Microbiology Specimen Collection and Handling Guide

PURPOSE:

The purpose is to establish proper protocol for the collection and transportation of patient specimens for routine microbiological testing (culture) and micro molecular testing.

PRINCIPLE:

To educate the staff of the importance of following accepted procedures when collecting and handling of specimens and body fluids for routine culture and molecular testing.

PATIENT IDENTIFICATION:

***Two patient identifiers are required on the labeled specimen container. ***

1. Patient name, medical record number or account number, date of birth and sex.

2. Requesting physician and phone number.

3. Date and time of collection.

4. Specimen type and/or site.

   **Location is not an acceptable identifier

   
   

   The patient's name and the source of specimen must be on both the requisition and the specimen. A culture is only as accurate as the method used for collection. Outside microorganisms may contaminate a specimen during each phase of handling. This can lead to misleading or erroneous results. Take care at all times to avoid contamination. Submit promptly for optimal recovery of pathogens. Submit in a sterile leak-proof container at room temperature unless otherwise specified.

   
   

   Aerobic Culture

   Fluid: Submit in a sterile tube or container, or syringe with needle removed and capped. Submit immediately to the laboratory. Swab: Submit a culture swab in transport media, COPAN eSwab or Port A Cult Media Vial. For optimal results, it should be received in the Microbiology laboratory within 24 hours after collection. Tissue: Submit in a sterile container immersed in a small amount sterile saline. Submit immediately

   
   

   
   

   Anaerobic Culture

   Be sure specimen is from suitable anaerobic sterile body site or deep body cavity. Send a culture swab immersed in transport media or fluid in syringe with air expelled and needle removed (with cap). Submit promptly for optimal recovery of pathogens. Must be received in microbiology laboratory within 24 hours of collection. Collection container should be a COPAN eSwab or Port A Cult Media Vial. For fluids, submit in a sterile container.

   
   

   Fungus Culture

   Submit specimens in sterile container. (Skin Scraping, Hair, Nails)

   
   

   Fungus Culture Other

   Submit specimens in sterile container. Swabs are acceptable but not recommended.

   
   

   Gram Stain

   Smear glass slide with specimen at time of collection and air dry. Always smear slide frosted side up. Label slide in pencil on frosted area with patient's name and source. Culture swabs and specimens submitted in sterile containers can also be submitted for gram stain. Alternately, liquid may be submitted.

   Any container can be used.

   
   

   Urine Culture

   Urine placed immediately in blue-top transport tube (Starplex boric acid preservative tube), is strongly preferred. Urine collected in a sterile container is also acceptable if refrigerated immediately after collection. Directions for proper collection: acceptable up to 72 hours after collection.

   1. Females should clean the periurethral area with water.

   2. Males should clean the glans penis area with water.

   3. Allow the initial flow of urine to commence and then collect a midstream portion into a sterile container.

   4. Store and submit sealed container refrigerated, or transfer urine immediately to a Starplex preservative tube, please note urine must be poured up to fill line and store/submit refrigerated or at room temperature. Susceptibility testing is not routinely performed on voided specimens with mixed urogenital flora or on colony counts below 50,000 CFU/mL. Unpreserved refrigerated urine must be received within 24 hours of collection. Urine grey top tubes are acceptable up to 48 hours after collection. Urine in blue topped "culture" tubes is

   Molecular Microbiology Tests Hologic Panther System

   From Cytology Media ThinPrep vial

   
   

   

   1. Chlamydia trachomatis/Neisseria gonorrhea NAAT Testing

      
      

   2. HPV High-risk testing

      
      

   3. Trichomonas vaginalis by NAAT testing

From Aptima® Multitest Swab Specimen (vaginal, Penile Meatal)

1. Chlamydia trachomatis/Neisseria gonorrhea NAAT Testing (can also perform from clinician collected throat or rectal swab)

   
   

2. Trichomonas vaginalis by NAAT testing

   
   

   

   
   

   After collection, transport and store the swab in the swab specimen transport tube at 2°C to 30°C until tested. Specimen is stable for 60 days of collection.

   
   

   From Aptima® Multitest Swab Specimen (vaginal)

   After collection, swab specimens in transport tubes can be stored at 15°C to 30°C for up to 30 days. See BV SOP for more details.

