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Microbiology

Microbiology Testing Services and Complex or Unknown Infections

Sometimes routine pathogen testing cannot identify an organism that is causing an infection. Microbiology testing allows for more in-depth investigation than other testing methods.

Routine Urine Culture and Antibiotic Sensitivity Testing

Routine PCR tests can identify most causes of illness in the human respiratory, GI, and urogenital tracts. But sometimes a person contracts an infection caused by an uncommon pathogen that routine tests do not identify.

Microbiology laboratories use both traditional and advanced diagnostic techniques to identify uncommon pathogens. Emerging pathogens and antibiotic-resistant bacteria require the use of microbial testing so that healthcare teams can develop treatment plans.

A microbial study can identify bacteria, fungi, or protozoans in a specimen collected from a patient. Microbiology testing may also be used when doctors suspect multiple infectious agents in a patient’s illness.

Madison Core Laboratories provide accurate and efficient microbiology testing services for complex infections and for infections where routine diagnostic testing is insufficient for a proper diagnosis.

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Clinical Significance

Urine culture is designed to quantitate the growth of significant bacteria when collected by the Clean Catch Guidelines or from indwelling catheters.  This test has a reference range of fewer than 1,000 bacteria per mL. More than 95% of Urinary Tract Infections (UTI) are attributed to a single organism. Infecting organisms are usually present at greater than 100,000 per mL, but a lower density may be clinically important. In cases of UTI where more than one organism is present, the predominant organism is usually significant, and others are probably urethral or collection contaminants. When multiple organisms are isolated from patients with indwelling catheters, UTI is doubtful and colonization likely.

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Appropriate Uses of Urine Cultures

Presence of symptoms suggestive of a urinary tract infection (UTI). For example,

  • Flank pain or costovertebral angle tenderness,
  • acute hematuria,
  • new pelvic discomfort
  • New onset or worsening sepsis without evidence of another source on history, physical examination, or laboratory testing
  • Fever or altered mental status without evidence of another source on history, physical examination, or laboratory testing
  • In spinal cord injury patients: increased spasticity, autonomic dysreflexia, sense of unease

Inappropriate Uses of Urine Cultures

  • Odorous, cloudy, or discolored urine in the absence of other localizing signs/symptoms
  • Reflex urine cultures based on urinalysis results, such as pyuria, in the absence of other indications (Absence of pyuria suggests a diagnosis other than CAUTI)
  • Urine culture to document response to therapy unless symptoms are failed to resolve

Reporting

Clinical reports will indicate the identification of any relevant pathogens, relative quantification of identified pathogens and a profile of antibiotic sensitivity testing performed. Preliminary reports are issued around 24 hours after the testing begins and will indicate growth or no growth, gram stain results, and relative quantification of the bacteria present. In some cases, the report will indicate that only normal flora was identified, and no further analysis is indicated.

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Specimen Collection

SPECIMEN STORAGE & TRANSPORT

Temperature: room temperature (15 °C – 25 °C / 59 °F – 77 °F) Maximum Holding Time: 72 hours

ACCEPTABLE SPECIMEN TYPES

Urine: ≈ 70 mL in Boritex Urine Culture Cup (enough to reach red fill line)

REJECTION CRITERIA 

  1. Transport time greater than 72 hours 
  2. Specimen container not labeled 
  3. Specimen container not sealed properly

SPECIMEN COLLECTION

Provider Instructions 

  1. Label the Boritex Cup with the patient’s information (Name and DOB). 
  2. Leave the white tablet in the cup. DO NOT INGEST. DO NOT TOUCH.
  3. Have the patient submit a clean-catch midstream urine sample in the Boritex Urine Cup. 
  4. Place the Boritex Urine Culture Cup inside the biohazard specimen bag and seal tightly. 
  5. Fill out the requisition form completely
  6. Transport to the laboratory within 72 hours of collection.

ACCEPTABLE SPECIMEN TYPES 

  1. Clean catch midstream urine specimen collected into a sterile container
  2. Proper collection from an in-dwelling catheter.

REJECTION CRITERIA 

  1. Transport time greater than 72 hours 
  2. Specimen container not labeled 
  3. Specimen container not sealed properly

SPECIMEN COLLECTION 

  1. Use only for the transport of urine specimens for culture and sensitivity (C&S) 
  2. A minimum volume of 5 ml of urine is required to ensure adequate fill to the 4 mL line on tube
  3. Transfer the urine from the collection container into the vacutainer tube immediately after collection. Do not fill tubes by pouring urine or injecting urine into the tube. 
  4. Aliquot the mid-stream urine specimen or catheter specimen into a grey topped urine C&S vacutainer tube using the provided transfer straw.
  5. Label the vacutainer urine tube with the patient’s information (Name and DOB).
  6. Place the vacutainer urine tube inside a biohazard specimen bag and seal tightly.
  7. Fill out the requisition form completely. Transport to the laboratory within 72 hours of collection.

    ACCEPTABLE SPECIMEN TYPES 

    1. Clean catch midstream urine specimen collected into a sterile container
    2. Proper collection from an in-dwelling catheter.

    REJECTION CRITERIA 

    1. Transport time greater than 24 hours 
    2. Specimen container not labeled 
    3. Specimen container not sealed properly

    SPECIMEN COLLECTION 

    Provider Instructions 

    1. Label the sterile specimen cup with the patient’s information (Name and DOB). 
    2. Have the patient submit a clean-catch midstream urine sample in a sterile specimen cup. If collecting an in-dwelling catheter specimen, make sure the proper procedure is followed and placed in a sterile urine cup.
    3. Place the sterile Cup inside the biohazard specimen bag and seal tightly. 
    4. Fill out the requisition form completely
    5. Transport to the laboratory within 24 hours of collection.

    Urinalysis criteria for culture
    and sensitivity workup

    If a urinalysis with culture and sensitivity (if indicated) flags any of the following, it will reflex for a urine culture.

    1. Positive for Blood, Nitrites, or Leukocytes
    2. Protein= Small, Moderate, Large
    3. WBC >10, RBC >10, or WBC clumps present
    4. Bacteria > Moderate
    5. Yeast present

    Antibiotics Reported for Gram Negative Bacteria:

    Gram Negative Antibiotics

    Gram Negative Antibiotics

    Amoxicillin/Clavulanic Acid

    Extended Spectrum Beta Lactamase (ESBL)

    Ampicillin

    Gentamicin

    Ampicillin/Sulbactam

    Imipenem

    Cefazolin

    Levofloxacin

    Cefepime

    Nitrofurantoin

    Ceftazidime

    Piperacillin/Tazobactam

    Ceftriaxone

    Tobramycin

    Ciprofloxacin

    Trimethoprim/Sulfamethoxazole

    Ertapenem

    Antibiotics Reported for Gram Positive Bacteria:

    Gram Positive Antibiotics

    Gram Positive Antibiotics

    Ampicillin (Enterococcus species, Streptococcus agalactiae)

    Moxifloxacin

    Benzylpenicillin (Enterococcus species, Staphylococcus species, Streptococcus agalactiae)

    Nitrofurantoin

    Cefoxitin Screen

    Oxacillin

    Ciprofloxacin

    Quinupristin/Dalfopristin (Synercid)

    Clindamycin

    Rifampin

    Erythromycin

    Streptomycin High Level (Synergy)

    Gentamicin

    Tetracycline

    Gentamicin High Level (Synergy)

    Tigecycline

    Inducible Clindamycin Resistance

    Trimethoprim/Sulfamethoxazole

    Levofloxacin

    Vancomycin

    Linezolid

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