Infectious Disease

What does an “inhibited” test result on a polymerase chain reaction (PCR) assay mean?

PCR inhibitors are factors that prevent the amplification of nucleic acids through PCR. PCR inhibition is the most common cause of amplification failure when sufficient copies of DNA are present. PCR inhibitors usually affect PCR through interaction with DNA or interference with DNA polymerase. Inhibitors can escape removal during the DNA purification procedure by binding directly to single- or double-stranded DNA.

Inhibitors may be present in the original specimen, such as blood or tissue, but may also be added as a result of the sample-processing and DNA-extraction techniques used. Excess salts, including KCl and NaCl, ionic detergents, ethanol, isopropanol, and phenol can contribute various inhibitory mechanisms and reduce PCR efficiency.

Why does the result for the Hepatitis C Virus Genotype by Sequencing, 0055593, assay state “1a or 1b”?

This test does not differentiate between HCV-1a and HCV-1b. Therefore, these subtypes will be reported as "1a or 1b."

Does a recent viral load need to be submitted for sequencing assays?

Each sequencing assay requires a minimal viral load for sequencing to be successful. Refer to the ARUP Laboratory Test Directory entry for each assay to determine the required viral load.

Is 2p a valid subtype for the HCV high-resolution assay?

Yes, 2p is a valid subtype.

How is it possible to have a detected result that is not quantitative?

When a sample has a viral load that is lower than the assay’s limit of quantification but at or above the limit of detection, the virus is detected, but the viral load is not high enough to quantify. Samples with a viral load below the assay’s limit of quantification are reported as detected with no quantitative value. Refer to the ARUP Laboratory Test Directory entry for each assay to determine the limit of quantification.

Why was the result indeterminate for genotyping but detected for viral load testing?

The viral load may not be high enough, and thereby indeterminate, for the genotyping assay.

What does it mean when a DFA result is reported as “sample inadequate”?

Sensitivity of DFA methodology is dependent upon adequacy of the specimen. If there are fewer than 20 cells, the DFA result will be reported as “sample inadequate.”

What identification methods are used to identify unusual bacteria?

ARUP uses phenotypic methods, as well as matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS) and 16S sequencing.

Why does ARUP no longer perform H. pylori serology?

Recent guidelines for testing strategies issued by the American Gastroenterology Association and American College of Gastroenterology do not recommend the use of serology for the diagnosis of active H. pylori infection. For these reasons, serological testing for H. pylori has been discontinued at ARUP to facilitate physician use of recommended testing methods.

What are the specimen transport requirements for 0060714, Unusual Organism Culture?

This culture is for uncommon organisms, such as Streptobacillus moniliformis, Haemophilus ducreyi, and certain fastidious organisms, such as Neisseria gonorrhoeae, for which standalone cultures are not available.
Transport for:

• S. moniliformis: Blood, fluid, wound, aspirate, and tissue; transport in blood culture bottles, blue-top vacutainer (citrate), or a sterile container
• H. ducreyi: Recovery of this pathogen is more likely if the specimen is immediately inoculated to chocolate agar and incubated onsite; if colonies resembling Haemophilus grow, they can be streaked to a chocolate agar slant and sent for identification. This organism is fragile and does not survive transport well. Organism will not survive for 24 hours in ambient air. Less optimal transport is a swab in Amies transport media at 4°C, <72 hours. 
• N. gonorrhoeae: Any body site or fluid should be sent ambient <2 hours. Specimen inoculated on Modified Thayer Martin (MTM) media can be sent ambient <24 hours. Specimens sent refrigerated or frozen are unacceptable.

A stool specimen was not placed in the preservative within one hour for Ova and Parasite Exam, Fecal (ARUP test code 2002272); is it still acceptable for testing?

To maintain proper morphology, intestinal parasites need to be preserved within one hour of collection. The specimen may be acceptable for the Gastrointestinal Parasite and Microsporidia PCR (ARUP test code 2011660) assay.

Is the Meridian Para-Pak SVT acceptable for Ova and Parasite Exam, Fecal (ARUP test code 2002272)?

We have not yet validated this media for use with the Ova and Parasite Exam; however, testing can be performed with a non-valid media disclaimer.

Is stool preserved in 10% formalin and PVA acceptable for Ova and Parasite Exam, Fecal (ARUP test code 2002272)?

Specimens preserved in 10% formalin and PVA are acceptable.

Can a specimen for Parasite Examination, Macroscopic (ARUP test code 2007361) be preserved in alcohol?

Alcohol, ethanol, or methanol of any concentration is acceptable as a preservative.

On which molds will ARUP perform susceptibility testing?

