A nucleic acid probe is used to detect and identify species or subspecies of organisms by identifying nucleic acid sequences in a sample. Nucleic acid probes detect genetic materials, such as RNA or DNA, unlike other tests, which use antigens or antibodies to diagnose organisms.

The availability of nucleic acid probes has permitted the rapid direct identification of microorganism DNA or RNA. Amplification techniques result in exponential increases in copy numbers of a targeted strand of microorganism-specific DNA. The most used amplification technique is polymerase chain reaction (PCR) or reverse transcriptase PCR. In addition to PCR, other nucleic acid amplification techniques have been developed, such as transcription-mediated amplification, loop-mediated isothermal DNA amplification, strand displacement amplification, nucleic acid sequence-based amplification, and branched-chain DNA signal amplification. After amplification, target DNA can be readily detected using a variety of techniques. The amplified product can also be quantified to assess how many microorganisms are present. Quantification of the number of nucleic acids permits serial assessments of response to treatment; the most common clinical application of quantification is the serial measurement of human immunodeficiency virus RNA (called viral load).

The direct probe technique, amplified probe technique, and probe with quantification methods vary based on the degree to which the nucleic acid is amplified and the method for measurement of the signal. The direct probe technique refers to detection methods in which nucleic acids are detected without an initial amplification step. The amplified probe technique refers to detection methods in which either target, probe, or signal amplification is used to improve the sensitivity of the assay over direct probe techniques, without quantification of nucleic acid amounts.

• Target amplification methods include PCR (including PCR using specific probes, nested or multiplex PCR), nucleic acid-based sequence amplification, transcription-mediated amplification, and strand displacement amplification. Nucleic acid-based sequence amplification and transcription-mediated amplification involve amplification of an RNA (rather than a DNA) target.
• Probe amplification methods include ligase chain reaction.
• Signal amplification methods include branched DNA (bDNA) probes and hybrid capture methods using an anti-DNA/RNA hybrid antibody.

Direct assays will generally have lower sensitivity than amplified probes. In practice, most commercially available probes are amplified, with a few exceptions. For this policy, indications for direct and/or amplified probes without quantification are considered together, while indications for a probe with quantification are considered separately.

Classically, identification of microorganisms relies either on the culture of body fluids or tissues or identification of antigens, using a variety of techniques including direct fluorescent antibody technique and qualitative or quantitative immunoassays. These techniques are problematic when the microorganism exists in very small numbers or is technically difficult to culture. Indirect identification of microorganisms by immunoassays for specific antibodies reactive with the microorganism is limited by difficulties in distinguishing between past exposure and current infection.

Potential reasons for a nucleic acid probe to be associated with improved clinical outcomes compared with standard detection techniques include the following (note: in all cases, for there to be clinical utility, making a diagnosis should be associated with changes in clinical management, which could include initiation of effective treatment, discontinuation of other therapies, or avoidance of invasive testing.):

• Significantly improved speed and/or efficiency in making a diagnosis.
• Improved likelihood of obtaining any diagnosis in cases where standard culture is difficult. Potential reasons for difficulty in obtaining standard culture include low numbers of the organisms (eg, HIV), fastidious or lengthy culture requirements (eg, Mycobacteria, Chlamydia, Neisseria species), or difficulty in collecting an appropriate sample (eg, herpes simplex encephalitis).
• There is no way to definitively make a diagnosis without nucleic acid testing.
• The use of nucleic acid probe testing provides qualitatively different information than that available from standard cultures, such as information regarding disease prognosis or response to treatment. These include cases where quantification of viral load provides prognostic information or is used to measure response to therapy.

• False-positive results can lead to unnecessary treatment, with its associated toxicities and side effects, including allergic reaction. In addition, true diagnosis and treatment could be delayed or missed altogether.
• False-negative results could delay diagnosis and initiation of proper treatment.
• It is possible that these risks can be mitigated by the use of a panel of selected pathogens indicated by the clinical differential diagnosis while definitive culture results are pending.

The U.S. Food and Drug Administration maintains a list of nucleic acid amplification tests (NAATs) that have been cleared by the Center for Devices and Radiological Health. NAATs have been cleared for many of the microorganisms discussed in this review and may be reviewed on this site.

Table 1 summarizes the NAATs cleared for central nervous system panels when diagnosing meningitis and/or encephalitis, for gastrointestinal panels when diagnosing gastroenteritis, and for respiratory panels.

Table 1. FDA Cleared NAATs for CNS, GI, and Respiratory Panels

NAAT	Manufacturer	510(k) Number	Product Code
Meningitis/Encephalitis (CNS) Pathogen Panels
FilmArray Meningitis/Encephalitis Panel	BioFire Diagnostics, LLC (Salt Lake City, UT)	DEN150013, K160462	PLO
Gastroenteritis Pathogen Panels
xTAG Gastrointestinal Pathogen Panel (GPP)	Luminex Molecular Diagnostics, Inc (Toronto, Ontario, CA)	DEN130003, K121454	PCH
Progastro SSCS Assay	Gen-Probe Prodesse, Inc (Waukesha, WI)	K123274	PCH
Biocode Gastrointestinal Pathogen Panel	Applied Biocode (Santa Fe Springs, CA)	K190585	PCH
EntericBio Dx Assay	Serosep, Ltd (Annacotty, IE)	K182703	PCH
Filmarray Gastrointestinal Panel	BioFire Diagnostics, LLC (Salt Lake City, UT)	K140407, K160459	PCH
ProGastro SSCS	Hologic/Genprobe (Waukesha, WA)	K123274	PCH
BD MAX Enteric Bacterial Panel (EBP)	BD Diagnostics (Sparks, MD)	K170308	PCH
Verigene Enteric Pathogen Panel (EP)	Nanosphere, Inc (Northbrook, IL)	K142033K140083	PCH
xTAG Gastroenterology Pathogen Panel (GPP) Multiplex Nucleic Acid-Based Assay System	Luminex Molecular Diagnostics, Inc (Toronto, Ontario, CA)	K121894	PCH
FilmArray GI Panel	BioFire Diagnostics, Inc (Salt Lake City, UT)	K140407	PCH
Respiratory Viral Panels
ID-TAG Respiratory Viral Panel Nucleic Assay System	Luminex Molecular Diagnostics, Inc (Toronto, Ontario, CA)	DEN070013, K063765	OCC
Biocode Respiratory Pathogen Panel	Applied BioCode, Inc. (Santa Fe Springs, CA)	K192485	OCC
Nxtag Respiratory Pathogen Panel	Luminex Molecular Diagnostics, Inc (Toronto, Ontario, CA)	K193167	OCC
xTAG Respiratory Virus Panel (RVP)	Luminex Molecular Diagnostics, Inc (Toronto, Ontario, CA)	K081483	OCC
Qiastat-Dx Respiratory Panel	QIAGEN GmbH (Germantown, MD)	K183597	OCC
xTAG Respiratory Virus Panel FAST	Luminex Molecular Diagnostics, Inc (Toronto, Ontario, CA)	K103776	OCC
eSensor® Respiratory Virus Panel (RVP)	Clinical Micro Sensors, Inc (Carlsbad, CA)	K113731	JJH
Verigene Respiratory Pathogens Plus Nucleic Acid Test	Nanosphere, Inc (Northbrook, IL)	K103209	OCC
BioFire FilmArray Respiratory Panel (RP)	BioFire Diagnostics, Inc (Salt Lake City, UT)	K123620	OCC

