Equine Disease Quarterly Newsletter5in high commercial demand was responsible for
spread of the virus to breeding stock in 18 states
and two provinces in Canada, all within a two- tothree-week period. This resulted in outbreaks ofequine viral arteritis, abortion in naïve pregnant
mares, and establishment of the carrier state in avariable number of exposed stallions.
It must be emphasized that stallions that
continue to harbor equine arteritis virus, equine
herpesvirus 3 or T. equigenitalis are asymptomaticor clinically inapparent carriers. With the exception of infection with T. equiperdum, there is nomeans of knowing whether a stallion is a carrierof a particular venereal pathogen or not without
subjecting it to appropriate testing protocols forwhatever the agent under consideration might
be. Regardless of what venereal infection is being
screened for, however, it is critically importantthat such testing is carried out by a reputable veterinary diagnostic laboratory with an establishedrecord of competency and experience in testingfor that infection. The reliability of laboratory
testing is crucially important to the success of any
prevention and control program especially in thecase of equine viral arteritis and contagious equine
metritis.
A further confounding factor when dealing withstallions that are asymptomatic carriers of equine

arteritis virus or T. equigenitalis is the fact that the
majority of naïve mares to which they are bred
may subsequently exhibit minimal, if any, clinical evidence of infection. This leaves the breeder/
mare owner unaware that transmission of infection
has occurred and that the stallion in question is acarrier of either of these two venereal pathogens.
This could have significant consequences in thecase of equine arteritis virus should such an acutely
infected mare be pastured with naïve pregnant
mares. The 2008-2010 CEM event in the USA
illustrated how easily a stallion that was a carrierof T. equigenitalis could escape detection at time ofimportation and ultimately be responsible for thevery costly event that first came to light in 2008.
Past and recent experiences underscore theimportance of screening breeding stallions regardless of breed, for presence of the carrier state. Thisapplies especially to equine arteritis virus. Moreover, the responsibility for ensuring the safety ofbreeding stallion populations ultimately resides
with the equine industry.

The Importance of Cleaning to Disinfection
leaning and disinfecting stalls is criticallyimportant for biosecurity, especially in controlling disease outbreaks. However, much misinformation exists.
The average 1,000-pound horse produces 50
pounds of manure and urine per day. Add on tothat other body fluids that potentially containpathogens (nasal discharges, abscess material,
blood, etc.), and significant organic load exists inthe average horse stall. Any surface that needs tobe disinfected (treated with chemicals in order tokill pathogens) must be cleaned of dirt and organic
material first.
Cleaning a stall takes detergent and manuallabor. Power washers should not be used to avoid
aerosolizing pathogens. Despite advertising claims,
no “one step” product exists that can be sprayed ona dirty stall and effectively kill pathogens. Surfaces
must be scrubbed with a detergent or cleaning

Department of Veterinary Science
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, Kentucky 40546-0099
Address Service Requested

F U N D E D B Y U N D E R W R I T E R S AT L LOY D ' S , LO N D O N

OCTOBER 2016
Volume 25, Number 4

C O M M E N TA RY
IN THIS ISSUE
Commentary
International
Second Quarter2016  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  . 2

CONTACT:
Peter Timoney, MVB, MS, PhD, FRCVS
ptimoney@uky.edu(859) 218-1094
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

KENTUCKYC

Presorted Standard
US Postage Paid
Permit 51
Lexington KY

agent to loosen and remove as much organic matteras possible.
Detergents are cleaning agents that emulsify(loosen) organic matter without forming a “soapscum” residue. A detergent should be used to scrub
stall surfaces followed by rinsing to physically remove dirt and organic matter. Only after surfaces
have been cleaned should they be sprayed with adisinfectant.
Studies have shown that over 90% of bacteria
are removed from surfaces that are thoroughly
cleaned first. Considering that equine herpesviruses, influenza viruses, and equine arteritis virus
are lipid-enveloped, cleaning surfaces with detergent will disrupt this envelope, helping to renderthese viruses inactive.
While bleach is an effective disinfectant on“hard, non-porous, previously cleaned surfaces,”
horse stalls on farms are rarely constructed of

Equine Genomics .  .  .  . 3National
Fire Ants .  .  .  .  .  .  .  .  .  .  .  .  . 3Asymptomatic Carrier
Stallion .  .  .  .  .  .  .  .  .  .  .  .  .  . 4

such materials. Bleach is also rapidly inactivatedby organic matter.
Disinfectant labels state: “It is a violation ofFederal law to use this product in a manner inconsistent with its labeling.” Users should understandand follow label instructions and call the manufacturer with any specific questions. If the label states“dilute ½ ounce of disinfectant concentrate in one
gallon of water,” use that dilution. Increasing theamount of chemical assuming it will overcome adirty surface is a waste of time and money andcould pose health hazards to people and animals.
Never mix different disinfectants together.
For example, bleach combined with ammonia
or strong oxiders can produce lethal gas anddangerous chemical compounds. Every approved
disinfectant in the USA has a Safety Data Sheet(previously known as Material Safety Data Sheet)
which is available from the manufacturer andcontains valuable information.

The statement “Proven effective against thefollowing organisms,” followed by a long list ofpathogens, is on many disinfectant labels. However, in the fine print is how this list was generated.
Most disinfectants have been tested in the presenceof 5% serum as the “organic” load. A feces-stained
stall wall has an organic load much higher than
5% serum, which is why cleaning is critical to theeffectiveness of any disinfectant.
Excellent infection control and disinfectant
information is available at www.cfsph.iastate.edu
and at www.aaep.org.
CONTACT:
Roberta M. Dwyer, DVM, MS, DACVPM
rmdwyer@uky.edu(859) 218-1122
Department of Animal and Food Sciences
University of Kentucky
Lexington, KY

Kentucky
Cleaning andDisinfection  .  .  .  .  .  .  .  .  . 5

College of Agriculture,
Food and Environment
Department of
Veterinary ScienceIn this issue of the Equine Disease Quarterly, Dr.
Emma Adam discusses the new genomics tools
available to study horse diseases. Her authorshipof this article is particularly noteworthy sinceEmma initially trained as a veterinary surgeon
before returning to university to complete a Ph.D.
studying joint diseases in horses. She discoveredthat genomic tools were an effective way to address
problems that were not resolvable using earlier
technologies. Her article presents the “nuts andbolts” of horse genomics. As a point of reference, in1990 we had only characterized 50-100 genes forthe horse and confirmed the chromosome location
for a mere seven of them. Fast forward to 2009,
and the whole genome sequence for the horse had
been determined. The immediate application of
the sequence data at the time was to identify DNA
mutations responsible for well-known diseases of
the horse. However, that was only the beginning.
There was a drive to find out how genes function.
Everything that we do to a horse turns genes
on or turns them off. If genes are defective, it can
result in development of disease. Genes are also
important for performance. Some genes have variants that affect such things as type of gait, optimal
racing distance to reach performance potential, andbehavior. Many genes interact with management
practices such that horses may be more reactive or,alternatively, less responsive to certain feeding programs, training regimens, or vaccinations. Breeders
and trainers attempt to optimize management.
These observations clearly suggest that genomics
information has a place both in veterinary practiceand in the stable-yard.

Emma also has been among the scientists
developing tools to investigate genes, their expression, and their impact on horses. Before genomics, we basically fed, trained, or treated horses
then observed them to assess what the clinicalor phenotypic effects might be. Emma’s studies
pioneered another approach. Her studies entailed
comparing gene expression in joints and othercollagenous tissues at different stages of life, including several stages of embryonic development,
and then assessing which genes had an impact on
healthy growth of that tissue. Understanding thegenes that contribute to tissue development andrepair should lead to development of veterinary
therapeutics that benefit the health and welfare of
the horse and rider.
Emma is not alone in pioneering the use of
genomics for research on horses. A quick surveyof veterinary publications reveals scientists using
genomics to study reproduction, lameness, respiratory diseases, infectious diseases, immunology,
and more. We do not need to become molecular
geneticists to enjoy horses any more than we need
to become mechanics to drive a car. But we needto know, appreciate and encourage developmentof these new approaches. Watch that space!
CONTACT:
Ernie Bailey, PhD
ebailey@uky.edu(859) 218-1105
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

Pandora’s Box – Equine Genomics

2

I N T E R N AT I O N A L

Second Quarter 2016*

T

Equine Disease Quarterly
Editors

Peter Timoney
Alan Loynachan
Cynthia Gaskill

Staff

Diane Furry
Tawana Brown
Dennis Duross

Correspondence should be
addressed to the editors,
Department of Veterinary
Science, Maxwell H. Gluck
Equine Research Center,
University of Kentucky,
Lexington, Kentucky USA,40546-0099
Telephone (859) 257-4757
Fax (859) 257-8542
Internet address:
http://www.ca.uky.edu/
gluck/index.htm
Material published in the
Quarterly is not subject tocopyright. Permission istherefore granted toreproduce articles, althoughacknowledgment of thesource and author is requested.
The University of Kentucky
is an Equal Opportunity
Organization.