   
   

   1. APTIMA Bacterial Vaginosis Assay (NAAT test)

   2. CV/TV Assay (NAAT test)

   3. Mycoplasma genitalium Assay (NAAT test)

From Urine Samples:

From urine collected on a sterile container and transferred to Hollogic APTIMA urine media: Urine specimens in the Aptima urine tube can be stored at 2°C to 30°C, until tested. In APTIMA tube sample is stable for 30 days. If longer storage is needed, freeze the specimen transport tube at ≤ –20°C for up to 24 months.

Note: Urine samples that are still in the primary collection container must be transported to the lab at 2°C to 30°C. Transfer the urine sample into the Aptima urine specimen transport tube within 24 hours of collection. Urine must be within the two black lines on the tube, do not overfill or underfill.

1. Chlamydia trachomatis/Neisseria gonorrhea (NAAT test)

   
   

2. Mycoplasma genitalium Assay (NAAT test)

APTIMA HSV 1 & 2 Test (collection must be from ano/genital lesion)

1. Aptima® Multitest Swab Specimen, orange swab

BioFire GI Panel (stool sample in cary blair media)

• Specimens should be processed and tested with the BioFire GI Panel as soon as possible.

• If storage is required, specimens can be held:

  
  

  At room temperature for up to 4 days (15-25 °C) Refrigerated for up to 4 days (2-8 °C)

  
  

  • Dysentery

  • Diarrhea with fever, severe abdominal cramps, or signs of sepsis

  • Moderate to severe disease

  • Symptoms lasting more than seven days

  • Immunocompromised patients with diarrhea

  • Individuals at high risk of spreading disease to others and during known or suspected outbreaks.1

  • Individuals presenting with:1,11

  Note: Formed stool samples will be rejected.

  
  

  Who Should Be Tested?

  Guidelines from American College of Gastroenterology and Infectious Disease Society of America:

  
  

  
  

  • Hologic Panther System SARS-CoV-2 APTIMA Test

  • Panther Fusion Respiratory Panels

The Panther Fusion® Flu A/B/RSV assay - Qualitative detection and differentiation of influenza A virus, influenza B virus and respiratory syncytial virus

The Panther Fusion® AdV/hMPV/RV assay - Qualitative detection and differentiation of adenovirus, human metapneumovirus and rhinovirus

The Panther Fusion® Paraflu assay - Qualitative detection and differentiation of parainfluenza 1 virus, parainfluenza 2 virus, parainfluenza 3 virus and parainfluenza 4 virus

• Specimens – Clinical material collected from patient placed in an appropriate transport system. For the Aptima SARS-CoV-2 assay or Panther Fusion respiratory panels, this includes NP, nasal, midturbinate and OP swab specimens, or nasopharyngeal wash/aspirate and nasal aspirate specimen collection in viral transport medium (VTM/UTM), saline, Liquid Amies, or specimen transport medium (STM).

  
  

• Samples - Represents a more generic term to describe any material for testing on the Panther System including specimens, specimens transferred into a Panther Fusion Specimen Lysis Tube, Hologic Specimen Lysis Tube with solid cap, Custom Specimen Lysis Tube, Aptima Specimen TransferTube, Aptima Multitest Transport Tubes, and controls.

  
  

  Swab Specimen Collection

• Collect NP swab, nasal swab, and OP swab specimens according to standard technique using a polyester-, rayon-, or nylon-tipped swab. Immediately place the swab specimen into 3mL of VTM or UTM.

  
  

• Swab specimens may alternatively be added to saline, Liquid Amies or STM. The Aptima Multitest Swab Specimen Collection Kit may be used for the collection of OP and nasal swab samples.

• After collection, specimens collected in VTM/UTM can be stored at 2°C to 8°C up to 96 hours before transferring to the Specimen Lysis Tube (i.e., Panther Fusion Specimen Lysis Tube, Hologic Specimen Lysis Tube with solid cap, or Custom Specimen Lysis Tube) or Aptima Specimen Transfer Tube as described in the specimen processing section below.

• Remaining specimen volumes in VTM/UTM can be stored at ≤-70°C.

  
  

  The following types of VTM/UTM can be used:

• Remel MicroTest M4, M4RT, M5 or M6 formulations

• Copan Universal TransportMedium

• BD Universal Viral TransportMedium

Note: Do not use medium that may contain Guanidium thiocyanate or any guanidine- containing material.