CDC: Centers for Disease Control and Prevention; CNS: central nervous system; DEN: de novo; GI: gastrointestinal; NAAT: nucleic acid amplification test; FDA: Food and Drug Administration.

Clinical laboratories may develop and validate tests in-house and market them as a laboratory service; laboratory-developed tests must meet the general regulatory standards of the Clinical Laboratory Improvement Amendments (CLIA). Laboratories that offer laboratory-developed tests must be licensed by the CLIA for high-complexity testing.

Related Policies:

• Multitarget Polymerase Chain Reaction Testing for Diagnosis of Bacterial Vaginosis (Policy #116 in the Pathology Section)
• Molecular Gastrointestinal Pathogen Panel (GIPP) Testing (Policy #138 in the Pathology Section)
• Intravenous Antibiotic Therapy for Lyme Disease (Policy #007 in the Treatment Section)

NOTE: For Medicare Advantage, Medicaid and FIDE-SNP, please refer to the Coverage Sections below for coverage guidance.)


1. The use of nucleic acid testing using a direct or amplified probe technique (without quantification of pathogen load) is considered medically necessary for the following microorganisms (See Policy Guidelines):

· Bartonella henselae or quintana
· Bordetella pertussis/Bordetella parapertussis
· Candida species
· Chlamydia pneumoniae
· Chlamydia trachomatis
· Clostridium difficile
· Enterococcus, vancomycin-resistant (eg, enterococcus vanA, vanB)
· Enterovirus
· Herpes simplex virus
· Human papillomavirus
· Influenza virus
· Legionella pneumophila
· Mycobacterium species
· Mycobacterium tuberculosis
· Mycobacterium avium intracellulare
· Mycoplasma pneumoniae
· Neisseria gonorrhoeae
· Rubeola (measles)
· Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
· Staphylococcus aureus
· Staphylococcus aureus, methicillin-resistant
· Streptococcus, group A
· Streptococcus, group B
· Trichomonas vaginalis
· Zika virus

· BK polyomavirus
· Cytomegalovirus
· Hepatitis B virus
· Hepatitis C virus
· HIV-1
· HIV-2
· Human herpesvirus 6

3. The use of nucleic acid testing with quantification of pathogen load is considered investigational for microorganisms that are not included in the list of microorganisms for which probes with or without quantification are considered medically necessary.

4. The use of nucleic acid testing using a direct or amplified probe technique with or without quantification of pathogen load is considered investigational for the following microorganisms:

· Gardnerella vaginalis
· Hepatitis G virus

5. The use of the following nucleic acid testing panel (without quantification of pathogen load):

a. Molecular Respiratory Virus Panel or Molecular Respiratory Infection Pathogen Panel (RIPP) (with or without SARS-CoV-2 as part of the panel);
i. it is considered medically necessary when the following criteria are met:
· the respiratory pathogen panel is FDA-approved/cleared or FDA-authorized under the Emergency Use Authorization (EUA); AND
· the member is 17 years of age or younger and has acute respiratory compromise; OR
· the member of any age has acute respiratory compromise and is:
o immunocompromised, OR
o immunocompetent and receiving care for acute respiratory symptoms in a hospital inpatient setting including the intensive care unit (ICU) when test results would influence care or management of the member; OR
o severely ill (i.e., respiratory decompensation) who is being considered for admission to the hospital.
ii. it should be limited to the minimum number of pathogens needed for therapeutic decision making. The member’s medical record should clearly indicate the differential diagnosis of possible microorganisms based on the member’s history and presenting signs and/or symptoms.

iii. it is not considered medically necessary for all other indications, including but not limited to the following:
· when utilized as a screening tool in the outpatient setting including screening for COVID-19 infection;
· in the presence of respiratory symptoms that suggest a specific respiratory pathogen in an immunocompetent member, molecular testing for the particular pathogen should be performed rather than pathogen panel testing;
· repeat respiratory pathogen panel test to ensure a causative organism is cleared. If test of cure is indicated for a particular pathogen, individual organism testing should be used.

b. Gastrointestinal Pathogen Panel - please refer to a separate policy on 'Molecular Gastrointestinal Pathogen Panel Testing' - Policy #138 in the Pathology Section.

c. All other nucleic acid testing panels (without quantification of pathogen load) are considered investigational.

· Central nervous system pathogen panel

FIDE-SNP:

For members enrolled in a Fully Integrated Dual Eligible Special Needs Plan (FIDE-SNP): (1) to the extent the service is covered under the Medicare portion of the member’s benefit package, the above Medicare Coverage statement applies; and (2) to the extent the service is not covered under the Medicare portion of the member’s benefit package, the above Medicaid Coverage statement applies.

Policy Guidelines: (Information to guide medical necessity determination based on the criteria contained within the policy statements above.)

The use of molecular diagnostics for the diagnosis and management of Borrelia burgdorferi infection (Lyme disease) is addressed in a separate policy on 'Intravenous Antibiotic Therapy for Lyme Disease' (Policy #007 in the Treatment Section).

Vaccine-preventable diseases surveillance for outbreaks and diagnosis of isolated cases: the Centers for Disease Control and Prevention (CDC) Pertussis and Diphtheria Laboratory has developed its own PCR and serological assays to diagnose pertussis, mumps and rubeola (measles) and has recommendations for their appropriate use.

The use of multitarget polymerase chain reaction testing for the diagnosis of Bacterial vaginosis is addressed in a separate policy on ''Multitarget Polymerase Chain Reaction Testing for Diagnosis of Bacterial Vaginosis' (Policy #116 in the Pathology Section).

