Phylogenomic Classification and the Evolution of Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere.
Phylogenomic Classification and the Evolution of Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere.
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DOI：
10.3389/fmicb.2018.01901
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发表时间：
2018
影响因子：
5.2
通讯作者：
Robinson DA
中科院分区：
文献类型：
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作者：
Challagundla L;Reyes J;Rafiqullah I;Sordelli DO;Echaniz-Aviles G;Velazquez-Meza ME;Castillo-Ramírez S;Fittipaldi N;Feldgarden M;Chapman SB;Calderwood MS;Carvajal LP;Rincon S;Hanson B;Planet PJ;Arias CA;Diaz L;Robinson DA
克隆复合物5耐甲氧西林金黄色葡萄球菌（CC 5-MRSA）包括在西半球引起医院相关感染的多个流行克隆。在这里，我们提出了一个新的基因组研究，这些MRSA揭示其遗传，空间和时间的人口结构，以及选定的性状的演变。我们研究了来自中美洲、北美洲和南美洲11个国家的598个基因组序列，包括409个新生成的序列，以及来自亚洲和欧洲的参考文献。早期分支的CC 5-基底进化枝在地理上分散良好，对甲氧西林敏感，MRSA主要是ST 5-IV，如USA 800克隆，并包括禽和猪菌株的单独亚进化枝。在20世纪70年代初和60年代初，分别出现了两个分支，随后在西半球进行了大规模的扩张：南美洲的CC 5-I分支和主要在中美洲和北美洲的CC 5-II分支。CC 5-I分支包括ST 5-I智利/Cordobes克隆和ST 228-I作为早期分支的南德克隆，但与其他来自欧洲的ST 5-I克隆不同，这些克隆嵌套在CC 5-Basal内。CC 5-II进化枝包括ST 5-II USA 100克隆的趋异菌株、各种其它克隆和大多数已知的万古霉素抗性S.金黄色葡萄球菌，但与嵌套在CC 5-Basal内的日本ST 5-II菌株N315不同。CC 5的重组率远低于其他S.金黄色葡萄球菌遗传背景，这表明在CC 5中万古霉素耐药性的复发不太可能是由于增强的滥交。随着离CC 5树根的距离的增加，抗生素抗性的数量增加，毒素的数量减少。值得注意的是，CC 5-I和CC 5-II进化枝在西半球的扩展之前，对氟喹诺酮、大环内酯类和林可酰胺类抗生素的耐药性的收敛性增加，以及来自噬菌体SA 3的免疫逃避基因簇的葡萄球菌肠毒素p（sep）基因的收敛性损失。这两个分支的表面蛋白的独特损失也被注意到。总之，我们的研究已经确定了CC 5的不同进化枝和克隆之间的关系，并揭示了与西半球这些MRSA扩张相关的抗生素耐药性增加和毒力降低的基因组变化。
Clonal complex 5 methicillin-resistant Staphylococcus aureus (CC5-MRSA) includes multiple prevalent clones that cause hospital-associated infections in the Western Hemisphere. Here, we present a phylogenomic study of these MRSA to reveal their phylogeny, spatial and temporal population structure, and the evolution of selected traits. We studied 598 genome sequences, including 409 newly generated sequences, from 11 countries in Central, North, and South America, and references from Asia and Europe. An early-branching CC5-Basal clade is well-dispersed geographically, is methicillin-susceptible and MRSA predominantly of ST5-IV such as the USA800 clone, and includes separate subclades for avian and porcine strains. In the early 1970s and early 1960s, respectively, two clades appeared that subsequently underwent major expansions in the Western Hemisphere: a CC5-I clade in South America and a CC5-II clade largely in Central and North America. The CC5-I clade includes the ST5-I Chilean/Cordobes clone, and the ST228-I South German clone as an early offshoot, but is distinct from other ST5-I clones from Europe that nest within CC5-Basal. The CC5-II clade includes divergent strains of the ST5-II USA100 clone, various other clones, and most known vancomycin-resistant strains of S. aureus, but is distinct from ST5-II strain N315 from Japan that nests within CC5-Basal. The recombination rate of CC5 was much lower than has been reported for other S. aureus genetic backgrounds, which indicates that recurrence of vancomycin resistance in CC5 is not likely due to an enhanced promiscuity. An increased number of antibiotic resistances and decreased number of toxins with distance from the CC5 tree root were observed. Of note, the expansions of the CC5-I and CC5-II clades in the Western Hemisphere were preceded by convergent gains of resistance to fluoroquinolone, macrolide, and lincosamide antibiotics, and convergent losses of the staphylococcal enterotoxin p (sep) gene from the immune evasion gene cluster of phage ϕSa3. Unique losses of surface proteins were also noted for these two clades. In summary, our study has determined the relationships of different clades and clones of CC5 and has revealed genomic changes for increased antibiotic resistance and decreased virulence associated with the expansions of these MRSA in the Western Hemisphere.
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影响因子：
16.6
作者：
Bradley P;Gordon NC;Walker TM;Dunn L;Heys S;Huang B;Earle S;Pankhurst LJ;Anson L;de Cesare M;Piazza P;Votintseva AA;Golubchik T;Wilson DJ;Wyllie DH;Diel R;Niemann S;Feuerriegel S;Kohl TA;Ismail N;Omar SV;Smith EG;Buck D;McVean G;Walker AS;Peto TE;Crook DW;Iqbal Z
通讯作者：
Iqbal Z
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
4.1
作者：
Egea, Ana L.;Gagetti, Paula;Sola, Claudia
通讯作者：
Sola, Claudia
影响因子：
6.4
作者：
Calderwood, Michael S.;Desjardins, Christopher A.;Huang, Susan S.
通讯作者：
Huang, Susan S.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
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