Specimen Collection and Transport Manual - Erie County

ECPHL ERIE COUNTY PUBLICHEALTH LABORATORIESSPECIMENCOLLECTIONandTRANSPORT MANUALECPHL ERIE COUNTYPUBLIC HEALTH LABORATORIES503 KENSINGTON AVENUEBUFFALO, NY 14214TEL: (716) 898-6100FAX: (716) 898-6110

ECPHL Specimen Collection and Transport ManualTABLE OF CONTENTSGeneral Laboratory1. Introduction2. Accreditation3. Location4. Department Contacts5. General Guidelines• Collection materials• Acceptance/Rejection• Lab requisition and Specimen labeling• Pack and Ship• Test Referral• Turn Around TimeClinical Public Health TestingGeneral ElementsSpecimen Collection Procedures (alpha by body source)Test ChartReference Range and Critical ValuesEmerging Infections and BiodefenseGeneral ElementsEnvironmental Sample Collection• Materials• ProcedureClinical Specimen Collection ProcedureEnvironmental TestingGeneral ElementsDirections for Sampling (alpha by analyte)Test Chart• Drinking Water• Environmental Waters and SolidsECPHL effective 3/1/2012 Page 2 of 38

ECPHL Specimen Collection and Transport Manual1. INTRODUCTIONErie County Public Health Laboratories (ECPHL) provides a wide range of clinical andenvironmental laboratory services. Our goal is to provide each client organization with qualityservices and programs as reflected in our mission statement.The Specimen Collection and Transport Manual (SCTM) details various laboratory services,contact information and many of the required elements for specimen submission. Accurate andtimely laboratory results are only possible when the sample collection and submission is optimal.To that end this manual was designed to provide much of the information needed to optimize thecollection and submission of specimens for testing.We appreciate your selection of ECPHL as a provider of quality, public health diagnosticservices and are available for any inquiries.Erie County Public Health Laboratories’Mission:To provide proficient, cost-effective laboratory services, educationalprograms, method evaluations, epidemiological support and scientificstudy resources to the health care, laboratory, environmental sciencesgovernment and private communities of Western New YorkECPHL effective 3/1/2012 Page 3 of 38

ECPHL Specimen Collection and Transport Manual2. ACCREDITATION• CLIA ’88 33D0654777 – Buffalo, NY• Federal I.D. Number 16-6002558• Medicaid Provider Number: 00623767• New York State Department of Health (NYSDOH)Clinical Laboratory Evaluation Program (CLEP) PFI: 1980 CODE#: 1401A100Environmental Laboratory Approval Program (ELAP) #: 10472Professional Affiliations• APHL - Association of Public Health Laboratories• NYAAEL – New York Association of Approved Environmental Laboratories• ASM - American Society for MicrobiologyQuality Control/Proficiency Testing Programs• NYSDOH - New York State Department of Health• CDC - Centers for Disease Control and Prevention• Nebraska Public Health LaboratoryECPHL effective 3/1/2012 Page 4 of 38

ECPHL Specimen Collection and Transport Manual3. LOCATIONECPHL ERIE COUNTYPUBLIC HEALTH LABORATORIES503 Kensington AvenueBuffalo, New York 14214Tel: (716) 898-6100Fax: (716) 898-6110Hours of OperationMonday – Friday 8:30am to 4:30pmIn the event of an emergency, call (716) 961-7898(MERS-Medical Emergency Radio System)Directions from NYS Thruway (I-90):• Traveling on the NYS Thruway, use exit 51W / Route 33W (Kensington Expressway) to downtownBuffalo.• Proceed on Route 33W to Grider Street exit.• Exit Route 33W and proceed through one (1) stop sign to Grider Street.• Turn left on Grider Street and proceed through one (1) traffic signal to the Erie County MedicalCenter campus.• Enter ECMC campus by turning right into the first entrance on Grider Street.• Use the map below and follow signage to the Erie County Public Health Laboratories.ECPHL effective 3/1/2012 Page 5 of 38

ECPHL Specimen Collection and Transport Manual4. DEPARTMENT CONTACTSDepartment Phone Room Email addressAdministration 716 898-6100 AA19DirectorScott J Zimmerman, DrPH, MPH 716 898-6105 AA15 scott.zimmerman@erie.govExecutive Assistant (Laboratory)Michael Simkins 716 898-6102 AA26 michael.simkins@erie.govCentral Receiving/Specimen 716 898-6111 AA6ProcessingExecutive Assistant (Laboratory)Michael Simkins 716 898-6102 AA18 michael.simkins@erie.govAdministrative Assistant (PHL)Joanne Kojm 716 961-7522joanne.kojm@erie.govClinical Public Health Lab 716 898-6116 AA11Chief PH MicrobiologistLinda Garringer 716 898-6117 AA14 linda.garringer@erie.govChief Laboratory Technologist (PH)Shirley Keenan 716 961-7593 AA13 shirley.keenan@erie.govEmerging Infections and BiodefenseChief Molecular ScientistCarleen Pope 716 961-7588 BB122 carleen.pope@erie.govEnvironmental Health Lab 716 961-7520 AA21Senior Sanitary ChemistGerhard Paluca 716 898-6118 AA23 gerhard.paluca@erie.govSanitary ChemistBryan Hill 716 961-7578 BB123 bryan.hill@erie.govECPHL effective 3/1/2012 Page 6 of 38