For Candida species, culture for yeast remains the criterion standard for identifying and differentiating these organisms. Although sensitivity and specificity are higher for NAATs than for standard testing methods, the CDC and other association guidelines do not recommend NAATs as first-line testing for Candida species. The CDC Centers for Disease Control and Prevention (2015) classifies uncomplicated vulvovaginal candidiasis as being sporadic or infrequent; or mild to moderate; or, in nonimmunocompromised women, as likely to be caused by C. albicans. A presumptive diagnosis can be made in the clinical care setting. However, for complicated infections, the CDC states that NAATs may be necessary to test for multiple Candida subspecies. Complicated vulvovaginal candidiasis is classified as being recurrent or severe; or, in women with uncontrolled diabetes, debilitation, or immunosuppression, as less likely to be caused by a C. albicans species.

Antibiotic sensitivity of streptococcus A culture is generally not performed for throat cultures. However, if an antibiotic sensitivity is considered, then the most efficient method of diagnosis would be a combined culture and antibiotic sensitivity.

In the evaluation of group B streptococcus, the primary advantage of a DNA probe technique compared with traditional culture techniques is the rapidity of results. This advantage suggests that the most appropriate use of the DNA probe technique is in the setting of impending labor, for which prompt results could permit the initiation of intrapartum antibiotic therapy.

Use of NAAT for SARS-CoV-2 is for confirming Coronavirus Disease 2019 (COVID-19) diagnoses. This medical policy does not address antibody testing (serological IgG assays).

It should be noted that the technique for quantification includes both amplification and direct probes; therefore, simultaneous coding for both quantification with either amplification or direct probes is not warranted.

Many probes have been combined into panels of tests. For the purposes of this policy, other than the respiratory pathogen panel, gastrointestinal pathogen panel and, central nervous system panel, only individual probes are reviewed.


[RATIONALE: This policy was created in 2012 and has been updated regularly with searches of the PubMed database. The most recent literature update was performed through May 27, 2020.

Evidence reviews assess whether a medical test is clinically useful. A useful test provides information to make a clinical management decision that improves the net health outcome. That is, the balance of benefits and harms is better when the test is used to manage the condition than when another test or no test is used to manage the condition.

The first step in assessing a medical test is to formulate the clinical context and purpose of the test. The test must be technically reliable, clinically valid, and clinically useful for that purpose.

The supplemental information section contains supporting information for the medical necessity of the use of the organism-specific nucleic acid amplification tests (NAATs) which have guideline support. Guidelines from the Centers for Disease Control and Prevention, National Institute of Health, Infectious Disease Society of America or America Academy of Pediatrics were used to evaluate appropriate indications for the following individual microorganisms; Bartonella henselae or Quintana, Candid Species, Chlamydia pneumoniae, Chlamydia trachomatis, Clostridium difficile, Cytomagolovirus, Enterovirus, Hepatitis B, Hepatitis C, Herpes Simplex Virus, Human Herpesvirus 6, Human Papillomavirus, HIV 1, Influenza virus, Legionella pneumophila, Mycobacteria Species, Mycoplasma pneumoniae, Neisseria gonorrhoeae, Staphylococcus aureus, Streptococcus Group A and Group B, and Vancomycin-resistant enterococcus, Zika virus.

Central Nervous System Bacterial and Viral Panel

Clinical Context and Test Purpose

The purpose of nucleic acid-based central nervous system (CNS) pathogen panels is to provide a diagnostic option that is an alternative to or an improvement on existing tests for patients with signs and/or symptoms of meningitis and/or encephalitis.

The question addressed in this policy is: Does testing for microorganisms using nucleic acid probes improve the net health outcome in individuals with suspected meningitis and/or encephalitis?

The following PICO was used to select literature to inform this review.

Patients

The relevant population of interest is individuals with signs and/or symptoms of meningitis and/or encephalitis.

Interventions

The therapy being considered is nucleic acid-based CNS pathogen panel.

Patients with signs and/or symptoms of meningitis and/or encephalitis are managed by infectious disease specialists and emergency medicine professionals in an emergency or inpatient clinical setting. Testing with a CNS pathogen panel leads to reduced time to diagnosis compared with standard laboratory techniques (approximately 1-8 hours).^1,

Comparators

Comparators of interest include no CNS pathogen-specific testing and culture or nucleic acid-based testing for individual pathogens.

Outcomes

The general outcomes of interest are test accuracy, test validity, other test performance measures, medication use, symptoms, and change in disease status.

True-positive and true-negative results lead to faster diagnosis and correct treatment, or no unnecessary treatment, as well as fewer repeated tests.

False-positive and false-negative results, inaccurate identification of a pathogen by the testing device, failure to correctly interpret test results, or failure to correctly operate the instrument may lead to misdiagnosis resulting in inappropriate treatment while postponing treatment for the true condition. Such a situation could lead to incorrect, unnecessary, or no treatment, necessity for additional testing, and delay of correct diagnosis and treatment.

Though not completely standardized, follow-up for suspected meningitis and/or encephalitis would typically occur in the days to weeks after a diagnosis decision and initiation of treatment.

Study Selection Criteria

Methodologically credible studies were selected using the following principles:

• The study population represents the population of interest. Eligibility and selection are described.
• The test is compared with a credible reference standard.
• If the test is intended to replace or be an adjunct to an existing test; it should also be compared with that test.
• Studies should report sensitivity, specificity, and predictive values. Studies that completely report true- and false-positive results are ideal. Studies reporting other measures (eg, receiver operating characteristic [ROC], area under receiver operating characteristic [AUROC], c-statistic, likelihood ratios) may be included but are less informative.
  • Reported on a validation cohort that was independent of the development cohort.
• Studies should also report reclassification of diagnostic or risk category.

The FilmArray Meningitis/Encephalitis (ME) Panel (BioFire Diagnostics, Salt Lake City, UT) is a nucleic acid-based test that simultaneously detects multiple bacterial, viral, and yeast nucleic acids from CSF specimens obtained via lumbar puncture from patients with signs and/or symptoms of meningitis and/or encephalitis. The test has been cleared for marketing through the U.S. Food and Drug Administration (FDA) 510(k) process. The test identifies 14 common organisms responsible for community-acquired meningitis or encephalitis:

Bacteria: Escherichia coli K1; Haemophilus influenzae; Listeria monocytogenes; Neisseria meningitides; Streptococcus agalactiae; Streptococcus pneumoniae;
Viruses: Cytomegalovirus; Enterovirus; Herpes simplex virus 1; Herpes simplex virus 2; Human herpesvirus 6; Human parechovirus; Varicella zoster virus;
Yeast: Cryptococcus neoformans/gattii.

Run-time is approximately 1 hour per specimen.

