Development of robust analytical pipelines for the analysis of microbial community data from clinical samples

开发强大的分析管道，用于分析临床样本中的微生物群落数据

• 批准号: MR/J014370/1
• 负责人: Nicholas Loman
• 金额: $ 36.26万
• 依托单位: University of Birmingham
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FJ014370%2F1
• 关键词: Development; robust; analytical; pipelines; analysis

Cystic fibrosis is an inherited disease which affects around 9,000 people in the UK. It is a recessive disorder, meaning that both parents have to carry a faulty copy of a gene for a child to be affected. Approximately 1 in 25 people carry this copy. Cystic fibrosis dramatically shortens the life of those affected and almost half do not live beyond their 30s. Cystic fibrosis has a negative effect on many parts of the body, but it particularly affects the lungs. The result of the defective gene is that thick secretions cannot be effectively cleared from the lungs, resulting in the airways becoming congested and damaged.This congestion results in frequent and severe exacerbations, sometimes requiring admission to hospital and treatment. We think exacerbations are often a result of infections, which may be caused by viruses and bacteria. One of the most common bacteria found is Pseudomonas aeruginosa. Microbiologists diagnose Pseudomonas by putting samples of sample onto plates and identifying the bacteria that grow in visible colonies. Often Pseudomonas is treated by antibiotics. Other bacteria may be found including Streptococcus and Staphylococcus.However when looking for causes of exacerbations we are limited to finding pathogens that we know about, and which grow on the types of culture plates we use. It may be that other bacteria are present that we can't see because they do not grow easily. Sometimes those bacteria may be a cause. However, in a similar way to the human gut it may be that there are "good" and "bad" bacteria. It is known that certain types of bacteria can prevent other types infecting and therefore they may help protect against exacerbations.A new technology utilises the idea of molecular barcodes which identify bacterial species from fragments of DNA in their cell. New instruments termed high-throughput sequencers permit these barcodes to be read from many samples easily and cheaply. This technology gives us a "parts list" of the bacterial species in a particular sample, and a rough idea of how frequently they occur. By reading this parts lists from patients with cystic fibrosis - when they are well, when they are very sick and when they are recovering, we may be able to tell the relative contribution of these unseen bacteria to the condition. For example a particular species increasing or reducing in abundance may be associated with recovery, giving us a potential therapeutic target.We are also interesting in seeing how patients end up being colonised with particular, commonly seen bacteria. For example in our local patients, about 30% have a particular type of Pseudomonas infection called Midlands 1. However, very little is known about how it is that so many patients end up being infected by the same strain. We are now able to sequence all the DNA in a bacterial cell (the genome) which gives very high resolution view of how it has evolved. By comparing genomes of strains from different patients, we can help determine whether patients are infecting each other with the same strain, or whether the strains are quite different and come from many different sources. We can also see how the Pseudomonas evolves whilst it is in a patients lungs. Previous studies have shown that the Pseudomonas adapts to the specific environment, which may give us clues as to why people with the same cystic fibrosis mutation have different courses and end up with more hospital admissions or exacerbations than others.The technology we are using is very new, and there are a number of difficulties with it before it can be a routine clinical test. One problem is that the machines generate plenty of sequencing "noise" which may look like species are present that aren't. I want to develop bioinformatics methods that try and increase the reliability of these techniques and generate information that would be useful for clinicians. We expect these techniques to enter the clinic within the next five years.

