Pennsylvania Animal Diagnostic Laboratory System
PADLS User Guide - Contents Tests Molecular Diagnostics
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9.3 Molecular Diagnostics

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. Call the laboratory running the test for more information.

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

Test/ Agent	Site	Procedure	Species	Tissue/ Specimen	Container	Shipping**	Turn- Around	Remarks
Avian Influenza (AI) Including H5/H7 subtyping	PSU PVL NBC	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)	PSU PVL NBC	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
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
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
Encephalomyocarditis 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 rhinopneumonitis 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 Standard delivery	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	Overnight	2-8 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	Urine collection-see below
Leptospirosis urine collection	For best recovery potential, inject with furosemide IV or IM. Clean vulva/prepuce and wait 10 min or 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. Including speciation	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^TM	PSU PVL NBC	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^TM for bacterial ID 28S for fugal 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
Porcine respiratory and reproductive syndrome (PRRS) Arterivirus:Lelystad agent	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 Circovirus type 2 (PCV-2)	PSU	PCR	Porcine	Lymph nodes, lung, spleen, tonsil Serum	Leak-proof container with VTM	Overnight on ice, do not freeze	1-5 days
Parainfluenza virus: type 3	PSU	PCR	Bovine, ovine	Nasal and ocular secretions, lung, tracheal swab	Leak-proof container with VTM	Overnight on ice, do not freeze	2-3 days	Test is set up on T
Salmonella spp.	NBC	Real time-PCR	All species	Feces (25 g)	Leak-proof container	Overnight on ice, do not freeze	2-3 days
West Nile Virus (WNV)	PVL	RT-PCR	All species	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

*preferred specimen
**If shipping to PSU, do not use the US Postal Service

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