Mechanisms for acquisition and transmission of successful antibiotic resistant pneumococcal clones pre- and post-vaccination

肺炎链球菌中的AMR通过有限数量的克隆在全球传播。PCV疫苗接种降低了疫苗型菌株的AMR。AMR现在通过非PCV类型的扩展而出现。该项目的重点是AMR克隆的遗传/功能特性，目标是在携带者群体中成功传播。目的是：1）对PCV引入后出现的AMR进行基于全基因组的分析，并与PCV前进行比较。序列数据将与宿主因素（包括临床患者信息）相关。将应用系统发生学和一般机器学习方法，并将创建数据库，以识别将AMR成功与传播、定殖和引起侵袭性疾病的能力联系起来的微生物特征2）将使用一组动物模型来研究AMR克隆的传播、定殖和疾病能力。通过改变宿主免疫防御、通过用甲型流感病毒致敏、通过暴露于长期抗生素以及通过影响环境中的物理或化学参数，将不同的内源性和环境线索应用于这些研究。3）将使用适当的突变体来鉴定影响传播/定殖/侵袭性疾病的驱动因素，和使用无菌小鼠监测宿主微生物组的影响4）抗性转移和感受态皮利的作用，将在存在和不存在呼吸道微生物组的情况下研究接合转移和缺乏CRISPR/Cas9干扰5）将在小鼠模型中尝试使用靶向AMR克隆的抗原并通过产生CRISPR/Cas9递送系统以在携带期间干扰AMR克隆来进行克隆消除。

AMR in Streptococcus pneumoniae is spread globally by a limited number of clones. PCV vaccination has decreased AMR among vaccine-type strains. AMR now emerges by expansion of non-PCV types. The project focuses on genetic/functional properties of AMR clones with the goal to target their success and transmission in the carrier population. The goals are to: 1) Perform whole genome based analyses on emerging AMR after PCV introduction, comparing with pre-PCV. Sequence data will be correlated to host factors including clinical patient information. Phylogenetic and general machine learning methods will be applied and a data base will be created to identify microbial traits that link success of AMR to transmission, colonization and ability to cause invasive disease 2) A set of animal models will be used to study transmission, colonization and disease capability of AMR clones. Different endogenous and environmental cues will be applied to these studies by altering host immune defense, by sensitizing with influenza A virus, by exposure to long term antibiotics, and by affecting physical or chemical parameters in the environment 3) Drivers affecting transmission/colonization/invasive disease will be identified using appropriate mutants, and monitoring the influence of the host microbiome using germ free mice 4) Resistance transfer and role of competence pili, conjugative transfer and lack of CRISPR/Cas9 interference will be studied in the presence and absence of a respiratory microbiome 5) Clonal elimination will be attempted in mice models using antigens targeting AMR clones and by generating a CRISPR/Cas9 delivery system for interference of AMR clones during carriage.