ECPHL Specimen Collection and Transport Manual5. GUIDELINES FOR SPECIMEN/SAMPLE COLLECTION AND HANDLINGThe following general guidance is applicable to both clinical specimen and environmentalsample collection. The following fundamentals should be considered when sending samples forlaboratory analysis:1. The sampling material must be truly representative of the site of interest. For clinicalmaterial it is the site of optimal recovery; for environmental material it is a homogenoussample.2. Sufficient quantity of sample must be obtained.3. The appropriate collection devices and sample containers must be used. Many containpreservatives or additives that ensure optimal holding and recovery of the analyte ofinterest.4. Storage and transport conditions must be followed for optimal analysis.The laboratory strongly encourages communication from the sender before the sample isreceived in the laboratory especially for new or unusual requests. This ensures guidance forproper specimen collection is up-to-date and correct. In an effort to provide accurate and timelyresults the laboratory reserves the right to reject specimens not properly collected, contained ortransported.Collection MaterialsSpecimen containers and supplies are provided by the laboratory according to the followingtable. Materials not listed below are deemed containers that may be supplied by clinics orcommonly submitted by clients. Requests for collection materials can be made in person at thelaboratory receiving area or by phone to ECPHL Central Receiving at 716 898-6111.Clinical PH TestingEnvironmental SamplingClinical lab requisitionEnvironmental lab requisitionEnteric transport cupsAlkalinity bottleJEMBEC culture platesBeachNAAT swabs, male/female Coliform testing Sterile, with sodiumisothiosulfateNAAT urine tubesColilert bottlesSST venipuncture tubes* Cyanide Sodium hydroxide at pH=12Specimen transport bags* Fluoride No preservativeViral transport tubesNitriteHaloacetic acid 250mL amber vialInorganics No preservativeMetals Nitric acid at pH less than 2.0Nitrate, chlorinatedNitrate, non-chlorinated* for designated providersSwimming poolsVolatile Organic Compound(VOC)2-40mL amber vials and adropper bottle with HClECPHL effective 3/1/2012 Page 7 of 38

ECPHL Specimen Collection and Transport ManualAcceptance / Rejection CriteriaThe laboratory will examine and analyze only those samples/specimens for which it holds a NYSPermit for Testing or Certificate of Approval. In addition, the laboratory will only acceptspecimens at the request of persons authorized by law to use the findings of the laboratoryexamination in their practice or performance of their official duties.Rejection criteria depend on several factors: the sample/specimen received, the test ordered andthe laboratory policy. Determining the acceptable condition of a specimen is often a judgmentcall based as much on good laboratory practice as on objective assessment of the sample. Inaddition to the specific criteria listed below a specimen should NOT be tested if• The apparent condition of the specimen indicates that it is unsatisfactory for testing or itis inappropriate for the test requested.• It has been collected, labeled, preserved or otherwise handled in such a manner that it isunreliable for testing.• It is perishable, that is, the time has lapsed between collection and receipt rendering thesample unreliable.• The date or time of collection is not furnished to the lab for those tests that require it.When a specimen is deemed unacceptable for testing the laboratory will promptly notify thesender and give the reason for rejection.Rejection criteria applicable to all submissions include:1. Requests for non-permitted laboratory tests.2. Unlabeled, mislabeled, mismatched identification on container or requisition.3. Incomplete information on requisition.4. No sample/specimen received.5. Improper, leaking or compromised sample container.6. Quantity insufficient for testing.7. Specimen receipt that exceeds the allowable time limit for testing.8. Laboratory accident preventing analysis.Additional rejection criteria related to specific tests and sources are listed in each laboratorysection.Laboratory Requisition and Specimen LabelingAll requests for testing are written not verbal. Laboratory requisitions both clinical andenvironmental serve as the written request and provide necessary information and identificationfor testing. Incomplete requisitions may require follow-up phone calls and can delay the start oftesting.Requisitions can be printed from the laboratory website:www.erie.gov/health/services/phlab_contact.aspClinical specimen labeling includes the following and MUST match the completed labrequisition:• Last name, First nameECPHL effective 3/1/2012 Page 8 of 38

ECPHL Specimen Collection and Transport Manual• Date of birth• Date of collectionEnvironmental sample requisition must include:• Complete sampling address• Submitter name and address• Complete sample description – see requisition.Packaging and TransportAppropriate packing and shipping of specimens is designed to follow all applicable federal andstate regulations and to provide for the safety of all who come in contact with the samples.Test Referral for Supplemental or ConfirmationTests that are listed on the clinical and environmental ECPHL requisitions are performed on-site.On occasion it may be necessary for a sample or specimen to be referred to another laboratoryfor testing not performed on-site or for confirmation. The following guidelines are in effect:1. Samples/specimens will either be returned to the submitter, if it is determined that therequest was sent by mistake or referred to NYS accredited laboratories to perform theadditional work2. Tests that are referred will be listed in the SCTM3. The laboratory report will contain the name of the testing lab and its NYS identificationnumber as well as the test result. Referral lab contact information will be available onrequest for any inquiries.The referral laboratories in current use include:Erie County Medical CenterLaboratory Medicine462 Grider StreetBuffalo New York 14215PFI# 2009Referrals:• HIV-1 Western Blot, serum• AFB smear• TB culture• TB susceptibilityWadsworth LaboratoriesDavid Axelrod Institute120 New Scotland AvenueAlbany New York 12208Referrals:• Bacterial Isolates for confirmationTurn Around TimeLaboratory turn around time (TAT) is the time from receipt of the specimen until testing resultsare available. The laboratory monitors this as a quality assurance measure to providers andclients. It is recognition of the necessity for timely reporting.ECPHL effective 3/1/2012 Page 9 of 38

