Core Module


The New York State Cattle Health Assurance Program (NYSCHAP) is an integrated disease prevention program that utilizes a team of advisors to develop a farm-specific herd health plan. 

The objectives of this integrated herd plan are to

  • increase the herd’s health, productivity and profitability
  • assure food safety, public health, and consumer confidence in animal agriculture
  • promote environmental stewardship

This Core Module is one of several modules that makes up NYSCHAP and is the starting point for enrollment in the program.  


An advisory team can help develop management plans to address complex issues faced by today’s farmers. One of the strengths of NYSCHAP is the strong emphasis on this cooperative "team" approach to develop and implement a health assurance program. Program success requires active participation from the producer, the herd veterinarian, employees, and advisors.  NYS Department of Agriculture and Markets' veterinarians or NYSCHAP certified veterinarians are involved with the initial risk survey and development of the herd plan. Additionally, they work with other team members to evaluate the herd plan annually and validate the farm’s implementation of the herd plan over the preceding year.

Implementing and adhering to disease prevention programs is challenging. Vitally important to success of this program is that team members, particularly the producer, veterinarian, and employees implementing the programs, are firmly committed to the principles and goals of the herd health plan. Accurate animal identification and health recording are also essential for program participation.

The NYSCHAP Concept

The core module of the program is represented by the hub of the wheel consisting of general "best management practices." These best management practices occupy the center of the health assurance wheel because they will benefit production, animal health, food safety, product quality and ultimately profit, regardless of the pathogen or herd stressor involved.
NYSCHAP logoThe individual modules "spin off" from the core and contain detailed and specific interventions designed to impact a particular issue or pathogen on the farm. The farm plan developed by the NYSCHAP team is farm-specific for each module. For example, if a producer wants to work towards the establishment of a Johne's disease control program, elements of the core best management practices are implemented, along with specific interventions designed to control and reduce Johne's disease on that farm.

NYSCHAP Farm Evaluation and Herd Plan Implementation

Step 1: Define Farm Goals and Areas of Concern

The core module provides the broadest level of risk assessment for the farm. The business plans and goals are reviewed. Areas of concern that members of the management team have are noted. Baseline farm data and information on current herd health status and production measures are collected to more appropriately develop the farm’s specific program.

Step 2: Assess the Risks

General biosecurity, animal health, quality assurance and environmental risks are then evaluated on the farm (see section below). The core module risk assessment considers the major pathways that disease organisms or conditions are introduced to and spread within the farm. Key management practices affecting food safety and quality and environmental stewardship are also reviewed.

Step 3: Develop the Herd Plan

The NYSCHAP team members (farm managers, farm employees, herd veterinarian, NYS Ag & Markets veterinarian, NYSCHAP certified veterinarian, etc.) develop a herd plan based on knowledge of conditions and goals specific to the farm. In putting the plan together, they will select only the appropriate best management practices for the farm’s goals, resources and risks.  Above all, the herd plan must be practical to implement.

Step 4: Implement the Herd Plan with All Farm Personnel

Upon completion of the enrollment visit, the NYS Ag & Markets veterinarian or NYSCHAP certified veterinarian documents the management practices in a herd plan, which is provide to the farm and the herd veterinarian. The herd plan, consisting of a prioritized list of best management practices specific to issues identified on the farm, is reviewed by the herd veterinarian and farm manager with farm personnel who have responsibility for the various procedures. This discussion explains the reasons for specific recommendations within the plan, allows for additional input from those actually performing the tasks, and acts to generate interest in and enthusiasm for the program.

Step 5: Evaluate the Herd Plan and Its Implementation

Annually, the entire team conducts a review of the herd plan. Modifications to the plan occur at this time and become the new herd plan. Depending on farm circumstance additional modules may be included in the updated herd plan.

Farms can request a certificate of participation that indicates the number of years of enrollment in the core program and any specific disease modules.  

Risk Factors Evaluated in the Core Module

The primary goal of the core module is to minimize disease introduction to, spread within, and transport off the farm. During the initial visit to the farm, the NYSCHAP team assesses the degree of risk to the farm in five key areas: biosecurity; manure management, feed and water management; facilities; and food quality assurance.

