General Farm Biosecurity Practices
Bacteria, viruses, or other microscopic organisms (microbes) are called
infectious when they are capable of causing disease in exposed animals.
Follow these biosecure farm practices to reduce the risks of transmitting
disease at your farm.
Manure handling
Many infectious agents pass in feces or urine of infected animals. To reduce
the risk of spreading disease via manure, prevent contamination of feed and
water, and clean resting areas daily.

Plan and install a manure system to prevent environmental
contamination and comply with Vermont’s Acceptable Agricultural
Practices.

Maintain clean water troughs, water bowls, and feed mangers.

Use a separate skidsteer or loader bucket for manure and feed
operations.

Use separate shovels and forks for feeding and manure handling.

Compost or store manure under conditions that destroy most diseaseproducing bacteria.

Remove manure frequently from barns, yards, and holding areas to
prevent completion of life cycles by intestinal parasites and flies.

Control the fly population. Methods include flypaper, parasitic wasps,
and insecticides.

Store manure so it is inaccessible to livestock, especially young stock.

Prevent runoff of adult manure to young stock rearing areas or
contamination of feed fed to young animals. (This is especially
important for Johne’s control.)

Do not feed refusals from older animals to youngstock.

Keep dogs and cats out of feeding areas.

Clean teats and udders of livestock immediately before or after
parturition (birthing) so nursing young will not ingest manure if birth
is unattended.

Remove young from dam as soon as possible, i.e. before a dairy calf
or kid nurses.

Clean maternity areas between births.
Equipment sanitation

Clean and disinfect any equipment used on sick animals prior to use
on healthy herd mates.

Clean and disinfect dehorners, hoof knives, and clippers between
animals.

Use your own halters and clippers rather than borrowing them.

Sanitize nursing bottles and buckets after each feeding.
Employee sanitation

Wash farm clothing with detergents and bleach or washing soda.

Insist workers wash their hands before milking dairy animals and after
working with sick animals. Nitrile gloves are recommended when
frequent cleaning between animals is necessary.

Insist workers wear protective plastic or rubber gloves when assisting
with births.
Farm traffic, animal transport, and sanitation

Keep visitor and service vehicles from driving over feed delivery or
manure handling routes if at all possible.

Keep visiting vehicles out of areas accessible to livestock.

Locate holding pens for animal pickups near the road and away from
the barns or livestock areas.

Use only clean well-bedded trucks to move livestock to avoid
introducing diseases and to avoid injuries during transport.
Thoroughly wash and disinfect the inside, outside, and tires of
livestock-hauling trucks or other implements of husbandry shared
with neighbors.

Housing for different animal groups
Young animals acquire infectious diseases primarily through exposure with
older infected or carrier animals. To minimize disease transmission, housing
and management systems should minimize contact between young stock and
older animals. Younger animals need time to develop immunity to diseases.
Although the following recommendations are written for cattle, similar
principles apply to all livestock.

Separate pre-weaned dairy calves from all other age groups.
House each dairy calf in an individual pen or hutch.

Place hutches away from dairy barn exhaust fans.

House 4- to 8-month-old dairy calves in small groups separate from
older heifers.

House yearling and breeding age dairy heifers separately.

Separate replacement heifers from cows.

Separate dry dairy cows from milking cows.

If overwintered on pasture, move cows to a clean pasture for calving.

Milk mastitic, treated, or sick cows last, and disinfect the milking
claw between such animals.

Provide adequate pen, stall, or bedded area per animal.

Provide adequate feed bunk length and water trough access per
animal.

Organize chore routines to feed and milk isolated cattle after the main
herd.

Make sure farm dogs and cats are vaccinated against rabies.

Prevent fence-line contact between your stock and other animals.

Maternity and sick pens

Use maternity pens only for birthing animals.

Move pregnant animals to clean pastures or paddocks prior to
birthing.

Use sick pens only for sick animals

Segregate sick animals and prevent animal-to-animal contact between
sick pens and maternity pens.

Provide a clean environment for birthing. In cattle, this is important
to prevent the spread of Johne’s and Salmonella, calf scours, and fresh
cow mastitis.

Clean all manure from the pens after use.

Disinfect the walls and floors after use.

Allow the pens to dry after disinfection.

Bed the pens before the next animal enters.
Pen/hutch disinfection

Remove all bedding.

