Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
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DOI：
10.1371/journal.pone.0022751
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Karch H
中科院分区：
文献类型：
--
作者：
Mellmann A;Harmsen D;Cummings CA;Zentz EB;Leopold SR;Rico A;Prior K;Szczepanowski R;Ji Y;Zhang W;McLaughlin SF;Henkhaus JK;Leopold B;Bielaszewska M;Prager R;Brzoska PM;Moore RL;Guenther S;Rothberg JM;Karch H
自2011年5月以来，以德国为中心的产特强滋贺毒素（Stx）大肠杆菌O 104：H4的持续爆发已造成830多例溶血性尿毒综合征（HUS）和46例死亡。血清型O 104：H4在动物中未检出，过去很少与HUS相关。为了前瞻性地阐明该菌株在此次暴发早期阶段的独特特征，我们在Life Technologies Ion Torrent PGM™测序仪和光学图谱上应用全基因组测序来表征一种暴发分离株（LB 226692）和一种来自2001年的历史O 104：H4 HUS分离株（01-09591）。在62小时内，用新引入的PGM™完成了两种菌株的参考引导拔模组装。HUS相关菌株均携带两种致病性大肠杆菌中常见的基因。大肠杆菌、肠聚集性E.大肠杆菌（EAEC）和肠出血性大肠杆菌（E.大肠杆菌（EHEC）。对1,144个核心E.大肠杆菌基因序列表明，引起HUS的O 104：H4菌株和先前公布的EAEC菌株55989的序列显示出密切的关系，但仅与常见的EHEC血清型有较远的关系。虽然密切相关，但爆发菌株在质粒含量和菌毛基因方面与2001年菌株不同。我们提出了一个模型，其中EAEC 55989和EHEC O 104：H4菌株从一个共同的EHEC O 104：H4祖先进化而来，并建议通过逐步获得和丢失染色体和质粒编码的毒力因子，EAEC和EHEC的高致病性杂交体成为当前爆发的克隆。总之，快速的下一代技术有助于在暴发的早期阶段进行前瞻性的全基因组表征。
An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with HUS in the past. To prospectively elucidate the unique characteristics of this strain in the early stages of this outbreak, we applied whole genome sequencing on the Life Technologies Ion Torrent PGM™ sequencer and Optical Mapping to characterize one outbreak isolate (LB226692) and a historic O104:H4 HUS isolate from 2001 (01-09591). Reference guided draft assemblies of both strains were completed with the newly introduced PGM™ within 62 hours. The HUS-associated strains both carried genes typically found in two types of pathogenic E. coli, enteroaggregative E. coli (EAEC) and enterohemorrhagic E. coli (EHEC). Phylogenetic analyses of 1,144 core E. coli genes indicate that the HUS-causing O104:H4 strains and the previously published sequence of the EAEC strain 55989 show a close relationship but are only distantly related to common EHEC serotypes. Though closely related, the outbreak strain differs from the 2001 strain in plasmid content and fimbrial genes. We propose a model in which EAEC 55989 and EHEC O104:H4 strains evolved from a common EHEC O104:H4 progenitor, and suggest that by stepwise gain and loss of chromosomal and plasmid-encoded virulence factors, a highly pathogenic hybrid of EAEC and EHEC emerged as the current outbreak clone. In conclusion, rapid next-generation technologies facilitated prospective whole genome characterization in the early stages of an outbreak.
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影响因子：
3.6
作者：
Bielaszewska M;Middendorf B;Tarr PI;Zhang W;Prager R;Aldick T;Dobrindt U;Karch H;Mellmann A
通讯作者：
Mellmann A
影响因子：
3.1
作者：
Dudley, EG;Abe, C;Nataro, JP
通讯作者：
Nataro, JP
影响因子：
3.7
作者：
Bielaszewska, Martina;Koeck, Robin;Mellmann, Alexander
通讯作者：
Mellmann, Alexander
影响因子：
11.8
作者：
Elias, Johannes;Harmsen, Dag;Vogel, Ulrich
通讯作者：
Vogel, Ulrich
DOI：
10.1093/bioinformatics/btp352
发表时间：
2009-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Handsaker B;Wysoker A;Fennell T;Ruan J;Homer N;Marth G;Abecasis G;Durbin R;1000 Genome Project Data Processing Subgroup
通讯作者：
1000 Genome Project Data Processing Subgroup