​Methodology and Clinical Interpretation for Microbiology Testing

Methodology​

​Clinical interpretation/ Performance Characteristics

• ​Gram stain
  
• Culture
  

• ​Swabs are suboptimal specimens from these sites and are less appropriate for anaerobic culture than tissue and aspirates
• Closed space specimens can also include aspirates or tissues from deep wounds that go across mucosal surface such as bite wounds, gunshots, stabs, punctures and third-degree burns due to electrocution

• Gram stain
• Culture​

• ​Organisms cultured from closed space sites should be identified and susceptibility testing performed, with the exception of mixed probable skin and/or bowel contaminants on swab specimens

• ​Gram stain
• Culture

• ​Gram stain (on STAT specimens)
• Culture

• ​Peritoneal fluid can be contaminated with numerous mixed gastrointestinal microbiotas in cases of ruptured intestine, but in patients with chronic ambulatory peritoneal dialysis or spontaneous bacterial peritonitis, the likely pathogen is usually present in very low numbers
  

• ​Antibiotic susceptibility testing is NOT done (since it is a self-limited disease) on Campylobacter, Yersinia, Aeromonas, Plesiomonas, and Vibrio
  
• E.coli 0157:H7 is not treated since treatment is associated with an increased risk of HUS
• Antibiotic susceptibility testing is note done on Salmonella/Shingella spp. (since the illness is also self-limiting); however the antibiogram is done and released only in specific circumstances (on request, immunosuppressed, neonates less than three (3) months, presence of S.typhi/paratyphi)

• ​Chromogenic culture media

• ​Other organisms such as Legionella pneumophilia, chlamydophilia (Chlamydia) pneumonia, Mycoplasma pneumonia, common respiratory viruses, Pneumocystis jirovecii and mycobacteria can cause lower repsiratory tract infections and necessitate specific testing
  

• ​Chromogenic culture media

• ​Positive culture for MRSA indicates carriage of the organism

• ​Culture
  

• ​Group A Streptococus (GAS) is the most common bacterial cause of acute pharyngitis and is primarily isolated in children 5-15 years of age
• Children may yield low numbers of streptococcus pyogenes (GAS) due to difficulty of collection
• A positive pharyngeal/throat culture indicates the presence of GAS but does not distinguish between infection and colonization
• Groups C and G beta-hemolytic stretococci can also cause acute phyaryngitis
• Arcanobacterium haemolyticum is a rare cause of acute pharyngitis that may be associated with a rash similar to that seen in scarlet fever
• Other possible agents of pharyngitis (e.g.. GC) would NOT be isolated unless specifically requested
• Penicillin or amoxicillin remain the treatments of choice for Group A streptococcal pharyngitis

• Mycoplasma DUO​

• ​Mycoplasma hominis has been implicated as a cause of endometritis and salpingitis and is associated with non-specific vaginitis
• Ureaplasma urealyticum in males mainly causes urethritis. It is occasionally found as the agent of prostatitis and epididymitis. It has been incriminated in the occurrence of reproductive disorders. In pregnant women it can lead to chorioamnionitis and premature rupture of the membranes which carry a risk of neonatal infection. it has been incriminated in the occurrence of reproductive disorders
  

• ​Direct microscopic examination under low-power (10x) objective
  

• Pinworms ova and/or adult worm seen on pinworm paddle indicates a pinworm infection
• Pinworm ova and/or adult worm not seen on one pinworm paddle will not determine if a patient is negative for infection. The female pinworm deposits eggs on the perianal skin sporadically. without multiple pinworm paddles (taken consecutively, one each morning), it is not possible to determine if patient is negative for the infection

• Gram stain​

• Presence of yeast indicates oral thrush
• If yeast is fount to be present and requires identification, please contact the Microbiologist-on-call at (306)655-1000 for further discussion​

• ​Real-time PCR amplification for detection of microbial DNA

• ​This test is a "Research Use Only" test and has not yet been fully validated
• intended to assist in the diagnosis of Acanthamoeba keratitis (AK). Clinical correlation is required
• The test will detect all species within the Acanthamoeba genus, but will not distinguish between them
• A positive result for Acanthamoeba does not necessarily indicate the presences of viable (infectious) microbes, PCR methods will detect infectious and non-infectious microbes with equal efficiency
• A negative result for Acanthamoeba does not exclude the possible presence of other viruses or bacteria
• Test results are qualitative only/ analytical sensitivity has not been determined

• ​Automated detection of growth by blood culture instrument

• ​Clinical correlation required
• M. tuberculosis bacteremia can be observed in immunocompromised patients with active TB disease
• Disseminated M. avium complex infection with bacteremia can develop in HIV positive individuals with low CD4 counts
• Central line-related bloodstream infections can be seen

