The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.
The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.
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整个醋酸杆菌属的基因组多样化：起源、机制和后果。
DOI：
10.1093/gbe/evu225
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发表时间：
2014-10-13
影响因子：
3.3
通讯作者：
Rocha EP
中科院分区：
文献类型：
--
作者：
Touchon M;Cury J;Yoon EJ;Krizova L;Cerqueira GC;Murphy C;Feldgarden M;Wortman J;Clermont D;Lambert T;Grillot-Courvalin C;Nemec A;Courvalin P;Rocha EP
细菌基因组学极大地扩展了我们对物种内微多样化模式的理解，但在更高的分类学水平上进行分析是必要的，以了解和预测一个属中病原体的独立崛起。我们对不动杆菌属的有效命名和暂定种的基因组多样性进行了采样、测序和评估，不动杆菌属包括主要的医院病原体和生物技术上重要的物种。我们推断了一个强大的全球系统发育，并划定了几个新的假定物种。这个属非常古老，而且极其多样化：高度分化的物种的基因组比一个物种内的某些菌株共享更多的同源物。我们系统地描述了驱动基因组多样化的元件和机制，如共轭元件、插入序列和自然转化。我们发现许多容易出错的聚合酶可能在对毒素、抗生素的抗性和遗传变异的产生中发挥作用。令人惊讶的是，在不动杆菌中研究较少的温带噬菌体被发现占大多数基因组的很大一部分。因此，许多基因组编码集群规则间隔短回文重复序列(CRISPR)-Cas系统，其中一些是迄今为止在细菌中发现的最大的CRISPR阵列。整合子在鲍曼不动杆菌中大量存在，这与它对抗生素的频繁耐药有关。我们的数据表明,a baumannii源自一个古老人口瓶颈人口膨胀下强大的净化选择紧随其后。突出的物种多样化主要是通过水平转移，包括一些等位基因重组，在靠近复制末端的特定热点上优先发生。我们的工作为了解不动杆菌向新兴耐药和多用途病原体的多样化奠定了定量基础。
Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens.
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影响因子：
9.9
作者：
de Berardinis, Veronique;Vallenet, David;Castelli, Vanina;Besnard, Marielle;Pinet, Agnes;Cruaud, Corinne;Samair, Sumitta;Lechaplais, Christophe;Gyapay, Gabor;Richez, Celine;Durot, Maxime;Kreimeyer, Annett;Le Fevre, Francois;Schaechter, Vincent;Pezo, Valerie;Doering, Volker;Scarpelli, Claude;Medigue, Claudine;Cohen, Georges N.;Marliere, Philippe;Salanoubat, Marcel;Weissenbach, Jean
通讯作者：
Weissenbach, Jean
影响因子：
3.7
作者：
Antunes LC;Imperi F;Carattoli A;Visca P
通讯作者：
Visca P
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
3.3
作者：
Didelot, Xavier;Falush, Daniel
通讯作者：
Falush, Daniel
DOI：
10.1099/ijs.0.043489-0
发表时间：
2013-04-01
影响因子：
2.8
作者：
Alvarez-Perez, Sergio;Lievens, Bart;Herrera, Carlos M.
通讯作者：
Herrera, Carlos M.