ECPHL Specimen Collection and Transport ManualClinical Public Health TestingGeneral ElementsClinical laboratory tests are conducted on specimens from a human source for the diagnosis orsurveillance of human illness. These laboratory tests are regulated by NYSDOH CLEP whichhas deemed status for federal CLIA regulations. In addition, clinical laboratory testing must beperformed by NYS licensed clinical laboratory technologists.Specimen Collection by Body SiteThe following procedures are designed as guidelines for the collection of human specimens forErie County Public Health Laboratory analysis. Most collection procedures are consideredinvasive. As such, the procedures should always be performed by trained, experienced medicalpersonnel. Individual collection methods may vary according to training but the followingprocedures highlight the basic steps to follow when collecting human specimens.In addition, standard precautions must be followed for the safety of patient and healthcarepersonnel. ‘Standard precautions’ refers to a set of practices used to prevent the transmission ofinfectious diseases. It applies to specimens from all individuals whether or not they appearinfectious or symptomatic. Personal protective equipment (PPE) should be worn according tothe policy and procedures of the facility. Depending on the risk assessment and the specimenbeing collected PPE should include:• disposable exam gloves• protective clothing: fluid resistant lab coat/smock• eyewear, safety glasses• respiratory barriers, face masksLaboratory analysis greatly depends on a properly collected, stored and transported specimen. Ingeneral, the sooner a specimen arrives in the testing laboratory the quicker the results and moreaccurate the analysis will be. However, appropriate storage and transport can be maintainedwhen immediate delivery is unavailable. The following instructions are guidelines and mayrepresent the optimum conditions. If there is an expectation that optimum collection, storage ortransport conditions can not be met, contact the laboratory for further instructions. The primeobjective is a properly maintained specimen for laboratory analysis.ECPHL effective 3/1/2012 Page 10 of 38

ECPHL Specimen Collection and Transport ManualBlood - Whole blood by venipuncture, including requests for plasma and serumIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsClinical chemistry: Alkaline Phosphate, ALT, AST, BilirubinHepatitis, HIV1-2, HSV-2, Syphilis EIA, RPR,Vacutainer: SST-marble top-preferred, red top- acceptableVenipuncture, phlebotomyPatient’s last, first name; date of birth, date of collection.At room temp

ECPHL Specimen Collection and Transport ManualCervical, EndocervicalIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsNucleic Acid Amplification Test (NAAT), GC Culture, Gram stainBD Dry Transport Swab Kit, JEMBEC, microscope slideInternal examPatient’s last, first name; date of birth, date and time of collection.Room temp

ECPHL Specimen Collection and Transport ManualFeces/StoolIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsEnteric cultureStool collection kit – ECPHL providedPatient’s last, first name; date of birth, date and time of collection.Refrigerate after collectionWithin 3 days of collectionPatients can self collect.Sterile cup with transport mediaDisposable spatulaPatient ID label and instructionsPlastic wrap or plastic-coated disposable plateProcedure1. Instruct patients who can, to excrete directly into the cup. Do not take specimen from thewater in the toilet or to allow urine to contaminate the specimen.2. Alternately, loosely attach plastic wrap to the sides of the toilet between the patient andthe water in the bowl or float a disposable plastic –coated (Styrofoam) plate in the toiletbowl.3. After defecation, use the disposable spatula to place approximately 10-20 grams of thespecimen into the transport cup. Specimen volume should be the size of a small egg.4. Cap specimen tightly, label and transport to the laboratory immediately or refrigerate anddeliver within three days of collection.ECPHL effective 3/1/2012 Page 13 of 38

ECPHL Specimen Collection and Transport ManualNasopharyngealIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsInfluenza A & BViral Transport media (VTM)Patient’s last, first name; date of birth, date and time of collection.Freeze (-20°C) after collectionWithin 7 daysPerformed by trained medical personnelSterile Dacron or rayon swab with plastic or aluminum shaftViral transport media in screw-cap tubesProcedure1. Remove the excess mucous by having the patient gently blow his nose.2. With patient’s head against a wall or firm surface, insert the swab into one nostril andproceed straight back until it reaches the nasopharynx. The length from the nose to theear gives an estimate of the distance the swab will travel. Do not force. If there is anobstruction try the other nostril.3. Rotate the swab gently for 5-10 seconds to loosen epithelial cells.4. Remove swab and place in VTM. Break or bend the swab to fit into the tube. Cap tightlyand label with patient indentity.5. Store frozen until transport.ECPHL effective 3/1/2012 Page 14 of 38