Remove sidewalls, gates, hog wire, if applicable.

Power wash or steam clean all wood, metal, or concrete surfaces.
 Note: ammonia compounds should not be mixed with chlorine
because the combination releases a harmful gas; acid compounds
mixed with chlorine release toxic chlorine gas.
 The hot water or steam will inactivate most pathogens.
 Protect yourself from aerosolized material; wear goggles and a
respirator.
 Rinse with a chlorox solution for additional sanitization.

If a high-temperature pressure washer is not available, scrub all
surfaces with detergent, rinse, and rinse again with a chlorox solution.

Let dry before bedding for next use.
Feed storage and bunk management

Make sure that feed bunks and storage areas are inaccessible to
rodents, birds, dogs, cats, and other wildlife.

Protect all feeding areas from animal carcasses and manure.

Follow optimal feed management practices.

Use smooth feeding bunks to minimize the surface area that could be
colonized by pathogens.

Dispose of feed refusals if not eaten within 24 hours. Do not feed
refusals from adult animals to youngstock. This is an important
Johne’s control measure.

Check for and dispose of moldy or spoiled material in silos, bunks,
and bins.

Clean in and around storage areas between batches of feed.

Rotate inventory to limit the amount of pathogens in stored feeds.

Keep covers on barrels and bins; make sure water is not getting into
storage areas.

Address any moisture problems periodically. Ensure that the storage
environment is appropriate for feed.

Apply manure to forages well before harvest.

Use optimal procedures for harvesting, handling, and storage of all
crops.
Water quality and trough management

Clean water troughs, buckets, or cups daily or weekly. Replace with
ones that are easier to clean if this is a bottleneck.

Protect all water sources from animal carcasses and manure.

Make sure a regular cleaning schedule of water troughs and tanks is
being followed.
Facility maintenance

Replace fly tape if necessary.

Be aware of hiding and denning places for rodents. Set baits or traps
accordingly. Use caution if dogs access same area.

Inspect and repair holes in buildings to prevent rodents from living
there.

Remove piles of boards, wood, or other junk.

Check for rain and storm water damage.

Identify and correct manure runoff problems.

Remove standing water, which can be a breeding ground for
mosquitoes.

Prevent standing water on the ground near water systems in pastures.

Check fences along farm and pasture perimeters; repair any damage.
Use electric fence wherever possible, if appropriate.

Make changes to bird detractors and fly tape or other control methods
as needed.

Replace bird netting where needed and change bird detractors so that
birds do not ignore their presence.
Boot cleaning and disinfection
Farms set up footbaths with the goal of preventing mechanical transmission
of pathogens among groups of animals. However, boot bath maintenance on
most facilities is poor, with gross contamination by organic matter
frequently observed. People commonly avoid stepping into boot baths or
simply step through the bath without stopping to clean their boots.
Organic material frequently inactivates or decreases the activity of
disinfectants. Thus, it is important to remove visible contamination with
soap and water to optimize the effectiveness of disinfection. Adopting the
following best management practices will minimize the risk of tracking
pathogens on footwear.

Clean visible dirt off of boots before
disinfecting.

Use water and a brush over a well-drained area.
A boot cleaning station (as pictured at right), in
which a hose is hooked up to a brush, is an
option.

Soak boots in a clean solution of an appropriate
disinfectant.

Use label recommendations for dilution rate and
exposure time.

Select disinfectants based on on-farm efficacy,
cost, ease of use, and environmental
friendliness. (See guide to disinfectants on next
5 pages.)
Disposable boots work well if protection is only needed for brief time
periods.
Photo: http://www.biosecuritycenter.org/bootdispr.htm
Disinfection in On-Farm Biosecurity
Choosing a disinfectant is a complex process. There is no one best product
for all situations. You must consider the disease risks about which you are
concerned, the type of surface you wish to disinfect, the conditions under
which the disinfectant will be used, and then select a disinfectant that best
suits your needs. When using a disinfectant, it is important to consider the
following points:
1. Most disinfectants won't work if the surface to be disinfected isn't
clean before applying the disinfectant.
 Organic materials such as soil, plant debris (like straw), milk,
blood, pus, and manure often inactivate some disinfectants or
protect germs from the disinfectant's active ingredients.
 Chlorine-based products are especially subject to this problem.

Wash boots, equipment, or housing areas first with water and
detergent.

