The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica.
The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica.
复制标题
作者：
Pettengill JB;Timme RE;Barrangou R;Toro M;Allard MW;Strain E;Musser SM;Brown EW
对成簇的规则间隔短回文重复序列(CRISPR)及其相关基因(CA)的进化研究可以提供对寄主-病原体共同进化动力学以及不同基因组事件(例如水平传播与垂直传播)发生频率的洞察。在这项研究中，我们使用全基因组序列(WGS)数据来确定CRISPR基因座和cas基因在427株不同的肠炎沙门氏菌中的进化历史和遗传多样性。代表不同血清型的肠杆菌分离株。我们还评估了CRISPR基因座在分型方面的性能，与全基因组和多位点序列分型(MLST)方法相比。我们发现CRISPR1(中位数=22；最小值=3；最大值=79)和CRISPR2(中位数=27；最小值=2；最大值=221)的阵列长度都具有很高的多样性。血清型之间也有很大的多样性(例如，沙门氏菌之间的阵列相差多达50个重复间隔单元。Senftenberg分离株)。有趣的是，我们发现有两个一般的cas基因图谱并不追踪系统发育关系，这表明在样本分离株的进化历史中，非垂直传播事件经常发生。在每个cas基因中估计的成对距离的范围也有相当大的差异，这可能表明对这些基因作用的自然选择的强度。我们开发了一种基于CRISPR间隔区内容的新的聚类方法，但发现基于CRISPR的分型不如基于MLST的分型准确；基于WGS数据的分型最准确。尽管成本和可及性很高，但我们预计，由于其更大的区分力，草案基因组测序最终将成为追溯调查的常规方法。
Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs. vertical transmission) occur. Within this study, we used whole genome sequence (WGS) data to determine the evolutionary history and genetic diversity of CRISPR loci and cas genes among a diverse set of 427 Salmonella enterica ssp. enterica isolates representing 64 different serovars. We also evaluated the performance of CRISPR loci for typing when compared to whole genome and multilocus sequence typing (MLST) approaches. We found that there was high diversity in array length within both CRISPR1 (median = 22; min = 3; max = 79) and CRISPR2 (median = 27; min = 2; max = 221). There was also much diversity within serovars (e.g., arrays differed by as many as 50 repeat-spacer units among Salmonella ser. Senftenberg isolates). Interestingly, we found that there are two general cas gene profiles that do not track phylogenetic relationships, which suggests that non-vertical transmission events have occurred frequently throughout the evolutionary history of the sampled isolates. There is also considerable variation among the ranges of pairwise distances estimated within each cas gene, which may be indicative of the strength of natural selection acting on those genes. We developed a novel clustering approach based on CRISPR spacer content, but found that typing based on CRISPRs was less accurate than the MLST-based alternative; typing based on WGS data was the most accurate. Notwithstanding cost and accessibility, we anticipate that draft genome sequencing, due to its greater discriminatory power, will eventually become routine for traceback investigations.
登录
查看更多内容
影响因子：
3.7
作者：
Fabre L;Zhang J;Guigon G;Le Hello S;Guibert V;Accou-Demartin M;de Romans S;Lim C;Roux C;Passet V;Diancourt L;Guibourdenche M;Issenhuth-Jeanjean S;Achtman M;Brisse S;Sola C;Weill FX
通讯作者：
Weill FX
影响因子：
1.7
作者：
Boisvert, Sebastien;Laviolette, Francois;Corbeil, Jacques
通讯作者：
Corbeil, Jacques
影响因子：
11.4
作者：
Beloglazova, Natalia;Petit, Pierre;Yakunin, Alexander F.
通讯作者：
Yakunin, Alexander F.
DOI：
10.1016/j.future.2006.07.009
发表时间：
2007-03-01
影响因子：
7.5
作者：
Bazinet, Adam L.;Myers, Daniel S.;Cummings, Michael P.
通讯作者：
Cummings, Michael P.
影响因子：
4.4
作者：
den Bakker HC;Moreno Switt AI;Govoni G;Cummings CA;Ranieri ML;Degoricija L;Hoelzer K;Rodriguez-Rivera LD;Brown S;Bolchacova E;Furtado MR;Wiedmann M
通讯作者：
Wiedmann M