Performing Department
(N/A)
Non Technical Summary
The goal of this project is to support long-term sustainability of organic dairies through improved young cow ("youngstock") liveability and performance. Three objectives support this goal: 1) Optimize youngstock management on organic dairy farms; 2) Identify on-farm source(s) and route(s) of Staphylococcus aureus intramammary infections in organic youngstock; and 3) Provide organic dairy educational materials to U.S. veterinary students.To accomplish these objectives, we assembled a national team spanning the Midwest, Northeast, Mountain West, Pacific Northwest and Southwest; with experts in youngstock health and welfare; organic dairy production; mastitis epidemiology; national farm surveys; and dairy education. The project is guided by an Advisory Board including major stakeholders in organic dairy production.Integrated project activities include national surveys of youngstock management practices; comprehensive on-farm youngstock health assessments; and multi-year data collection to document long-term outcomes that directly impact farm profitability. Innovative statistical and molecularmethods will beused to analyze these information-rich datasets to findrelationships between on-farm practices, youngstock health and performance, and profit-bearing outcomes. Findings are brought back to farmers through practical, evidence-based recommendations and support for youngstock management. Project outcomes address a critical need for organic dairy farmers to optimize youngstock outcomes for sustained herd size.
Animal Health Component
100%
Research Effort Categories
Basic
25%
Applied
75%
Developmental
0%
Goals / Objectives
The long-term goal of this project is to improve the profitability of organic dairy producers through optimal youngstock performance, health and welfare. To acheive this goal, we propose three major objectives,as follows:Objective #1 is to optimize youngstock management on organic dairy farms. To accomplish this, we have 3 sub-objectives: 1a) Establish a network focused on management of organic youngstock ("MOODY"); 1b) Identify management risk factors associated with youngstock health, welfare and performance; and 1c) Provide evidence-based guidance to producers, veterinarians and extension agents to enhance management for optimized youngstock health, welfare and performance.Objective #2 is to identify the on-farm source(s) and route(s) of S. aureus intramammary infections in organic youngstock. We accomplish this through an on-farm research campaign that is integrated with the on-farm activities conducted under objective #1.Objective #3 is to provide organic dairy educational materials to U.S. veterinary schools and students. We will do this through two sub-objectives: 3a) Develop and deliver a modular curriculum focused on veterinary-relevant issues related to organic dairy farms; and 3b) Train veterinary and animal science students to conduct on-farm youngstock health assessments specific to organic dairy farms.
Project Methods
There are several important methods components for Objective #1 activities:The "survey sandwich" method: This term refers to our flipped approach for administering a nationwide survey, and was developed in consultation with key stakeholders. Specifically, our partners reported a notable decrease in survey and research participation by organic dairy farmers over the past 1-2 years. Based on this input, we greatly increased the amount of pre-survey outreach in our approach, leading to the "sandwich method", i.e., pre-survey outreach → survey → post-survey outreach. The pre-survey outreach will significantly increase: 1) farmer participation rates; 2) survey relevance for farmer-drive priorities.Choice of scoping review. The choice of a scoping review (versus a systematic review) was made because we expect that the scope of available relevant literature may not be large enough to support a formal systematic review. However, if sufficient literature is identified, we will define a question for full systematic review.Use of DAGs and target trials analysis. Causal diagrams (such as DAGs) are increasingly used in epidemiological research to better identify true causal relationships between study variables [21]. DAGs have been shown to improve systematic review and survey usability [22] and generate more accurate results from statistical analyses of applied health datasets, particularly when multiple confounders are present [23, 24]. Target trials are also built on a causal inference framework and can be used to emulate a randomized controlled trial using observational "big data" [18]. We decided to use these methods to maximize the utility of the data being collected, and to generate more useful causal inferences from the datasets. While causal inference has made significant headway in human research, it is relatively novel within livestock research.Longitudinal calf-level follow-up. Individual, serial calf measurements are a major portion of our project budget and effort. We decided to make this investment for several key reasons: 1) provides robust data for causal inference methods; 2) allows us to collect prospective health and outcome data, greatly increasing the accuracy of these key metrics; 3) provides an estimate of variability over time and season. Thus, our investment pays off in terms of accuracy and utility.Objective 2 MethodsOn-farm samples will be collected from possible S. aureus sources, includinglactating cows, whole waste milk fed to calves, nurse cows, biting flies, cross-sucking behavior, and skin lesions. All samples will be subjected to culture for S. aureus using standard methods and in-depth strain typing of S. aureus isolates. To obtain strain-level information, we will extract DNA from cultured isolates and subject the DNA to library preparation and short- and long-read whole-genome sequencing (WGS). Resulting data will be analyzed using the Bactopia pipeline, including use of subworkflows specific to S. aureus.We will combine the S. aureus prevalence information with the management and health data collected in Objective #1 to identify farm- and animal-level risk factors for S. aureus. For strains with high enough prevalence, we will conduct a strain-specific risk factor analysis. We will use the WGS strain-level data to identify likely routes of S. aureus transmission to youngstock. Specifically, we will use SNPs as markers for a modified microbial source tracking (MST) analysis, which supports identification of source(s) and sink(s) of specific populations of bacteria (in this case, strains of S. aureus), within a defined environment (in this case, the farm). If not enough strain-specific data exist for MST, we will evaluate phylogenetic clustering patterns to identify strains found across youngstock and environmental samples within a farm, indicating a likely transmission route.Objective 3 MethodsWe will use a four-step process to complete the objective: 1) Information-gathering; 2) Online modules development; 3) Online modules implementation and evaluation; 4) Fine tuning and dissemination.The decision to develop online modules was driven by the realities of dairy education at U.S. institutions of higher education. In essence, individual veterinary or animal science programs are unlikely to possess the requisite students, resources, faculty expertise, or facilities to adequately address the needs of the organic dairy industry on a national scale. Therefore, we decided to pursue a modular online curriculum, which can be an effective education tool for topical areas experiencing faculty shortages; in some cases, such tools even facilitate cross-institutional collaborations.