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Molecular Diagnostics

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General guidance about swab selection for PCR: Cotton/Dacron/Polyester Swabs are acceptable. Calcium alginate and gel swabs should not be used and, where possible, use of wooden swabs should be avoided. Swabs can be submitted dry when indicated or in appropriate medium as recommended below.  Contact us for more information.

 

 *Preferred specimen Additional fees may apply
**Additonal fees may apply, click Here for more information.
***If shipping to PSU, do not use the US Postal Service

Test Agent

Site

Procedure

Species

Tissue/ Specimen

Container

Shipping***

Turn-Around

Remarks

 Actinobacillus pleuropneumoniae  PSU   PCR   porcine
tissues (lung, tonsil), tonsil swabs, pure or mixed cultures
 sterile container  overnight on ice / gel packs  2 - 3 days  Set-up on Tuesdays and Fridays
 Anaplasma marginale  PVL  PCR  Bovine  5 mL blood in Heparin or EDTA (lavender top tub  lavender top tube  overnight on ice / gel packs  3 5 days  This test detects the DNA of Anaplasma marginale, the agent of bovine Anaplasmosis. This test is not designed to detect other Anaplasma species

Avian Influenza (AI) Including H5/H7 subtyping

All

RRT-PCR

Avian: chickens, turkeys, and other gallinaceous birds, wild birds, ducks

Tracheal swab* (for gallinaceous birds), cloacal swab* (for waterfowl), intestine, lung, trachea, air sac, sinus

Leak-proof container with VTM or BHI broth.  Don't use wooden swabs

Overnight on ice, do not freeze

1-3 days

Up to 5 swabs can be pooled in a tube containing BHI broth or VTM.  VTM/BHI available from NBC, PVL, PSU

Avian paramyxovirus-1 (APMV-1) Including Exotic New castle Disease

All

RRT-PCR

Avian: chickens, turkeys, and other gallinaceous birds, wild birds, ducks

Tracheal swab* (for gallinaceous birds), cloacal swab* (for waterfowl), intestine, lung, trachea, air sac, sinus

Leak-proof container with VTM or BHI broth.  Don't use wooden swabs

Overnight on ice, do not freeze

1-3 days

Up to 5 swabs can be pooled in a tube containing BHI broth or VTM.  VTM/BHI available from NBC, PVL, PSU

Bluetongue (BTV) PVL              
Bovine coronavirus  PSU  RRT-PCR  Bovine  Feces, fecal swab, intestine, intestinal contents, lung (respiratory cases)  leak proof container
Brain Heart Infustion (BHI) broth or viral transport media (VTM
Use Dacron swab
 Overnight on ice or gel packs

Do not freeze
 2-5 days  PCR is run on M-F
 Bovine herpesvirus (BHV1) or infectious bovine rhinotrachitis (IBR) virus  PSU PVL  PCR  Bovine  bovine lung, fetal thoracic fluid, nasal swabs, conjunctival swabs  leak proof container
Brain Heart Infusion (BHI) broth or Viral Transport Media (VTM)
use a Dacron swab
 overnight on ice or gel packs  2 - 5 days  PCR is run on M-F

Bovine viral diarrhea virus (BVD)

PSU PVL

RRT-PCR

Bovine

Serum-red top tube.  Whole blood-lavender top tube.  Tissues (including ear notches)

Leak-proof container

Overnight on ice/gel packs

2-5 days

Pooling of serum samples is recommended when testing whole herds.  Up to 30 serum samples are pooled for cattle.  Confirmation of individual positives is done at no charge by virus isolation.

Bovine respiratory syncitial virus (BRSV)  PSU  PCR  Bovine  Fresh respiratory tissues   Overnight on ice packs    
Campylobacter jejuni  PVL  PCR    Feces milk  Leak proof container Overnight on ice packs  2-5 days  
Classical Swine Fever virus (CSFV) PVL RRT-PCR Swine Nasal swabs
tonsils
Use Dacron swab with Brain Heart Infusion (BHI) broth or Viral Transport Media Overnight on ice packs 24-48 hrs For PCR, organism needs to be cultured

Clostridium perfringens toxin typing 

PSU PVL

PCR

All species

Feces or intestinal loop.  Isolated organism

Sterile container.  Anaerobic BA in AnaPak

Overnight on ice/gel packs

2-8 days

For PCR, organism needs to be cultured

Eastern Equine Encephalitis (EEE)