Use steam and high-pressure washers to clean porous surfaces.
2. Disinfectants vary considerably in their activity against the assorted
germs—bacteria, viruses, fungi, and protozoa—associated with
livestock.
 Plain vinegar (4% acetic acid) will readily kill the Foot and
Mouth Disease virus, but is not effective against
Mycobacterium avium paratuberculosis (MAP), the cause of
Johne's disease.
 Most commonly used disinfectants are not active against
bacterial spores, which are the environmentally hardy life form
of the germs that cause tetanus, blackleg, botulism, and anthrax.
 The spectrum of activity of various classes of disinfectants is
shown in a chart later in this section.
3. It is important to select a disinfectant that will be active across a wide
spectrum of germs under the conditions in which it will usually be
used.

Check the pH (acidity or alkalinity) of your water. Hard water can
reduce or destroy the activity of some disinfectants.

Use the recommended water temperature for dilution or maintain
at the recommended ambient temperature to ensure optimal
activity.

Know the shelf life of the chemical or the age of the mixture.
Some lose activity fairly quickly after being diluted.

Record when you mix each solution of disinfectant and refresh
regularly. A solution that has been contaminated by organic
material like manure, will have decreased effectiveness.

Wear protective equipment if indicated. Some chemicals,
especially at full strength, may be toxic or cause damage to skin,
clothing, or environmental surfaces.
4. Disinfectants must have sufficient contact time with the surfaces to
allow them to kill the germs. The required contact time varies with
the product and the germ. In any case, a quick splash of a dirty boot
in a footbath is not likely to accomplish anything except to give a
false sense of security.

Allow sufficient contact time for the disinfectant to do its job.

Follow label directions closely and do not mix different classes of
disinfectants.
5. Disinfectants are not to be applied to animals directly, unless labeled
for such use.

Consult the label to make sure there are no warnings against using
them around feeders and in animal quarters.

Rinse disinfectants off after the appropriate amount of contact time
if animals will have contact with the disinfected surfaces.
Guide to Disinfectants
On most farms, disinfectants will be used in footbaths or for cleaning
equipment and livestock premises. The most commonly used disinfectants
fall into the following six classes.
Iodophors (e.g., Betadine® and Weladol®)
 Iodine compounds have been used as antiseptics and
disinfectants for many years.
 They are good disinfectants but are not as effective in the
presence of organic debris.
 Iodophors are generally less toxic than other disinfectants but
can stain clothes and some surfaces.

Keep away from metals and out of sunlight. These may
inactivate iodophor compounds.

Do not mix iodophors with quaternary ammonium
disinfectants. This will inactivate them.
Chlorine & Chloramines (e.g., bleach, Halazone®)
 Chlorine compounds are good disinfectants on clean surfaces
and have a broad spectrum of activity.
 They generally are more active in warm water.
 They can be somewhat irritating and can be harmful to clothing,
rubber goods, and some metals.
 Chlorine-based disinfectants are generally compatible with
soaps but should never be mixed with acids.

Use only after removing organic matter to optimize their
activity.

Mix a new solution of chlorine at least every 24 hours. Most
chlorine solutions are unstable and lose activity over time.
Chlorhexidine (e.g., Nolvasan® -S)
 Active against many bacteria and viruses.
 Not effective against spore-forming bacteria.