ECPHL Specimen Collection and Transport ManualRectalIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsGC cultureJEMBEC or Culture swabPatient’s last, first name; date of birth, date and time of collection.Incubated 34-36°CWithin 1-2 daysPerformed by trained medical personnelSterile swab: Dacron, rayon or cotton with plastic or aluminum shaftJEMBEC plate systemProcedure - JEMBEC1. Prepare the patient for collection procedure.2. Gently insert the swab 1-2 cm beyond the anal sphincter, rotate it swabbing the analcrypts. Remove swab, avoiding fecal contamination as much as possible3. Inoculate the JEMBEC plate by rolling the rectal swab onto the media. Place thebicarbonate tablet in the well, label the bottom of the plate with the patient identity andplace the covered plate into the zipper lock bag.4. Incubate at 34-36°C until transport to the laboratory.Procedure – Culture Swab1. Prepare the patient for collection procedure.2. Using the culture swab unit, gently insert the swab 1-2 cm beyond the anal sphincter,rotate it swabbing the anal crypts. Remove swab, avoiding fecal contamination as muchas possible.3. Place swab into plastic holder, label with patient identity and transport to the laboratory.ECPHL effective 3/1/2012 Page 15 of 38

ECPHL Specimen Collection and Transport ManualThroatIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsGC cultureJEMBEC or Culture swabPatient’s last, first name; date of birth, date and time of collection.Incubated at 34-36°CWithin 1-2 daysPerformed by trained medical personnelSterile swab: Dacron, rayon, or cotton with plastic or aluminum shaftTongue depressorJEMBEC plate systemProcedure for JEMBEC1. Position patient for throat collection.2. Use the depressor to hold tongue down and local areas of inflammation or exudate3. Firmly rub the swab over posterior pharynx.4. Withdraw the swab, avoiding any contact with cheek, teeth, gums or tongue.5. Inoculate JEMBEC plate, rolling swab over the surface of media, add bicarbonate tabletto well, label the bottom of the plate with the patient identity and enclose covered plate inzipper lock bag.6. Incubate 34-36°C until transport to the laboratory.Procedure for Culture Swab1. Position patient for throat collection.2. Use the depressor to hold tongue down and local areas of inflammation or exudate3. Firmly rub the swab over posterior pharynx.4. Withdraw the swab, avoiding any contact with cheek, teeth, gums or tongue.5. Replace inoculated swab into the original plastic holder, label with the patient identityand transport to the laboratory.ECPHL effective 3/1/2012 Page 16 of 38

ECPHL Specimen Collection and Transport ManualUrethralIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsNAAT, GC culture, Gram stainBD urethral swab, JEMBECPatient’s last, first name; date of birth, date and time of collection.Refrigerate urine, Incubate JEMBECWithin 1-2 daysPerformed by trained medical personnelSterile swab: Dacron, rayon or cotton, with plastic or aluminum shaftBD Male Swab kit (blue),JEMBEC plate systemMicroscope slideProcedureNote: Patient should not have urinated one hour before collection. Material from a siteabout 2 cm inside the urethra or expressed exudate is the specimen of choice.1. Clean external skin flora of urethral meatus.2. Strip the urethra toward the orifice to express the exudate and collect on a swab.3. Alternately, insert a thin calcium alginate swab into the urethra 1-2 cm, gently rotate,4. Withdraw the swab and inoculate as follows:a. For NAAT: Using the BD kit, place cap and swab into the transport tube and captightly. Label and transportb. For GC culture: Gently roll swab onto the surface of a JEMBEC plate. Place thetablet (sodium bicarbonate/citric acid) into the well. Label the plate and place itinto the zipper lock bag and incubate at 34-36°C or transport to the laboratory.c. For Gram stain: gently roll swab onto the center of glass microscope slide, withthe frosted edge up. Air dry, label and transport to laboratory in protective slideholder.ECPHL effective 3/1/2012 Page 17 of 38

ECPHL Specimen Collection and Transport ManualUrineIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsNucleic Acid Amplification Test (NAAT), pregnancy testingSterile cup with screw-capFirst voidPatient’s last, first name; date of birth, date and time of collection.Refrigerate 1-2 daysWithin 2 daysPatient collected or by trained medical personnelSterile cup with screw-capProcedureNote: Patient should not have urinated one hour before collection.1. Do not remove the beads or the liquid preservative in the cup.2. Collect the first 15-60mL of voided urine. Use line on cup as guideline, do not overfill.3. Cap tightly, label with patient identity, store refrigerated until transport to laboratory.ECPHL effective 3/1/2012 Page 18 of 38

ECPHL Specimen Collection and Transport ManualVaginalIntended UseContainerMethodLabelingStorageTransportCommentsMaterialsWet PrepMicroscopic slide with protective holderPatient’s last, first name; date of birth, date and time of collection.noneTo on-site lab within 15 minutesPerformed by trained medical personnelGlass microscope slides, and cover slipsProtective slide holdersSterile saline,Procedure1. Prepare the patient for an internal examination2. Using a speculum and a sterile swab, obtain the specimen from the posterior vaginalvault. If the hymen is intact a swab of the vaginal orifice is sufficient.3. Allow the exudate to absorb onto the swab for a few seconds.4. Dab the swab onto the slide under the frosted area, removing an adequate amount ofvaginal material from swab to slide5. Immediately add one drop of saline to vaginal material. AVOID touching the specimenwith the saline dropper.6. Place slide with moist vaginal specimen into the slide holder and deliver to the on-sitelaboratory within 15 minutes of collection.ECPHL effective 3/1/2012 Page 19 of 38

