯曲杆菌，食源性胃肠炎的主要原因。通过估计精心挑选的分离对的经验核苷酸变化率来重建种群历史，并评估多个谱系随时间的维持，我们提供了有关菌株多样化的信息。我们的方法是细菌基因组学工具包的一个新补充，将有助于了解机会性病原体的传播。
Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the ‘birthday problem’. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10−6 s/s/y) and Campylobacter jejuni (3.4 x 10−6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame–analogous to a shared birthday–and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species. Growth and reproduction in living organisms require DNA replication but this process is error prone. Along with variation introduced by horizontal gene transfer, it can lead to alterations in the nucleotide sequence. These nucleotide changes accumulate over time in successive generations at an approximately constant rate termed the molecular clock. Therefore, if this rate is known, one can estimate the date when two or more lineages diverged. In bacteria, this can be informative for understanding the time-scale of emergence and spread of pathogenic strains. Such analyses are robust when the ancestral population is known, such as for obligate pathogens that only infect humans. However, when the bacterium inhabits multiple hosts or niches it is difficult to infer direct ancestry from one strain to another, reducing the accuracy of molecular clock estimates. Here we focus on one such multi-host organism, Campylobacter, a leading cause of food-borne gastroenteritis. Reconstructing the population history by estimating empirical nucleotide change rates from carefully selected isolate pairs, and evaluating the maintenance of multiple lineages over time, we provide information about strain diversification. Our method is a new addition to the bacterial genomics toolkit that will help in understanding the spread of opportunistic pathogens.
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通才弯曲杆菌菌株中快速的宿主切换侵蚀了追踪人类感染的信号。
DOI：
10.1038/ismej.2015.149
发表时间：
2016-03
期刊：
The ISME journal
影响因子：
--
作者：
Dearlove BL;Cody AJ;Pascoe B;Méric G;Wilson DJ;Sheppard SK
通讯作者：
Sheppard SK
DOI：
10.1098/rspb.2014.0732
发表时间：
2014-07-07
影响因子：
4.7
作者：
Duchene, Sebastian;Holmes, Edward C.;Ho, Simon Y. W.
通讯作者：
Ho, Simon Y. W.
影响因子：
1.4
作者：
Dhillon, AS;Shivaprasad, HL;Bandli, D
通讯作者：
Bandli, D
影响因子：
3.3
作者：
Didelot, Xavier;Falush, Daniel
通讯作者：
Falush, Daniel
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.