Genomic Epidemiology and Transmission of Campylobacter in Africa (GETcampy-Africa)

非洲弯曲杆菌的基因组流行病学和传播 (GETcampy-Africa)

• 批准号: MR/V001213/1
• 负责人: Samuel Sheppard
• 金额: $ 127.36万
• 依托单位: University of Bath
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FV001213%2F1
• 关键词: Genomic; Epidemiology; Transmission; Campylobacter; Africa

Diarrhoeal disease remains a major cause of child morbidity, growth faltering and mortality in low and middle income countries (LMICs), with Campylobacter among the most common causes. The major infection sources in the UK include contaminated food, but transmission routes in LMICs are unknown. This means that transmission among the children at highest risk (85% infected before 1yr in LMICs) is the least studied. House crowding, cohabitation with animals and poor sanitation/food safety are all potential risk factors, but effective interventions depend upon quantitative estimates of infection sources. So why is Campylobacter largely overlooked in LMICs? While the answer to this question, in part, relates to the perceived sub-clinical sporadic nature of infection and difficulties in culturing microaerophilic bacteria, a more unsettling reason is that the countries where people are at the greatest risk have low economic and development status. This realisation led to my decision to devote future research, and the knowledge and resources I have developed, to combat Campylobacter where my skills are most needed, in LMICs.The epidemiology of campylobacteriosis is poorly understood in LMICs. In pilot studies, we have identified genomic variation in strains that may indicate differences in source, survival, transmission and virulence (compared to the UK). In particular, we have identified globally and locally distributed strains, evidence of within household spread and strains associated with asymptomatic infection and infection with other enteropathogens. Genome sequencing technologies and bioinformatics analysis provide a means for explaining these cryptic disease networks by identifying differences between strains from multiple sources, and tracking their transmission. However, the effective implementation of genomic source attribution relies not only on advanced comparative genomics techniques, but also the deployment of an appropriate sample frame and access to microbiology laboratories. To achieve this I have developed a network of collaborators, through several visits to Africa, that can undertake the required multicentre sampling (consistent with previous national-scale studies) including both broad cross-sectional sampling and sentinel site surveillance allowing calculation of the overall Campylobacter burden as well as case-control comparison to quantify asymptomatic infection. Information will feed into source attribution and monetised decision support models, to allow informed assessment of risk and targeted intervention through public health contacts. If funded, I will re-locate to The Gambia for 3-6 months of each year, at my own expense.Building on an established collaborative network in the UK and Africa (The Gambia, Ghana, Burkina Faso), we will develop a program of globalized Campylobacter NGS surveillance. Specifically, we will: (i) sample and genome sequence thousands of isolates from animals, food, environmental sources and people (symptomatic, asymptomatic, and matched cases and controls); (ii) develop open-access databases and novel analysis pipelines (association study and machine learning) to characterize Campylobacter population structure and identify source attribution markers; (iii) quantify the relative contribution of different human infection sources; (iv) use a cost-benefit risk models to identify the most effective interventions in the transmission network. This evidence-based approach will enable effective local public health and policy interventions and focus efforts to reducing the burden of diarrhoeal disease in Africa.