Clinical Testing ChartKEY• SST/gold: Serum separator tube, gold top. Note: Multiple tests using serum can be performed on one full SST.• Venipuncture: whole blood, serum or plasma.• CB -Cary-Blair• JEMBEC – John E. Martin Biological Environmental Chamber• VTM – Viral transport Media• SA – Select AgentCode Test Name Method Source Container/Qtyprovided by LABStorageBACTERIOLOGYBacterial isolate, Rule-out LRN/PCR IsolateCulture tube-5mLPrior Notification Needed SA Rule-outslantCulture, Enteric Culture Feces, Stool CB transportGC Culture, N. gonorrhoeae Culture Cervical, RectalThroat, UrethralVaginal10-20 gramsJEMBEC orculture swabTransportTAT(days)Rejection CriteriaIn addition to p.7Room temp 24 hrs 3 days Uninoculated.Refrigerate 1-3 days 7 days Greater than 72 hrs aftercollectionRoom temp 1-3 days 7 days Expired, frozen or& Incubatedehydrated media; noCLINICAL CHEMISTRYALK Alkaline Phosphatase Enzymatic Serum SST Refrigerate 24 hrs 3 daysALT Alanine transaminase Enzymatic Serum SST Refrigerate 24 hrs 3 daysAST Aspartate transaminase Enzymatic Serum SST Refrigerate 24 hrs 3 daysTBIL Bilirubin, total Photometric Serum SST Refrigerate 24 hrs 3 daysDIAGNOSTIC IMMUNOLGYHBsAb Hepatitis B surface antibody EIA Serum SST Refrigerate 1-3 days 7 daysHBsAg Hepatitis B surface antigen EIA Serum SST Refrigerate 1-3 days 7 daysHCV Hepatitis C antibody EIA Serum SST Refrigerate 1-3 days 7 daysHIV HIV-1,2 antibody EIA Serum SST Refrigerate 1-3 days 7 daysWestern Blot confirmatory –automatic specimen referralHSV-2 Herpes Simplex Virus-2 EIA Serum SST Refrigerate 1-3 days 7 daystype specificSYPH Syphilis EIA and RPR Serum SST Refrigerate 1-3 days 7 daysMOLECULAR MICROBIOLOGYFLU Influenza AB (A subtyping) PCR NasopharyngealNasal swabVTM, 2mL Freeze 1-3 days 7 daysNAATNucleic Acid AmplificationTest for CT and NGStranddisplacementamplificationEndocervicalUrethralUrineFemale/Male kitSterile cup,minimum 30mLCO2 pellet; refrigerated.Hemolyzed or lipemicReceipt 7 days aftercollectionRefrigerate 1-3 days 7 days Receipt 7 days aftercollection.ECPHL effective 3/1/2012 Page 20 of 38

ECPHL Specimen Collection and Transport ManualREFERENCE RANGESThe reference range for each clinical chemistry test is listed below. This range is the 95th percentile of resultsfrom a study of apparently healthy individuals. The number tested and the gender distribution variesaccording to each analyte and is listed in the manufacturer’s package insert.ANALYTEREFERENCE RANGEAlkaline Phosphatase Male: 40–129 U/LFemale: 35-104 U/LALT (alanine aminotransferase) Male:

ECPHL Specimen Collection and Transport ManualEmerging Infections and BiodefenseGeneral ElementsThe ECPHL Emerging Infections and Biodefense Laboratory serves Erie County and the western16 counties of New York as a Biological Reference Level laboratory within the LaboratoryResponse Network (LRN). The laboratory analyzes environmental samples for the identificationof biothreat agents as directed by the LRN under permit through the NYSDOH ELAP regulatoryagency. For environmental samples the analysis is bacterial culture and PCR for Bacillusanthracis, Francisella tularensis, Yersinia pestis, Brucella spp., Burkholderia spp., Orthopoxvirus and Ricin toxin. In addition, the laboratory analyzes clinical isolates for the rule-out ofbiothreat agents submitted by sentinel laboratories under permit through NYSDOH CLEP.Analysis of biothreat culture isolates for PCR and culture include Bacillus anthracis, Brucellaspp., Francisella tularensis and Yersinia pestis. Note: This is specialized testing requiringlaboratory preparation and trained personnel.It is important to notify the laboratory prior to collection.Environmental Sample Collection• Environmental samples include direct samples of small (less than 1 cubic foot) biothreatmaterial such as powders, liquids or small particles and indirect samples such as swipesof larger environmental surfaces.• All samples are collected by trained and experienced HAZMAT specialists who followthe NYSDOH CODE RED sampling protocol (see attachment #1).• The decision to collect samples should follow a risk assessment by law enforcement orauthorized local health officials and a determination of ‘credible threat’ that follows theNYS Guidance on Initial Response to a Letter/Container Containing a SuspiciousSubstance and /or Threat Statement (see attachment #2).• Samples submitted for analysis are considered legal evidence for law enforcementpurposes and will follow chain of custody (COC) requirements.• The laboratory will only accept samples for analysis that it is permitted to perform. Inaddition, the submitted samples must be screened for radiological, chemical, andexplosive hazards before acceptance into the laboratory.• It is strongly advised that all submitting agencies contact the laboratory prior tosample collection both as notification for laboratory testing preparation and to ensure thatproper methods of collection are followed.Collection Material• Personal Protective Equipment (PPE)o Gloves, minimum 2 per sampleo Respirators, N95o Protective clothing as necessary.• Permanent marker for sample labeling• Evidence tape• Sterile 2” x 2” Dacron gauze pads• Sterile water or saline in 6oz/10mL vialECPHL effective 3/1/2012 Page 22 of 38