Printed on recycled paper

he International Collating Centre, Newmarket, United Kingdom, and other sources
reported the following disease outbreaks.
In early April, a case of African horse sickness wasreported in the Surveillance Zone, Western Cape
Province, Republic of South Africa. A total of 20 additional cases of infection with serotype 1 virus were
subsequently identified on seven other premises.
Equine influenza was reported by the UK and
the USA. One outbreak involving a limited number of cases was recorded in the UK. The disease isendemic in the USA; it was confirmed in six states.
Equine herpesvirus 1 and 4 (EHV-1, -4) related diseases were reported by France, Germany,
Ireland, Japan, Korea, Switzerland, the UK, andthe USA. Respiratory disease was diagnosed in
France (seven outbreaks, all isolated cases), Germany (nine cases involving eight premises), Ireland (four cases), and the USA (activity recorded
in various states). Abortion due to EHV-1 was
confirmed in France (two outbreaks), Germany(five cases), Japan (single cases on three premises),South Korea (one case), Switzerland (two cases inneonatal foals, one co-infected with Actinobacillus equuli), the UK (three outbreaks), and theUSA (three cases). EHV-1 neurologic disease
was reported by France (two outbreaks) andthe USA (four outbreaks ). Neuropathogenic or
non-neuropathogenic virus strains were involved.
EHV-4 respiratory disease was recorded by France(14 outbreaks), Germany (nine cases on six premises), and Switzerland (one outbreak involving
co-infection with EHV-1 and -4).
Strangles was reported by France (eightoutbreaks), Germany (10 cases involving eightpremises), Switzerland (three affected premises),
and the USA in which the disease was considered
endemic, with 57 affected premises recorded in 17
states, 10 with multiple outbreaks.
The USA identified two Warmblood stallion
carriers of equine arteritis virus.
A limited number of cases of EHV-2 and/or -5
infection also were recorded in the USA.

Equine infectious anemia was reported by
Canada and the USA. Canada confirmed a totalof 15 cases, one on a premises in British Columbia
and 14 divided between four premises in Saskatchewan, two linked epidemiologically. One case wasdiagnosed in a non-racing horse in Colorado, USA.
France (endemic), Spain (endemic), and the
USA reported cases of equine piroplasmosis. There
was an increase in case numbers in the USA; allwere Theileria equi positive Quarter horse racehorses, the majority in Texas, with some involvedin bush track racing.
Salmonellosis was recorded in Germany (onecase) and the USA (seven outbreaks involving
Group B Salmonella spp. and one Group C1
Salmonella spp.). Outbreaks of rotavirus infection
were confirmed in France (13 outbreaks). One
involved co-infection with rotavirus and coronavirus. The USA reported outbreaks of clostridial
enteritis; C. difficile was implicated in two outbreaks and C. perfringens in seven others. Isolatedcases of coccidiosis and Mycobacterium avium wererecorded by Switzerland and Singapore, respectively. Contagious equine metritis was reported byGermany, with 20 cases confirmed on 12 premises,
the majority in stallions. Icelandic, Warmblood,and Coldblood breeds were involved. The USA
diagnosed five cases of equine coital exanthema(EHV-3) and one case of nocardioform placentitis(Amycolatopsis spp.).
A total of 18 cases of Eastern Equine Encephalomyelitis were recorded in the USA, withthe majority identified in Florida (11) and South
Carolina (5).
West Nile Encephalitis reappeared in the second
quarter, with single cases confirmed in California
and Florida.
The USA reported one case of equine rabies in
Arizona.
Switzerland recorded two cases of ehrlichiosis
on separate premises.

T

he genetics of horses has been of great interest
to humans for millennia. While we may nothave used that term specifically, the recording ofequine parentage, births, and deaths was a practicethat pre-dated the compulsory recording of human births and deaths in Great Britain by over a
century. The term “genomics” covers all aspects ofgenes, including their structure and function, notjust the science of heredity.
The genome is all of the DNA, divided up
and packaged as chromosomes, in each cell. The
DNA molecule, the unit of heredity, is made up
of four nucleotide bases, guanine (G), cytosine(C), adenine (A), and thymine (T) in a sequence.
The equine genome consists of ~2,700 million
base pairs, which is similar in size to the humangenome.
Less than 3% of the genome actually codes forproteins. The remaining 97% was formerly termed“junk DNA” but we now know it orchestrates theuse of the entire genome, as regulatory elements.
Individuals have differences in the sequences of
the nucleotides. This is pretty obvious - we havegreys and bays but they are still horses. However, not all of the sequence differences are that
obvious, and sequence differences can be whole
sections of sequence or just single nucleotides. A
Single Nucleotide Polymorphism (SNP, usuallypronounced “snip”) is a single nucleotide in asequence that differs between individuals at a low
population frequency.
Approximately 10 million SNPs have beenfound in the collective equine genome. It is important to remember that SNPs are not necessarily
mutations that have any effect on the organism.
Indeed, SNPs are less likely to be found in theprotein coding genes of the genome as these areas
have been heavily selected for functionality by
evolution. Any change in DNA sequence that did
not benefit the animal would reduce its chances ofsurvival in the gene pool.

Science uses selected SNPs as a crude roadmap of the genome. By way of analogy, a set of
directions are like a SNP map. If I gave you somedirections, they might be: “Turn right at the pub,then take the second left after the church.” The
pub and the church have no actual bearing on thedestination, they are just guiding landmarks, andso it is with SNPs. SNPs that sit close together ona chromosome are likely to be inherited together.
Using commercial SNP arrays (“SNP chips”),
molecular biology techniques can rapidly hone inon a region of the genome that is different between
horses in terms of its SNP frequency.
SNP analysis is an immensely useful tool tonarrow down the search for areas of the genome
harboring genetic traits of interest, whether they
be a trait relating to disease or a desired trait.
Studies using this approach are called Genome
Wide Association Studies or GWAS (pronounced‘gee-waahs’).
The SNP-GWAS approach has helped identify
regions of interest in the genome in diseases such as
Lavender Foal Syndrome, Polysaccharide Storage Myopathy, recurrent laryngeal neuropathy, Foal Immunodeficiency Syndrome in the Fell and Dales pony,osteochondrosis dissecans (OCD), guttural pouch
tympany in Arabians and German warmbloods,
recurrent uveitis in German warmbloods, insect bite
hypersensitivity, and hydrocephalus in Friesians.
We have only just started to uncover the wealthof information the equine genome holds. Continued efforts for funding and research will yield
more mind-blowing results than our imagination
can fathom. Watch this space!
CONTACT:
Emma N. Adam, BVetMed, MRCVS,DACVIM-LA, DACVS-LA, PhD
emma.adam@uky.edu(859) 218-1175
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

N AT I O N A L

Fire Ant Surveillance for Horse Farms*First Quarter Report from AustraliaT

he red imported fire ant occurs in parts or allof Alabama, Arkansas, California, Florida,
Georgia, Louisiana, Mississippi, New Mexico,
North Carolina, Oklahoma, Puerto Rico, South
Carolina, Tennessee, Texas, and Virginia. Occa-

sionally, it has been found in Kentucky, Maryland,and Missouri (Figure 1). Fire ants like to establish
colonies in open sunny fields and pastures. Soil
moisture and winter temperatures round out the
major environmental factors that limit the spread

3

Figure 1. Fire ant colonies in the U.S.

Fire ant range:
Documented expansion
Possible expansion

4of this invasive insect. Changes in climate, alongwith the adaptability of the insect point to a continued gradual expansion of its boundaries.
The impact of the fire ant extends beyond thepain of its legendary sting. No significant adverse
effects to the health of foals or mature horses havebeen reported in states in which fire ants are widely
established. In addition to causing injury to workers, animals, and wildlife, this small insect affects
pasture maintenance, hay production, damages
equipment, and increases costs. Horse-farm managers in fire ant-infested areas have adjusted their
management practices and developed strategies
to live with this pest. The gradual northward andwestward expansion of the fire ant’s range exposes
more farm managers and stable and pleasure horseowners to this important pest. Those living along
the expansion front should become familiar withsome of the basics of fire ants and watch for ant
activity that seems out of the ordinary.
The familiar mound is the ant’s hallmark, butthere is one major difference when it comes tofire ants: Their mound is the typical pile of loose,fine soil but there is no central opening. Instead,fire ants enter and leave their colonies throughunderground tunnels that radiate from the mound.
Mound heights range from a few inches in mowed
areas to 18 inches in undisturbed areas. Repair ofa fire ant mound collapsed by a heavy rain results
in a loose, fluffy pile of soil a few days later.
Fire ants look like typical ants. They are small
but vary from 1/8- to 1/4-inch in length. The
head, thorax, and legs are red to brown with ablack abdomen. Positive identification of fireants requires collecting approximately a dozen
specimens in rubbing alcohol and taking themto your local Cooperative Extension Office. This
must be done carefully. Disturbing the moundusually prompts numerous ants to pour out andclimb up any vertical surface to sting the intruder.
Other ant species scurry about when the colony is
disrupted, working to protect the queen and movetheir brood to a safe place.
Collect the ants carefully to prevent being
stung. Dust baby powder on dishwashing gloves
and wear them because the ants cannot crawl up
dusted surfaces. Stay as far away from the moundas possible during collection and watch for ants
crawling on your shoes.
Follow up a positive identification of fire ants
with a careful examination of the property inspring or late fall to determine the number andlocation of active mounds. Fire ants are managed
by careful application of baits or mound drenchesof insecticides labeled for fire-ant control. Take
advantage of the excellent information available
on fire-ant management.
For more information, see Identifying Fire
Ants, http://articles.extension.org/pages/11278/
identifying-fire-ants.
CONTACT:
Lee Townsend, MS, PhD
Lee.Townsend@uky.edu(859) 257-7455
Department of Entomology
University of Kentucky
Lexington, KY