Technically Reliable

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this policy and alternative sources exist. This policy focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

Review of Evidence

The systematic review and meta-analysis by Tansarli and Chapin (2019) examined the diagnostic accuracy of the BioFire FilmArray ME panel. ^2,Thirteen prospective and retrospective studies conducted from 2016 through 2019 were reviewed (N=3764 patients); 8 were included in the meta-analysis (n=3059 patients). Included in the meta-analysis is the study by Leber et al [2016]^3,, which is discussed below. Risk of bias among the studies was mixed but tended toward low-risk, with the index test aspect being most questionable. No applicability concerns were found in any studies. To be eligible, studies had to provide sensitivity and specificity data compared with a reference standard. Patients in the studies had infections caused by a variety of components found on the panel (bacterial, viral, Cryptococcus neoformans/gatti). Table 2 summarizes the sensitivity, specificity, and other measurements of accuracy. The highest proportions of false-positive results were for Streptococcus pneumoniae (17.5%) and Streptococcus agalactiae (15.4%). The highest proportion of false negatives was seen for Herpes Simplex Virus 1 and 2, Enterovirus, and C. neoformans/gatti. The rate of false-positive results with the ME panel suggests this method should be used with caution, and additional diagnostic methods should be used to confirm panel results.

Table 2. Accuracy of BioFire FilmArray Meningitis/Encephalitis Panel

Measurement	Sensitive, Mean %	Specificity, Mean	PPV %	NPV %	False-Positive Results Before and After Adjudication,a %		False-Negative Results Before and After Adjudication, %
					Before	After	Before	After
Value	90.2	97.7	85.1	98.7	11.4	4.0	2.2	1.5
95% CI	86.2–93.1	94.6–99.0	NR	NR	NR	NR	NR	NR
Range	60–100	88–100	NR	NR	NR	NR	NR	NR

Source: Tansarli and Chapin (2019)^2,
CI: confidence interval; NPV: negative predictive value; NR: not reported; PPV: positive predictive value.
^a Adjudication is further investigation of results, which could include further testing, clinician input, or chart review. In this study, it was performed for discordant results between index and reference tests.

The study by Leber et al. (2016) was the FDA pivotal study, as well as the largest and one of the only prospective studies available.^3, A total of 1560 samples were tested, which were takenfrom children and adults with available CSF but not limited to those with high pretest probability for an infectious cause for meningitis or encephalitis. (See Table 3 for study characteristics.) Even the most prevalent organisms were present only a small number of times in the samples. The specificities ranged from 98% to 100% and, given the high number of true negatives, the specificities were estimated with tight precision. However, given the small number of true positives, the sensitivities to detect any given organism could not be estimated with precision. A total of 141 pathogens were detected in 136 samples with the FilmArray and 104 pathogens were detected using comparator methods; 43 FilmArray results were false-positive compared with the comparator method and 6 were false-negative. For 21 of the 43 false-positives, repeat testing of the FilmArray, comparator, or additional molecular testing supported the FilmArray results. The remaining 22 false-positives (16% of all positives) were unresolved. Codetections were observed in 3.7% (5/136) positive specimens. All 5 included a bacterial and viral positive result, and all 5 specimens were found to have a false-positive result demonstrated by comparator testing. (See Table 4 for detailed clinical validity data.) The investigators suggested that the discrepancies could have been due to specimen contamination or another problem with the assay configuration or testing process.

The smaller studies^4,5, were consistent with Leber (2016) in estimating the specificities for all included pathogens to be greater than 98%. However, there were also a very low number of true-positives for most pathogens in these studies and thus the estimates of sensitivities were imprecise. Relevance, study design, and trial conduct limitations are shown in Tables 5 and 6.

Table 3. Characteristics of Clinical Validity Studies of Central Nervous System Panel

Author (Year)	Study Population	Design	Reference Standard	Timing of Reference and Index Tests	Blinding of Assessors
Leber et al. (2016)3,	Children and adults from whom a CSF specimen was available from standard care testing for bacterial culture; not limited to those with high pretest probability for an infectious cause for meningitis or encephalitis	Nonconcurrent prospective	Culture and PCR	Processed within 7 days of collection or immediately frozen for future testing	Yes
Hanson et al. (2016)5,	Children and adults from whom a CSF specimen was available who had been tested with at least 1 conventional method	Retrospective, selection method not clear	Culture and PCR with discrepancy resolution LDT PCR	Stored up to 2 y after collection	Yes
Graf et al. (2017)4,	Positive samples (children) selected based on positivity of reference method for any of targets on the CNS panel. Negative samples selected based on negativity of reference sample and with preference for samples highly suggestive of meningitis or encephalitis	Retrospective, convenience	Culture and PCR	Stored up to 2 y after collection	NR

CNS: central nervous system; CSF: cerebrospinal fluid; LDT: laboratory-developed test; NR: not reported; PCR: polymerase chain reaction.