Use the formulation appropriate for what you are disinfecting.
There are formulations appropriate for hand washing and
sanitizing equipment such as Nolvasan® Skin and Wound
Cleanser or Surgical Scrub and Nolvasan® Solution
respectively.
Quaternary ammonium (e.g., Roccal DT)
 The older quaternary ammonium compounds are good for some
situations and relatively clean surfaces.
 They will not be particularly effective against the Foot and
Mouth Disease (FMD) virus or the cause of Johne's disease and
have markedly reduced activity in the presence of organic
material.
 Some of the newer quaternary ammonium preparations have
improved activity.
 Compounds in this class usually have some detergent action;
however, most are inactivated by contact with soaps or soap
residues.
Phenolic compounds (e.g., One Stroke Environ®, Osyl®, Amphyl®).
 Phenolics have good activity in hard water and in the presence
of some organic material.
 They are considered active against many bacteria, viruses, and
fungi, including the bacteria that cause tuberculosis and Johne's
disease.
 They are not effective against the FMD virus.
 They are good all-purpose disinfectants for farm use.
Per-oxygen compounds (e.g., Virkon S®, Oxy-Sept 333®
 Oxidizing agents such as Virkon S® appear to have a wide
spectrum of activity against many kinds of germs (including the
FMD virus). They are relatively stable in the presence of some
organic material.
 Oxy-Sept 333®, based on peroxyacetic acid, has been EPAapproved for killing the FMD virus and is reportedly active
against a broad spectrum of germs.
General Use Disinfectants
The following chart outlines the properties of disinfectants that are legal for
general use in Vermont.
Iodophors
Chlorine &
Chloramines
Quanternary
ammoniums
Phenols
Chlorhexidine
Per-oxy
compounds
Gram +
(Anthrax)
Good
Good
Good
Good
Some activity
Good
Gram –
(Brucella)
Good
Good
Some
activity
Good
Some activity
Good
Acid-fast
(TB)
Some
activity
Some
activity
Bad
Good
Some activity
Good
Spores
(Tetanus)
Some
activity
Some
activity
Bad
Bad
Some activity
Good
Viruses
(FMD)
Some
activity
Good
Variable
Some activity
Good
Good
Fungi
(Ringworm)
Good
Good
Some
activity
Some activity
Some activity
Good
Best pH
Acid
Acid
Basic
Acid
Wide Range
Acid
Activity
with
Organic
Material
Fair to poor
Very Poor
Very Poor
Excellent
Good
Good
Residual
activity
Yes
Yes
(Bleach : no)
No
Yes
Good
Good
Common
uses
On clean
equipment
On clean
equipment
On clean
equipment
On equipment
On premises
In footbaths
On equipment
On premises
In footbaths
On equipment
On premises
In footbaths
This table has been compiled from information gathered from the following three sites.
Virginia Polytechnic Institute and State University and Virginia State University
http://www.ext.vt.edu/pubs/poultry/408-310/table1.html
The Veterinary Service in Northern Ireland
http://www.dardni.gov.uk/vetservice/biosecurity/biodisinfectanttable.htm
Purdue University Cooperative Extension Bulletin PIH-80; reprints can be ordered through
http://www.agriculture.purdue.edu/agcomm/campus/other/mdc/order.html
FMD Disinfectants
The USDA has compiled the following table for field use in the event of a
Foot and Mouth Disease (FMD) outbreak.
Product
Dilution
Mixing Instructions
5.25% Sodium
Hypochlorite (NaOCI)
(household bleach)
3%
Add 3 gallons of
chlorine bleach to 2
gallons of water; mix
thoroughly.
Add 6.5 ounces of
glacial acetic acid to 1
gallon of water; mix
thoroughly.
Follow label instructions
Acetic acid*
4-5%
Potassium
Peroxymonosulfate and
Sodium Chloride
(i.e Virkon-S)
Sodium Carbonate
(soda ash)*
1%
Sodium Hydroxide
(NaOH)
(lye)*
2%
4%
Add 5.33 ounces of
sodium carbonate to 1
gallon of hot water (or 1
pound to 3 gallons of hot
water); mix thoroughly
Add 1/3 cup of NaOH
pellets (2.7 ounces of the
lye) to 1 gallon of cold
water; mix thoroughly
Notes
Vinegar is a 4%
solutions of acetic acid
Virkon-S
The solution is mildly
caustic but can dull paint
and varnished surfaces.
This solution is highly
caustic. Use protective
rubber clothing, gloves
and safety glasses.
WARNING: Always
add the lye to the water.
Never pour the water
over the lye.
* Section 18 application submitted and EPA approval pending.
** From National Emergency Response to a Highly Contagious Animal Disease, Executive Summary, March 30, 2001.
<http://www.aphis.usda.gov/oa/pubs/fco412.pdf>
Although common household bleach would be an effective disinfectant for
the FMD virus, the recommended concentration (3% sodium hypochlorite)
is 60% of full strength as it comes from the bottle. This concentration would
damage clothing, shoes, and rubber goods and is mildly corrosive to steel
surfaces. It can be used on an infected premise in an outbreak of FMD, but
probably wouldn't be a good choice as a general-purpose disinfectant for
equipment and footbaths. Vinegar will also kill the virus, but wouldn't be a
good choice for general use because of its lack of effectiveness against many
other important germs. Obviously, lye is too caustic for general use. See the
table on the previous page for disinfectants good for general use.