The devil we know? Using sequencing and metagenomics to assess the diversity of bacteria and antimicrobial resistance captured by passive surveillance

细菌感染的抗菌素耐药性（AMR）是对公共卫生的严重威胁，为了阻止或控制其上升，了解其来源和传播方式至关重要。非伤寒沙门氏菌（NTS）是一种感染动物和人类的细菌，对抗菌药物的耐药性是一个日益严重的问题，可能导致更严重的感染并使治疗复杂化。我们对NTS和AMR的模式和来源的大量理解是基于实验室监测和疾病暴发调查的数据。这些系统主要从临床患病个体收集数据和样本，这些数据和样本存在严重的漏报，并且仅代表那些导致疾病的细菌。因此，这些数据仅占总细菌种群的相对较小比例。本奖学金提案中概述的研究建立在我以前在流行病学，生态学和基因组学方面的经验基础上，并将解决五个关键问题：1）临床患病和非患病宿主的NTS和AMR有多相似？2)对于在不同NTS亚型中发现的常见AMR模式，耐药基因是否相同？3)AMR在同一地点的不同宿主种群之间是如何分布的，观察到的耐药性与已鉴定的AMR基因的相关性如何？4)在工业化国家和工业化国家之间，不同宿主人群的AMR如何比较？5)样本中的总AMR（包括无法在标准实验室条件下生长的细菌）中有多少是由可以在标准实验室条件下生长的单一微生物NTS中的AMR代表的？我将使用从加拿大和越南收集的NTS来解决这些问题，在每个地方，NTS都可以从患病和未患病的个体中获得。这项研究将在剑桥大学进行，与牛津大学临床研究单位/威康信托基金会越南主要海外项目、加拿大渥太华大学和英国威康信托基金会桑格研究所的合作者一起进行。全基因组测序提供了最高的分辨率，可用于研究生物体在遗传水平上如何相互关联，我将利用这项技术来评估患病和非患病宿主的分离株彼此之间的相似程度，在每个宿主中发现的AMR的类型和多样性，以及来自不同疾病状态宿主的分离株群体的混合程度。我还将生成一个试验数据集，将宏基因组测序应用于粪便样本，检查样本中的所有细菌，包括那些可以和不能在标准实验室条件下生长的细菌，并比较NTS分离株中的AMR代表总细菌种群中发现的AMR的程度。此外，我将使用这些分离的样本来检查越南动物和人群的AMR和NTS;鉴于食品供应的全球性以及世界各地农业、政治和社会学环境的广泛差异，在许多不同的国家进行此类评估非常重要，因为AMR不太可能有一个单一的普遍条件。如果我们有能力采取措施阻止AMR的上升，我们需要知道它在哪里，我们目前的测量情况如何，以及我们可能遗漏了什么-本提案所包含的研究将提供重要的见解和关键数据来解决这些问题。

Antimicrobial resistance (AMR) of bacterial infections is a serious threat to public health, and in order to halt or control its rise, understanding where it comes from and how it spreads is essential. Resistance to antimicrobial drugs in non-typhoidal Salmonella (NTS), a bacterium that infects both animals and humans, is an increasing problem, one that can lead to more severe infections and complicates treatment. A great deal of our understanding of the patterns and sources of NTS and AMR is based on data from laboratory-based surveillance and from disease outbreak investigations. These systems collect data and samples from primarily clinically ill individuals, for which there is significant under-reporting and which represent only those bacteria that cause disease. Therefore, these data characterise a relatively small proportion of the overall bacterial population. The research outlined in this fellowship proposal builds on my previous experience in epidemiology, ecology and genomics, and will address five key questions: 1) How similar are NTS and AMR from clinically diseased and non-diseased hosts? 2) For common AMR patterns found in different subtypes of NTS, are the resistance genes the same? 3) How is AMR distributed between different host populations in the same location, and how well does the observed resistance correlate with identified AMR genes? 4) How does AMR in different host populations compare between an industrialised and an industrialising country? 5) How much of the total AMR in a sample, including in bacteria that cannot be grown in standard laboratory conditions, is represented by the AMR within a single organism, NTS, which can be grown in standard laboratory conditions? I will address these questions using NTS collections from Canada and Vietnam, where in each location NTS are available from diseased and non-diseased individuals. This research will be undertaken at the University of Cambridge, in conjunction with collaborators at the Oxford University Clinical Research Unit/Wellcome Trust Major Overseas Programme in Vietnam, the University of Ottawa, Canada, and the Wellcome Trust Sanger Institute, UK. Whole genome sequencing provides the highest resolution available to investigate how organisms are related to each other on a genetic level, and I will utilise this technology to assess how similar isolates from diseased and non-diseased hosts are to each other, the type and diversity of AMR found in each, and the degree of mixture of the populations of isolates from differing disease status hosts. I will also generate a pilot dataset applying metagenomic sequencing to faecal samples, examining all bacteria in the samples, including those can and cannot grow in standard laboratory conditions, and compare how well the AMR in the NTS isolate represents the AMR found within the total bacterial population. In addition, I will use these isolate collections to examine AMR and NTS from animal and human populations in Vietnam; given the global nature of the food supply and the wide variability of agricultural, political and sociological settings across the world, it is important to conduct such assessments in many different countries, as there is unlikely to be a single universal condition for AMR. If we are going to have the ability to do something to halt the rise in AMR, we need to know where it is, how well we are currently measuring it, and what we may be missing - the research encompassed by this proposal will provide important insight and critical data with which to address these questions.