囊性纤维化是一种遗传性疾病，影响英国约9，000人。这是一种隐性疾病，意味着父母双方都必须携带一个有缺陷的基因拷贝，孩子才会受到影响。大约每25个人中就有一个人携带这本书。囊性纤维化大大缩短了受影响者的寿命，几乎一半的人活不过30多岁。囊性纤维化对身体的许多部位都有负面影响，但它特别影响肺部。这种基因缺陷的结果是，肺部无法有效清除粘稠的分泌物，导致气道堵塞和受损。这种堵塞导致频繁和严重的病情加重，有时需要住院治疗。我们认为病情加重通常是感染的结果，感染可能是由病毒和细菌引起的。最常见的细菌之一是铜绿假单胞菌。微生物学家诊断假单胞菌的方法是将样品放在平板上，并识别在可见菌落中生长的细菌。假单胞菌通常用抗生素治疗。其他细菌可能会被发现，包括链球菌和葡萄球菌。然而，当寻找恶化的原因时，我们仅限于寻找我们已知的病原体，以及在我们使用的培养板上生长的病原体。这可能是其他细菌存在，我们看不到，因为他们不容易生长。有时这些细菌可能是一个原因。然而，与人类肠道相似的是，可能存在“好”和“坏”细菌。众所周知，某些类型的细菌可以防止其他类型的感染，因此它们可能有助于防止病情恶化。一项新技术利用分子条形码的想法，从细胞中的DNA片段中识别细菌物种。被称为高通量测序仪的新仪器允许从许多样品中容易且便宜地读取这些条形码。这项技术为我们提供了特定样本中细菌种类的“部件列表”，以及它们出现的频率的大致概念。通过阅读囊性纤维化患者的这部分列表-当他们健康时，当他们病得很重时，当他们正在康复时，我们可能能够说出这些看不见的细菌对病情的相对贡献。例如，一个特定的物种数量的增加或减少可能与康复有关，这给了我们一个潜在的治疗目标。我们也很有兴趣了解患者最终是如何被特定的常见细菌定殖的。例如，在我们当地的患者中，约30%患有一种称为Midlands 1的特定类型的假单胞菌感染。然而，很少有人知道这么多患者最终是如何被同一菌株感染的。我们现在能够对细菌细胞（基因组）中的所有DNA进行测序，这为它如何进化提供了非常高的分辨率。通过比较来自不同患者的菌株的基因组，我们可以帮助确定患者之间是否感染了相同的菌株，或者这些菌株是否完全不同，来自许多不同的来源。我们还可以看到假单胞菌是如何在患者肺部进化的。以前的研究表明假单胞菌适应特定的环境，这可能会给我们一些线索，为什么具有相同囊性纤维化突变的人会有不同的病程，最终比其他人有更多的住院或病情加重。我们使用的技术非常新，在成为常规临床测试之前，它还有很多困难。一个问题是，这些机器会产生大量测序“噪音”，这些噪音可能看起来像是存在但实际上不存在的物种。我想开发生物信息学方法，试图提高这些技术的可靠性，并产生对临床医生有用的信息。我们预计这些技术将在未来五年内进入临床。

项目成果

A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

• DOI: 10.1371/journal.pone.0083158
• 发表时间: 2013
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Davis IJ;Wallis C;Deusch O;Colyer A;Milella L;Loman N;Harris S
• 通讯作者: Harris S

Defining bacterial species in the genomic era: insights from the genus Acinetobacter.

• DOI: 10.1186/1471-2180-12-302
• 发表时间: 2012-12-23
• 期刊: BMC microbiology
• 影响因子: 4.2
• 作者: Chan JZ;Halachev MR;Loman NJ;Constantinidou C;Pallen MJ
• 通讯作者: Pallen MJ

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

• DOI: 10.1126/science.abf2946
• 发表时间: 2021-02-12
• 期刊: Science (New York, N.Y.)
• 作者: du Plessis L;McCrone JT;Zarebski AE;Hill V;Ruis C;Gutierrez B;Raghwani J;Ashworth J;Colquhoun R;Connor TR;Faria NR;Jackson B;Loman NJ;O'Toole Á;Nicholls SM;Parag KV;Scher E;Vasylyeva TI;Volz EM;Watts A;Bogoch II;Khan K;COVID-19 Genomics UK (COG-UK) Consortium;Aanensen DM;Kraemer MUG;Rambaut A;Pybus OG
• 通讯作者: Pybus OG

Treatment of COVID-19 with remdesivir in the absence of humoral immunity: a case report.

• DOI: 10.1038/s41467-020-19761-2
• 发表时间: 2020-12-14
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Buckland MS;Galloway JB;Fhogartaigh CN;Meredith L;Provine NM;Bloor S;Ogbe A;Zelek WM;Smielewska A;Yakovleva A;Mann T;Bergamaschi L;Turner L;Mescia F;Toonen EJM;Hackstein CP;Akther HD;Vieira VA;Ceron-Gutierrez L;Periselneris J;Kiani-Alikhan S;Grigoriadou S;Vaghela D;Lear SE;Török ME;Hamilton WL;Stockton J;Quick J;Nelson P;Hunter M;Coulter TI;Devlin L;CITIID-NIHR COVID-19 BioResource Collaboration;MRC-Toxicology Unit COVID-19 Consortium;Bradley JR;Smith KGC;Ouwehand WH;Estcourt L;Harvala H;Roberts DJ;Wilkinson IB;Screaton N;Loman N;Doffinger R;Lyons PA;Morgan BP;Goodfellow IG;Klenerman P;Lehner PJ;Matheson NJ;Thaventhiran JED
• 通讯作者: Thaventhiran JED