• ​Real-time PCR amplification for detection of viral DNA

• This test will detect all serotypes of Adenovirus but will not discriminate between them
• A positive result for Adenovirus does not necessarily indicate the presence of viable (infectious) virus. PCR methods will detect infectious and non-infectious virus with equal efficiency
• a negative result for Adenovirus does not exclude the possible presence of other respiratory viruses or bacteria
• Test results are qualitative only. Analytical sensitivity has not been determined
• This test has been validated in-house using published data as a source (reference available upon request)​

• ​Real-time PCR amplification for detection of bacterial DNA

• ​This test will not discriminate between the closely related species B. pertussis, B. bronchoseptica, and B. holmseii. However, because these latter two species rarely cause human disease, a positive result is most likely to be B. pertussis
• The test does not distinguish between viable and non-viable organisms- both are detected with equal efficiency
• A negative result for B. pertussis does not exclude the possible presence of other microorganisms
• Test results are qualitative only. Analytical sensitivity has not been determined
• This test has been validated in-house using published data as a source (reference available upon request)
  

• Real-time PCR amplification for detection of bacterial DNA​

• ​This test is specific for C. trachomatis and will not cross-react with other species of Chlamydia. The assay targets the cryptic plasmid found in all C. trachomatis and have a genetic deletion of this plasmid
• The test does not distinguish between viable and non-viable organisms - both are detected with equal efficiency
• A negative result for C. trachomatis does not exclude the possible presence of other microorganisms
• Test results are qualitative only. Analytical sensitivity has not been determined
• This test has been validated in-house using published data as a source (reference available upon request)

• ​Cepheid GeneXpert system: Real-time PCR amplification of C. difficile- specific gene targets
  

• ​This test is intended to aid in the diagnosis of patients suspected of having C. dificile disease. The test is a multiplexed PCR that targets genetic regions encoding the Toxin B gene (tcdB) and the binary toxin gene present in all toxigenic C. difficile. in addition, a third gene (tcdC) may be amplified which allows the hypervirulent 027/NAP1?B1 C. difficile ribotype to be differentiated from non-NAP1 C. difficile
• The test does not distinguish between viable and non-viable C. difficile - both are detected with equal efficiency
• A negative result for C. difficile does not exclude the possible presence of other pathogens
• A positive result should be correlated with clinical symptoms because of the possibility of asymptomatic carriage of C. difficile in healthy children and adults
• The manufacturer reports analytical sensitivity between 75 and 460 organisms per test, depending on the toxin type, and clinical sensitivity of at least 93% depending on the patient population. No cross-reactivity with other fecal organisms has been noted
  

• ​Eragen (Luminex) system: Real-time PCR amplification for detection of CMV DNA
  

• ​This assay is to be used to quantitate the amount of Cytomegalovirus DNA in the plasma of patients undergoing anti-CMV therapy. It is not indicated for the initial diagnosis of a CMV infection, nor for screening of asymptomatic patients who do not have risk factors for CMV disease
• This assay employs real-time PCR technology and has been calibrated against an international reference standard. Results are expressed as International Units per mL(IU/mL) of plasma
• This assay has a quantitation range of 200 to 5,000,000 IU/mL; a result reported as "detected, less than 200 IU/mL" or "detected, greater than 5,000,000 IU/mL" indicates that although CMV DNA is present, accurate quantitation is not possible
• The limit of detection of this assay is approximately 50 IU/mL of plasma. Therefore, a result of "Not Detected" does not necessarily indicate the complete absence of CMV if the viral load is below this detection limit
• The assay has an inherent technical variability that may be as high as 25%; for example, a viral load reported 1000 IU/mL. For this reason, changes in viral loads of less than 25% in serially collected specimens may not be meaninful and should be interpreted in the clinical context. Similarly, caution should be used if comparing quantitative results from this assay to those generated by different laboratories, or published in the literature

• ​Standard PCR amplification followed by agarose gel electrophoretic detection of viral DNA

• ​This is a "Research Use Only" test and has not yet been fully validated for diagnostic use
• This test is specific for EBV and will not cross-react with other members of the Herpes Virus family
• Intended to assist in the diagnosis of disease caused by this virus, in particular, central nervous system infectious mononucleosis
• The test does not distinguish between infectious and non-infectious viruses - both are detected with equal efficiency
• A negative result for EBV does not exclude the possible presence of other microorganisms
• Test results are qualitative only. Analytical sensitivity has not been determined
  

• ​Real-time PCR amplification from detection of viral DNA

• ​This test will specifically detect HSV Type 1 and HSV Type 2 and differentiate between these two types. The report will indicate which HSV type has been detected. The test does not cross-react with other members of Herpes Virus family
• Test results are qualitative only. Analytical sensitivity is between 2000 and 5000 copies of HSV1 or 2 per mL of primary specimen.
• False negative results may occur for dermal specimens (vesicular lesions) if the base of the lesion is not sampled properly, or if the specimens is collected late in the course of the infection
• False negative results may occur for cerebrospinal specimens if the specimen is collected during the very early stages of CNS disease when the viral load is expected to be very low. in addition, HSV DNA may only persist in CSF for 3 to 4 weeks after initial presentation of symptoms and be undetectable in the very late stages of disease
• A positive result does not necessarily indicate the presence of viable (infectious) virus. PCR methods will detect infectious and non-infectious virus with equal efficiency
• A positive result does not exclude the possible presence of other microbial pathogens
• This test has been validated in-house using published data as a source (references available upon request)

