Genome analysis following a national increase in Scarlet Fever in England 2014
Genome analysis following a national increase in Scarlet Fever in England 2014
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DOI：
10.1186/s12864-017-3603-z
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发表时间：
2017-03-10
期刊：
影响因子：
4.4
通讯作者：
Underwood, Anthony
中科院分区：
文献类型：
--
作者：
Chalker, Victoria;Jironkin, Aleksey;Underwood, Anthony
背景：在 2014 年猩红热 (SF) 通报数量大幅增加期间，对从 SF 患者中分离出的化脓性链球菌（A 组链球菌，GAS）与从侵袭性疾病患者 (iGAS) 中分离出的分离株进行了一项全国基因组研究，以检验以下假设：SF 的增加是由于英格兰人群中一种或多种新/新兴菌株的引入或已知遗传因素在英格兰人群中的传播所致。水平基因转移 (HGT) 导致的 GAS 导致感染，导致 SF 的可能性增加。收集分离株以提供地理代表性，从 2014 年 4 月 1 日至 2014 年 6 月 18 日，每个地区大约有 5% SF 分离株。包含可获得基因组数据的同期 iGAS 分离株以进行比较。分析数据以确定 emm 基因序列类型、系统发育谱系和基因组进化枝代表性、已知原噬菌体元件的存在以及已知赋予致病性和抗生素抗性的基因的存在。结果：分析了 555 个分离株，其中 303 个来自 SF 患者，252 个来自 iGAS 患者。来自 SF 患者的分离株具有多种不同的 emm 序列类型和系统发育谱系。在数据标准化之前，emm3 是主要类型（占 SF 分离株的 42.9%，130/303 95% CI 37.5-48.5；比 iGAS 分离株中发现的 emm3 分离株百分比高 14.7%）。与 iGAS 患者相比，SF 患者中正常化后的 emm 类型 4 和 12 较多（p < 0.001）。单一基因 ssa 在 SF 患者的分离株中出现过多。与 iGAS 相比，没有发现单个噬菌体在 SF 中出现过多。然而，由 315.2、SPsP6、MGAS10750.3 或 HK360ssa 的存在定义的“meta-ssa”噬菌体被发现过多。 HKU360。 HKU360 尚未检测到 vir 噬菌体。 ssa 噬菌体存在于 43/63 emm12 分离株中，但在 SF 患者的分离株中并未发现过多。结论：没有证据表明 SF 病例数量的增加是菌株特异性或已知的移动元件特异性现象，因为 SF 病例的增加与 GAS 的多个谱系相关。
Background: During a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with comparison to isolates from patients with invasive disease (iGAS) to test the hypotheses that the increase in SF was due to either the introduction of one or more new/emerging strains in the population in England or the transmission of a known genetic element through the population of GAS by horizontal gene transfer (HGT) resulting in infections with an increased likelihood of causing SF. Isolates were collected to provide geographical representation, for approximately 5% SF isolates from each region from 1st April 2014 to 18th June 2014. Contemporaneous iGAS isolates for which genomic data were available were included for comparison. Data were analysed in order to determine emm gene sequence type, phylogenetic lineage and genomic clade representation, the presence of known prophage elements and the presence of genes known to confer pathogenicity and resistance to antibiotics.Results: 555 isolates were analysed, 303 from patients with SF and 252 from patients with iGAS. Isolates from patients with SF were of multiple distinct emm sequence types and phylogenetic lineages. Prior to data normalisation, emm3 was the predominant type (accounting for 42.9% of SF isolates, 130/303 95% CI 37.5-48.5; 14.7% higher than the percentage of emm3 isolates found in the iGAS isolates). Post-normalisation emm types, 4 and 12, were found to be over-represented in patients with SF versus iGAS (p < 0.001). A single gene, ssa, was over-represented in isolates from patients with SF. No single phage was found to be over represented in SF vs iGAS. However, a "meta-ssa" phage defined by the presence of : 315.2, SPsP6, MGAS10750.3 or HK360ssa, was found to be over represented. The HKU360. vir phage was not detected yet the HKU360. ssa phage was present in 43/63 emm12 isolates but not found to be over-represented in isolates from patients with SF.Conclusions: There is no evidence that the increased number of SF cases was a strain-specific or known mobile element specific phenomenon, as the increase in SF cases was associated with multiple lineages of GAS.