U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

1

Contagious Equine Metritis (CEM) Testing for Imported Horses at Approved Quarantine Facilities 

 

1. Purpose and Background 

This document outlines procedures for testing imported horses for permanent entry 

from regions that the Animal and Plant Health Inspection Service (APHIS) considers 

affected with CEM and the approval criteria for CEM quarantine facilities.

This guidance document represents the Agency’s position on this topic and is intended 

solely as guidance. It does not have the force and effect of law, does not create, or confer 

any rights for or on any person, and does not bind the U.S. Department of Agriculture 

(USDA) or the public. Language suggesting that this guidance is mandatory (e.g., “shall,” 

“must,” “required,” or “requirement”) should not be construed as binding unless the 

terms quote from a statutory or regulatory requirement. The information this document 

contains may be made available to the public. While this document provides guidance for 

users outside APHIS, APHIS employees may not deviate from the directions provided 

herein without appropriate justification and supervisory concurrence.

2. Document Status 

A. Review date: 11/22/2026.

B. This document replaces Veterinary Services (VS) Guidance 13406.2, which is 

canceled.

3. Reason for Reissuance 

VS updated this document to reflect its reorganization and refinement of field practices.

4. Authority and References 

A. Authorities (Code of Federal Regulations (CFR)):

7 CFR 371.4

9 CFR 93.300

9 CFR 93.301

9 CFR 93.308 

B. References

Laboratories approved to conduct CEM tests.

VS Guidance 15202, Approval and Requirements for Laboratories to Conduct Tests for 

Contagious Equine Metritis
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

2

C. Definitions

1) Contagious equine metritis (CEM): A venereal disease of horses caused by

Taylorella equigenitalis, a Gram-negative coccobacillus.

2) Detergent (mild): A water-soluble cleansing agent that combines with impurities 

and dirt to make them miscible. It is more effective at removing fine dirt particles 

than soap when dissolved in water.

3) Disinfectant: A solution or product prepared at such a concentration to be 

bactericidal or bacteriostatic, and which does not cause tissue inflammation or 

irritation. This includes any solution that has been demonstrated to be bactericidal 

or bacteriostatic against Taylorella equigenitalis.

4) Equids: Horses, asses, mules, and zebras.

5) Facility: A building or designated area specifically approved for VS-mandated CEM 

quarantine and testing.

6) National CEM Coordinator: A VS Veterinary Medical Officer who oversees activities 

and duties of State CEM Coordinators. The National Coordinator prepares 

necessary documentation and reviews data submitted monthly from State CEM 

Coordinators.

7) State Animal Health Official (SAHO): A State Veterinarian or State Animal Health 

Technician.

8) State CEM Coordinator: A SAHO or a VS official who oversees operations at stateapproved CEM quarantine facilities. The State Coordinator is responsible for 

inspecting CEM quarantine facilities and monthly record keeping/reporting.

9) Test mare: A mare designated for testing stallions for CEM.

10) VS official: A full-time salaried employee who represents VS in the capacity of 

veterinary medical officer or animal health technician.

5. Audience 

VS employees, other federal and state agencies, and members of the public.

6. Guidance 

A. General

1) The 9 CFR 93.301(c) regulations contain provisions for importing horses for 

permanent entry from regions VS considers affected with CEM. After completing 

federal import quarantine, sexually intact horses over 731 days of age must be 

tested for CEM in an approved facility supervised by state or federal authorities 

prior to release for entry to the United States.

2) APHIS delegates authority to U.S. SAHOs to carry out certain CEM program 

responsibilities per 9 CFR 93.301 and this guidance, as well as inspection and 

approval of CEM quarantine facilities per 9 CFR 93.308. The responsibilities of 
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

3

both parties are described in a Memorandum of Understanding (MOU) (see 

Appendix 1).

3) Each state participating in testing imported horses under the CEM program at 

approved quarantine facilities must identify a State CEM Coordinator. VS 

designates a National CEM Coordinator who relays updates and other 

communications concerning CEM import testing to State CEM Coordinators.

4) T. equigenitalis is a fastidious organism, and adherence to sampling protocols is 

necessary to reduce the risk of false negative results. Testing methodology is a 

series of bacterial cultures, using samples obtained from various anatomical sites 

depending on gender, and by the serological testing of mares using a complement 

fixation test (CFT) for CEM antibodies.

5) An accredited veterinarian, state veterinarian, or VS veterinarian must collect test 

samples and monitor test breeding and treatments. When an accredited 

veterinarian performs the treatments, a SAHO or VS official must observe at least 

one treatment during the five-day treatment period.

6) The horses must not be treated with antibiotics or disinfectants while undergoing 

T. equigenitalis testing to avoid false negative culture results.

a. If a horse requires systemic antibiotic treatment, at least seven days between 

the last systemic treatment and an initial CEM culture must elapse.

b. If a horse receives topical antibiotic or disinfectant treatment of the external 

genitalia, at least 21 days between the last topical treatment and an initial 

CEM culture test must elapse.