• ​Enzyyme-linked Immunosorbent Assay (ELISA)

• This test cannot distinguish between tuberculosis disease and latent tuberculosis infection (LTB)
• This test is tended for use in conjunction with risk management, radiography, and other medical and diagnostic evaluations
• Infections with other mycobacteria (M. kansasii, M. szulgai, and M. marinum) may also cause false results

• ​GeneXpert system: Real-time PCR amplification for detection of bacterial DNA

• ​This test will detect all members of the Mycobacterium tuberculosis MTB Complete which includes M. tuberculosis, M. bovis, M. africanum, M.canetti, and M. microti. it will not distinguish between the members of the MTB complex
  
• Culture should be performed as it is the gold standard for testing and is necessary for susceptibility and fingerprinting (for epidemiology).
• This test does not distinguish between viable organisms, non-viable organisms', or nucleic acids persisting from a prior infection. Test results must be correlated with clinical presentation before a definitive diagnosis is made. Similarly, the test has not been studied in patients undergoing antimicrobial chemotherapy and should not be used to assess therapeutic success or failure
• A negative result does not rule out the presence of MTB complex if the organisms are present below the limit of detection for the assay. Manufacturer data suggests that the limit of detection is approximately 130 organisms per mL of primary specimen.
• Clinical sensitivity of this test, based on manufacturer data, is approximately 99.5% for smear-positive, culture-positive specimens, and 90% for smear negative, culture-positive specimens. Clinical specificity is approximately 98%
• Test results are qualitative only (positive or negative)

• ​Real-time PCR amplification for detection of viral RNA

• ​This assay is specific for the Genotypes I and II Noroviruses and will distinguish between the two genotypes. Within the Genotype II group, this assay will also detect the newly emerged Sydney GII.4 variant. The assay does not cross-react with other gastrointestinal viruses or bacteria
• Test results are qualitative only. Analytical sensitivity has not been determined
• A positive result for Norovirus does not necessarily indicate the presence of viable (infectious) virus. PCR methods will detect infectious and non-infectious virus with equal efficiency. Similarly, Norovirus will be present in stool for several days after complete resolution of symptoms in the patient, yielding positive PCR result. results of a PCR test must be correlated with other clinical and diagnostic findings
• A negative result for Norovirus does not exclude the possible presence of other gastrointestinal viruses or bacteria
• This test has been validated in-house using published data as a source (reference available upon request)

• ​Real-time PCR amplification for detection of viral RNA

• ​This test will specifically detect Respiratory Syncytial Virus (RSV) Types A and B and distinguish between them. the report will indicate which RSV type has been detected. The test does not cross-react other common respiratory viruses or bacteria
• A positive result does not necessarily indicate the presence of viable (infectious) virus. PCR methods will detect infectious and non-infectious virus with equal efficiency
• A negative result does not rule out the presence of RSV if the virus is present below the limit of detection of the assay. Data suggests that the assay has a detection limit of approximately 9000 viral copies per mL of primary specimen
• Test results are qualitative only (positive or negative)
• A positive result does not exclude the possible presence of other microbial pathogens
• The test has been validated in-house using published data as a source (references are available upon request)

• ​Real-time PCR amplification for detection of viral DNA

• ​This test will specifically detect Varicella Zoster Virus (VSV). The test does not cross-react with other known herpes viruses.
• Test results are qualitative only. Analytical sensitivity has not been determined
• False negative results may occur for dermal specimens (vesicular lesions) if the base of the lesion is not sampled properly, or if the specimen is collected late in the course of the infection.
• False negative results may occur for dermal specimens (vesicular lesions) if the base of the lesion is not sampled properly, or if the specimen is collected late in the course of the infection
• False negative results may occur for cerebrospinal specimens if the specimen is collected during the very early stages of CNS disease when the viral load is expected to be very low. In addition, VSV DNA may become undetectable in the very late stages of CNS disease
• A positive result does not exclude the possible presence of other microbial pathogens
• This test has been validated in-house using published data as a source (reference available upon request)

• ​Referred out to National Microbiology Laboratory (NML), Winnipeg

• ​Zika virus serology cross reacts with dengue and yellow fever, therefore positive results require further evaluation using PRINT (plaque reduction neutralization test)
  
• A convalescent sample taken for serology 2-4 weeks after the acute onset of illness is recommended to confirm exposure to Zika virus. If initial PCR and IgM tests negative
• Refer to the most recent guidelines for recommendations on Zika virus testing. Please contact the microbiologist on call at (306)655-1000 if consultation is required.