To accomplish this, all areas where infectious organisms could be introduced to the herd are evaluated. Disease problems in many herds originate when purchased animals enter the herd or home-raised animals return to the herd following a show or fair or raising at a contract grower. In other herds, the infectious organism may enter on the boots or clothing of a visitor, or perhaps on foot trimming equipment or with the livestock truck. The potential for introduction by feed and water is also evaluated.

Once in the herd, the spread of infectious organisms must be contained. Areas that can affect the spread of disease within the herd, such as the vaccination program, housing, animal grouping and density, personnel and equipment hygiene, and the order in which farm responsibilities are completed are also reviewed.

Manure may contain animal pathogens and it can be an environmental hazard. Therefore, manure must be managed to minimize the chances of ingestion by other farm livestock, particularly calves and young heifers. Manure must also be managed to minimize runoff into wellheads, streams and lakes. Feed and water can also harbor pathogens and contaminants, so management procedures affecting each of these areas are considered.

The facilities where animals are housed can have a major impact on animal health, well-being, and production. Facilities, equipment, animal handling, or treatment methods must be designed to minimize physical trauma and stress and maximize animal comfort and welfare. Areas including stall or housing design, footing, traffic alleys and flow, air quality, and over-crowding are assessed in the core module.

Consumer confidence in food safety and quality is very important to the success of the dairy and beef industries. Dairy cows, beef cows and bob veal calves supply approximately one third of the total non-fed beef produced in the United States. According to the National Market Cow and Bull Beef Quality Audit, food safety, animal welfare/handling, poor condition, antibiotic residues, carcass bruising, hide damage, lameness, condemnations/downer cows and injection site prevalence all decrease the quality of marketed beef and income for the producer. The quality assurance portion of the core module is designed to evaluate the use of antibiotics and drugs in order to minimize the chances of contaminated milk or meat. Treatment protocols, injection sites and cattle handling practices are reviewed to minimize damage to the carcass and maximize animal welfare. The goal of this part of the core program is to promote consumer confidence and product quality and enhance farm profitability.  

The Core Best Management Practices


  • Cattle should come from a reputable source. If possible, the attending herd veterinarian and the source herd's veterinarian need to establish a reasonable program for testing, vaccination, transport, and quarantine for purchased or re-entering cattle. Whenever possible, bring cattle in from a source herd with a defined health history for diseases of concern, including contagious mastitis, Johne’s disease, bovine viral diarrhea, bovine leukosis, heel warts, and Salmonella species infection. Quarantine incoming animals for a minimum of three to four weeks and use this time to monitor for clinical disease. Test additions if their health history is unknown.
  • Enhance immunity by maintaining an appropriate vaccination program for incoming and resident animals. Be certain that all calves have adequate colostrum in an appropriate timeframe.
  • Fenceline contact, contact at exhibitions etc. may also serve as sources of infection to the herd. Minimize contact with non-resident animals including cattle, other livestock, pets, pests, and wildlife to prevent introduction of infections spread by saliva, respiratory secretions, blood, urine, and feces. Use vaccination and segregation protocols to minimize these risks.


  • Farm visitors should not enter any facilities on the farm unless they have a real need to do so.
  • Visitors who have to enter animal facilities should wash their boots with a disinfectant or put on plastic boots before doing so. Likewise, insist that all employees, advisors and visitors enter only with clean clothing and disinfected equipment. Use good hygiene to prevent movement of manure around the farm. Provide boot brushes, disinfectant, and boot wash areas or disposable boots when there is movement between areas on the farm.
  • Start work routines with young stock and move toward adults to prevent contamination of young stock areas with adult manure. Handle sick animals last.
  • Work with every person who routinely enters the barn to make sure they understand concerns for biosecurity.

Vehicles and Equipment:

Establish parking areas away from any animals. Prevent movement of and contact with mud and feces introduced from other farms. Haul dead or down cows out to the rendering or cattle hauling vehicle as far away from the barn as possible.