Table 4. Results of Clinical Validity Studies of Central Nervous System Panel

Author (Year)	Initial N	Final N	Excluded Samples	Prevalence of Condition, %	Clinical Validity (95% CI)
					Sensitivity/ Positive % Agreement	Specificity/ Negative % Agreement
Leber et al. (2016)3,	1643	1560	Insufficient volume, outside the 7-d window, repeat subject, or invalid FilmArray test.
Bacteria
Escherichia coli K1				0.1	100 (34 to 100)	99.9 (99.6 to 100)
Haemophilus influenzae				0.06	100 (NA)	99.9 (99.6 to 100)
Listeria monocytogenes				0		100 (99.8 to 100)
Neisseria meningitides				0		100 (99.8 to 100)
Streptococcus agalactiae				0.06	0 (NA)	99.9 (99.6 to 100)
Streptococcus pneumoniae				0.3	100 (51 to 100)	99.2 (98.7 to 99.6)
Viruses
Cytomegalovirus				0.2	100 (44 to 100)	99.8 (99.4 to 99.9)
Enterovirus				2.9	96 (86 to 99)	99.5 (99.0 to 99.8)
Herpes simplex virus 1				0.1	100 (34 to 100)	99.9 (99.5 to 100)
Herpes simplex virus 2				0.6	100 (72 to 100)	99.9 (99.5 to 100)
Human herpesvirus 6				1.3	86 (65 to 95)	99.7 (99.3 to 99.9)
Human parechovirus				0.6	100 (70 to 100)	99.8 (99.4 to 99.9)
Varicella zostervirus				0.3	100 (51 to 100)	99.8 (99.4 to 99.9)
Yeast
Cryptococcusneoformans/Cryptococcus gattii				0.06	100 (NA)	99.7 (99.3 to 99.9)
Hanson et al. (2016)5,	342	342	NR
Bacteria
Escherichia coli K1				0.3	100 (3 to 100)	100 (98 to 100)
Haemophilus influenza				1.5	100 (48 to 100)	100 (97 to 100)
Listeria monocytogenes				0	NA	100 (98 to 100)
Neisseria meningitides				0.3	100 (3 to 100)	100 (98 to 100)
Streptococcus agalactiae				0.9	67 (9 to 99)	99 (95 to 100)
Streptococcus pneumoniae				1.5	100 (48 to 100)	99 (96 to 100)
Viruses
Cytomegalovirus				2.0	57 (18 to 90)	100 (91 to 100)
Enterovirus				11.1	97 (86 to 100)	100 (69 to 100)
Herpes simplex virus 1				3.5	93 (66 to 100)	98 (89 to 100)
Herpes simplex virus 2				8.5	100 (88 to 100)	100 (82 to 100)
Human herpesvirus 6				5.6	95 (74 to 100)	100 (93 to 100)
Human parechovirus				0.3	100 (3 to 100)	100 (93 to 100)
Varicella zostervirus				9.4	100 (89 to 100)	100 (79 to 100)
Yeast
Cryptococcus neoformans/Cryptococcus gattii				2.6	64 (35 to 87)	NA
Graf et al (2017)4,	133	133	NR
Bacteria
Haemophilus influenzae				NAa	100 (1 to 100)b	100 (96 to 100)b
Streptococcus agalactiae				NAa	100 (1 to 100)b	100 (96 to 100)b
Streptococcus pneumoniae				NAa	100 (28 to 100)b	100 (96 to 100)b
Viruses
Enterovirus				NAa	95 (82 to 99)b	100 (94 to 100)b
Herpes simplex virus 1				NAa	50 (7 to 93)b	100 (96 to 100)b
Herpes simplex virus 2				NAa	100 (1 to 100)b	100 (96 to 100)b
Human herpesvirus 6				NAa	100 (9 to 100)b	100 (96 to 100)b
Human parechovirus				NAa	94 (70 to 100)b	100 (95 to 100)b

CI: confidence interval; CNS: central nervous system; NA: not available; NR: not reported.
a Positives and negatives retrospectively selected from a convenience sample with different selection criteria; prevalence is unknown.
b Confidence intervals not provided in publication; estimated based on available information.

The purpose of the limitations tables (see Tables 5 and 6) is to display notable limitations identified in each study. This information is synthesized as a summary of the body of evidence following each table and provides the conclusions on the sufficiency of the evidence supporting the position statement.

Table 5. Study Relevance Limitations of Studies of Central Nervous System Panels

Study	Populationa	Interventionb	Comparatorc	Outcomesd	Duration of Follow-Upe
Leber et al. (2016)3,	4. Participants not limited to those with high pretest probability for an infectious cause for meningitis or encephalitis	3. Used investigational version of test but varies from marketed version only in that Epstein-Barr virus is not available in the marketed version
Hanson et al. (2016)5,	3. Selection criteria with respect to clinical characteristics not described	3. Used investigational version (see above)
Graf et al. (2017)4,	4. Selection criteria varied for positive and negative samples
Key	1.Intended use population unclear 2.Clinical context for test is unclear 3.Study population unclear 4.Study population not representative of intended clinical use 5.Study population is subpopulation of intended use	1.Classification thresholds not defined 2.Version used unclear 3.Not version currently in clinical use	1.Classification thresholds not defined 2.Not compared with credible reference standard 3.Not compared with other tests in use for same purpose	1.Study does not directly assess a key health outcome 2.Evidence chain or decision model not explicated 3.Key clinical validity outcomes not reported (sensitivity, specificity, predictive values) 4.Reclassification of diagnostic or risk categories not reported 5.Adverse events of the test not described (excluding minor discomforts and inconvenience of venipuncture or noninvasive tests)	1.Follow-up duration not sufficient with respect to natural history of disease (TP, TN, FP, FN cannot be determined)

CNS: central nervous system; FN: false-negative; FP: false-positive; TN: true-negative; TP: true-positive.
The evidence limitations stated in this table are those notable in the current review; this is not a comprehensive gaps assessment.
^a Population key: 1. Intended use population unclear; 2. Clinical context is unclear; 3. Study population is unclear; 4. Study population not representative of intended use.
^b Intervention key: 1. Classification thresholds not defined; 2. Version used unclear; 3. Not intervention of interest (e.g., older version of test, not applied as intended).
^c Comparator key: 1. Classification thresholds not defined; 2. Not compared to credible reference standard; 3. Not compared to other tests in use for same purpose.
^d Outcomes key: 1. Study does not directly assess a key health outcome; 2. Evidence chain or decision model not explicated; 3. Key clinical validity outcomes not reported (see template Results tables; 4. Reclassification of diagnostic or prognostic risk categories not reported; 5. Adverse events of the test not described (excluding minor discomforts and inconvenience of venipuncture or noninvasive tests).
^e Follow-Up key: 1. Follow-up duration not sufficient with respect to natural history of disease (true positives, true negatives, false positives, false negatives cannot be determined).

Table 6. Study Design and Conduct Limitations

Study	Selectiona	Blindingb	Delivery of Testc	Selective Reportingd	Completeness of Follow-Upe	Statisticalf
Leber et al. (2016)3,			2.Many tests performed on frozen samples
Hanson et al. (2016)5,	1. Not clear if participants were consecutive		2. Many tests performed on frozen samples		1. Not clear if there were indeterminate samples
Graf et al. (2017)4,	3.Selection not random or consecutive and varied for positive and negatives	1. Not clear if blinded	2.Many tests performed on frozen samples		1.Not clear if there were indeterminate samples	1. Confidence intervals not provided
Key	1.Selection not described 2.Selection not random nor consecutive (ie, convenience)	1.Not blinded to results of reference or other comparator tests	1.Timing of delivery of index or reference test not described 2.Timing of index and comparator tests not same 3.Procedure for interpreting tests not described 4.Expertise of evaluators not described	1.Not registered 2.Evidence of selective reporting 3.Evidence of selective publication	1.Inadequate description of indeterminate and missing samples 2.High number of samples excluded 3.High loss to follow-up or missing data	1.Confidence intervals and/or p values not reported 2.No statistical test reported to compare with alternatives

The evidence limitations stated in this table are those notable in the current review; this is not a comprehensive gaps assessment.
^a Selection key: 1. Selection not described; 2. Selection not random or consecutive (ie, convenience).
^b Blinding key: 1. Not blinded to results of reference or other comparator tests.
^c Test Delivery key: 1. Timing of delivery of index or reference test not described; 2. Timing of index and comparator tests not same; 3. Procedure for interpreting tests not described; 4. Expertise of evaluators not described.
^d Selective Reporting key: 1. Not registered; 2. Evidence of selective reporting; 3. Evidence of selective publication.
^e Data Completeness key: 1. Inadequate description of indeterminate and missing samples; 2. High number of samples excluded; 3. High loss to follow-up or missing data.
^f Statistical key: 1. Confidence intervals and/or p values not reported; 2. Comparison to other tests not reported; 3: Insufficient consideration of potential confounding.
Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from randomized controlled trials (RCTs).