B. Procedures for Approval of CEM Testing Facilities

A facility must meet the following minimum requirements for approval as described 

in this VSG to quarantine and treat imported horses for CEM. Individual states may 

institute additional standards for approval and inspection of facilities.

1) A facility must be approved before horses may be placed for CEM quarantine.

2) The state is responsible for inspecting and approving proposed quarantine 

facilities using the facility inspection report form in Appendix 2. CEM quarantine 

facilities must meet all requirements listed in this VSG and the inspection report 

form before approval. The State and National CEM Coordinators must review any 

requested deviation from these requirements for authorization.

3) The State CEM Coordinator must notify the National CEM Coordinator within ten

days of approving a facility, provide the completed facility inspection report form, 

and indicate the anticipated duration of the approval.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

4

a. The National CEM Coordinator reviews the inspection report form, notes any 

concerns, and addresses them with the State CEM Coordinator.

b. The facility may lose approval if the State CEM Coordinator does not give the 

inspection report to the National CEM Coordinator within ten days or address 

the National coordinator’s concerns in a timely manner.

4) Each State CEM Coordinator maintains a list of currently approved facilities and 

makes that list available to the National CEM Coordinator upon request.

5) The State CEM Coordinator must immediately notify the National CEM 

Coordinator when the state cancels the approval of a CEM facility for any reason.

C. Procedure for Reapproval of CEM Testing Facilities

1) Each state may determine the duration of approval of CEM quarantine facilities 

within that state; however, state personnel must inspect and re-approve active 

facilities at least every 365 days. States may elect to inspect and re-approve a 

facility each time horses are placed in quarantine.

2) The State CEM Coordinator is responsible for coordinating the re-approval of 

quarantine facilities with the National CEM Coordinator as per 6.B.3.

D. Facility Construction, Sanitation, and Security

1) The CEM quarantine facility must be an enclosed, sound, permanent building with 

surfaces (walls, floors, and ceilings) able to withstand frequent and effective 

cleaning and disinfection without deteriorating.

2) The facility must contain stalls where individual imported horses can be separated 

from each other, either by an empty stall, an empty area where horses cannot 

touch each other, or by a solid wall that is at least 8 feet (2.4 m) high.

3) The facility must provide separation and isolation from other horses and common 

traffic.

4) No physical contact may occur between horses in CEM import quarantine.

5) The owner may house test mares in a secure temporary stabling structure on the 

same premises as the facility if the structure can be effectively cleaned and 

disinfected.

a. Test mares housed in a secure temporary stabling structure may be 

commingled if the mares are not being used for test breeding and remain on 

the same premises as the CEM quarantine facility.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

5

b. Test mares must remain in the CEM quarantine facility while being used for 

test breeding until they meet all release requirements.

6) All entrances to the facility must clearly identify it as a quarantine area. Access to 

the facility must be limited to authorized personnel.

7) The facility must be large enough to accommodate the maximum number of 

horses indicated in the quarantine facility inspection report form.

8) The facility must be secure so that horses cannot escape or be removed without 

authorization and to prevent other animals from entering.

9) Drainage from the facility must not flow into parts of the premises containing 

other horses.

10) During the quarantine period, all equipment used for feeding, watering, 

grooming, and cleaning must remain in the quarantine area, and its use is limited 

only to the animals in quarantine. Personnel must clean and disinfect larger 

equipment (tractors, farm trucks, stalls) in the quarantine area before and after 

shared use on the same premises.

11) After each culture or treatment, personnel must place all gloves, sleeves, 

speculums, and other disposable materials in plastic garbage bags to be disposed 

of through incineration or burial. Alternatively, these materials may be stored 

until the quarantine is released (providing that all culture results are negative), 

when they may be disposed of as domestic waste.

12) The facility must be available to attending accredited veterinarians and state and 

VS personnel at any time necessary to conduct required testing or observe 

quarantine.

13) State or VS personnel must oversee horse owners and grooms in the quarantine 

area. All visitors must sign a visitor log on entry to the quarantine area. No pets 

may enter the quarantine area.

14) All horses under CEM quarantine must remain in the facility until released by a 

SAHO.

E. Quarantine and Biosecurity for Imported Horses

1) Quarantined horses must always be segregated.

a. Quarantined horses may be exercised in arenas or turned out into paddock 

areas separated from all other horses, maintaining the “no physical contact” 

requirement with quarantined and non-quarantined horses.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

6

b. Do not share grooming, cleaning supplies, or tack between quarantined and 

non-quarantined horses.

2) Do not breed, collect samples from, or subject horses under quarantine to genital 

examination or cleaning beyond what is required for CEM testing and treatment 

as detailed in section 6.F.

3) Fomites, especially contaminated reproductive equipment and contaminated 

artificial insemination equipment can transmit T. equigenitalis.

a. Use separate buckets, brushes, sponges, tack, etc., for each horse under 

quarantine.

b. Personnel must clean and disinfect all reusable equipment between 

quarantines.