Susceptibility testing on mold species that may not be clinically relevant are not routinely performed. If the mold is identified as Penicillium species, Cladosporium species, Phoma species, Myrothecium species, Trichothecium species, or Basidiomycete mold and susceptibly is requested, the test will have the following result: Susceptibility testing is not recommended for this organism. Clinical and pathologic correlation is required to determine the significance of this isolate. Contact ARUP if susceptibility testing is clinically indicated (e.g., the isolate was recovered from multiple specimens); organism saved for one week.

For clinically significant molds, the following antifungals are reported with MIC values only: amphotericin B, anidulafungin, caspofungin, itraconazole, micafungin, posaconazole, and voriconazole.

What are the turnaround times for mycology cultures?

• Final report on negative fungal cultures is available at 28 days.
• Preliminary report on negative fungal cultures is available on a Saturday following one to two weeks.
• Positive results are reported as soon as detected.
• Phenotypic methods, MALDI-TOF, and ITS sequencing are performed daily and begun on an organism as soon as there is sufficient  growth.

What information is needed when susceptibility testing is ordered?

Specimen source, organism name, and drugs requested are required to determine if test requested is appropriate. ARUP uses CLSI susceptibility testing documents for result interpretation.

What does SDD mean on susceptibility reports?

The susceptible-dose dependent category implies that the susceptibility of an isolate is dependent on the dosing regimen used in the patient. To achieve levels likely to be clinically effective against isolates for which the susceptibility testing results (either MICs or disk diffusion) are in the SDD category, it is necessary to use a dosing regimen (i.e., higher doses, more frequent doses, or both) that results in higher drug exposure than the dose used to establish the susceptible breakpoint.

Why doesn’t ARUP report MIC values on the Carba NP test?

The Carba NP assay is a biochemical test based on the ability of an organism with a carbapenem resistant gene (KPC, NDM, VIM, IMP, etc.) to hydrolize the β-lactam ring of the carbapenem (imipenem), resulting in a pH-dependent color change in the testing substrate. This assay is not an MIC test.

What is the difference between Antimicrobial Susceptibility MIC, Individual (ARUP test code 0060201) and Antimicrobial Susceptibility Not Otherwise Specified (ARUP test code 0060200)?

Submitting an organism under test code 0060200 generates a standard susceptibility panel based on organism and source. Test code 0060201 is appropriate if specific antibiotics are requested.

What susceptibility methods does ARUP utilize?

ARUP’s automated susceptibility system is the BD Phoenix. We also use broth microdilution, Etest, and disk diffusion.

Does ARUP perform respiratory specimen testing on Mycobacterium tuberculosis Complex Detection and Rifampin Resistance by PCR, 2010775?

Acceptable sources for MTBRIF PCR are respiratory specimens, cerebrospinal fluid (CSF), and pleural fluid or tissue. Body fluids other than pleural fluid will be performed with a disclaimer. Unacceptable specimens include blood, paraffin blocks, stool, swabs, and urine.

Once received at ARUP, unprocessed respiratory samples are first decontaminated/concentrated using NaOH NALC and then tested using the MTBRIF PCR assay. Specimen volume is critical to receive an accurate result; the optimal volume is 5–10 mL, and the minimum volume is 1.0 mL.

For Chlamydia trachomatis Culture test code 0060850, can you explain why there is no stability for these specimens at -20°C? It seems odd that it is stable for 48 hours refrigerated, and stable for 1 month frozen at -70°C, but if you freeze at -20°C it loses stability.

The published stability for Chlamydia trachomatis Culture (0060850) is listed in the LTD correctly.

• Stability: Ambient: 1 hour; Refrigerated: 48 hours; Frozen at -20°C: Unacceptable; Frozen at -70°C: 1 month

ARUP validated storage for this testing at -70°C to increase the stability option for transport. The science behind this conundrum has to do with the freezing process. At -20°C the freezing process is slower allowing for ice crystals to form, which can harm the organism and patient host cells. That is why ultra-low freezers (-70°C) are standard units in microbiology laboratories. Chlamydia Culture detects live organisms, these stringent stability requirements are necessary to provide a quality test result.¹

Here are two options for resolution to this tests stability challenge.

1. Per the CDC, in most cases nucleic acid amplification tests should be used to detect chlamydia (https://www.cdc.gov/std/laboratory/2014labrec/default.htm).

   • See ARUP test 0060243 Chlamydia trachomatis by Transcription-Mediated Amplification (TMA).

2. Hold the specimen refrigerated (</= 48 hours), then ship on dry ice.

¹Manual of Clinical Microbiology. 11th ed. 1109-1110.