The Asymptomatic Carrier Stallion:
Critical Role in Venereal Disease Transmission

Source: http://www.ars.usda.gov/Research/docs.htm?docid=9165&pf=1&cg_id=0

A

range of venereally transmissible agents—viral, bacterial, and protozoal—have long been
known to establish persistence or the carrier state
in stallions, mares, or both. Some of these agents(e.g. Pseudomonas aeruginosa, certain capsule typesof Klebsiella pneumoniae and Streptococcus zooepidemicus) are commonplace in most domesticatedhorse populations. Others such as equine herpesvirus 3, equine arteritis virus, Taylorella equigenitalis,or T. asinigenitalis are less frequently encountered.
Of additional significance is Trypanosoma equiperdum, the causal agent of dourine, which thoughrarely reported nowadays, is reputedly still present
in certain regions/countries of the world.
Even though some but not all of the foregoing
agents can establish persistent infection in both thestallion and the mare, it is the carrier stallion thatplays a more important role in the epidemiologyof the respective infections. Not only has it thepotential to disseminate a particular infectious
agent among the mares to which it is bred, but ofeven greater long-term significance, it ensures thetransfer of infection from one breeding season to
the next.
While some of these agents, such as equine
arteritis virus and T. equigenitalis, can be transmitted either through natural service or artificial
insemination, the risk of more widespread transmission is much greater through the practice ofartificial insemination with fresh-chilled or frozen
semen from a carrier stallion. This was borne out
in the course of the 2006 equine viral arteritis
disease event in the USA, when fresh-chilled semen from a well-known Quarter horse stallion

Pandora’s Box – Equine Genomics

2

I N T E R N AT I O N A L

Second Quarter 2016*

T

Equine Disease Quarterly
Editors

Peter Timoney
Alan Loynachan
Cynthia Gaskill

Staff

Diane Furry
Tawana Brown
Dennis Duross

Correspondence should be
addressed to the editors,
Department of Veterinary
Science, Maxwell H. Gluck
Equine Research Center,
University of Kentucky,
Lexington, Kentucky USA,40546-0099
Telephone (859) 257-4757
Fax (859) 257-8542
Internet address:
http://www.ca.uky.edu/
gluck/index.htm
Material published in the
Quarterly is not subject tocopyright. Permission istherefore granted toreproduce articles, althoughacknowledgment of thesource and author is requested.
The University of Kentucky
is an Equal Opportunity
Organization.

Printed on recycled paper

he International Collating Centre, Newmarket, United Kingdom, and other sources
reported the following disease outbreaks.
In early April, a case of African horse sickness wasreported in the Surveillance Zone, Western Cape
Province, Republic of South Africa. A total of 20 additional cases of infection with serotype 1 virus were
subsequently identified on seven other premises.
Equine influenza was reported by the UK and
the USA. One outbreak involving a limited number of cases was recorded in the UK. The disease isendemic in the USA; it was confirmed in six states.
Equine herpesvirus 1 and 4 (EHV-1, -4) related diseases were reported by France, Germany,
Ireland, Japan, Korea, Switzerland, the UK, andthe USA. Respiratory disease was diagnosed in
France (seven outbreaks, all isolated cases), Germany (nine cases involving eight premises), Ireland (four cases), and the USA (activity recorded
in various states). Abortion due to EHV-1 was
confirmed in France (two outbreaks), Germany(five cases), Japan (single cases on three premises),South Korea (one case), Switzerland (two cases inneonatal foals, one co-infected with Actinobacillus equuli), the UK (three outbreaks), and theUSA (three cases). EHV-1 neurologic disease
was reported by France (two outbreaks) andthe USA (four outbreaks ). Neuropathogenic or
non-neuropathogenic virus strains were involved.
EHV-4 respiratory disease was recorded by France(14 outbreaks), Germany (nine cases on six premises), and Switzerland (one outbreak involving
co-infection with EHV-1 and -4).
Strangles was reported by France (eightoutbreaks), Germany (10 cases involving eightpremises), Switzerland (three affected premises),
and the USA in which the disease was considered
endemic, with 57 affected premises recorded in 17
states, 10 with multiple outbreaks.
The USA identified two Warmblood stallion
carriers of equine arteritis virus.
A limited number of cases of EHV-2 and/or -5
infection also were recorded in the USA.

Equine infectious anemia was reported by
Canada and the USA. Canada confirmed a totalof 15 cases, one on a premises in British Columbia
and 14 divided between four premises in Saskatchewan, two linked epidemiologically. One case wasdiagnosed in a non-racing horse in Colorado, USA.
France (endemic), Spain (endemic), and the
USA reported cases of equine piroplasmosis. There
was an increase in case numbers in the USA; allwere Theileria equi positive Quarter horse racehorses, the majority in Texas, with some involvedin bush track racing.
Salmonellosis was recorded in Germany (onecase) and the USA (seven outbreaks involving
Group B Salmonella spp. and one Group C1
Salmonella spp.). Outbreaks of rotavirus infection
were confirmed in France (13 outbreaks). One
involved co-infection with rotavirus and coronavirus. The USA reported outbreaks of clostridial
enteritis; C. difficile was implicated in two outbreaks and C. perfringens in seven others. Isolatedcases of coccidiosis and Mycobacterium avium wererecorded by Switzerland and Singapore, respectively. Contagious equine metritis was reported byGermany, with 20 cases confirmed on 12 premises,
the majority in stallions. Icelandic, Warmblood,and Coldblood breeds were involved. The USA
diagnosed five cases of equine coital exanthema(EHV-3) and one case of nocardioform placentitis(Amycolatopsis spp.).
A total of 18 cases of Eastern Equine Encephalomyelitis were recorded in the USA, withthe majority identified in Florida (11) and South
Carolina (5).
West Nile Encephalitis reappeared in the second
quarter, with single cases confirmed in California
and Florida.
The USA reported one case of equine rabies in
Arizona.
Switzerland recorded two cases of ehrlichiosis
on separate premises.

T

he genetics of horses has been of great interest
to humans for millennia. While we may nothave used that term specifically, the recording ofequine parentage, births, and deaths was a practicethat pre-dated the compulsory recording of human births and deaths in Great Britain by over a
century. The term “genomics” covers all aspects ofgenes, including their structure and function, notjust the science of heredity.
The genome is all of the DNA, divided up
and packaged as chromosomes, in each cell. The
DNA molecule, the unit of heredity, is made up
of four nucleotide bases, guanine (G), cytosine(C), adenine (A), and thymine (T) in a sequence.
The equine genome consists of ~2,700 million
base pairs, which is similar in size to the humangenome.
Less than 3% of the genome actually codes forproteins. The remaining 97% was formerly termed“junk DNA” but we now know it orchestrates theuse of the entire genome, as regulatory elements.
Individuals have differences in the sequences of
the nucleotides. This is pretty obvious - we havegreys and bays but they are still horses. However, not all of the sequence differences are that
obvious, and sequence differences can be whole
sections of sequence or just single nucleotides. A
Single Nucleotide Polymorphism (SNP, usuallypronounced “snip”) is a single nucleotide in asequence that differs between individuals at a low
population frequency.
Approximately 10 million SNPs have beenfound in the collective equine genome. It is important to remember that SNPs are not necessarily
mutations that have any effect on the organism.
Indeed, SNPs are less likely to be found in theprotein coding genes of the genome as these areas
have been heavily selected for functionality by
evolution. Any change in DNA sequence that did
not benefit the animal would reduce its chances ofsurvival in the gene pool.

Science uses selected SNPs as a crude roadmap of the genome. By way of analogy, a set of
directions are like a SNP map. If I gave you somedirections, they might be: “Turn right at the pub,then take the second left after the church.” The
pub and the church have no actual bearing on thedestination, they are just guiding landmarks, andso it is with SNPs. SNPs that sit close together ona chromosome are likely to be inherited together.
Using commercial SNP arrays (“SNP chips”),
molecular biology techniques can rapidly hone inon a region of the genome that is different between
horses in terms of its SNP frequency.
SNP analysis is an immensely useful tool tonarrow down the search for areas of the genome
harboring genetic traits of interest, whether they
be a trait relating to disease or a desired trait.
Studies using this approach are called Genome
Wide Association Studies or GWAS (pronounced‘gee-waahs’).
The SNP-GWAS approach has helped identify
regions of interest in the genome in diseases such as
Lavender Foal Syndrome, Polysaccharide Storage Myopathy, recurrent laryngeal neuropathy, Foal Immunodeficiency Syndrome in the Fell and Dales pony,osteochondrosis dissecans (OCD), guttural pouch
tympany in Arabians and German warmbloods,
recurrent uveitis in German warmbloods, insect bite
hypersensitivity, and hydrocephalus in Friesians.
We have only just started to uncover the wealthof information the equine genome holds. Continued efforts for funding and research will yield
more mind-blowing results than our imagination
can fathom. Watch this space!
CONTACT:
Emma N. Adam, BVetMed, MRCVS,DACVIM-LA, DACVS-LA, PhD
emma.adam@uky.edu(859) 218-1175
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

N AT I O N A L

Fire Ant Surveillance for Horse Farms*First Quarter Report from AustraliaT

he red imported fire ant occurs in parts or allof Alabama, Arkansas, California, Florida,
Georgia, Louisiana, Mississippi, New Mexico,
North Carolina, Oklahoma, Puerto Rico, South
Carolina, Tennessee, Texas, and Virginia. Occa-

sionally, it has been found in Kentucky, Maryland,and Missouri (Figure 1). Fire ants like to establish
colonies in open sunny fields and pastures. Soil
moisture and winter temperatures round out the
major environmental factors that limit the spread

3

Figure 1. Fire ant colonies in the U.S.