PVL

PCR

All species

Brain tissue

Fresh or formalin fixed paraffin embedded tissue, slide mailer

Fresh tissue, overnight shipment, on ice, do not freeze

3-5 days

FFPE tissue preferred with histologic lesions

Encephalo-myocarditis Virus (EMCV)

PSU

RT-PCR

Porcine

Heart, brain, spleen, liver, pancreas, and skeletal muscle tissue

Fresh or formalin fixed paraffin embedded tissue

Fresh tissue, overnight shipment, on ice, do not freeze

3-5 days

Equine rhino-pneumonitis herpesvirus (EHV)                        EHV-1 PCR EHV-4 PCR                    

 PVL

PCR

Equine

15 ml blood in heparin or EDTA (lavender top tube), nasal swab, tissues including placenta-fetus, lung, nasal secretions, lymph nodes, thymus, brain.  Unstained slide, FFPE tissues

Leak-proof container.  Tissue materials for virus isolation and PCR should be submitted in VTM.  Slide mailer.

Overnight shipment, on ice

3-5 days

For PCR only, nasal swab samples without VTM are also acceptable

Escherichia coli toxin typing and virulence testing

PSU

PCR

All species

Feces or other tissues

Sterile container

Standard delivery Overnight

2-8 days

 Fowl adenovirus (FAdV)  NBC
PSU
  PCR  avian  cecal tonsil
bursa of Fabricius liver
   overnight on ice/gel packs    
Herpesvirus, Koi/Carp  All    fish (carp)  fresh gill, kidney, spleen, intestine, brain  leak proof container  overnight on ice/gel packs  3 – 5 days  
Infectious Bronchitis (IBV)  All  RRT-PCR Avian  tracheal swab  leak-proof with VTM or BHI broth
Don’t use wooden swabs
 overnight on ice, do not freeze  3 - 5 days  Mass., Conn., Ark. strains
Infectious Laryngotracheitis (ILT)  All  PCR  Avian  tracheal swabs
tissue
 leak-proof with VTM or BHI broth
Don’t use wooden swabs
leak proof container
 overnight on ice, do not freeze   3 - 5 days  

Leptospira spp 

PVL

PCR

All species

urine, kidney, placenta, spleen, liver

Sterile container.  Paraffin embedded tissues (FFPE)

Overnight on ice/gel packs

1-3 days

Leptospirosis urine collection:                For best recovery potential, inject with furosemide IV or IM. Clean vulva/prepuce and wait 10 min for second urination. Collect 10 ml urine midstream

Mycobacterium paratuberculosis (Johne's disease)

PVL

PCR

Bovine

Feces (5-10 g) ileocecal valve, mesenteric lymph node (FFPE) blocks

Wide-mouth screw-top container, child-resistant prescription vial, sterile container

Overnight on ice/gel packs

Once a week.  1-5 days

Mycoplasma spp.  

PSU PVL

PCR  AFLP-PCR

All species

Culture broth, plates.  Tissues (1.5 in3), aspirates.  Swabs

Sterile-capped vial.  Sterile container

Overnight on ice packs

1-5 days

Avoid the use of calcium alginate or wooden shaft swabs

Mycoplasma gallisepticum

PSU PVL

PCR

Avian

Culture broth, plates.  Tissues (1.5 in3), aspirates.  Swabs

Sterile-capped vial

Overnight on ice packs

1-5 days

Avoid the use of calcium alginate or wooden shaft swabs

Mycoplasma synoviae

PSU PVL

PCR

Avian

Culture broth, plates.  Tissues (1.5 in3), aspirates.  Swabs

Sterile-capped vial

Overnight on ice packs

1-5 days

Avoid the use of calcium alginate or wooden shaft swabs

Mycoplasma bovis

PSU PVL

PCR

Bovine

Culture broth, plates.  Tissues (1.5 in3), aspirates.  Swabs

Sterile-capped vial

Overnight on ice packs

1-5 days

Avoid the use of calcium alginate or wooden shaft swabs

Mycoplasma hyopneumoniae

PSU

PCR

Swine

Culture broth, plates.  Tissues (1.5 in3), aspirates.  Swabs

Sterile-capped vial

Overnight on ice packs

1-5 days

Avoid the use of calcium alginate or wooden shaft swabs

 Microbial Sequencing Including viral, bacterial fungal *MicroSeq™  All   PCR  All species isolate(s) on plate, broth, or in suitable medium *Sterile body fluids  sterile container overnight on ice
*overnight Frozen
 5-15 days  16S or MicroSeq™ for bacterial
28S for fungal ID
viral gene sequencing
 Neospora Caninum  PSU PVL  PCR  All species  

