A recalibrated molecular clock and independent origins for the cholera pandemic clones.
A recalibrated molecular clock and independent origins for the cholera pandemic clones.
复制标题
DOI：
10.1371/journal.pone.0004053
复制
发表时间：
2008
期刊：
影响因子：
3.7
通讯作者：
Wang L
中科院分区：
文献类型：
--
作者：
Feng L;Reeves PR;Lan R;Ren Y;Gao C;Zhou Z;Ren Y;Cheng J;Wang W;Wang J;Qian W;Li D;Wang L
由霍乱弧菌引起的霍乱在南亚全球爆发了7次大流行，但在第6次（1899-1923）和第7次（1961年至今）大流行之间也有局部暴发。上述所有菌株均为血清型O 1，而环境或无脊椎动物分离株的抗原性不同。上述第7次大流行前的分离株和其他次要致病性克隆与第7次大流行克隆相关，而第6次大流行克隆在同一谱系中但关系更远，非致病性分离株未显示克隆结构。为了了解大流行克隆的起源和关系，我们对1937年大流行前菌株和第6次大流行分离株的基因组进行了测序，并将其与已发表的第7次大流行基因组进行了比较。我们区分了突变和重组事件，并将这些事件和其他事件分配到进化树中的特定分支。突变事件比重组事件多，但更多的基因和44倍多的碱基对被重组改变。我们使用突变的单核苷酸多态性和已知的分离日期的大流行前和第7次大流行的分离株，以估计突变率，并发现它是100倍高于通常假设。然后，我们用它来估计第6次和第7次大流行克隆的分歧日期约为1880年。虽然存在很大的误差，但这比使用通常假设估计的10，000 - 50，000年前更加现实。我们的结论是，这2个大流行克隆独立地获得了大流行潜力，总共有29个插入或缺失一个或多个基因。主要整合子也发生了实质性变化，这归因于单个盒的获得（包括从内部复制）或盒块的丢失。所使用的方法为分析其他重要病原体的起源和历史开辟了新的途径。
Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6th (1899–1923) and 7th (1961–present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to the 7th pandemic clone, while the 6th pandemic clone is in the same lineage but more distantly related, and non-pathogenic isolates show no clonal structure. To understand the origins and relationships of the pandemic clones, we sequenced the genomes of a 1937 prepandemic strain and a 6th pandemic isolate, and compared them with the published 7th pandemic genome. We distinguished mutational and recombinational events, and allocated these and other events, to specific branches in the evolutionary tree. There were more mutational than recombinational events, but more genes, and 44 times more base pairs, changed by recombination. We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7th pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed. We then used this to estimate the divergence date of the 6th and 7th pandemic clones to be about 1880. While there is a large margin of error, this is far more realistic than the 10,000–50,000 years ago estimated using the usual assumptions. We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes. There were also substantial changes in the major integron, attributed to gain of individual cassettes including copying from within, or loss of blocks of cassettes. The approaches used open up new avenues for analysing the origin and history of other important pathogens.
登录
查看更多内容
影响因子：
11.4
作者：
Bouvier, M;Demarre, G;Mazel, D
通讯作者：
Mazel, D
DOI：
10.1073/pnas.0408026101
发表时间：
2004-12-21
影响因子：
11.1
作者：
Achtman, M;Morelli, G;Keim, P
通讯作者：
Keim, P
影响因子：
6.5
作者：
Ho, Simon Y. W.;Shapiro, Beth;Drummond, Alexei J.
通讯作者：
Drummond, Alexei J.
影响因子：
3.6
作者：
Collis, CM;Kim, MJ;Hall, RM
通讯作者：
Hall, RM
影响因子：
64.8
作者：
Heidelberg JF;Eisen JA;Nelson WC;Clayton RA;Gwinn ML;Dodson RJ;Haft DH;Hickey EK;Peterson JD;Umayam L;Gill SR;Nelson KE;Read TD;Tettelin H;Richardson D;Ermolaeva MD;Vamathevan J;Bass S;Qin H;Dragoi I;Sellers P;McDonald L;Utterback T;Fleishmann RD;Nierman WC;White O;Salzberg SL;Smith HO;Colwell RR;Mekalanos JJ;Venter JC;Fraser CM
通讯作者：
Fraser CM