Fire ant range:
Documented expansion
Possible expansion

4of this invasive insect. Changes in climate, alongwith the adaptability of the insect point to a continued gradual expansion of its boundaries.
The impact of the fire ant extends beyond thepain of its legendary sting. No significant adverse
effects to the health of foals or mature horses havebeen reported in states in which fire ants are widely
established. In addition to causing injury to workers, animals, and wildlife, this small insect affects
pasture maintenance, hay production, damages
equipment, and increases costs. Horse-farm managers in fire ant-infested areas have adjusted their
management practices and developed strategies
to live with this pest. The gradual northward andwestward expansion of the fire ant’s range exposes
more farm managers and stable and pleasure horseowners to this important pest. Those living along
the expansion front should become familiar withsome of the basics of fire ants and watch for ant
activity that seems out of the ordinary.
The familiar mound is the ant’s hallmark, butthere is one major difference when it comes tofire ants: Their mound is the typical pile of loose,fine soil but there is no central opening. Instead,fire ants enter and leave their colonies throughunderground tunnels that radiate from the mound.
Mound heights range from a few inches in mowed
areas to 18 inches in undisturbed areas. Repair ofa fire ant mound collapsed by a heavy rain results
in a loose, fluffy pile of soil a few days later.
Fire ants look like typical ants. They are small
but vary from 1/8- to 1/4-inch in length. The
head, thorax, and legs are red to brown with ablack abdomen. Positive identification of fireants requires collecting approximately a dozen
specimens in rubbing alcohol and taking themto your local Cooperative Extension Office. This
must be done carefully. Disturbing the moundusually prompts numerous ants to pour out andclimb up any vertical surface to sting the intruder.
Other ant species scurry about when the colony is
disrupted, working to protect the queen and movetheir brood to a safe place.
Collect the ants carefully to prevent being
stung. Dust baby powder on dishwashing gloves
and wear them because the ants cannot crawl up
dusted surfaces. Stay as far away from the moundas possible during collection and watch for ants
crawling on your shoes.
Follow up a positive identification of fire ants
with a careful examination of the property inspring or late fall to determine the number andlocation of active mounds. Fire ants are managed
by careful application of baits or mound drenchesof insecticides labeled for fire-ant control. Take
advantage of the excellent information available
on fire-ant management.
For more information, see Identifying Fire
Ants, http://articles.extension.org/pages/11278/
identifying-fire-ants.
CONTACT:
Lee Townsend, MS, PhD
Lee.Townsend@uky.edu(859) 257-7455
Department of Entomology
University of Kentucky
Lexington, KY

The Asymptomatic Carrier Stallion:
Critical Role in Venereal Disease Transmission

Source: http://www.ars.usda.gov/Research/docs.htm?docid=9165&pf=1&cg_id=0

A

range of venereally transmissible agents—viral, bacterial, and protozoal—have long been
known to establish persistence or the carrier state
in stallions, mares, or both. Some of these agents(e.g. Pseudomonas aeruginosa, certain capsule typesof Klebsiella pneumoniae and Streptococcus zooepidemicus) are commonplace in most domesticatedhorse populations. Others such as equine herpesvirus 3, equine arteritis virus, Taylorella equigenitalis,or T. asinigenitalis are less frequently encountered.
Of additional significance is Trypanosoma equiperdum, the causal agent of dourine, which thoughrarely reported nowadays, is reputedly still present
in certain regions/countries of the world.
Even though some but not all of the foregoing
agents can establish persistent infection in both thestallion and the mare, it is the carrier stallion thatplays a more important role in the epidemiologyof the respective infections. Not only has it thepotential to disseminate a particular infectious
agent among the mares to which it is bred, but ofeven greater long-term significance, it ensures thetransfer of infection from one breeding season to
the next.
While some of these agents, such as equine
arteritis virus and T. equigenitalis, can be transmitted either through natural service or artificial
insemination, the risk of more widespread transmission is much greater through the practice ofartificial insemination with fresh-chilled or frozen
semen from a carrier stallion. This was borne out
in the course of the 2006 equine viral arteritis
disease event in the USA, when fresh-chilled semen from a well-known Quarter horse stallion

Pandora’s Box – Equine Genomics

2

I N T E R N AT I O N A L

Second Quarter 2016*

T

Equine Disease Quarterly
Editors

Peter Timoney
Alan Loynachan
Cynthia Gaskill

Staff

Diane Furry
Tawana Brown
Dennis Duross

Correspondence should be
addressed to the editors,
Department of Veterinary
Science, Maxwell H. Gluck
Equine Research Center,
University of Kentucky,
Lexington, Kentucky USA,40546-0099
Telephone (859) 257-4757
Fax (859) 257-8542
Internet address:
http://www.ca.uky.edu/
gluck/index.htm
Material published in the
Quarterly is not subject tocopyright. Permission istherefore granted toreproduce articles, althoughacknowledgment of thesource and author is requested.
The University of Kentucky
is an Equal Opportunity
Organization.

Printed on recycled paper

he International Collating Centre, Newmarket, United Kingdom, and other sources
reported the following disease outbreaks.
In early April, a case of African horse sickness wasreported in the Surveillance Zone, Western Cape
Province, Republic of South Africa. A total of 20 additional cases of infection with serotype 1 virus were
subsequently identified on seven other premises.
Equine influenza was reported by the UK and
the USA. One outbreak involving a limited number of cases was recorded in the UK. The disease isendemic in the USA; it was confirmed in six states.
Equine herpesvirus 1 and 4 (EHV-1, -4) related diseases were reported by France, Germany,
Ireland, Japan, Korea, Switzerland, the UK, andthe USA. Respiratory disease was diagnosed in
France (seven outbreaks, all isolated cases), Germany (nine cases involving eight premises), Ireland (four cases), and the USA (activity recorded
in various states). Abortion due to EHV-1 was
confirmed in France (two outbreaks), Germany(five cases), Japan (single cases on three premises),South Korea (one case), Switzerland (two cases inneonatal foals, one co-infected with Actinobacillus equuli), the UK (three outbreaks), and theUSA (three cases). EHV-1 neurologic disease
was reported by France (two outbreaks) andthe USA (four outbreaks ). Neuropathogenic or
non-neuropathogenic virus strains were involved.
EHV-4 respiratory disease was recorded by France(14 outbreaks), Germany (nine cases on six premises), and Switzerland (one outbreak involving
co-infection with EHV-1 and -4).
Strangles was reported by France (eightoutbreaks), Germany (10 cases involving eightpremises), Switzerland (three affected premises),
and the USA in which the disease was considered
endemic, with 57 affected premises recorded in 17
states, 10 with multiple outbreaks.
The USA identified two Warmblood stallion
carriers of equine arteritis virus.
A limited number of cases of EHV-2 and/or -5
infection also were recorded in the USA.

Equine infectious anemia was reported by
Canada and the USA. Canada confirmed a totalof 15 cases, one on a premises in British Columbia
and 14 divided between four premises in Saskatchewan, two linked epidemiologically. One case wasdiagnosed in a non-racing horse in Colorado, USA.
France (endemic), Spain (endemic), and the
USA reported cases of equine piroplasmosis. There
was an increase in case numbers in the USA; allwere Theileria equi positive Quarter horse racehorses, the majority in Texas, with some involvedin bush track racing.
Salmonellosis was recorded in Germany (onecase) and the USA (seven outbreaks involving
Group B Salmonella spp. and one Group C1
Salmonella spp.). Outbreaks of rotavirus infection
were confirmed in France (13 outbreaks). One
involved co-infection with rotavirus and coronavirus. The USA reported outbreaks of clostridial
enteritis; C. difficile was implicated in two outbreaks and C. perfringens in seven others. Isolatedcases of coccidiosis and Mycobacterium avium wererecorded by Switzerland and Singapore, respectively. Contagious equine metritis was reported byGermany, with 20 cases confirmed on 12 premises,
the majority in stallions. Icelandic, Warmblood,and Coldblood breeds were involved. The USA
diagnosed five cases of equine coital exanthema(EHV-3) and one case of nocardioform placentitis(Amycolatopsis spp.).
A total of 18 cases of Eastern Equine Encephalomyelitis were recorded in the USA, withthe majority identified in Florida (11) and South
Carolina (5).
West Nile Encephalitis reappeared in the second
quarter, with single cases confirmed in California
and Florida.
The USA reported one case of equine rabies in
Arizona.
Switzerland recorded two cases of ehrlichiosis
on separate premises.

