Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain.
Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain.
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DOI：
10.1099/mgen.0.000511
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发表时间：
2021-03
影响因子：
3.9
通讯作者：
Winstanley C
中科院分区：
文献类型：
--
作者：
Moore MP;Lamont IL;Williams D;Paterson S;Kukavica-Ibrulj I;Tucker NP;Kenna DTD;Turton JF;Jeukens J;Freschi L;Wee BA;Loman NJ;Holden S;Manzoor S;Hawkey P;Southern KW;Walshaw MJ;Levesque RC;Fothergill JL;Winstanley C
利物浦流行株(LES)是一种重要的可传播的铜绿假单胞菌克隆血统，慢性感染囊性纤维化(CF)患者的肺部。以前的研究主要集中在有限数量的分离株中LES的基因组学，主要来自英国的一个CF中心，以及来自加拿大LES鉴定的研究。在这里，我们通过对来自英国多个CF中心的91个分离物进行基因组测序，显著扩展了当前的LES基因组数据库，并描述了来自英国和加拿大的这一大批LES分离物的比较基因组学。系统发育分析表明，与更广泛的铜绿假单胞菌种群相比，所分析的145个LES基因组形成了一个明显的克隆谱系。值得注意的是，这些分离物形成了两个分支：一个与来自加拿大的分离物有关，另一个与英国分离物有关。对英国LES分离株的进一步分析揭示了临床地理分布的聚集性。在分离株紧密聚集的地方，这种联系通常得到了联系分离株或患者的临床数据的支持。与已知最早的分离株LESB58(1988年)相比，许多英国LES分离株具有共同的功能丧失突变，如基因gltR和fler。在先前的研究中确认的其他功能丧失突变在慢性肺循环感染期间是常见的适应性变化，在多个LES分离株中也被发现。对LES辅助基因组(包括基因组岛和前噬菌体)的分析显示，大基因组区域的携带存在差异，根据临床位置的不同，有一些证据表明共享基因组岛/前噬菌体互补。我们的研究揭示了LES在英国内部和大陆之间传播过程中的分歧和适应。
The Liverpool epidemic strain (LES) is an important transmissible clonal lineage of Pseudomonas aeruginosa that chronically infects the lungs of people with cystic fibrosis (CF). Previous studies have focused on the genomics of the LES in a limited number of isolates, mostly from one CF centre in the UK, and from studies highlighting identification of the LES in Canada. Here we significantly extend the current LES genome database by genome sequencing 91 isolates from multiple CF centres across the UK, and we describe the comparative genomics of this large collection of LES isolates from the UK and Canada. Phylogenetic analysis revealed that the 145 LES genomes analysed formed a distinct clonal lineage when compared with the wider P. aeruginosa population. Notably, the isolates formed two clades: one associated with isolates from Canada, and the other associated with UK isolates. Further analysis of the UK LES isolates revealed clustering by clinic geography. Where isolates clustered closely together, the association was often supported by clinical data linking isolates or patients. When compared with the earliest known isolate, LESB58 (from 1988), many UK LES isolates shared common loss-of-function mutations, such as in genes gltR and fleR. Other loss-of-function mutations identified in previous studies as common adaptations during CF chronic lung infections were also identified in multiple LES isolates. Analysis of the LES accessory genome (including genomic islands and prophages) revealed variations in the carriage of large genomic regions, with some evidence for shared genomic island/prophage complement according to clinic location. Our study reveals divergence and adaptation during the spread of the LES, within the UK and between continents.
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DOI：
10.1093/bioinformatics/btp347
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Assefa S;Keane TM;Otto TD;Newbold C;Berriman M
通讯作者：
Berriman M
影响因子：
--
作者：
Ashish, Abdul;Shaw, Matthew;Walshaw, Martin J
通讯作者：
Walshaw, Martin J
影响因子：
3.3
作者：
Fischer, Sebastian;Klockgether, Jens;Tuemmler, Burkhard
通讯作者：
Tuemmler, Burkhard
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：
10
作者：
Al-Aloul, M;Crawley, J;Walshaw, MJ
通讯作者：
Walshaw, MJ