  • Don't allow off-farm vehicles to drive into or through the barn. The potential to contaminate feed with manure from another farm and for fecal-oral transmission of disease is very real.
  • Equipment, such as hoof-trimming tables, should be washed thoroughly before it is brought into the facility. Equipment must be cleaned and disinfected between cows, groups, and farms.
  • Make sure that the feed wagon doesn't have to drive through manure before entering the barn or bunk silo. KEEP MANURE OUT OF THE FEED!
  • Use separate equipment for handling feed and manure.

Environment and Facilities:

  • Pay attention to ventilation in the barn, cow resting behavior and posture, stall design, footing, etc. Minimize overcrowding. Cow comfort plays a large role in the health of the animals.
  • Facilities must be maintained to eliminate risk of injury to cattle.
  • Be certain that facilities protect animals sufficiently from extreme environmental conditions.
  • Flooring, movement and handling of cows should be maintained and conducted in a way that minimizes the prevalence of lameness in the herd and allows as much time as possible for the cows to lie down. The natural resting behavior for cows includes 12-14 hours of rest per day. Cows that are non-ambulatory should be moved in a humane manner to an appropriate site that allows for access to feed and water, protection from environmental extremes and other animals, with non-slip flooring.

Nutrition & Feeding:

  • Provide feed that meets the physiological state of the animals and enhance immune function. Analyze forages to meet animal requirements and quality standards. Use clean equipment to mix and deliver feeds. Label pesticides and additives and store them safely away from feeds.
  • Buy feeds from dealers with quality controls in place. Ensure that the feedmill adheres to the FDA regulations regarding the ban on feeding mammalian proteins to ruminants. Adopt rodent control programs and keep pets and pests out of feedstuffs. The opportunity for feeds to be contaminated with salmonella or other organisms by rodents, birds or pets at the feedmill, or in storage on the farm is quite real.  


  • Be certain that all animals on the farm have free-choice access to water.
  • Check water occasionally for microbial contamination and other quality measures.
  • Keep cattle away from surface water sources that may be a point of entry or export for disease.

Manure Management:

  • Ensure that cow, people or vehicular traffic does not carry manure into feed or feed storage areas or between animal groups.
  • It is imperative to minimize adult manure in youngstock areas. Risk areas to be assessed include the maternity area, equipment that is used in both adult and youngstock areas and personnel that move between the groups.
  • Manure removal must be of sufficient frequency to avoid accumulation on animals, facilities and equipment.

Environmental Stewardship:

  • Manure must not be spread near watercourses, on hydrologically sensitive areas, or at times where the probability of runoff or subsurface flows is high.
  • Minimize potential for manure runoff from barnyards. Seal household and barnyard wells to prevent contamination of ground water.

Product Quality Assurance:

  • Accurate animal identification and health records are essential for health and quality assurance programs on farms.
  • Prevent meat and milk residues from drug or chemical contaminants by providing written standard operating procedures and employee training for drug use and storage, animal treatments, records, and drug withdrawal from milk and beef.
  • Prevent bruising and carcass condemnations. Handle and transport cattle in a way that minimizes stress, injury and/or bruising.
  • Inspect animal facilities and housing for sharp objects that can injure cattle.
  • Market cattle before they become either too fat or too thin and emaciated.
  • Market cattle with physical or health-related disorders in a timely manner to avoid condemnations and minimize unnecessary suffering. Euthanize animals that have health conditions that would increase the risk of becoming non-ambulatory in transport or those that may be condemned.
  • Eliminate all intramuscular injections in the hindquarters to protect the higher-value cuts obtained from this area.
  • Administer products labeled for subcutaneous (SQ) use in front of the shoulders. The preferred sites for intramuscular injection include the large muscle masses of the shoulder and neck only (no exceptions, regardless of age).

That sounds like a lot to keep track of on the farm. The best management practices described here represent a "laundry list" of most of the practices promoted by NYSCHAP. On any particular farm, only a handful of these might be included in the herd plan. The farm advisory team develops the priorities and decides how to address them. That's why it is especially important to involve everyone in the effort. If everyone takes responsibility for their part of a good herd plan the return to the farm is healthier more productive cows and a more profitable operation.

NYSCHAP can provide the structure to assess the most important disease issues on the farm and then develop a practical plan to reduce those risks.