T

he genetics of horses has been of great interest
to humans for millennia. While we may nothave used that term specifically, the recording ofequine parentage, births, and deaths was a practicethat pre-dated the compulsory recording of human births and deaths in Great Britain by over a
century. The term “genomics” covers all aspects ofgenes, including their structure and function, notjust the science of heredity.
The genome is all of the DNA, divided up
and packaged as chromosomes, in each cell. The
DNA molecule, the unit of heredity, is made up
of four nucleotide bases, guanine (G), cytosine(C), adenine (A), and thymine (T) in a sequence.
The equine genome consists of ~2,700 million
base pairs, which is similar in size to the humangenome.
Less than 3% of the genome actually codes forproteins. The remaining 97% was formerly termed“junk DNA” but we now know it orchestrates theuse of the entire genome, as regulatory elements.
Individuals have differences in the sequences of
the nucleotides. This is pretty obvious - we havegreys and bays but they are still horses. However, not all of the sequence differences are that
obvious, and sequence differences can be whole
sections of sequence or just single nucleotides. A
Single Nucleotide Polymorphism (SNP, usuallypronounced “snip”) is a single nucleotide in asequence that differs between individuals at a low
population frequency.
Approximately 10 million SNPs have beenfound in the collective equine genome. It is important to remember that SNPs are not necessarily
mutations that have any effect on the organism.
Indeed, SNPs are less likely to be found in theprotein coding genes of the genome as these areas
have been heavily selected for functionality by
evolution. Any change in DNA sequence that did
not benefit the animal would reduce its chances ofsurvival in the gene pool.

Science uses selected SNPs as a crude roadmap of the genome. By way of analogy, a set of
directions are like a SNP map. If I gave you somedirections, they might be: “Turn right at the pub,then take the second left after the church.” The
pub and the church have no actual bearing on thedestination, they are just guiding landmarks, andso it is with SNPs. SNPs that sit close together ona chromosome are likely to be inherited together.
Using commercial SNP arrays (“SNP chips”),
molecular biology techniques can rapidly hone inon a region of the genome that is different between
horses in terms of its SNP frequency.
SNP analysis is an immensely useful tool tonarrow down the search for areas of the genome
harboring genetic traits of interest, whether they
be a trait relating to disease or a desired trait.
Studies using this approach are called Genome
Wide Association Studies or GWAS (pronounced‘gee-waahs’).
The SNP-GWAS approach has helped identify
regions of interest in the genome in diseases such as
Lavender Foal Syndrome, Polysaccharide Storage Myopathy, recurrent laryngeal neuropathy, Foal Immunodeficiency Syndrome in the Fell and Dales pony,osteochondrosis dissecans (OCD), guttural pouch
tympany in Arabians and German warmbloods,
recurrent uveitis in German warmbloods, insect bite
hypersensitivity, and hydrocephalus in Friesians.
We have only just started to uncover the wealthof information the equine genome holds. Continued efforts for funding and research will yield
more mind-blowing results than our imagination
can fathom. Watch this space!
CONTACT:
Emma N. Adam, BVetMed, MRCVS,DACVIM-LA, DACVS-LA, PhD
emma.adam@uky.edu(859) 218-1175
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

N AT I O N A L

Fire Ant Surveillance for Horse Farms*First Quarter Report from AustraliaT

he red imported fire ant occurs in parts or allof Alabama, Arkansas, California, Florida,
Georgia, Louisiana, Mississippi, New Mexico,
North Carolina, Oklahoma, Puerto Rico, South
Carolina, Tennessee, Texas, and Virginia. Occa-

sionally, it has been found in Kentucky, Maryland,and Missouri (Figure 1). Fire ants like to establish
colonies in open sunny fields and pastures. Soil
moisture and winter temperatures round out the
major environmental factors that limit the spread

3

Figure 1. Fire ant colonies in the U.S.

Fire ant range:
Documented expansion
Possible expansion

4of this invasive insect. Changes in climate, alongwith the adaptability of the insect point to a continued gradual expansion of its boundaries.
The impact of the fire ant extends beyond thepain of its legendary sting. No significant adverse
effects to the health of foals or mature horses havebeen reported in states in which fire ants are widely
established. In addition to causing injury to workers, animals, and wildlife, this small insect affects
pasture maintenance, hay production, damages
equipment, and increases costs. Horse-farm managers in fire ant-infested areas have adjusted their
management practices and developed strategies
to live with this pest. The gradual northward andwestward expansion of the fire ant’s range exposes
more farm managers and stable and pleasure horseowners to this important pest. Those living along
the expansion front should become familiar withsome of the basics of fire ants and watch for ant
activity that seems out of the ordinary.
The familiar mound is the ant’s hallmark, butthere is one major difference when it comes tofire ants: Their mound is the typical pile of loose,fine soil but there is no central opening. Instead,fire ants enter and leave their colonies throughunderground tunnels that radiate from the mound.
Mound heights range from a few inches in mowed
areas to 18 inches in undisturbed areas. Repair ofa fire ant mound collapsed by a heavy rain results
in a loose, fluffy pile of soil a few days later.
Fire ants look like typical ants. They are small
but vary from 1/8- to 1/4-inch in length. The
head, thorax, and legs are red to brown with ablack abdomen. Positive identification of fireants requires collecting approximately a dozen
specimens in rubbing alcohol and taking themto your local Cooperative Extension Office. This
must be done carefully. Disturbing the moundusually prompts numerous ants to pour out andclimb up any vertical surface to sting the intruder.
Other ant species scurry about when the colony is
disrupted, working to protect the queen and movetheir brood to a safe place.
Collect the ants carefully to prevent being
stung. Dust baby powder on dishwashing gloves
and wear them because the ants cannot crawl up
dusted surfaces. Stay as far away from the moundas possible during collection and watch for ants
crawling on your shoes.
Follow up a positive identification of fire ants
with a careful examination of the property inspring or late fall to determine the number andlocation of active mounds. Fire ants are managed
by careful application of baits or mound drenchesof insecticides labeled for fire-ant control. Take
advantage of the excellent information available
on fire-ant management.
For more information, see Identifying Fire
Ants, http://articles.extension.org/pages/11278/
identifying-fire-ants.
CONTACT:
Lee Townsend, MS, PhD
Lee.Townsend@uky.edu(859) 257-7455
Department of Entomology
University of Kentucky
Lexington, KY

The Asymptomatic Carrier Stallion:
Critical Role in Venereal Disease Transmission

Source: http://www.ars.usda.gov/Research/docs.htm?docid=9165&pf=1&cg_id=0

A

range of venereally transmissible agents—viral, bacterial, and protozoal—have long been
known to establish persistence or the carrier state
in stallions, mares, or both. Some of these agents(e.g. Pseudomonas aeruginosa, certain capsule typesof Klebsiella pneumoniae and Streptococcus zooepidemicus) are commonplace in most domesticatedhorse populations. Others such as equine herpesvirus 3, equine arteritis virus, Taylorella equigenitalis,or T. asinigenitalis are less frequently encountered.
Of additional significance is Trypanosoma equiperdum, the causal agent of dourine, which thoughrarely reported nowadays, is reputedly still present
in certain regions/countries of the world.
Even though some but not all of the foregoing
agents can establish persistent infection in both thestallion and the mare, it is the carrier stallion thatplays a more important role in the epidemiologyof the respective infections. Not only has it thepotential to disseminate a particular infectious
agent among the mares to which it is bred, but ofeven greater long-term significance, it ensures thetransfer of infection from one breeding season to
the next.
While some of these agents, such as equine
arteritis virus and T. equigenitalis, can be transmitted either through natural service or artificial
insemination, the risk of more widespread transmission is much greater through the practice ofartificial insemination with fresh-chilled or frozen
semen from a carrier stallion. This was borne out
in the course of the 2006 equine viral arteritis
disease event in the USA, when fresh-chilled semen from a well-known Quarter horse stallion

Equine Disease Quarterly Newsletter5in high commercial demand was responsible for
spread of the virus to breeding stock in 18 states
and two provinces in Canada, all within a two- tothree-week period. This resulted in outbreaks ofequine viral arteritis, abortion in naïve pregnant
mares, and establishment of the carrier state in avariable number of exposed stallions.
It must be emphasized that stallions that
continue to harbor equine arteritis virus, equine
herpesvirus 3 or T. equigenitalis are asymptomaticor clinically inapparent carriers. With the exception of infection with T. equiperdum, there is nomeans of knowing whether a stallion is a carrierof a particular venereal pathogen or not without
subjecting it to appropriate testing protocols forwhatever the agent under consideration might
be. Regardless of what venereal infection is being
screened for, however, it is critically importantthat such testing is carried out by a reputable veterinary diagnostic laboratory with an establishedrecord of competency and experience in testingfor that infection. The reliability of laboratory
testing is crucially important to the success of any
prevention and control program especially in thecase of equine viral arteritis and contagious equine
metritis.
A further confounding factor when dealing withstallions that are asymptomatic carriers of equine

arteritis virus or T. equigenitalis is the fact that the
majority of naïve mares to which they are bred
may subsequently exhibit minimal, if any, clinical evidence of infection. This leaves the breeder/
mare owner unaware that transmission of infection
has occurred and that the stallion in question is acarrier of either of these two venereal pathogens.
This could have significant consequences in thecase of equine arteritis virus should such an acutely
infected mare be pastured with naïve pregnant
mares. The 2008-2010 CEM event in the USA
illustrated how easily a stallion that was a carrierof T. equigenitalis could escape detection at time ofimportation and ultimately be responsible for thevery costly event that first came to light in 2008.
Past and recent experiences underscore theimportance of screening breeding stallions regardless of breed, for presence of the carrier state. Thisapplies especially to equine arteritis virus. Moreover, the responsibility for ensuring the safety ofbreeding stallion populations ultimately resides
with the equine industry.

