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Q&A with the Laboratory: What’s Important to Know to Submit Samples for TB Testing

Q&A with the Laboratory: What’s Important to Know to Submit Samples for TB Testing. 2017 World TB Day Jessica Gentry Tuberculosis Laboratory Supervisor. Outline. Packaging and Shipping LimsNet Ordering Testing Timeline for Results. Packaging and Shipping. How Much Sputa is Enough?.

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Q&A with the Laboratory: What’s Important to Know to Submit Samples for TB Testing

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  1. Q&A with the Laboratory:What’s Important to Know to Submit Samples for TB Testing 2017 World TB Day Jessica Gentry Tuberculosis Laboratory Supervisor

  2. Outline • Packaging and Shipping • LimsNet • Ordering Testing • Timeline for Results

  3. Packaging and Shipping

  4. How Much Sputa is Enough? • 5-10 mL is optimal, however, we’ll accept any amount • More is better • Samples of <0.5 mL will be noted on the report • Collect 3 sputa; at least 8 hours apart; at least one first thing in the morning • Make sure the patient is not just producing saliva • Refrigerate if not shipping immediately

  5. How Do I Package a TB Specimen? ISDH shipping supplies are available for Local Health Departments • To order 6A containers: 317-921-5875 containers@isdh.in.gov

  6. Be Sure to Send this…

  7. …and Not This!

  8. What if I don’t have any ISDH Containers and I Really Need to Ship? • Any sterile, leak-proof, screw capped collection container should be fine—for example, urine collection tubes from the hospital • Remember to package as Category B, Biological Substances, including leak-proof secondary packaging and rigid outer packaging

  9. How Do I Get my Sputa to the Lab? • Use UPS bags provided by ISDH—FREE!!! • Deliver them yourself—open 8:15 am to 4:45 pm • 550 West 16th Street, Suite B, Indianapolis, 46202 • Remember not to ship on Friday or the day before a state holiday www.google.com/maps

  10. What are Transit Times and Why Should I be Concerned About them? • Transit time is defined as the length of time between sample collection and receipt at the lab • The sooner the sample arrives here, the faster it can be tested, and the faster new TB cases can be identified • ISDH must report transit time data to the CDC as part of the TB Cooperative grant—the goal is 24 hours from collection • Do not “BATCH” your specimens! • Ship one immediately, and the others the next day • Remember, UPS shipping is FREE!

  11. LimsNet

  12. How Do I Sign up for LimsNet? • Contact the LIMS helpdesk at LimsAppSupport@isdh.in.gov • Provide your name, contact info, organization, IP address https://eportal.isdh.in.gov/limsnet/login.aspx

  13. How do I add New Tests to my Account? • Contact the helpdesk and let them know what test type you need to add • Currently Available Tests: • Blood Lead •Pertussis • CRE •Syphilis • CT/GC •TB • Enterics •Virology • Hepatitis/HIV •Trioplex (Zika) • Rabies Note: some tests may be restricted based on organization type

  14. How do I Add a New User? • Contact the LIMS helpdesk at LimsAppSupport@isdh.in.gov • Provide the user’s name, contact info, organization, IP address • Help Desk may require email or fax from supervisor to validate user • This is just to ensure we assign the user to the correct account

  15. LimsNet Tip #1 • Patient’s Clinic ID Number—use this feature to autofill patient demographics when more than one sample will be submitted for the same patient • Enter an ID number for the first sample • Enter this number for the next sample and click Lookup Info

  16. LimsNet Tip #2 • Specimen Collection, Packaging & Shipping Instructions link • The instructions provided will match the test type selected in the drop down

  17. LimsNet Tip #3 • If the coversheet doesn’t pop up as a PDF, you can retrieve it in the Packages screen

  18. LimsNet Tip #4 • Email Alerts—if you wish to receive an email each time there is a new result, you can select this in the Personalized Settings tab, under Change my Personal Information

  19. What’s the Status of my Sample? Test order has been completed but sample has not yet been shipped Sample has been shipped but not received Sample has been received at the lab (no results yet) Preliminary report is available (unviewed) Preliminary report is available (after viewing) Final report is available Awaiting Approval and Generating Report—testing has been completed but report isn’t released into LimsNet yet

  20. Ordering Testing

  21. What Testing is Available for Specimens? • Acid Fast Microscopy (AFB Smear)—sputum smeared on a glass slide, stained, and examined under a microscope. When we see any AFB, we quantify them as number/field. • AFB Positive-->50/field, >10/field, 1-10/field, <1/field • Equivocal—we see 1, 2, or 3 bacteria on the entire slide • Positive result could indicate TB or some other mycobacteria (M. avium, M. abscessus, etc.)

  22. What Testing is Available for Specimens? • Sputum PCR—molecular test that detects MTBC DNA—very sensitive, can detect very small quantities, specific to TB • Not quite the same as a probe, but the results are equivalent • Pyrosequencing—molecular test that detects mutations which commonly cause antibiotic resistance to RIF and INH • Mutation not detected—approx. 90% chance the strain will be susceptible—culture DST will be performed to confirm • Mutation detected—strain will most likely be resistant

  23. What Testing is Available for Cultures? • Two sets of media are inoculated for all specimens—liquid and solid. Once growth is detected in either, we will try to identify it • Culture PCR—same test as sputum PCR, but performed on the culture instead of the specimen • MALDI-TOF Mass Spec—molecular test that can identify hundreds of different mycobacteria (ex. M. avium, M. abscessus) • Drug Susceptibility Testing RIPE Rifampin Isoniazid Pyrazinamide Ethambutol

  24. What Tests Do I Need to Order? • The lab will automatically perform a smear and culture for every specimen submitted • If the smear is positive, TB PCR will be performed (for new patients) • Susceptibility testing and pyrosequencing will be performed once per TB patient • PCR can also be performed on smear negative sputa upon special request—make sure to note this on the coversheet or in LimsNet as “MTB other” test • When a culture grows, culture TB PCR will be performed

  25. Timeline for Results

  26. How Long Does All this Take? • Acid Fast Microscopy (AFB Smear)—Day 1 (if received before 10 am) • Sputum PCR—Day 2 • Pyrosequencing—within 7 days • Culture PCR—within 3-4 weeks • MALDI-TOF Mass Spec—within 4-5 weeks • Drug Susceptibility Testing –within 6 weeks • Negative Culture—42 days from date started These times are approximate; dependent on how fast the strain grows and how many bacteria are present

  27. Who’s Doing all this Great Work? Edita Doraci, Microbiologist Lee Maggard, Microbiologist Brandon Watson, Lab Tech Erica Vecchio, Microbiologist Jessica Gentry, Supervisor

  28. When Should I Call the Lab? • If you have a question • If you have a special test request • If you need testing expedited • If you need help interpreting a lab report • If you need help finding lab results • If you have a patient at a hospital and want to arrange for testing from ISDH

  29. More Questions? Jessica Gentry Tuberculosis Laboratory Supervisor Indiana State Department of Health jgentry@isdh.in.gov Phone: (317) 921-5858

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