Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks.
Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks.
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DOI：
10.1099/mgen.0.000084
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发表时间：
2016-09
影响因子：
3.9
通讯作者：
Gally DL
中科院分区：
文献类型：
--
作者：
Cowley LA;Dallman TJ;Fitzgerald S;Irvine N;Rooney PJ;McAteer SP;Day M;Perry NT;Bono JL;Jenkins C;Gally DL
产志贺毒素的大肠杆菌(STEC)O157：H7是一种公共卫生威胁，在全球范围内都有暴发。在这里，我们调查了相关STEC O157：H7之间的基因组差异，这两个STEC O157：H7在同一家餐厅引发了两次相隔八周的疫情。短读基因组测序将暴发毒株分为两个亚群，两个亚群之间只有核心基因组中的三个单核苷酸多态，而传统的分型方法将它们鉴定为不同的噬菌体类型，PT8和PT54。分离株不是与当地菌株聚集在一起，而是与前往中东/北非的外国旅行相关的菌株聚集在一起。长读测序和光学作图相结合的方法显示，这两个暴发毒株在附属基因组上经历了显著的微进化，并伴随着前噬菌体的获得、丢失和重组。此外，PT54亚型还获得了一个240kbp的多药耐药(MDR)IncHI2质粒，负责噬菌体类型的转换。在富营养液中，PT54菌株比PT8菌株具有普遍的适应性优势，包括更强的利用特定氨基酸和二肽作为氮源的能力。第二次暴发的规模要大得多，有多个继发性病例表明有效的人与人之间的传播。我们推测，多药耐药质粒的获得和前噬菌体的改变使PT54菌株适应了人类感染和传播。我们的研究显示了通过结合全基因组测序方法进行疫情调查所提供的额外见解。
Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC O157:H7 that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided the outbreak strains into two sub-clusters separated by only three single-nucleotide polymorphisms in the core genome while traditional typing identified them as separate phage types, PT8 and PT54. Isolates did not cluster with local strains but with those associated with foreign travel to the Middle East/North Africa. Combined long-read sequencing approaches and optical mapping revealed that the two outbreak strains had undergone significant microevolution in the accessory genome with prophage gain, loss and recombination. In addition, the PT54 sub-type had acquired a 240 kbp multi-drug resistance (MDR) IncHI2 plasmid responsible for the phage type switch. A PT54 isolate had a general fitness advantage over a PT8 isolate in rich medium, including an increased capacity to use specific amino acids and dipeptides as a nitrogen source. The second outbreak was considerably larger and there were multiple secondary cases indicative of effective human-to-human transmission. We speculate that MDR plasmid acquisition and prophage changes have adapted the PT54 strain for human infection and transmission. Our study shows the added insights provided by combining whole-genome sequencing approaches for outbreak investigations.