4) If an imported mare foals or aborts before completing CEM testing, personnel 

should consider placental tissue, fetal membranes, and amniotic fluid as potential 

sources of T. equigenitalis transmission.

a. These materials, along with soiled bedding and any other potentially 

contaminated materials from foaling, should be properly disposed of by 

burial, incineration, or composting to minimize any risk of T. equigenitalis 

transmission.

b. Otherwise-soiled bedding and manure from the quarantine do not pose a risk 

for infection and can be disposed of as domestic waste as per standard 

practices for the facility.

5) Any horse found positive for T. equigenitalis on any testing performed (serology 

or culture) must remain in quarantine for additional treatment and testing until 

the horse tests negative for T. equigenitalis. The positive horse could be reexported before quarantine ends with the consent of the competent authority of 

the country of destination. The horse must be transported under official seal 

directly from the quarantine facility to the port of exit.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

7

F. Procedures for Imported Mares

NOTE: To exempt an imported mare in foal from the final cervical or endometrial 

culture, the owner or person transporting the mare must have an original letter 

signed by the examining veterinarian in the country of origin or a U.S. accredited 

veterinarian confirming that the mare is in foal and the approximate breeding date.

1) Arrival: Collect a serum sample and submit it to an approved laboratory for CFT 

(see Section K for additional guidance).

2) Culture sample collection.

a. Culture the mare 3 times over 12 days, with at least 72 hours between culture 

sets from the clitoral sinuses (use 1 small diameter (approximately 2 mm tip) 

swab for the 3 sinuses and separate swabs for the clitoral fossa). If the mare is 

not pregnant, the last set of culture samples must include a distal cervix or 

endometrium swab using a guarded uterine swab.

1. Do not scrub or use soap, disinfectant, or mild detergent on the sample 

sites before taking clitoral sinus or fossa swabs.

2. Use dry cleanup or minimal water if necessary to remove excess organic 

debris.

3. After collecting the third set of swabs from the clitoral sinuses and fossa, 

the external genitalia may be scrubbed using soap, disinfectant, or mild 

detergent before swabbing the distal cervix or endometrium.

4. Submit culture samples to an approved laboratory as per Section K.

b. If the mare requires medical treatment with antibiotics at any time during this 

culturing period, the mare must first complete the medical treatment and 

then restart the 12-day culturing period adhering to guidance in section 6.F.3

of this document.

c. For non-pregnant mares, include a swab of the distal cervix or endometrium 

with the third culture set.

1. Use 1 swab for the 3 sinuses and separate swabs for the clitoral fossa and 

the cervix or endometrium.

2. Pregnant mares do not need to have the distal cervix or endometrium 

cultured.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

8

3) CEM treatment

NOTE: VS strongly recommends delaying the treatment described in this section 

until you obtain negative culture results from the laboratory.

a. Plating and culture incubation of T. equigenitalis takes a minimum of 7 days. If 

a laboratory reports it is unable to perform a culture (e.g., overgrowth on the 

plate1 or delayed arrival of samples to the lab), then the mare will need to be 

re-cultured. If antibiotic or disinfectant treatment has already begun, 21 days 

must elapse from the end of treatment until the mare can be re-cultured.

b. Imported mares are treated for 5 consecutive days. A delay will occur if it is 

necessary to repeat culturing or if there is overgrowth that requires 

treatment.

c. First day of CEM treatment (prophylactic and clinical) procedures:

1. Infuse the clitoral sinuses with a small volume of a cerumenolytic agent, 

such as hydrogen peroxide or sodium bicarbonate, using either a curved 

tip 12-cc syringe or a syringe attached to a disposable 1-1/3 inch plastic 

teat infusion cannula.

2. Alternatively, bathe the clitoral area with the cerumenolytic agent and 

infuse the sinuses using digital manipulation. The difficulty you encounter 

in softening the smegma (“bean”) or other debris sufficiently for removal,

as described below, will determine the amount of cerumenolytic agent 

required.

3. Express the smegma from the central sinus of the clitoris by grasping the 

clitoris between the thumb and forefinger and gently squeezing while 

simultaneously pulling down and out. This method should displace the 

frenulum sufficiently to allow access to the central sinus.

4. Flush the sinuses with a small volume (e.g., 5.0-10.0 ml) of at least 2%

chlorhexidine scrub solution to remove all residual smegma and 

cerumenolytic agent.

5. Following flushing, clean and scrub the clitoral sinuses and clitoral fossa 

area using 2% or greater chlorhexidine scrub solution. Rinse the scrubbed 

areas.

1 Approved State laboratories or NVSL report bacterial overgrowth occurrences resulting from Pseudomonas, 

Proteus, etc., to the SAHO and National CEM coordinator, who address the occurrences case by case.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

9

6. After cleaning and rinsing, infuse the sinuses with an antibiotic ointment 

effective against T. equigenitalis, such as silver sulfadiazine or 0.2%

nitrofurazone. Personnel can accomplish infusion by working the ointment 

into the sinuses by hand.

7. After infusing the sinuses, coat the entire clitoral area, sinuses, and fossa 

with the antibiotic ointment.

d. Days 2 to 5 of treatment:

1. Clean and scrub the clitoral sinuses and clitoral fossa area using at least 

2% chlorhexidine scrub solution. Rinse the scrubbed areas.

