Evaluating Microbial and Molecular Mechanisms that Affect Changes in Antibiotic Resistance during Anaerobic Digestion of Manure

评估粪便厌氧消化过程中影响抗生素耐药性变化的微生物和分子机制

• 批准号: RGPIN-2022-03670
• 负责人: Cicek, Nazim
• 金额: $ 3.13万
• 依托单位: University of Manitoba
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=746300
• 关键词: Evaluating; Microbial; Molecular; Mechanisms; Affect

Livestock production and animal husbandry are considered key contributors responsible for generating and emitting antibiotic-resistant bacteria (ARB) due to the extensive use of veterinary antibiotics. Antibiotic resistance genes (ARG), the genetic units encoding the diverse mechanisms of resistance, play an important role in disseminating antibiotic resistance because they are usually located in mobile genetic elements (MGE) that are easily transferred between microbial species. Therefore, bacteria that are not directly exposed to antibiotics are also susceptible to acquiring antibiotic resistance mechanisms. Since the application of animal manures as soil fertilizers is a common agricultural practice, there is increasing concern about the proliferation of ARB and ARG in agricultural fields and surrounding waterways and ultimately the consequences this will have on public and ecosystem health. One alternative to address this problem is to design manure treatment processes that ensure the reduction of ARB and ARG before they reach the environment. Anaerobic digester installations are readily expanding across Canada (at farm level or larger regional plants) to meet the growing demand in sustainable waste management and renewable energy. We propose using manure anaerobic digestion as a model to better understand microbial and molecular mechanisms involved in the evolution of ARG. Developing effective strategies for ARB and ARG mitigation through manure treatment will provide an additional incentive to build and operate anaerobic digestion systems, which will enhance the long-term sustainability and resilience of Canadian agriculture. The specific objectives of this research program are to: 1) Determine the presence, levels, and prevalence of ARGs in raw and treated manures in dairy farms with different sizes, operations, and manure management systems; 2) Assess the long-term impact of different operational parameters on the resistome (total ARG) and mobilome (total MGE) profiles and microbial population dynamics in anaerobic digesters; 3) Identify specific microbial groups responsible for carrying and spreading ARG, through the use of metagenomic and bioinformatic tools and biostatistics; 4) Validate potential microbial group hosts of ARG by comparing their presence and prevalence (co-occurrence) in other anaerobic digestion applications, such as in municipal wastewater treatment and industrial wastewater treatment; 5) Develop and validate a computational algorithm to estimate the potential risk associated with the presence of ARG, MGE, and microbial communities in raw and treated animal manures that can be used for the systematic comparison between samples and processes. This research program will provide multidisciplinary training in bioprocessing, waste treatment, and metagenomics, and supply highly skilled professionals (2 PhD, 2 MSc, 5 BSc) to Canada's growing bio-economy, where companies reported significant labour and skill shortages.

由于兽用抗生素的广泛使用，畜牧生产和畜牧业被认为是产生和排放耐药性细菌（ARB）的关键因素。抗生素耐药基因（Antibiotic resistance genes，ARG）是编码多种抗生素耐药机制的遗传单位，由于ARG通常位于可移动的遗传元件（移动的genetic element，MGE）中，易于在微生物种间转移，因此ARG在抗生素耐药传播中起着重要作用。因此，不直接接触抗生素的细菌也容易获得抗生素耐药机制。由于将动物粪便用作土壤肥料是一种常见的农业做法，人们越来越担心ARB和ARG在农田和周围水道中的扩散，以及最终对公众和生态系统健康的影响。解决这一问题的一个替代办法是设计粪便处理工艺，确保在ARB和ARG进入环境之前减少它们。厌氧消化器装置正在加拿大各地（农场或大型区域工厂）迅速扩大，以满足可持续废物管理和可再生能源日益增长的需求。我们建议使用粪便厌氧消化作为一个模型，以更好地了解微生物和分子机制参与ARG的演变。通过粪便处理制定有效的ARB和ARG缓解战略将为建设和运营厌氧消化系统提供额外的激励，这将提高加拿大农业的长期可持续性和复原力。该研究计划的具体目标是：1）确定不同规模，运营和粪便管理系统的奶牛场中未处理和处理粪便中ARGs的存在，水平和患病率; 2）评估不同操作参数对抗性组的长期影响。（总ARG）和mobilome厌氧消化池中的总MGE谱和微生物种群动态; 3）通过使用宏基因组和生物信息学工具以及生物统计学，确定负责携带和传播ARG的特定微生物组; 4）通过比较ARG的存在和流行来确定ARG的潜在微生物群宿主（共现）在其它厌氧消化应用中，例如在城市废水处理和工业废水处理中; 5）开发并验证计算算法，以估计与原始和处理过的动物粪便中存在的ARG、MGE和微生物群落相关的潜在风险，该算法可用于样品和工艺之间的系统比较。该研究计划将提供生物加工，废物处理和宏基因组学方面的多学科培训，并为加拿大不断增长的生物经济提供高技能专业人员（2名博士，2名硕士，5名理学士），公司报告了显著的劳动力和技能短缺。