ECPHL Specimen Collection and Transport Manual• Zippered plastic bags, minimum 3 per sample.• Sterile spatula, scoop etc.• Large rigid transport container, plastic or cardboard.• 0.5% bleach, freshly diluted 1:10. (1 part bleach to 9 parts water).• Laboratory requisition or COC form for each submitted sample.Collection ProcedureCollectors must be trained in CODE RED Biothreat sample collection or equivalent proceduresprior to beginning threat assessment and sample collection. CODE RED sample collectionshould be performed as a two-person team consisting of a Collector (considered dirty) and aFacilitator (considered clean). If the collection area requires HAZMAT containment, pre-labelthe specimen containers as much as possible. It is very important if more than one sample iscollected at the scene that each item is labeled for identification.The following is an annotated collection procedure from CODE RED:1. In a clean area, outside the contaminated zone, don 2 layers of sterile, disposable gloves,N95 respirator and all protective clothing deemed necessary.2. For Envelopes: Collector will directly place item into zippered bag held open byFacilitator. Do not try to remove excess air from bag. Proceed to Step 5.3. For Bulk powder samples: Collector will use a card and dry swab to move powder to acollection cup or bag held open by Facilitator. Proceed to Step 5.4. For Surface swipe samples: Collector will use moist swab for small surfaces or moistgauze for larger areas. Use a gentle back and forth sweeping motion to cover the surface.Place swab or swipe into the cup or tube and place that container into a zippered bag.Proceed to Step 5.5. Wipe the outside of the bag with the disinfecting bleach solution and place it in a secondzippered bag and seal. Remove first layer of gloves and dispose properly.6. Again wipe outside of second bag and place into a 3 rd zippered bag and seal.7. Place the triple contained sample into a rigid-walled transport container, sealing withevidence tape.8. Complete the laboratory requisition and chain of custody forms with all pertinentinformation.9. Dispose of PPE properly or send to the laboratory for disposal.10. It is expected that law enforcement will transport the samples and the completed forms toECPHL for testing.Clinical Specimen CollectionECPHL will also accept clinical specimens for rule-out testing targeting Bacillus anthracis,Brucella spp., Francisella tularensis, and Yersinia pestis by PCR and subculture. Thesespecimens must be submitted as a bacterial isolate on an agar slant or plate.1. Notify ECPHL that a culture isolate from a clinical/patient source is being submitted for arule-out of biothreat agentsECPHL effective 3/1/2012 Page 23 of 38

ECPHL Specimen Collection and Transport Manual2. Include all results of testing performed by the submitting sentinel laboratory andcomplete an ECPHL laboratory requisition with all patient information and anatomicalsource. Please include the submitting laboratory contact information and the physicianname and contact information.3. Culture isolate should be grown on blood or chocolate agar, on a plate taped closed or onan agar slant in a screw capped tube. Place item in a zippered bag, decontaminate theoutside with 0.5% freshly made bleach.4. Place in a second zippered bag and then in a rigid transport carrier and deliver to thelaboratory for testing.If a biothreat agent is presumptively identified, the submitting sentinel laboratory is responsibleto collect and secure all subcultures and aliquots of the specimen as required by the FederalSelect Agent Rule.ECPHL effective 3/1/2012 Page 24 of 38

ECPHL Specimen Collection and Transport ManualEnvironmental TestingGeneral ElementsThe Environmental Health Laboratory performs testing for the following:Drinking Water1. Bacterial Analysis2. Mineral Content3. Trace Metal Content4. Trace OrganicsEnvironmental Water1. Bacterial Analysis2. Mineral Content3. Biological or Chemical Demand4. Oil and Grease / Total Petroleum HydrocarbonsSample Collection ProceduresThe laboratory will supply appropriate sample containers for all requested testing and willONLY accept samples containers meeting test requirements as stated in the followingprocedures.ECPHL effective 3/1/2012 Page 25 of 38

ECPHL Specimen Collection and Transport ManualColiform TestingContainerContentsNotesColiform / Colilert bottleSterile, with sodium isothiosulfateDo not open until ready to sampleDirection for Sampling1. Select a sample point, the faucet that is representative of the service throughout thelocation. Do not choose a faucet connected to a storage tank. In addition, choose a sitethat looks clean.2. If faucet is a mixing type, that is one handle, carefully remove the faucet screen oraerator, if possible. Do NOT force removal.3. Open cold water faucet and allow water to run for at least 2-3 minutes or sufficient timefor service line to clear. If faucet is mixing type, run hot water for 2 minutes followed bycold water for 2-3 minutes. NOTE: If sample is collected from a well fitted with a handpump, pump water for about 5 minutes before collection.4. Reduce flow of water to avoid splashing.a. Unscrew cap but do not place it on the surface to avoid contamination.b. Sample bottle contains a powder that will remove residual chlorine, if present.DO NOT RINSE OUT BOTTLE!5. Fill the bottle just over the molded fill line that surrounds the bottle, cap immediately.6. Bring sample to the testing laboratory by 2:00 PM the day of collection or refrigerate anddeliver the next day. Sample must be processed with 24 hrs of collection.7. Complete a requisition for each sample bottle includinga. Date and Time of collectionb. Name of collectorc. Sample location (address and location with the residence (i.e. kitchen)d. Billing addressECPHL effective 3/1/2012 Page 26 of 38