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

Section Summary: Central Nervous System Bacterial and Viral Panel

The FilmArray ME Panel provides fast diagnoses compared with standard culture and pathogen-specific PCR, and because it combines multiple individual nucleic acid tests, clinicians can test for several potential pathogens simultaneously. The test uses only a small amount of CSF, leaving remaining fluid for additional testing if needed. The test is highly specific for the included organisms. However, due to the low prevalence of these pathogens overall, the sensitivity for each pathogen is not well-characterized. More than 15% of positives in the largest study were reported to be false-positives, which could cause harm if used to make clinical decisions. Also, a negative panel result does not exclude infection due to pathogens not included in the panel.

Gastrointestinal Pathogen Panel

Clinical Context and Test Purpose

The purpose of nucleic acid-based gastrointestinal (GI) pathogen panels is to provide a treatment option that is an alternative to or an improvement on existing therapies in patients with signs and/or symptoms of GI conditions.

The question addressed in this policy is: Does testing for microorganisms using nucleic acid probes improve the net health outcome in individuals with suspected GI infections?

The following PICO was used to select literature to inform this review.

Patients

The relevant population of interest is individuals with signs and/or symptoms of gastroenteritis and GI conditions.

The most common 2 types of GI pathogens are either bacterial or viral, including but not limited to the following^6,7,8,:

• Bacterial (common to U.S. and may be foodborne): Bacillus cereus, Campylobacter, Clostridium difficile, Clostridium botulinum, Clostridium perfringens, Cronobacter sakazakii, Esherichia coli, Listeria monocytogenes, Salmonella spp., Shigella spp., Staphylococcus aureus, Yersinia enterocolitica
• Viral: norovirus, rotavirus, adenovirus, astrovirus, sapovirus

Interventions

The intervention being considered is testing with a nucleic acid-based GIpathogen panel.

These panels are capable of qualitatively detecting the DNA or RNA of multiple pathogens, including but not limited to Campylobacter, Clostridioides (Clostridium) difficile, Plesiomonas shigelloides, Salmonella spp., Yersinia spp., enteroaggregative Escherichia coli, enteropathogenic E coli, enterotoxigenic E coli, Shiga toxin-producing E coli, E coli O157, Shigella/enteroinvasive E coli, adenovirus F 40/41, astrovirus, norovirus, rotavirus, and sapovirus.

For community-acquired diarrheal illness, extensive GI panels for parasites and viruses may be unnecessary because these illnesses are usually self-limited and, as viruses, are treated with supportive care and hydration.^10, In situations in which the GI condition is likely foodborne based on patient history, GI pathogen panels may be limited to the most common pathogens typically found with foodborne illness. For patients who are immune competent, such a panel could include Salmonella, Campylobacter, Shigella, Cryptosporidium (parasite), Shiga toxin-producing E. coli (STEC), and STEC O157. More pathogen targets may be included if testing for C. difficile or testing patients who are critically ill or immunocompromised.^10,

Patients with signs and/or symptoms of gastroenteritis and GI conditions are managed by primary care clinicians, infectious disease specialists, and emergency medicine professionals in an emergency or inpatient clinical setting. Time to a result of testing with a gastrointestinal pathogen panel is reduced compared with standard laboratory techniques (< 6 hours).^11,

Comparators

Comparators of interest include no GI pathogen-specific testing and culture or nucleic acid-based testing for individual pathogens.

Outcomes

The general outcomes of interest are test accuracy, test validity, other test performance measures, medication use, symptoms, and change in disease status.

True-positive and true-negative results lead to faster diagnosis and correct treatment, or no unnecessary treatment, as well as fewer repeated tests.

False-positive and false-negative results, inaccurate identification of a pathogen by the testing device, failure to correctly interpret test results, or failure to correctly operate the instrument may lead to misdiagnosis resulting in inappropriate treatment while postponing treatment for the true condition. Such a situation could lead to incorrect, unnecessary, or no treatment, subsequent testing, and delay of correct diagnosis and treatment.^12,13,

Though not completely standardized, follow-up for suspected gastroenteritis or GI conditions would typically occur in the weeks to months after a diagnosis decision and initiation of treatment.

Study Selection Criteria

Methodologically credible studies were selected using the following principles:

• The study population represents the population of interest. Eligibility and selection are described.
• The test is compared with a credible reference standard.
• If the test is intended to replace or be an adjunct to an existing test; it should also be compared with that test.
• Studies should report sensitivity, specificity, and predictive values. Studies that completely report true- and false-positive results are ideal. Studies reporting other measures (eg, ROC, AUROC, c-statistic, likelihood ratios) may be included but are less informative.
  • Reported on a validation cohort that was independent of the development cohort.
• Studies should also report reclassification of diagnostic or risk category.

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this policy and alternative sources exist. This policy focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

Review of Evidence

Infectious gastroenteritis may be caused by a broad spectrum of pathogens resulting in the primary symptom of diarrhea. Panels for GI pathogens use multiplex amplified probe techniques and multiplex reverse transcription for the simultaneous detection of many GI pathogens such as C. difficile, E. coli, Salmonella, Shigella, norovirus, rotavirus, and Giardia. The performance study of the first FDA-cleared GI panel (xTAG Gastrointestinal Pathogen Panel [GPP], Luminex Molecular Diagnostics, Inc, Toronto, Ontario, CA), showed high sensitivity and specificity and overall strong positive percent agreement for the organisms on the panel (Table 7).^14,

Table 7. Prospective Performance Data by Organism

Organism	Sensitivity, %	95% CI, %	Specificity, %	95% CI, %
Campylobacter	100	43.8–100	98.2	97.3–98.8
Cryptosporidium	9.23	66.7–98.6	95.5	94.2–96.6
E. coli O157	100	34.2–100	99.2	98.5–99.6
Giardia	100	51.0–100	96.7	95.5–97.6
Salmonella	100	72.2–100	98.4	97.6–99.0
STEC	100	20.7–100	98.6	97.8–99.2
Shigella	100	34.2–100	98.5	97.7–99.1
Organism	Positive Percent Agreement	95% CI, %	Negative Percent Agreement
C. difficile Toxin A/B	93.9	87.9–97.0	89.8	87.8–91.5
ETEC	25.0	7.1–59.1	99.7	99.1–99.9
Norovirus GI/GII	94.9	87.5–98.0	91.4	89.6–92.9
Rotavirus A	100	34.2–100	99.8	99.4–100

Source: FDA Decision Summary.^14,
CI: Confidence Interval; ETEC: enterotoxigenic Escherichia coli; GI: gastrointestinal; STEC: Shiga toxin–producing E. coli.