2. After cleaning and rinsing, infuse the sinuses with an antibiotic ointment 

effective against T. equigenitalis, such as silver sulfadiazine or 0.2%

nitrofurazone. Personnel can accomplish infusion by working the ointment 

into the sinuses by hand.

3. After infusing the sinuses, coat the entire clitoral area, sinuses, and fossa 

with the antibiotic ointment.

4. Systemic and/or intrauterine antibiotics are not required, but the 

attending veterinarian, in consultation with regulatory officials, may 

authorize their use with topical treatment.

4) Release

The SAHO may release the mare from quarantine if all cultures and CFT results 

are negative, 5 days of wash and pack are completed, and no further treatment is 

required. If the CFT or any culture results are positive, the mare must be treated 

and re-cultured according to sections 6.F.2 through 6.F.3 of this document before 

release.

G. Procedure for Imported Mares Positive for T. equigenitalis

1) A mare is positive for T. equigenitalis when the CFT or culture results are positive.

2) Treat the mare as described in section 6.F.3 of this document.

3) No sooner than 21 days after the last topical or intrauterine treatment, repeat 3

sets of cultures on the mare as described in section 6.F.2.

4) If all culture sets are negative, perform treatment as described in section 6.F.3 of 

this document, then release the mare following re-treatment. A repeat CFT test is 

not required for release.

5) A positive mare must remain in quarantine until the mare is treated and culture 

negative for T. equigenitalis.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

10

H. Procedures for Imported Stallions

1) On arrival, collect 1 set of culture specimens from the stallion, ensuring samples 

arrive at the laboratory within 48 hours of culture collection.

a. Collect samples from the shaft of the penis and prepuce, urethral sinus, fossa 

glandis, and distal urethra using a separate swab for each of these 4 sites.

b. If necessary, clean swab sites with cotton and plain water to remove excess 

organic debris.

c. Do not scrub or use soap, disinfectant, or mild detergent cleaners on the 

sample sites before swabbing.

d. Submit samples to an approved laboratory as per Section K.

2) CEM culture results, test breeding, and treatment

a. Plating and culture incubation of T. equigenitalis takes a minimum of 7 days.

b. If the culture results are negative, proceed to breed 2 qualified test mares 

(see section 6.J of this document).

c. If a stallion is determined to be positive at any time during the process, 

suspend further testing and initiate treatment without test breeding mares 

(see section 6.F of this document).

d. Test breeding

1. Do not begin test breeding until negative culture results return for the 

imported stallion. After obtaining negative culture results, test breed the 

stallion to 2 qualified test mares (6.J).

2. Do not clean the external genitalia before or during testing since cleaning 

may lead to false negative culture results.

3. Do not scrub or use soap, disinfectant, or detergent cleaners on the test 

mare or stallion before breeding.

4. Test breeding consists of live cover of 2 qualified mares (see section 6.H of 

this document). The goal is to maximize contact time between the 

external genitalia of the stallion and the mare. At a minimum, each test 

mare must experience at least 2 complete penetrations from the stallion, 

at least one of which must result in ejaculation. Complete penetration 

means full insertion of the shaft of the penis into the vaginal vault of the 

mare.

5. The state is responsible for ensuring adequate oversight of test breeding.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

11

e. Treatment

1. After completing both test breedings, the stallion's prepuce, penis, fossa 

glandis, and urethral sinus must be thoroughly scrubbed with a cleansing 

agent such as 2% chlorohexidine while the stallion is in full erection (or 

using sedation to allow for exteriorization of the penis) once a day for five 

consecutive days.

2. After each cleaning, coat the penis, prepuce, and sheath with an antibiotic 

ointment effective against T. equigenitalis, such as silver sulfadiazine or 

0.2%) nitrofurazone, once a day for five consecutive days.

3. Systemic antibiotics may be used with topical treatment at the discretion 

of the attending accredited or regulatory veterinarian.

3) Post-breeding testing of test mares

a. Begin culture testing of test mares on the third day post-breeding. For the 

purposes of this section, the day after the date of breeding is considered the 

first day post-breeding.

b. Culture the mare 3 separate times during a 12-day period with at least 72

hours between culture sets from the clitoral sinuses (1 small diameter 

(approximately 2mm tip) swab for 3 sinuses) and clitoral fossa (1 swab). Swab 

the clitoral fossa as well as the distal cervix or endometrium.

c. Refer to section 6.K of this document for complete culture sample collection 

procedures.

d. Collect and submit a serum sample for CFT from test mares between days 21

and 28 post-breeding (6.K).

4) Release of import stallions

The SAHO may release a stallion from quarantine once it meets all the following 

requirements:

a. The stallion is negative on the pre-breeding culture set.

b. Post-breeding diagnostic tests are negative on the 2 qualified test mares (CFT 

and all post-breeding cultures).

c. The stallion has completed treatment.