ECPHL Specimen Collection and Transport ManualHaloacetic Acids in Drinking WaterContainerNotes250mL amber bottleSample bottle contains preservative. Do not open until ready to sampleDirections for Sampling1. Select a sample point that is used mainly for drinking and cooking purposes, such as thekitchen faucet. Allow the water to run for at least 1 minute.2. Unscrew the sample bottle cap, then immediately and slowing fill to the neck of thesample bottle being careful not to let the preservative out of the bottle.3. Slowly screw the cap back on the bottle and deliver it to the testing laboratory.Note: Common practice dictates collection of the sample after 2-3 minutes of flushing thefaucet. The use of a Trip Blank (a contaminant-free water sample provided by the lab) is tocompensate for any environmental contaminants that may be present during the transport andcollection of samples between the sample source and the laboratory.ECPHL effective 3/1/2012 Page 27 of 38

ECPHL Specimen Collection and Transport ManualInorganics in Drinking WaterContainerNotesInorganicsUsed for sampling for the following tests:Color, Total Dissolved Solids, Calcium Hardness, Chloride, Fluoride, ortho-Phosphate, and SulfateDirections for Sampling1. Select a sample point that is used mainly for drinking and cooking purposes, such as thekitchen faucet.2 Turn on faucet and let cold water flush for 2-3 minutes.3. Unscrew sample bottle and slowly fill to the shoulder of the bottle just below thethreaded portion of the bottle neck.4. Screw cap back on the sample bottle and promptly deliver to testing laboratory in coolercontaining ice. If sample cannot be delivered on the day of collection, place sample inrefrigerator and keep cold until transport to the laboratory on ice.Note: Color and ortho-Phosphate require analysis within 48 hours of collection.ECPHL effective 3/1/2012 Page 28 of 38

ECPHL Specimen Collection and Transport ManualLead or Metals in Drinking WaterContainer Metals bottleContents Nitric acid , pH

ECPHL Specimen Collection and Transport ManualNitrates in Drinking WaterContainerNotesNitrate bottle, chlorinated, Nitrate bottle unchlorinated.For chlorinated well water use chlorinated sample bottleFor unchlorinated well water use unchlorinated sample bottleDirections for Sampling1. Select a sample point that is used mainly for drinking and cooking purposes, such as thekitchen faucet.2. Turn on faucet and let cold water flush for 2-3 minutes.3. Unscrew sample bottle and slowly fill to the shoulder of the bottle just below thethreaded portion of the bottle neck.4. Screw cap back on the sample bottle and promptly deliver to testing laboratory in coolercontaining ice. If sample cannot be delivered on the day of collection, place sample inrefrigerator and keep cold until transport to the laboratory on ice.Note: Unchlorinated water sample requires analysis within 48 hours of collection.ECPHL effective 3/1/2012 Page 30 of 38

ECPHL Specimen Collection and Transport ManualVolatile Organic Compounds in Drinking WaterContainerNote2 40mL amber vials and a dropper bottle of HClTwo 40mL sample vials are pre-preserved in the lab. A small dropper bottle containing dilutehydrochloric acid is obtained with the sample vials. Do not open either until ready to sampleDirections for Sampling1. Select a sample point that is used mainly for drinking and cooking purposes such as thekitchen faucet. Allow the water to run for at least 1 minute.2. Unscrew the sample bottle cap, then immediately and slowly fill the first sample vial halfway. Cautiously, add 5 drops of hydrochloric acid and continue filling the vial until it isjust about to overflow. (Use hydrochloric acid with caution as it burns skin whenspilled).3. Slowly screw cap back on sample to prevent air bubbles in the vial and deliver to testinglaboratory along with the hydrochloric acid dropper bottle.4. Repeat the process in steps 1 through 3 for the second sample vial.Note: Common practice dictates collection of two samples vials after 2-3 minutes of flushingthe faucet. The use of a Trip Blank (a contaminant-free water sample provided by the lab) is tocompensate for any environmental contaminants that may be present during the transport andcollection of samples between the sample source and the laboratory.ECPHL effective 3/1/2012 Page 31 of 38

ECPHL Specimen Collection and Transport ManualEnvironmental Testing Chart - Sample: Drinking WaterTest Name Method Container(provided by ECPHL)CodeBACTERIOLOGYTC Total coliform-E.coli Colilert Sterile with sodium thiosulfate,Bottled waterSPC Standard Plate Count Pour plate Sterile with sodium thiosulfate,Bottled waterStorageECPHL effective 3/1/2012 Page 32 of 38Allowable timeCollection to testTATRejection Criteria2-6°C 30 hrs 18-24 hrs More than 30 hrs old2-6°C 8 hrs 2-3 days More than 8 hrs oldCHEMISTRY-INORGANICS-RESIDUESTDS Total Dissolved Solids Evaporation Inorganics 2-6°C 7 days 3 days Greater than 6°CMore than 7 days oldCHEMISTRY-ORGANICSHAA Haloacetic acid GC-ECD 250mL amber vial 2-6°C 28 days 5 days Greater than 6°CMore than 28 days oldTHM Trihalomethanes GC/MS 40mL amber vial with ascorbic acid 2-6°C 14 days 5 days Greater than 6°CMore than 14 days oldVOC Volatile Organic Compounds GC/MS 40 mL amber vial with ascorbic acid 2-6°CpH