Several studies of GIpathogen panels have demonstrated overall high sensitivities and specificities and indicated the panels might be useful for detecting causative agents for GI infections, including both foodborne and infectious pathogens. Claas et al. (2013) assessed the performance characteristics of the xTAG Gastrointestinal Pathogen Panel (GPP; Luminex, Toronto, ON, Canada) compared with traditional diagnostic methods (ie, culture, microscopy, enzyme immunoassay/direct fluorescent antibody, real-time PCR (rtPCR), or sequencing) using 901 stool samples from multiple sites^15,. The sensitivity of GPP againstrtPCR was > 90% for nearly all pathogens tested by rtPCR; the 1 exception was adenovirus at 20%, but sensitivity could be higher because rtPCR did not distinguish between adenovirus species. Kahre et al. (2014) found similar results when they compared the FilmArray GI panel (BioFire Diagnostics, Salt Lake City, UT, USA) with the xTag GPP. Both panels detected more pathogens than routine testing. Of 230 prospectively collected samples, routine testing identified 1 or more GI pathogens in 19 (8.3%) samples; FilmArray detected 76 (33.0%), and xTag detected 69 (30.3%). Two of the most commonly detected pathogens in both assays were C. difficile (12.6%–13.9% prevalence) and norovirus (5.7%–13.9% prevalence). Both panels showed > 90% sensitivity for the majority of targets.

Using the xTAG GPP, Beckmann et al (2014) evaluated 296 patients who were either children with gastroenteritis (n = 120) or patients who had been to the tropics and had suspected parasite infestation (adults, n = 151; children, n = 25).^11, Compared with conventional diagnostics, the GPP showed 100% sensitivity for rotavirus, adenovirus, norovirus, C. difficile, Salmonella species, Cryptosporidium, and Giardia lamblia. Specificity was >90% for all but norovirus (42%) and G. lamblia (56%), which both also had lower positive predictive value (PPV) at 46% and 33%, respectively. Salmonella species also had low PPV at 43%; all others had 100% PPV. Negative predictive value was 100% for all pathogens.

Buchan et al. (2013) evaluated a multiplex rtPCR assay (ProGastro SSCS, Gen-Probe Prodesse, San Diego, CA) limited to Campylobacter spp., Salmonella spp., and Shigella spp. against culture; and they tested for Shiga toxin-producing Escherichia coli (STEC) against broth enrichment followed by enzyme immunoassay^16,. A total of 1244 specimens from 4 U.S. clinical laboratories were tested. Bidirectional sequencing was used to resolve discrepancies between ProGastro and culture or enzyme immunoassay. The overall prevalence of pathogens detected by culture was 5.6%, whereas the ProGastro assay and bidirectional sequencing showed an overall prevalence of 8.3%. The ProGastro SSCS assay showed a sensitivity of 100% and a specificity of 99.4% to 100% for all pathogens. This is compared with a sensitivity of 52.9% to 76.9% and a specificity of 99.9% to 100% for culture compared with ProGastro SSCS assay.

Al-Talib et al. (2014) assessed the diagnostic accuracy of a pentaplex PCR assay with specific primers to detect hemorrhagic bacteria from stool samples.^17, The primers, which were mixed in a single reaction tube, were designed to detect Salmonella spp., Shigella spp., enterohemorrhagic E. coli , and Campylobacter spp., all of which are a particular danger to children in developing countries. The investigators used 223 stool specimens from healthy children and spiked them with hemorrhagic bacteria. All primers designed had 100% sensitivity, specificity, PPV, and negative predictive value.

Jiang et al. (2014) developed a reverse transcription and multiplexrtPCR assay to identify 5 viruses in a single reaction.^18, The viruses included norovirus genogroups I and II; sapovirus genogroups I, I, IV, and V; human rotavirus A; adenovirus serotypes 40 and 41; and human astrovirus. Compared with monoplex rtPCR, multiplex rtPCR assay had sensitivity ranging from 75% to 100%; specificity ranged from 99% to 100%.

The health technology assessment and systematic review by Freeman et al (2017) evaluated multiplex texts to identify GI pathogens in people suspected of having infectious gastroenteritis.^19, Tests in the assessment were xTAG® GPP and FilmArray GI Panel. Eligible study included patients with acute diarrhea, compared multiplex GI pathogen panels tests with standard microbiology tests, and assessed patient, management, and/or test accuracy outcomes. Of the 23 identified studies, none provided an adequate reference standard for comparing the accuracy of GI panels with standard tests, so sensitivity and specificity analyses were not performed. Positive and negative test agreement were analyzed for individual pathogens for the separate panel products and are not detailed in this review. The meta-analysis of 10 studies found high heterogeneity in participants, country of origin, conventional methods used, and pathogens considered. Using conventional methods as the determinant of clinically important disease, the meta-analysis results suggested GI panel testing is reliable and could supplant current microbiological methods. An increase in false positives would result, along with the potential for overdiagnosis and incorrect treatment. However, if GI panel testing is identifying important pathology being missed with conventional methods, the result could be more appropriate treatments. The clinical importance of these findings is unclear, and assessment of GI panel testing effect on patient management and outcomes, compared with conventional testing, is needed.

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Review of Evidence

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from RCT.

No RCTs were available that evaluated clinical utility

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity.

A 9-month, prospective, multi-center study by Cybulski et al. (2018) assessed the effect of the BioFire FilmArray GI PCR panel on clinical diagnosis and decision-making. It also compared the diagnostic accuracy for patients with positive results obtained exclusively using the GI panel with results obtained using conventional stool culture.^20, (Study characteristics in Table 8.) Testing on 1887 consecutive fecal samples was performed in parallel using the GI panel and stool culture. The GI panel detected pathogens in significantly more samples than culture; median time from collection to results and collection to initiation of treatment was also significantly less. The use of a GI panel also led to a significant trend toward targeted therapy rather than empirical (r²=0.65; p=0.009 by linear regression). Results of the GI panels resulted in discontinuation of antimicrobials in 8 of 9 Shiga toxin-producing E. coli (STEC), with just 1 example of GI panel results affecting clinical decision-making. (Other results summarized in Table 9.) Limitations of the study include the limit to 2 hospitals within a single healthcare system and certain subgroups that were too small for analysis. In addition, it was unclear how the historic controls were used since the current samples tested were both tested with GI panel and culture.