5) Release of test mares

a. Test mares must remain in quarantine until negative results return for all tests 

for both test mares.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

12

b. If a test mare is confirmed positive on CFT or culture during post-breeding 

testing, treat and re-culture both test mares associated with the test breeding 

in accordance with section 6.J.

I. Procedures for Stallions Positive for T. equigenitalis

1) A stallion is positive for T. equigenitalis if any testing performed returns positive: 

Culturing of stallion, post-breeding cultures of test mares, or post-breeding CFT of 

test mares. An infected stallion must remain in quarantine until the stallion is 

treated and retested negative for T. equigenitalis.

2) Treat positive stallions according to Section 6.H.2) e.

3) After treatment, retest by culture according to Section 6.H.1) no fewer than 21

days after the last day of topical antibiotic treatment, and no fewer than 7 days 

after systemic antibiotic treatment.

4) If cultures are again negative, test breed the stallion according to Section 6.H.2

and post-breeding test the test mares according to Section 6.H.3.

5) For any positive stallions, repeat the culture, test mare breeding and testing, and 

treatment process until the stallion tests negative on all pre-breeding and test 

mare breeding cultures.

J. Qualifying Test Mares

1) Test mares must test negative for T. equigenitalis by CFT and by culture before 

any test breeding to imported stallions. Follow the culture sample collection 

protocol in Section 6.F.2.

2) After completing the 3 sets of cultures and determining the test mares are 

negative for T. equingenitalis by both culture and CFT, and before the mares are 

used for test breeding, they must be permanently identified with the capital letter 

“T” or other permanent identification approved by APHIS on a case-by-case basis. 

The letter “T” may be applied by hot branding, freeze branding, or lip tattooing, 

overseen by VS personnel, state authorities, or accredited veterinarians.

a. Apply brands on the left shoulder or left neck area, at least 2 inches high.

b. Apply lip tattoos to the inside surface of the upper lip. They must be at least 1

inch high and 0.75 inches wide.

3) Negative post-breeding cultures and CFTs within 45 days of initial blood draw on a 

test mare can serve as the qualifying tests, making the mare eligible for use as a 

test mare again if the mare remains on the same premises as the CEM quarantine 

facility.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

13

4) If a candidate test mare is positive on the CFT or cultures, this mare is considered 

positive for CEM and must be quarantined. Follow the procedures in Section 6.G. 

to release the mare from quarantine and requalify it.

K. Sample Collection and Submission

NOTE: Refer to VSG 15202 for additional guidance on specimen collection, 

identification, and transport.

1) Send all culture samples to a laboratory approved to conduct CEM testing within

the National Animal Health Laboratory Network (NAHLN) or to the National 

Veterinary Services Laboratories (NVSL). Send serum samples for CFT to NVSL, 

Cornell University, Ithaca, NY, or the University of Kentucky at Lexington.

2) Place swabs in Amies transport medium with charcoal (each swab in a single tube) 

and refrigerate.

3) The swabs that come in the Amies sample collection tubes are adequate to collect 

stallion samples and clitoral fossa samples from mares but are too large for the 

clitoral sinuses of mares. Cut off and discard the large swab from the tube cap 

and swab the sinuses with a small diameter swab, put the swab in the Amies, and 

replace the cap.

4) Specimens must include equine identification, collection date and time, and 

anatomical sites of the sample collected.

5) Submit completed specimen submission forms with the name, address, and 

phone/fax number of the submitting veterinarian, name of the owner or person 

responsible for the horse, location of the horse, complete animal identification, 

anatomical location sampled, and the date and time of collection.

6) Swabs must be shipped with ice packs to keep the specimens cold (4oC) on arrival. 

Use a commercial overnight service provider (Federal Express, United Parcel 

Service, etc.) or an approved third-party courier (as identified by the State CEM 

Coordinator) to ship the samples to the VS-approved CEM diagnostic laboratory.

7) All samples must reach the lab and be plated within 48 hours after collection. If 

the samples arrive more than 48 hours after collection, the laboratory must notify 

the facility to repeat the cultures.

8) NVSL must confirm all suspect samples. Approved CEM laboratories should send a 

swab of suspect T. equigenitalis colonies to NVSL in Amies media with charcoal. If 

suspect colonies are noted on multiple anatomical locations from the same set of 

swabs, send a suspect colony from each location in individual Amies media. Do 

not send the original swabs to NVSL.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

14

9) Specimens shipped to NVSL should be addressed to:

National Veterinary Services Laboratories,

Diagnostic Bacteriology Pathology Laboratory (DBPL) 

1920 Dayton Ave.

Ames, IA 50010

L. Communications, Recordkeeping, and CEM Database

1) The State and National CEM Coordinators will abide by all provisions for 

communications on approval of CEM quarantine facilities in Section 6.B.

2) The State CEM Coordinators will use a CEM Quarantine Tracking Spreadsheet 

provided by the National CEM Coordinator to capture testing and other 

information pertinent to imported stallions and mares in CEM quarantine 

facilities. The State CEM coordinator must email the completed spreadsheet 

monthly to VS.CEM.Data@usda.gov for entry into a national CEM database.

