Genomic Epidemiology of Campylobacter in Poultry to Enable the Effective Control of Human Campylobacteriosis in a Middle Income Country

项目总结 人畜共患病病原体弯曲杆菌是引起低收入地区儿童腹泻的主要原因之一。 资源设置。出现对临床相关抗菌药的多重耐药性，包括 氟喹诺酮类和大环内酯类使其成为世界卫生组织高度重视的病原体。然而， 这种病原体在中低收入国家(LMICs)的分子流行病学和生态学 悬而未决。这种知识差距在病原体的主要宿主--鸡身上尤为明显。初步 有证据表明，有足够的基因组特征来区分弯曲杆菌种群和 小规模和工业化规模的家禽。这项K43新兴全球领导者职业发展奖旨在 研究和比较耐多药弯曲杆菌病的分子流行病学和生态学。 在高度流行的环境中饲养的家禽。这将通过以下方式实现：i)详细研究 后院饲养和工厂化生产家禽中弯曲菌种群的基因组特征，II) 后院饲养和工业化生产中多药耐药弯曲杆菌基因组决定因素的评估 以及三)当地报告的抗生素暴露与基因组学数据之间的联系 抗药性的信号。这项研究的结果将对人类来源归因做出重要贡献 在该项目所在的研究中建立的疾病模型(正在进行的儿科队列和 研究秘鲁亚马逊地区弯曲杆菌传播动态的嵌套式病例对照)。履行 为了实现这些目标，一群有成就的导师将共同提供指导，并培训候选人。 弗朗西丝卡·希亚菲诺。Schiaffino博士提出了一项职业发展计划，其中包括先进的方法 基因组分析培训(通过课程作业、个性化培训课程和现场学术轮换)， 出版物、资助人精神和在以下背景下负责任地开展研究的持续培训 全球健康。主要的指导委员会由该领域的世界级专家组成，其中包括Dr。 玛格丽特·科塞克(传染病，流行病学)，卡洛斯·希瓦博士(兽医微生物学，家禽 科学)、克雷格·T·帕克博士(微生物基因组学)、克里·库珀博士(细菌基因组学和靶向 元基因组分析)，塞缪尔·谢泼德博士和本·帕斯科博士(弯曲杆菌生态和进化， 来源归因研究)和Maribel Paredes夫人(基于社区的参与性研究，项目 管理)。Schiaffino博士的职业发展计划是按顺序设计的，目标是 将她定位为具有细菌基因组学专业知识的独立兽医科学家和流行病学家 总体目标是通过安全和强大的食品系统改善人类和动物健康。

PROJECT SUMMARY The zoonotic pathogen Campylobacter is among the principal etiologies of diarrhea in children living in low resource settings. Emergence of multi drug resistance against clinically relevant antimicrobials including fluroquinolones and macrolides make it a high-priority pathogen by the World Health Organization. However, the molecular epidemiology and ecology of this pathogen in low- and middle- income countries (LMICs) remains unresolved. This knowledge gap is especially evident in the pathogen’s main host: the chicken. Preliminary evidence suggests that there are sufficient genomic features to differentiate Campylobacter populations between small-scale and industrially scaled poultry. This K43 Emerging Global Leader career development award aims to study and compare the molecular epidemiology and ecology of MDR Campylobacteriosis in industrially and domestically reared poultry within a highly endemic setting. This will be achieved through i) the detailed study of genomic features of Campylobacter populations from backyard reared and industrially produced poultry, ii) the assessment of Campylobacter genomic determinants of multi-drug resistance in backyard reared and industrially produced poultry, and iii) the linkage of epidemiologic data of locally reported antibiotic exposures and genomic signals of drug resistance. The results from this study will critically contribute to the human source attribution models of disease being built in the study under which this project is nested (an ongoing pediatric cohort and nested case control studying the transmission dynamics of Campylobacter in the Peruvian Amazon). To fulfill these goals, an accomplished group of mentors will collectively provide mentorship and train the candidate, Dr. Francesca Schiaffino. Dr. Schiaffino proposes a career development plan that includes advanced methodological training in genomic analysis (through coursework, personalized training sessions and on-site scholarly rotations), publications, grantsmanship and continued training in responsible conduct of research within the context of global health. The main mentoring committee is composed of world-class experts in the field, including Dr. Margaret N. Kosek (infectious diseases, epidemiology), Dr. Carlos Shiva (veterinary microbiology, poultry science), Dr. Craig T. Parker (microbial genomics), Dr. Kerry Cooper (bacterial genomics and targeted metagenomic analysis), Dr. Samuel Sheppard and Dr. Ben Pascoe (Campylobacter ecology and evolution, source attribution studies), and Mrs, Maribel Paredes (community based participatory research, project management). Dr. Schiaffino’s career development plan has been sequentially designed with the objective of positioning her as an independent veterinary scientist and epidemiologist with expertise in bacterial genomics with the overall objective of improving human and animal health through safe and robust food systems.