Formalin fixed paraffin embedded tissue (FFPE) or fresh tissue (heart and brain)

 Sterile-capped vial or tissue block  Fresh tissues overnight on ice packs.  Fixed tissue via standard mail  1-5 days  FFPE tissues preferred with histologic lesions
 Parainfluenza virus: type 3 (PI-3)  PSU RRT-PCR  bovine
ovine
 nasal and ocular secretions, lung, tracheal swab  leak-proof container with BHI  overnight shipment, on ice
do not freeze
 2 - 3 days  Test is set up on T
Pastuerella multocida – toxin typing  PSU  PCR  Porcine isolated organism  sterile container  overnight on ice/gel packs  2 - 3 days  Set up on T & F
 Porcine circovirus type 2 (PCV-2)  PSU  RRT-PCR  porcine  lymph nodes, lung, spleen, tonsil, serum  leak-proof container with BHI  overnight on ice
do not freeze
 1 – 5 days  

Porcine respiratory and reproductive syndrome (PRRS)

PSU

RRT-PCR

Porcine

Lung, lymphoid tissue. Serum

Leak-proof container with or without  VTM

Overnight on ice, do not freeze

5-6 days

PCR is run on F

 Porcine parvovirus
(PPV)
 PSU  RRT-PCR  porcine  lymph nodes, tonsils, thymus, spleen, lung, fetal thoracic fluid
lymph nodes, tonsils, thymus, spleen, lung, fetal thoracic fluid
 leak proof container
Brain Heart Infusion (BHI) broth or Viral Transport Media (VTM)
use a Dacron swab
 overnight on ice or gel packs  2 - 5 days  PCR is run on M-F
 Porcine respiratory coronavirus (PRCV) and transmissible gastroenteritis virus (TGEV)  PSU  Duplex PCR  porcine  fecal swabs, intestine, intestinal contents (for TGEV)
nasal swabs, lung (for PRCV)
 leak-proof container
Brain Heart Infusion (BHI) broth or Viral Transport Media (VTM)
Use Dacron swab
 overnight on ice or gel packs  2 – 5 days  PCR is run on M-F

Salmonella spp.
including Salmonella enteriditis (SE)

All

Real time PCR

All species

feces 10g feed
environmental swabs
10 mL fluid, tissue, milk filter
eggs

Leak-proof container

Overnight on ice, do not freeze

2-3 days

 SE PCR satisfies FDA, NPIP or PEQAP test requirements for poultry.
Call laboratories for details.

 Salmonella genomic fingerprinting    PFGE            
 

Sequencing including viral, bacterial, fungal

 

All

 

*MicroSeqTM

 

All species

 

Isolate(s) on plate, broth, or in suitable medium.  *Sterile body fluids

 

Sterile container

 

Overnight on ice.  *Overnight frozen

 

5-15 days

 

16S or MicroSeqTM for bacterial ID.  28S for fugal ID.  Viral Gene sequencing

 Streptococcus equi subspecies equi  NBC  PCR          
 Swine Influenza  PSU  Including novel H1N1            
 Transmissible gastroenteritis virus (TGEV)  PSU  RRT-PCR  swine  fecal swabs, intestine, intestinal contents  Leakproof container
Brain Heart Infusion (BHI) broth or Viral Transport Media (VTM)
Use Dacron swab
 overnight on ice or gel packs  2 – 5 days  PCR is run on M-F
 Tritrichomonas  PVL  PCR  bovine  cow: vaginal
wash/cervical
mucus
bull: preputial wash, semen
fetal fluids
 In Pouch media or Lactated Ringers Solution (LRS)  sterile capped
vial
 2 - 3 days  Contact lab prior to collection for instructions and transport media.

West Nile Virus (WNV)

PVL

Real Time PCR

equine and avian

Brain tissue from mammals.  Kidney, brain, intestine, spleen, lung, etc., from avian spp.

Fresh, formalin fixed tissue.  Slide mailer

For fresh tissue, overnight on ice, do not freeze

3-5 days

FFPE tissues preferred with histologic lesions

Procedure codes

BHI - brain heart infusion broth

PCR - polymerase chain reaction

VTM - viral transport media

FFPE - formalin fixed paraffin embedded

RRT-PCR - real time reverse transcriptase polymerase chain reaction