3) The National CEM Coordinator reviews the tracking spreadsheet data monthly to 

ensure compliance with testing and treatment protocols. When the National CEM 

Coordinator detects a discrepancy, they notify the State CEM Coordinator.

4) The National CEM Coordinator reviews all State CEM data and provides a 

quarterly summary report of CEM import data to State CEM Coordinators to 

review for accuracy.

5) The State CEM Coordinators must retain identification and horse treatment and 

release records of CEM quarantine facilities for at least 7 years.

6) The State CEM Coordinators will send copies of release records to the VS Animal 

Import Center or Port Services Office at the port of entry electronically (email 

addresses listed below) so office staff are aware of horses departing CEM state 

quarantine facilities.

7) If a horse tests positive for CEM while in quarantine, the State CEM Coordinator 

will notify the National CEM Coordinator within 24 hours via 

VS.CEM.Data@usda.gov.

7. Inquiries 

A. Ask the National CEM Coordinator for information about the national CEM database by 

emailing VS.CEM.Data@usda.gov.

B. Contact the office for the relative port of entry.

Port of Entry Email Address 
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

15

New York VSPSNIC@usda.gov

Miami notifymaic@usda.gov

Chicago VSDesPlaines@usda.gov

Los Angeles VSPSLAX@usda.gov

Puerto Rico Collateral.Port.Offices@usda.gov

All other ports Collateral.Port.Offices@usda.gov
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

16

Appendix I: EXAMPLE Memorandum of Understanding (MOU) 

State Contagious Equine Metritis Testing 

 

MEMORANDUM OF UNDERSTANDING (MOU) 

BETWEEN 

THE STATE OF _________(COOPERATOR) AND 

THE UNITED STATES DEPARTMENT OF AGRICULTURE ANIMAL AND PLANT HEALTH 

INSPECTION SERVICE (APHIS) VETERINARY SERVICES 

 

ARTICLE 1 - PURPOSE 

This MOU establishes the responsibilities of the Cooperating State in carrying out testing and 

treatment of horses imported into the United States from countries or regions affected with 

contagious equine metritis (CEM). CEM is a venereal disease of equines and is foreign to the 

United States. Horses subject to CEM regulations must remain under State quarantine until 

completing all required testing and treatment.

ARTICLE 2 - BACKGROUND 

To be permanently imported into the United States, stallions and mares over 731 days of age 

from CEM-affected countries must test negative for CEM and be treated, in accordance with 

9 CFR 93.301. Any State wishing to participate in CEM testing must enter into a written 

agreement with the APHIS Administrator that the State will conduct testing and treatment as 

specified in 9 CFR 93.301 and VS Guidance 13406.3, Contagious Equine Metritis (CEM) 

Testing for Imported Horses at Approved Quarantine Facilities.

 ARTICLE 3 - AUTHORITIES 

Under the Farm Security and Rural Investment Act of 2002, PL 107-171, Subtitle E, Animal 

Health Protection, Section 10401-10418 [subsequently the Animal Health Protection Act, 7 

U.S.C. 8301 et. seq.], the Secretary of Agriculture, to protect the agriculture, environment, 

economy, and health and welfare of the people of the United States by preventing, 

detecting, controlling, and eradicating diseases and pests of animals, is authorized to 

cooperate with foreign countries, States, and other jurisdictions, or other persons, to prevent 

and eliminate burdens on interstate commerce and foreign commerce, and to regulate 

effectively interstate commerce and foreign commerce.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

17

ARTICLE 4 - MUTUAL RESPONSIBILITIES 

The Cooperator and APHIS mutually agree to designate, in writing, an authorized 

representative for each party who shall be responsible for collaboratively administering the 

activities conducted under this MOU.

ARTICLE 5 - COOPERATOR RESPONSIBILITIES 

a. The State has entered into this written agreement with the Deputy Administrator, 

Veterinary Services, Animal and Plant Health Inspection Service (APHIS), United States 

Department of Agriculture or his or her designee, whereby the State agrees to 

enforce its laws and regulations to control CEM and to abide by the conditions of 

approval established by the regulations in Title 9, Code of Federal Regulations (9 CFR) 

Section 93.301.

b. The State agrees that stallions and mares shall be quarantined under State or Federal 

supervision until testing and treatment requirements have been met in accordance 

with 9 CFR 93.301(e)(2).

c. The State agrees to quarantine all stallions and mares over 731 days of age imported 

under 9 CFR 93.301 until the stallions have been treated in accordance with 9 CFR 

93.301(e)(3) and the mares have been treated in accordance with 9 CFR 93.301(e)(5).

d. The State agrees to quarantine all mares used to test stallions for CEM until the 

mares have been released from quarantine in accordance with 9 CFR 93.301(e)(4).

e. The State has laws or regulations requiring that stallions over 731 days of age 

imported under 9 CFR 93.301(e) be treated in the manner specified in 9 CFR 

93.301(e)(3), and that mares over 731 days of age imported under paragraph 9 CFR 

93.301(e) be treated in the manner specified in 9 CFR 93.301(e)(5).