The Importance of Cleaning to Disinfection
leaning and disinfecting stalls is criticallyimportant for biosecurity, especially in controlling disease outbreaks. However, much misinformation exists.
The average 1,000-pound horse produces 50
pounds of manure and urine per day. Add on tothat other body fluids that potentially containpathogens (nasal discharges, abscess material,
blood, etc.), and significant organic load exists inthe average horse stall. Any surface that needs tobe disinfected (treated with chemicals in order tokill pathogens) must be cleaned of dirt and organic
material first.
Cleaning a stall takes detergent and manuallabor. Power washers should not be used to avoid
aerosolizing pathogens. Despite advertising claims,
no “one step” product exists that can be sprayed ona dirty stall and effectively kill pathogens. Surfaces
must be scrubbed with a detergent or cleaning

Department of Veterinary Science
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, Kentucky 40546-0099
Address Service Requested

F U N D E D B Y U N D E R W R I T E R S AT L LOY D ' S , LO N D O N

OCTOBER 2016
Volume 25, Number 4

C O M M E N TA RY
IN THIS ISSUE
Commentary
International
Second Quarter2016  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  . 2

CONTACT:
Peter Timoney, MVB, MS, PhD, FRCVS
ptimoney@uky.edu(859) 218-1094
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

KENTUCKYC

Presorted Standard
US Postage Paid
Permit 51
Lexington KY

agent to loosen and remove as much organic matteras possible.
Detergents are cleaning agents that emulsify(loosen) organic matter without forming a “soapscum” residue. A detergent should be used to scrub
stall surfaces followed by rinsing to physically remove dirt and organic matter. Only after surfaces
have been cleaned should they be sprayed with adisinfectant.
Studies have shown that over 90% of bacteria
are removed from surfaces that are thoroughly
cleaned first. Considering that equine herpesviruses, influenza viruses, and equine arteritis virus
are lipid-enveloped, cleaning surfaces with detergent will disrupt this envelope, helping to renderthese viruses inactive.
While bleach is an effective disinfectant on“hard, non-porous, previously cleaned surfaces,”
horse stalls on farms are rarely constructed of

Equine Genomics .  .  .  . 3National
Fire Ants .  .  .  .  .  .  .  .  .  .  .  .  . 3Asymptomatic Carrier
Stallion .  .  .  .  .  .  .  .  .  .  .  .  .  . 4

such materials. Bleach is also rapidly inactivatedby organic matter.
Disinfectant labels state: “It is a violation ofFederal law to use this product in a manner inconsistent with its labeling.” Users should understandand follow label instructions and call the manufacturer with any specific questions. If the label states“dilute ½ ounce of disinfectant concentrate in one
gallon of water,” use that dilution. Increasing theamount of chemical assuming it will overcome adirty surface is a waste of time and money andcould pose health hazards to people and animals.
Never mix different disinfectants together.
For example, bleach combined with ammonia
or strong oxiders can produce lethal gas anddangerous chemical compounds. Every approved
disinfectant in the USA has a Safety Data Sheet(previously known as Material Safety Data Sheet)
which is available from the manufacturer andcontains valuable information.

The statement “Proven effective against thefollowing organisms,” followed by a long list ofpathogens, is on many disinfectant labels. However, in the fine print is how this list was generated.
Most disinfectants have been tested in the presenceof 5% serum as the “organic” load. A feces-stained
stall wall has an organic load much higher than
5% serum, which is why cleaning is critical to theeffectiveness of any disinfectant.
Excellent infection control and disinfectant
information is available at www.cfsph.iastate.edu
and at www.aaep.org.
CONTACT:
Roberta M. Dwyer, DVM, MS, DACVPM
rmdwyer@uky.edu(859) 218-1122
Department of Animal and Food Sciences
University of Kentucky
Lexington, KY

Kentucky
Cleaning andDisinfection  .  .  .  .  .  .  .  .  . 5

College of Agriculture,
Food and Environment
Department of
Veterinary ScienceIn this issue of the Equine Disease Quarterly, Dr.
Emma Adam discusses the new genomics tools
available to study horse diseases. Her authorshipof this article is particularly noteworthy sinceEmma initially trained as a veterinary surgeon
before returning to university to complete a Ph.D.
studying joint diseases in horses. She discoveredthat genomic tools were an effective way to address
problems that were not resolvable using earlier
technologies. Her article presents the “nuts andbolts” of horse genomics. As a point of reference, in1990 we had only characterized 50-100 genes forthe horse and confirmed the chromosome location
for a mere seven of them. Fast forward to 2009,
and the whole genome sequence for the horse had
been determined. The immediate application of
the sequence data at the time was to identify DNA
mutations responsible for well-known diseases of
the horse. However, that was only the beginning.
There was a drive to find out how genes function.
Everything that we do to a horse turns genes
on or turns them off. If genes are defective, it can
result in development of disease. Genes are also
important for performance. Some genes have variants that affect such things as type of gait, optimal
racing distance to reach performance potential, andbehavior. Many genes interact with management
practices such that horses may be more reactive or,alternatively, less responsive to certain feeding programs, training regimens, or vaccinations. Breeders
and trainers attempt to optimize management.
These observations clearly suggest that genomics
information has a place both in veterinary practiceand in the stable-yard.

Emma also has been among the scientists
developing tools to investigate genes, their expression, and their impact on horses. Before genomics, we basically fed, trained, or treated horses
then observed them to assess what the clinicalor phenotypic effects might be. Emma’s studies
pioneered another approach. Her studies entailed
comparing gene expression in joints and othercollagenous tissues at different stages of life, including several stages of embryonic development,
and then assessing which genes had an impact on
healthy growth of that tissue. Understanding thegenes that contribute to tissue development andrepair should lead to development of veterinary
therapeutics that benefit the health and welfare of
the horse and rider.
Emma is not alone in pioneering the use of
genomics for research on horses. A quick surveyof veterinary publications reveals scientists using
genomics to study reproduction, lameness, respiratory diseases, infectious diseases, immunology,
and more. We do not need to become molecular
geneticists to enjoy horses any more than we need
to become mechanics to drive a car. But we needto know, appreciate and encourage developmentof these new approaches. Watch that space!
CONTACT:
Ernie Bailey, PhD
ebailey@uky.edu(859) 218-1105
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

Equine Disease Quarterly Newsletter5in high commercial demand was responsible for
spread of the virus to breeding stock in 18 states
and two provinces in Canada, all within a two- tothree-week period. This resulted in outbreaks ofequine viral arteritis, abortion in naïve pregnant
mares, and establishment of the carrier state in avariable number of exposed stallions.
It must be emphasized that stallions that
continue to harbor equine arteritis virus, equine
herpesvirus 3 or T. equigenitalis are asymptomaticor clinically inapparent carriers. With the exception of infection with T. equiperdum, there is nomeans of knowing whether a stallion is a carrierof a particular venereal pathogen or not without
subjecting it to appropriate testing protocols forwhatever the agent under consideration might
be. Regardless of what venereal infection is being
screened for, however, it is critically importantthat such testing is carried out by a reputable veterinary diagnostic laboratory with an establishedrecord of competency and experience in testingfor that infection. The reliability of laboratory
testing is crucially important to the success of any
prevention and control program especially in thecase of equine viral arteritis and contagious equine
metritis.
A further confounding factor when dealing withstallions that are asymptomatic carriers of equine

arteritis virus or T. equigenitalis is the fact that the
majority of naïve mares to which they are bred
may subsequently exhibit minimal, if any, clinical evidence of infection. This leaves the breeder/
mare owner unaware that transmission of infection
has occurred and that the stallion in question is acarrier of either of these two venereal pathogens.
This could have significant consequences in thecase of equine arteritis virus should such an acutely
infected mare be pastured with naïve pregnant
mares. The 2008-2010 CEM event in the USA
illustrated how easily a stallion that was a carrierof T. equigenitalis could escape detection at time ofimportation and ultimately be responsible for thevery costly event that first came to light in 2008.
Past and recent experiences underscore theimportance of screening breeding stallions regardless of breed, for presence of the carrier state. Thisapplies especially to equine arteritis virus. Moreover, the responsibility for ensuring the safety ofbreeding stallion populations ultimately resides
with the equine industry.