ECPHL Specimen Collection and Transport ManualCodeTest Name Method Container(provided by ECPHL)StorageAllowable timeCollection to testTATRejection CriteriaCHEMISTRY-INORGANICSAlkalinity Titrimetric AlkalinityFill completely to exclude all air2-6°C 14 days 5 days Air present in containerMore than 14 days oldGreater than 6°CCalcium, hardness Titrimetric Metals 18-24°C 6 months 10 days More than 6 months oldChloride Titrimetric Inorganics 18-24°C 28 days 5 days More than 28 days oldColorVisual Inorganics 2-6°C 48 hrs 24 hrs Greater than 6°CPrior notification neededMore than 48 hrs oldCyanide Lachat FIA Cyanide 2-6°C 14 days 5 days Greater than 6°CMore than 14 days oldFluoride Selective electrode Fluoride 18-24°C 28 days 5 days More than 28 days oldNitrate Lachat FIA Nitrate, chlorinated 2-6°C 14 days 10 days Greater than 6°CMore than 14 days oldNitrate Lachat FIA Nitrate, non-chlorinated 2-6°C 48 hrs 24 hrs More than 48 hrs oldNitrite Spectrophotometer Nitrite 2-6°C 48 hrs 24 hrs Greater than 6°CMore than 48 hrs oldpHPrior notification neededElectrometric P or G 18-24°C 1 hr 24 hrs More than 1 hr oldPhosphate (ortho-) Spectrophoto-metric Inorganics 2-6°C 48 hrs 24 hrs More than 48hrs oldSulfate Turbidimetric Inorganics 2-6°C 28 days 5 days Greater than 6°CMore than 28 days oldECPHL effective 3/1/2012 Page 33 of 38

ECPHL Specimen Collection and Transport ManualEnvironmental Testing Chart - Sample: Environmental Water and SolidsCode Test Name Method Sample Container(provided byECPHL)BACTERIOLOGYTC Total coliform Membrane filterquantitationTC-SPCFC Fecal coliform Membrane filterquantitationEC E.coli Membrane filterStorageAllowabletransport timeCollection to testTATRejection CriteriaNon-turbid Coliform 2-6°C 8 hrs 24 hrs More than 8 hrs oldTotal coliform, SPC Pour plate Frozen dessert Sterile -4-0°C No set time 24-48 Greater than 0°ChrsEW Coliform 2-6°C 8 hrs 24 hrs More than 8 hrs oldquantitationSPC Standard Plate Count Pour plate EW Sterile with sodiumthiosulfateBeach, EW Coliform 2-6°C 8 hrs 24 hrs More than 8 hrs old2-6°C 8 hrs 2daysSterility/Biological Culture other Attest vials 18-24°C 24 hrs 2IndicatordaysFood Culture 2x2 inch food Sterile whirl pack 2-6°C or 24 hrs 7sample

ECPHL Specimen Collection and Transport ManualCode Test Name Method Sample Container(*provided byECPHL)CODEWChemical oxygendemandSpectrophotometricHach 8000½ gallon bottle,P/GStorage2-6°CpH 12days oldFluoride Selective electrode EW Fluoride 18-24°C 28 days 5 More than 28 daysdays oldHardness EDTA titrimetic EW Metals 18-24°C 6 months 10 More than 6 monthsdays oldNitrateReduction flow EW nonchlorinatechlorinatedNitrate, non-2-6°C 48 hrs 2 Greater than 6°Cinjectiondays More than 48 hrs oldNitrite Spectrophotometer EW Nitrite 2-6°C 48 hrs Greater than 6°CMore than 48 hrs oldO&G Oil and Grease Extraction EW 1 Liter Amber Glass 2-6˚C 28 days 5BottlepH

ECPHL Specimen Collection and Transport ManualAttachment #1NYSDOH Code RedECPHL effective 3/1/2012 Page 36 of 38

ECPHL Specimen Collection and Transport ManualAttachment #2NYS Guidance on Initial Response to a Letter/Container Containing a SuspiciousSubstance and /or Threat StatementThis is a restricted document for official use only.The document may be accessed by authorized individuals at the NYS Health Commercewebsite or may be obtained by contacting the Erie County Public Health Laboratories.ECPHL effective 3/1/2012 Page 37 of 38

ECPHL Specimen Collection and Transport ManualReferences1. Miller, J Michael. Specimen Management in Clinical Microbiology 1999 ASM.Washington DC2. Clinical Laboratory Standards of Practice 2011 Wadsworth Laboratory, Albany NY3. Environmental Laboratory Approval Program Certification Manual 2011, Albany NY4. Erie County Public Health Laboratory Specimen Collection and Transport Manual 2007,Buffalo NY.ECPHL effective 3/1/2012 Page 38 of 38