f. The Administrator may suspend a State’s approval to receive stallions or mares 

imported from regions affected with CEM if they determine that the State is not 

meeting the requirements of 9 CFR 93.301. After the Administrator takes such action, 

APHIS will inform the State’s animal health authorities of the reasons for the action 

and afford them an opportunity to present their views before APHIS finalizes the 

suspension; however, such suspension of approval shall continue in effect unless the 

Administrator orders otherwise. In those instances where there is a disagreement as 

to the facts, a hearing shall be held to resolve such disagreements.

g. The proposed CEM quarantine facility will be inspected and/or reinspected and 

approved by a State or Federal official based on provisions established by the State 

Veterinarian and APHIS. Facility inspection and approvals will be renewed at least 
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

18

annually as the State Veterinarian or APHIS deems necessary. Quarantine facilities 

must meet all requirements listed in VSG 13406 and on the inspection report form 

prior to approval. Any requested deviation from these requirements must be 

authorized by both the State and National CEM Coordinators. Failure to provide the 

inspection report to the National CEM Coordinator within 10 days or to adequately

address their concerns in a timely manner may result in the facility losing approval. 

Each State may determine the duration of approval of CEM quarantine facilities 

within that State if State personnel inspect and re-approve active facilities at least 

annually. States may elect to inspect and re-approve a facility each time horses are 

placed for quarantine. The State CEM Coordinator is responsible for coordinating reapproval of quarantine facilities with the National CEM Coordinator.

h. The State CEM Coordinators will use a CEM quarantine tracking spreadsheet provided 

by the National CEM Coordinator to capture testing and other information pertinent 

to imported stallions and mares in CEM quarantine facilities. The National CEM 

Coordinator reviews the tracking spreadsheet data monthly (including number of 

horses in quarantine and positive cases, if any) to ensure compliance with testing and 

treatment protocols. When the National CEM Coordinator detects a discrepancy, he 

or she notifies the State CEM Coordinator.

i. The collection of blood samples, culture specimens, and CEM treatment will be 

performed by a veterinarian who is accredited in the State of the CEM quarantine 

facility and approved by the State CEM coordinator. Specimen collections, test 

breeding, and/or treatments will be monitored by a State or Federal official.

j. All blood samples and culture specimens will be collected at the appropriate sampling 

frequency and delivered to the appropriate APHIS-approved testing laboratory to 

conduct CEM testing following the procedures specified in 9 CFR 93.301.

k. If the State wishes to withdraw its approval to conduct CEM quarantine and testing of 

horses imported from countries affected with CEM, the State Veterinarian may 

submit this request in writing to APHIS.

ARTICLE 6 - STATEMENT OF NO FINANCIAL OBLIGATION 

Signature of this MOU does not constitute a financial obligation on the part of APHIS. Each 

signatory party is to use and manage its own funds in carrying out the purpose of this MOU. 

Transfers of funds or items of value are not authorized under this MOU.

ARTICLE 7 - LIMITATIONS OF COMMITMENT 

This MOU and any continuation thereof shall be contingent upon the availability of funds 

appropriated by the Congress of the United States. It is understood and agreed that any 

monies allocated for purposes covered by this MOU shall be expended in accordance with its 
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

19

terms and the manner prescribed by the fiscal regulations and/or administrative policies of 

the party making the funds available. If fiscal resources are to transfer, a separate agreement 

must be developed by the parties.

ARTICLE 8 - CONGRESSIONAL RESTRICTION 

Under 41 USC 22, no member of, or delegate to, Congress shall be admitted to any share or 

part of the MOU or to any benefit to arise therefrom.

ARTICLE 9 – NONDISCRIMINATION CLAUSE 

The United States Department of Agriculture prohibits discrimination in all its programs and 

activities on the basis of race, color, national origin, age, disability, and where applicable, sex, 

marital status, familial status, parental status, religion, sexual orientation, genetic 

information, political beliefs, reprisal, or because all or a part of an individual’s income is 

derived from any public assistance program. Not all prohibited bases apply to all programs.

ARTICLE 10 - LIABILITIES 

APHIS assumes no liability for any actions or activities conducted under this agreement 

except to the extent the recourse or remedies are provided by Congress under the Federal 

Tort Claims Act (28 U.S.C. 1346(b), 2401(b), 2671-2680).

ARTICLE 11 - AMENDMENTS 

This MOU may be amended at any time by mutual agreement of the parties in writing.

ARTICLE 12 - TERMINATION 

This MOU may be terminated at any time by mutual agreement of the parties in writing, or 

by either party upon 60 days’ written notice to the other party.

ARTICLE 13 - EFFECTIVE DATE AND DURATION 

This MOU will be in effect upon date of final signature and shall remain in effect for 5 years.