The Importance of Cleaning to Disinfection
leaning and disinfecting stalls is criticallyimportant for biosecurity, especially in controlling disease outbreaks. However, much misinformation exists.
The average 1,000-pound horse produces 50
pounds of manure and urine per day. Add on tothat other body fluids that potentially containpathogens (nasal discharges, abscess material,
blood, etc.), and significant organic load exists inthe average horse stall. Any surface that needs tobe disinfected (treated with chemicals in order tokill pathogens) must be cleaned of dirt and organic
material first.
Cleaning a stall takes detergent and manuallabor. Power washers should not be used to avoid
aerosolizing pathogens. Despite advertising claims,
no “one step” product exists that can be sprayed ona dirty stall and effectively kill pathogens. Surfaces
must be scrubbed with a detergent or cleaning

Department of Veterinary Science
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, Kentucky 40546-0099
Address Service Requested

F U N D E D B Y U N D E R W R I T E R S AT L LOY D ' S , LO N D O N

OCTOBER 2016
Volume 25, Number 4

C O M M E N TA RY
IN THIS ISSUE
Commentary
International
Second Quarter2016  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  . 2

CONTACT:
Peter Timoney, MVB, MS, PhD, FRCVS
ptimoney@uky.edu(859) 218-1094
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

KENTUCKYC

Presorted Standard
US Postage Paid
Permit 51
Lexington KY

agent to loosen and remove as much organic matteras possible.
Detergents are cleaning agents that emulsify(loosen) organic matter without forming a “soapscum” residue. A detergent should be used to scrub
stall surfaces followed by rinsing to physically remove dirt and organic matter. Only after surfaces
have been cleaned should they be sprayed with adisinfectant.
Studies have shown that over 90% of bacteria
are removed from surfaces that are thoroughly
cleaned first. Considering that equine herpesviruses, influenza viruses, and equine arteritis virus
are lipid-enveloped, cleaning surfaces with detergent will disrupt this envelope, helping to renderthese viruses inactive.
While bleach is an effective disinfectant on“hard, non-porous, previously cleaned surfaces,”
horse stalls on farms are rarely constructed of

Equine Genomics .  .  .  . 3National
Fire Ants .  .  .  .  .  .  .  .  .  .  .  .  . 3Asymptomatic Carrier
Stallion .  .  .  .  .  .  .  .  .  .  .  .  .  . 4

such materials. Bleach is also rapidly inactivatedby organic matter.
Disinfectant labels state: “It is a violation ofFederal law to use this product in a manner inconsistent with its labeling.” Users should understandand follow label instructions and call the manufacturer with any specific questions. If the label states“dilute ½ ounce of disinfectant concentrate in one
gallon of water,” use that dilution. Increasing theamount of chemical assuming it will overcome adirty surface is a waste of time and money andcould pose health hazards to people and animals.
Never mix different disinfectants together.
For example, bleach combined with ammonia
or strong oxiders can produce lethal gas anddangerous chemical compounds. Every approved
disinfectant in the USA has a Safety Data Sheet(previously known as Material Safety Data Sheet)
which is available from the manufacturer andcontains valuable information.

The statement “Proven effective against thefollowing organisms,” followed by a long list ofpathogens, is on many disinfectant labels. However, in the fine print is how this list was generated.
Most disinfectants have been tested in the presenceof 5% serum as the “organic” load. A feces-stained
stall wall has an organic load much higher than
5% serum, which is why cleaning is critical to theeffectiveness of any disinfectant.
Excellent infection control and disinfectant
information is available at www.cfsph.iastate.edu
and at www.aaep.org.
CONTACT:
Roberta M. Dwyer, DVM, MS, DACVPM
rmdwyer@uky.edu(859) 218-1122
Department of Animal and Food Sciences
University of Kentucky
Lexington, KY

Kentucky
Cleaning andDisinfection  .  .  .  .  .  .  .  .  . 5

College of Agriculture,
Food and Environment
Department of
Veterinary ScienceIn this issue of the Equine Disease Quarterly, Dr.
Emma Adam discusses the new genomics tools
available to study horse diseases. Her authorshipof this article is particularly noteworthy sinceEmma initially trained as a veterinary surgeon
before returning to university to complete a Ph.D.
studying joint diseases in horses. She discoveredthat genomic tools were an effective way to address
problems that were not resolvable using earlier
technologies. Her article presents the “nuts andbolts” of horse genomics. As a point of reference, in1990 we had only characterized 50-100 genes forthe horse and confirmed the chromosome location
for a mere seven of them. Fast forward to 2009,
and the whole genome sequence for the horse had
been determined. The immediate application of
the sequence data at the time was to identify DNA
mutations responsible for well-known diseases of
the horse. However, that was only the beginning.
There was a drive to find out how genes function.
Everything that we do to a horse turns genes
on or turns them off. If genes are defective, it can
result in development of disease. Genes are also
important for performance. Some genes have variants that affect such things as type of gait, optimal
racing distance to reach performance potential, andbehavior. Many genes interact with management
practices such that horses may be more reactive or,alternatively, less responsive to certain feeding programs, training regimens, or vaccinations. Breeders
and trainers attempt to optimize management.
These observations clearly suggest that genomics
information has a place both in veterinary practiceand in the stable-yard.

Emma also has been among the scientists
developing tools to investigate genes, their expression, and their impact on horses. Before genomics, we basically fed, trained, or treated horses
then observed them to assess what the clinicalor phenotypic effects might be. Emma’s studies
pioneered another approach. Her studies entailed
comparing gene expression in joints and othercollagenous tissues at different stages of life, including several stages of embryonic development,
and then assessing which genes had an impact on
healthy growth of that tissue. Understanding thegenes that contribute to tissue development andrepair should lead to development of veterinary
therapeutics that benefit the health and welfare of
the horse and rider.
Emma is not alone in pioneering the use of
genomics for research on horses. A quick surveyof veterinary publications reveals scientists using
genomics to study reproduction, lameness, respiratory diseases, infectious diseases, immunology,
and more. We do not need to become molecular
geneticists to enjoy horses any more than we need
to become mechanics to drive a car. But we needto know, appreciate and encourage developmentof these new approaches. Watch that space!
CONTACT:
Ernie Bailey, PhD
ebailey@uky.edu(859) 218-1105
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

Pandora’s Box – Equine Genomics

2

I N T E R N AT I O N A L

Second Quarter 2016*

T

Equine Disease Quarterly
Editors

Peter Timoney
Alan Loynachan
Cynthia Gaskill

Staff

Diane Furry
Tawana Brown
Dennis Duross

Correspondence should be
addressed to the editors,
Department of Veterinary
Science, Maxwell H. Gluck
Equine Research Center,
University of Kentucky,
Lexington, Kentucky USA,40546-0099
Telephone (859) 257-4757
Fax (859) 257-8542
Internet address:
http://www.ca.uky.edu/
gluck/index.htm
Material published in the
Quarterly is not subject tocopyright. Permission istherefore granted toreproduce articles, althoughacknowledgment of thesource and author is requested.
The University of Kentucky
is an Equal Opportunity
Organization.

Printed on recycled paper

he International Collating Centre, Newmarket, United Kingdom, and other sources
reported the following disease outbreaks.
In early April, a case of African horse sickness wasreported in the Surveillance Zone, Western Cape
Province, Republic of South Africa. A total of 20 additional cases of infection with serotype 1 virus were
subsequently identified on seven other premises.
Equine influenza was reported by the UK and
the USA. One outbreak involving a limited number of cases was recorded in the UK. The disease isendemic in the USA; it was confirmed in six states.
Equine herpesvirus 1 and 4 (EHV-1, -4) related diseases were reported by France, Germany,
Ireland, Japan, Korea, Switzerland, the UK, andthe USA. Respiratory disease was diagnosed in
France (seven outbreaks, all isolated cases), Germany (nine cases involving eight premises), Ireland (four cases), and the USA (activity recorded
in various states). Abortion due to EHV-1 was
confirmed in France (two outbreaks), Germany(five cases), Japan (single cases on three premises),South Korea (one case), Switzerland (two cases inneonatal foals, one co-infected with Actinobacillus equuli), the UK (three outbreaks), and theUSA (three cases). EHV-1 neurologic disease
was reported by France (two outbreaks) andthe USA (four outbreaks ). Neuropathogenic or
non-neuropathogenic virus strains were involved.
EHV-4 respiratory disease was recorded by France(14 outbreaks), Germany (nine cases on six premises), and Switzerland (one outbreak involving
co-infection with EHV-1 and -4).
Strangles was reported by France (eightoutbreaks), Germany (10 cases involving eightpremises), Switzerland (three affected premises),
and the USA in which the disease was considered
endemic, with 57 affected premises recorded in 17
states, 10 with multiple outbreaks.
The USA identified two Warmblood stallion
carriers of equine arteritis virus.
A limited number of cases of EHV-2 and/or -5
infection also were recorded in the USA.

