Characterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking Listeria monocytogenes from Food Processing Environments.
Characterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking Listeria monocytogenes from Food Processing Environments.
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DOI：
10.3390/pathogens9100822
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发表时间：
2020-10-07
期刊：
影响因子：
--
通讯作者：
Chen Y
中科院分区：
文献类型：
--
作者：
Kwon HJ;Chen Z;Evans P;Meng J;Chen Y
最近开发的纳米孔测序技术提供了一个独特的机会来快速关闭基因组并识别移动遗传元件（MGE）的完整序列。在这项研究中，对来自七个即食肉类或家禽加工设施的 17 个单增李斯特菌 (Lm) 流行克隆 II (ECII) 分离株进行了鸟枪法测序，其中 5 个分离株进一步进行了长读长测序。此外，从国家生物技术信息中心 (NCBI) 数据库中获取了与美国和南非三起李斯特菌病爆发相关的 26 个 Lm ECII 分离株基因组，并进行了分析，以评估 MGE 是否可用作识别和采购 Lm 来源的高分辨率遗传标记。分析在来自 4 个设施的 11 个非暴发分离株中鉴定出 4 个 comK 前噬菌体，在与美国发生的两起暴发相关的 20 个分离株中鉴定出 3 个 comK 前噬菌体。此外，在 10 个非暴发分离株和 14 个暴发分离株中鉴定出了 3 个不同的质粒。每个 comK 原噬菌体和质粒在共享它的分离株中都是保守的。来自不同设施或爆发的不同噬菌体具有显着的遗传变异，这可能是由于水平基因转移所致。系统发育分析表明，来自同一设施或同一爆发的分离株总是紧密聚集在一起。 Lm ECII 分离株最近共同祖先的时间估计为 1816 年 3 月，平均核苷酸取代率为每年每个位点 3.1 × 10−7 次取代。这项研究表明，完整的 MGE 序列为确定 Lm 分离株的遗传相关性、识别食品加工环境中发生的持久性或重复污染以及研究密切相关的分离株之间的进化历史提供了良好的信号。
Recently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of Listeria monocytogenes (Lm) epidemic clone II (ECII) from seven ready-to-eat meat or poultry processing facilities, not known to be associated with outbreaks, were shotgun sequenced, and among them, five isolates were further subjected to long-read sequencing. Additionally, 26 genomes of Lm ECII isolates associated with three listeriosis outbreaks in the U.S. and South Africa were obtained from the National Center for Biotechnology Information (NCBI) database and analyzed to evaluate if MGEs may be used as a high-resolution genetic marker for identifying and sourcing the origin of Lm. The analyses identified four comK prophages in 11 non-outbreak isolates from four facilities and three comK prophages in 20 isolates associated with two outbreaks that occurred in the U.S. In addition, three different plasmids were identified among 10 non-outbreak isolates and 14 outbreak isolates. Each comK prophage and plasmid was conserved among the isolates sharing it. Different prophages from different facilities or outbreaks had significant genetic variations, possibly due to horizontal gene transfer. Phylogenetic analysis showed that isolates from the same facility or the same outbreak always closely clustered. The time of most recent common ancestor of the Lm ECII isolates was estimated to be in March 1816 with the average nucleotide substitution rate of 3.1 × 10−7 substitutions per site per year. This study showed that complete MGE sequences provide a good signal to determine the genetic relatedness of Lm isolates, to identify persistence or repeated contamination that occurred within food processing environment, and to study the evolutionary history among closely related isolates.
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影响因子：
4.4
作者：
Elhanafi, Driss;Dutta, Vikrant;Kathariou, Sophia
通讯作者：
Kathariou, Sophia
影响因子：
9.4
作者：
Graves, LM;Hunter, SB;Swaminathan, B
通讯作者：
Swaminathan, B
影响因子：
4.4
作者：
Dutta, Vikrant;Elhanafi, Driss;Kathariou, Sophia
通讯作者：
Kathariou, Sophia
DOI：
10.1128/genomea.00538-18
发表时间：
2018-06-21
期刊：
Genome announcements
影响因子：
--
作者：
Allam M;Tau N;Smouse SL;Mtshali PS;Mnyameni F;Khumalo ZTH;Ismail A;Govender N;Thomas J;Smith AM
通讯作者：
Smith AM
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.