STATE OF _____________________________________ 

______________________________________________ Date _________________

State Veterinary Official

______________________________________________ Date _________________

National CEM Coordinator
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

20

National CEM coordinator Date
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

21

Appendix 2: CONTAGIOUS EQUINE METRITIS (CEM) QUARANTINE FACILITY INSPECTION 

REPORT FORM 

NAME OF OWNER/OPERATOR OF 

PREMISES 

 STATE ANIMAL HEALTH OFFICIAL (SAHO) 

SERVING AS STATE CEM COORDINATOR 

STREET ADDRESS STREET ADDRESS 

CITY STATE ZIP CITY STATE ZIP 

TELEPHONE NUMBER TELEPHONE NUMBER 

MOBILE TELEPHONE NUMBER MOBILE TELEPHONE NUMBER 

EMAIL EMAIL 

 

Describe facility being inspected (attach map of facility or floor plan of barn if available): 

 

 

 

 

 

Facility can accommodate (maximum number) _________horses. 

 

Facility is approved to house: Mares / Stallions / Both 
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

22

 YES NO 

1. The facility owner, operator (if different), and attending personnel have 

read and agree to carry out the provisions in Title 9, Code of Federal 

Regulations (9 CFR) 93.308(c)(3) and the recommendations in VS Guidance 

13406 that pertain to the quarantine of horses from CEM-affected regions or 

countries. 

 

2. The facility includes a separate enclosed building or separate area of the 

building of sound permanent construction, capable of being effectively 

cleaned and disinfected. 

 

3. The quarantine area is clearly identified by posted signs. 

4. The facility is large enough to accommodate all animals involved in the 

quarantine. 

 

5. The facility contains stalls where individual horses can be kept separate 

from each other by either an empty stall, an empty area where horses cannot 

touch each other, or by a solid wall that is at least 8 feet (2.4 m) high. The 

facility provides isolation from other horses and common traffic. Nose-to-nose 

contact does not occur. 

 

6. The facility is secure so that horses may not escape or be removed from the 

facility without authorization and to prevent other animals or unauthorized 

personnel from entering. 

 

7. The facility has an adequate drainage setup so that discharge shall not flow 

into areas where other horses are being maintained. 

 

8. The facility can dispose of manure, bedding, waste, and any related shipping 

materials in a manner that will prevent the dissemination of disease and that 

is approved by a SAHO. 

 

9. During the quarantine period, the facility will keep all equipment used for 

feeding, watering, grooming, and cleaning in the quarantine area. Use of the 

equipment will be limited to the animals in quarantine. 

 

10. After each culture or treatment, the facility can place all gloves, sleeves, 

speculums, and other disposable material in plastic garbage bags and dispose 

of them as regulated garbage through incineration or burial. Alternatively, the 

facility can store these materials until the quarantine is released, when (if all 

cultures are negative), they may be disposed of as non-regulated garbage. 

 
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

23

11. The facility will not permit pets in the quarantine area. Horse owners and 

visitors must be authorized by State or APHIS personnel to enter the 

quarantine area. Authorized visitors are to sign a logbook upon entering and 

exiting the quarantine area. 

 

12. The facility agrees that all horses under CEM quarantine must remain in 

the facility until released by a SAHO. Horses under CEM quarantine may be 

moved under permit for emergency medical care. 

 

13. The facility can keep horses separated at all times; see #5 for details. 

Grooming and cleaning supplies and tack are not shared. 

 

14. The facility agrees that horses under quarantine will not be bred, collected, 

or subjected to genital examination or cleaning beyond what is required for 

CEM testing as detailed in the VS Guidance 13406. 

 

15. The facility uses separate buckets, brushes, sponges, tack, etc., for each 

horse under quarantine unless the equipment is cleaned and disinfected 

between each horse as approved by the SAHO. All reusable equipment is 

cleaned and disinfected between quarantines. 

 

16. The facility has adequate food, water, and shelter for all horses being 

tested/treated in the CEM quarantine facility. 

 

17. The facility has sufficient protective clothing (disposable gloves, at a 

minimum) available for all facility personnel at the entrance of the CEM 

quarantine facility. 

 

18. The facility has footbath containers at the entrance and exit of the facility 

or rubber boots or disposable plastic shoe covers to be worn within the 

facility. 

 

19. The facility has a supply of disinfectant approved by the SAHO to apply to 

all fixed and movable surfaces and equipment exposed to the quarantined 

animal prior to use. 

21. The facility personnel know the appropriate restricted physical contact 

between horses in the quarantine facility. Personnel will not share daily care 

equipment between horses. 

22. The facility agrees to oversee the cleaning and disinfection by horse 

transport personnel of all trailers with an approved disinfectant before leaving 

the premises when any transportation of CEM quarantined horses occurs as 

required by VS Form 1-27 (if item 16 is marked “Yes” by the form preparer). 
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 13406.3 

___________________________________________________________________ 

24

23. Additional State facility checklist items (attached). 

Entrance to this facility shall be granted to personnel authorized by the SAHO or USDA/APHIS 

official at any time necessary to inspect the premises or to observe required testing. 

 

 

 

 

 

 

Print - Owner/Operator of Facility Print - State or Federal Official Conducting Inspection

Signature – Owner/Operator of Facility Signature – State or Federal Official Conducting Inspection

 Date Date