腹泻病仍然是低收入和中等收入国家儿童发病、生长迟缓和死亡的主要原因，弯曲杆菌属是最常见的原因之一。英国的主要感染源包括受污染的食物，但LMIC的传播途径尚不清楚。这意味着对高危儿童（低收入国家中85%的儿童在1岁以前感染）的传播研究最少。房屋拥挤、与动物同居和卫生/食品安全不良都是潜在的风险因素，但有效的干预措施取决于对感染源的定量估计。那么，为什么弯曲杆菌在中低收入国家中很大程度上被忽视呢？虽然这一问题的答案部分涉及感染的亚临床散发性质和培养微需氧细菌的困难，但更令人不安的原因是，人们面临最大风险的国家经济和发展状况较低。这一认识促使我决定将未来的研究以及我开发的知识和资源投入到LMIC中最需要我的技能的弯曲杆菌中。弯曲杆菌病的流行病学在LMIC中知之甚少。在试点研究中，我们已经确定了菌株的基因组变异，这些变异可能表明来源、存活、传播和毒力（与英国相比）的差异。特别是，我们已经确定了全球和本地分布的菌株，家庭内传播的证据，以及与无症状感染和其他肠道病原体感染相关的菌株。基因组测序技术和生物信息学分析通过识别来自多个来源的菌株之间的差异并跟踪其传播，为解释这些隐性疾病网络提供了一种手段。然而，基因组来源归属的有效实施不仅依赖于先进的比较基因组学技术，而且还依赖于部署适当的样本框架和进入微生物实验室。为了实现这一目标，我通过对非洲的几次访问建立了一个合作者网络，可以进行所需的多中心采样（与以前的国家规模研究一致），包括广泛的横断面采样和哨点监测，从而计算弯曲杆菌的总体负担以及病例对照比较，以量化无症状感染。信息将输入来源归属和货币化决策支持模型，以便通过公共卫生联系人进行知情的风险评估和有针对性的干预。如果获得资助，我将自费每年3-6个月重新安置到冈比亚。在英国和非洲（冈比亚，加纳，布基纳法索）建立合作网络的基础上，我们将制定全球化的弯曲杆菌NGS监测计划。具体而言，我们将：（i）从动物、食物、环境来源和人身上抽取数以千计的分离物样本并进行基因组测序（有症状、无症状和匹配的病例和对照）;（ii）开发开放获取的数据库和新的分析管道（iii）量化不同人类感染源的相对贡献;（iv）使用成本效益风险模型，以确定输电网络中最有效的干预措施。这一循证方法将使地方公共卫生和政策干预措施有效，并将工作重点放在减轻非洲的疟疾负担上。

项目成果

Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs.

• DOI: 10.1099/mgen.0.000882
• 发表时间: 2022-11
• 期刊: MICROBIAL GENOMICS
• 影响因子: 3.9
• 作者: Kittiwan, Nattinee;Calland, Jessica K.;Mourkas, Evangelos;Hitchings, Matthew D.;Murray, Susan;Tadee, Pakpoom;Tadee, Phacharaporn;Duangsonk, Kwanjit;Meric, Guillaume;Sheppard, Samuel K.;Patchanee, Prapas;Ben Pascoe
• 通讯作者: Ben Pascoe

Contrasting genes conferring short- and long-term biofilm adaptation in Listeria.

• DOI: 10.1099/mgen.0.001114
• 发表时间: 2023-10
• 期刊: Microbial genomics
• 影响因子: 3.9
• 作者: Monteith W;Pascoe B;Mourkas E;Clark J;Hakim M;Hitchings MD;McCarthy N;Yahara K;Asakura H;Sheppard SK
• 通讯作者: Sheppard SK

Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance.

• DOI: 10.1099/mgen.0.000834
• 发表时间: 2022-06
• 期刊: MICROBIAL GENOMICS
• 影响因子: 3.9
• 作者: Mouftah, Shaimaa F.;Pascoe, Ben;Calland, Jessica K.;Mourkas, Evangelos;Tonkin, Naomi;Lefevre, Charlotte;Deuker, Danielle;Smith, Sunny;Wickenden, Harry;Hitchings, Matthew D.;Sheppard, Samuel K.;Elhadidy, Mohamed
• 通讯作者: Elhadidy, Mohamed

Genome-based analysis of infrequent Salmonella serotypes through the Thai pork production chain.

• DOI: 10.3389/fmicb.2022.968695
• 发表时间: 2022
• 期刊: Frontiers in microbiology
• 影响因子: 5.2

Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages.

• DOI: 10.1371/journal.pgen.1009829
• 发表时间: 2021-09
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Calland JK;Pascoe B;Bayliss SC;Mourkas E;Berthenet E;Thorpe HA;Hitchings MD;Feil EJ;Corander J;Blaser MJ;Falush D;Sheppard SK
• 通讯作者: Sheppard SK