Equine infectious anemia was reported by
Canada and the USA. Canada confirmed a totalof 15 cases, one on a premises in British Columbia
and 14 divided between four premises in Saskatchewan, two linked epidemiologically. One case wasdiagnosed in a non-racing horse in Colorado, USA.
France (endemic), Spain (endemic), and the
USA reported cases of equine piroplasmosis. There
was an increase in case numbers in the USA; allwere Theileria equi positive Quarter horse racehorses, the majority in Texas, with some involvedin bush track racing.
Salmonellosis was recorded in Germany (onecase) and the USA (seven outbreaks involving
Group B Salmonella spp. and one Group C1
Salmonella spp.). Outbreaks of rotavirus infection
were confirmed in France (13 outbreaks). One
involved co-infection with rotavirus and coronavirus. The USA reported outbreaks of clostridial
enteritis; C. difficile was implicated in two outbreaks and C. perfringens in seven others. Isolatedcases of coccidiosis and Mycobacterium avium wererecorded by Switzerland and Singapore, respectively. Contagious equine metritis was reported byGermany, with 20 cases confirmed on 12 premises,
the majority in stallions. Icelandic, Warmblood,and Coldblood breeds were involved. The USA
diagnosed five cases of equine coital exanthema(EHV-3) and one case of nocardioform placentitis(Amycolatopsis spp.).
A total of 18 cases of Eastern Equine Encephalomyelitis were recorded in the USA, withthe majority identified in Florida (11) and South
Carolina (5).
West Nile Encephalitis reappeared in the second
quarter, with single cases confirmed in California
and Florida.
The USA reported one case of equine rabies in
Arizona.
Switzerland recorded two cases of ehrlichiosis
on separate premises.

T

he genetics of horses has been of great interest
to humans for millennia. While we may nothave used that term specifically, the recording ofequine parentage, births, and deaths was a practicethat pre-dated the compulsory recording of human births and deaths in Great Britain by over a
century. The term “genomics” covers all aspects ofgenes, including their structure and function, notjust the science of heredity.
The genome is all of the DNA, divided up
and packaged as chromosomes, in each cell. The
DNA molecule, the unit of heredity, is made up
of four nucleotide bases, guanine (G), cytosine(C), adenine (A), and thymine (T) in a sequence.
The equine genome consists of ~2,700 million
base pairs, which is similar in size to the humangenome.
Less than 3% of the genome actually codes forproteins. The remaining 97% was formerly termed“junk DNA” but we now know it orchestrates theuse of the entire genome, as regulatory elements.
Individuals have differences in the sequences of
the nucleotides. This is pretty obvious - we havegreys and bays but they are still horses. However, not all of the sequence differences are that
obvious, and sequence differences can be whole
sections of sequence or just single nucleotides. A
Single Nucleotide Polymorphism (SNP, usuallypronounced “snip”) is a single nucleotide in asequence that differs between individuals at a low
population frequency.
Approximately 10 million SNPs have beenfound in the collective equine genome. It is important to remember that SNPs are not necessarily
mutations that have any effect on the organism.
Indeed, SNPs are less likely to be found in theprotein coding genes of the genome as these areas
have been heavily selected for functionality by
evolution. Any change in DNA sequence that did
not benefit the animal would reduce its chances ofsurvival in the gene pool.

Science uses selected SNPs as a crude roadmap of the genome. By way of analogy, a set of
directions are like a SNP map. If I gave you somedirections, they might be: “Turn right at the pub,then take the second left after the church.” The
pub and the church have no actual bearing on thedestination, they are just guiding landmarks, andso it is with SNPs. SNPs that sit close together ona chromosome are likely to be inherited together.
Using commercial SNP arrays (“SNP chips”),
molecular biology techniques can rapidly hone inon a region of the genome that is different between
horses in terms of its SNP frequency.
SNP analysis is an immensely useful tool tonarrow down the search for areas of the genome
harboring genetic traits of interest, whether they
be a trait relating to disease or a desired trait.
Studies using this approach are called Genome
Wide Association Studies or GWAS (pronounced‘gee-waahs’).
The SNP-GWAS approach has helped identify
regions of interest in the genome in diseases such as
Lavender Foal Syndrome, Polysaccharide Storage Myopathy, recurrent laryngeal neuropathy, Foal Immunodeficiency Syndrome in the Fell and Dales pony,osteochondrosis dissecans (OCD), guttural pouch
tympany in Arabians and German warmbloods,
recurrent uveitis in German warmbloods, insect bite
hypersensitivity, and hydrocephalus in Friesians.
We have only just started to uncover the wealthof information the equine genome holds. Continued efforts for funding and research will yield
more mind-blowing results than our imagination
can fathom. Watch this space!
CONTACT:
Emma N. Adam, BVetMed, MRCVS,DACVIM-LA, DACVS-LA, PhD
emma.adam@uky.edu(859) 218-1175
Maxwell H. Gluck Equine Research Center
University of Kentucky
Lexington, KY

N AT I O N A L

Fire Ant Surveillance for Horse Farms*First Quarter Report from AustraliaT

he red imported fire ant occurs in parts or allof Alabama, Arkansas, California, Florida,
Georgia, Louisiana, Mississippi, New Mexico,
North Carolina, Oklahoma, Puerto Rico, South
Carolina, Tennessee, Texas, and Virginia. Occa-

sionally, it has been found in Kentucky, Maryland,and Missouri (Figure 1). Fire ants like to establish
colonies in open sunny fields and pastures. Soil
moisture and winter temperatures round out the
major environmental factors that limit the spread

3

Figure 1. Fire ant colonies in the U.S.

Fire ant range:
Documented expansion
Possible expansion

4of this invasive insect. Changes in climate, alongwith the adaptability of the insect point to a continued gradual expansion of its boundaries.
The impact of the fire ant extends beyond thepain of its legendary sting. No significant adverse
effects to the health of foals or mature horses havebeen reported in states in which fire ants are widely
established. In addition to causing injury to workers, animals, and wildlife, this small insect affects
pasture maintenance, hay production, damages
equipment, and increases costs. Horse-farm managers in fire ant-infested areas have adjusted their
management practices and developed strategies
to live with this pest. The gradual northward andwestward expansion of the fire ant’s range exposes
more farm managers and stable and pleasure horseowners to this important pest. Those living along
the expansion front should become familiar withsome of the basics of fire ants and watch for ant
activity that seems out of the ordinary.
The familiar mound is the ant’s hallmark, butthere is one major difference when it comes tofire ants: Their mound is the typical pile of loose,fine soil but there is no central opening. Instead,fire ants enter and leave their colonies throughunderground tunnels that radiate from the mound.
Mound heights range from a few inches in mowed
areas to 18 inches in undisturbed areas. Repair ofa fire ant mound collapsed by a heavy rain results
in a loose, fluffy pile of soil a few days later.
Fire ants look like typical ants. They are small
but vary from 1/8- to 1/4-inch in length. The
head, thorax, and legs are red to brown with ablack abdomen. Positive identification of fireants requires collecting approximately a dozen
specimens in rubbing alcohol and taking themto your local Cooperative Extension Office. This
must be done carefully. Disturbing the moundusually prompts numerous ants to pour out andclimb up any vertical surface to sting the intruder.
Other ant species scurry about when the colony is
disrupted, working to protect the queen and movetheir brood to a safe place.
Collect the ants carefully to prevent being
stung. Dust baby powder on dishwashing gloves
and wear them because the ants cannot crawl up
dusted surfaces. Stay as far away from the moundas possible during collection and watch for ants
crawling on your shoes.
Follow up a positive identification of fire ants
with a careful examination of the property inspring or late fall to determine the number andlocation of active mounds. Fire ants are managed
by careful application of baits or mound drenchesof insecticides labeled for fire-ant control. Take
advantage of the excellent information available
on fire-ant management.
For more information, see Identifying Fire
Ants, http://articles.extension.org/pages/11278/
identifying-fire-ants.
CONTACT:
Lee Townsend, MS, PhD
Lee.Townsend@uky.edu(859) 257-7455
Department of Entomology
University of Kentucky
Lexington, KY

The Asymptomatic Carrier Stallion:
Critical Role in Venereal Disease Transmission

Source: http://www.ars.usda.gov/Research/docs.htm?docid=9165&pf=1&cg_id=0

A

range of venereally transmissible agents—viral, bacterial, and protozoal—have long been
known to establish persistence or the carrier state
in stallions, mares, or both. Some of these agents(e.g. Pseudomonas aeruginosa, certain capsule typesof Klebsiella pneumoniae and Streptococcus zooepidemicus) are commonplace in most domesticatedhorse populations. Others such as equine herpesvirus 3, equine arteritis virus, Taylorella equigenitalis,or T. asinigenitalis are less frequently encountered.
Of additional significance is Trypanosoma equiperdum, the causal agent of dourine, which thoughrarely reported nowadays, is reputedly still present
in certain regions/countries of the world.
Even though some but not all of the foregoing
agents can establish persistent infection in both thestallion and the mare, it is the carrier stallion thatplays a more important role in the epidemiologyof the respective infections. Not only has it thepotential to disseminate a particular infectious
agent among the mares to which it is bred, but ofeven greater long-term significance, it ensures thetransfer of infection from one breeding season to
the next.
While some of these agents, such as equine
arteritis virus and T. equigenitalis, can be transmitted either through natural service or artificial
insemination, the risk of more widespread transmission is much greater through the practice ofartificial insemination with fresh-chilled or frozen
semen from a carrier stallion. This was borne out
in the course of the 2006 equine viral arteritis
disease event in the USA, when fresh-chilled semen from a well-known Quarter horse stallion