The prospective study by Beal et al. (2017) also aimed to assess the clinical impact of the BioFire FilmArry GI panel.^21, (Study characteristics in Table 8.) Stool samples from 241 patients (180 adults and 61 children) were tested with the GI panel and compared with 594 control patients from the previous year who were tested via culture. The most common pathogens detected by the GI panel were enteropathogenic E. coli (n=21), norovirus (n=21), rotavirus (n=15), sapovirus (n=9), and Salmonella (n=9). GI panel patients had significantly fewer subsequent infectious stool tests compared with the control group. GI panel patients also had 0.18 imaging studies per patient compared with 0.39 (p=.0002) in the control group. The GI panel group spent fewer days on antibiotic(s) per patient: 1.73 versus 2.12 in the control group. In addition, average length of time from stool culture collection to discharge was 3.4 days for the GI panel group and 3.9 days for the controls (p=.04). (Other results summarized in Table 9.) The GI panel improved patient care in several ways: (1) it identified a range of pathogens that might not have been detected by culture, (2) it reduced the need for other diagnostic tests, (3) it resulted in less unnecessary use of antibiotics, and (4) it led to shorter length of hospital stay. Some limitation of the study include not confirming the results in which the GI panel did not agree with standard testing, and the study used a historical cohort as a control group.

Table 8. Summary of Key Observational Comparative Study Characteristics

Study	Study Type	Country	Dates	Participants	Test 1	Test 2
Cybulski (2018)20,	Prospective multi-center, parallel design	U.S.	Jan-Sep 2017 (controls from 2016)	Newly admitted inpatients (<3 d) and outpatients aged 0-91 y; historical control group was patients with positive stool samples from same laboratory during the same period the previous year. (N=1887 specimens)	BioFire FilmArray GI panel (n=1887 specimens)	Stool culture (n=1887)
Beal (2017)21,	Prospective single-center	U.S.	Jun 2016-Jun 2017 (controls from Jun-Dec 2015)	ED or admitted patients with stool samples submitted with an order for culture; historical controls were from a previous period.(N=835)	BioFire FilmArray GI Panel (n=241)	Stool culture (n=594)

ED: emergency department; GI: gastrointestinal.

Table 9. Summary of Key Observational Comparative Study Results

Study	Pathogens Detected, % of specimens	Time to Results	Time From Collection to Treatment	Empirical Initiation of Antimicrobial, %	Overall Positivity Rate, %	No. of Additional Stool Tests
Cybulski et al. (2018)20,		Median	Median
GI panel	35.3	18 h	26 h	23.5	NR	NR
Culture	6.0	47 h	72 h	40.0	NR	NR
p-value	NA	<.0001	<.0001	.015	NR	NR
Beal et al (2017)21,		Mean
GI panel	NR	8.94 h	NR	NR	32.8	0.58
Culture	NR	54.75 h	NR	NR	6.7	3.02
95% CI	NA	1.44 to 82.8	NR	NR	NR	2.89 to 3.14
p-value	NA	<.0001	NR	NR	NR	.0001

CI: confidence interval; GI: gastrointestinal; NA: not applicable; NR: not reported.

Section Summary: Gastrointestinal Pathogen Panel

Most GI panels combining multiple individual nucleic acid tests provide faster results compared standard stool culture. Sensitivity and specificity are generally high, but the yield of testing may be affected by the panel composition. Results of comparisons of conventional methods for ova and parasites to nucleic acid tests are limited. No direct evidence is available to assess clinical utility. Prospective observational studies were available to evaluate the clinical utility of a GI panel, which was shown in faster turnaround times leading to quicker treatment and a trend away from empirical treatment toward targeted therapy. However, both studies were limited by lack of adjudication of discordant results or the use of only a historical control. Access to a rapid method for etiologic diagnosis of GI infections may lead to more effective early treatment and infection-control measures. However, in most instances, when there is suspicion for a specific pathogen, individual tests could be ordered or a limited pathogen panel could be used. There may be a subset of patients with an unusual presentation who would warrant testing for a larger panel of pathogens at once, but that subset has not been well defined.

Respiratory Pathogen Panel

Clinical Context and Test Purpose

The purpose of the nucleic acid-based respiratory pathogen panel is to provide a diagnostic option that is an alternative to or an improvement on existing tests in patients with signs and/or symptoms of viral or bacterial respiratory infections.

The question addressed in this policy is: Does testing for microorganisms using nucleic acid-based respiratory pathogen probes improve the health outcome in individuals with suspected viral or bacterial respiratory infections?

The following PICO was used to select literature to inform this review.

Patients

The relevant population of interest is individuals with signs and/or symptoms of viral or bacterial respiratory infections.

The available evidence also notes that respiratory pathogen panels are particularly effective for high-risk individuals.

High-risk individuals can include:

• Immunocompromised individuals, such as
  • Hematopoietic stem cell or solid organ transplant recipients
  • Individuals receiving high-dose chemotherapy and/or steroids
  • These individuals can be adult or pediatric patients
• Adults who appear acutely ill with respiratory conditions—particularly in certain settings such as influenza outbreaks
• Critically ill adult individuals—particularly ICU patients

The test being considered is the nucleic acid-based respiratory pathogen panel.

The respiratory pathogens panel is used to diagnosis respiratory infection due to bacteria or viruses and to help guide management of the infection. This panel is performed primarily when a patient is seriously ill, hospitalized, and/or at an increased risk for severe infection with complications or multiple infections. Not everyone with symptoms is tested (eg, fever, aches, sore throat, and cough). Samples are collected by nasopharyngeal swab in universal transport medium or respiratory wash (ie, nasal wash, nasal aspirate, or bronchoalveolar lavage wash). Examples of these pathogens include adenovirus, coronavirus (HKU1, NL63, 229E, OC43), human metapneumovirus, human rhinovirus/enterovirus, influenza A (H1, H1-2009, H3), influenza B, parainfluenza (1, 2, 3, 4), respiratory syncytial virus, Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae.

Patients are tested in an outpatient setting.

Comparators

Comparators of interest include no respiratory pathogen-specific testing and culture or nucleic acid-based testing for individual pathogens.

Outcomes

The general outcomes of interest are test accuracy, test validity, and other test performance measures, medication use, symptoms, and change in disease status.

True-positive and true-negative results lead to faster diagnosis and correct treatment, or no unnecessary treatment, as well as fewer repeated tests.

False-positive and false-negative results, inaccurate identification of a pathogen by the testing device, failure to correctly interpret test results, or failure to correctly operate the instrument may lead to misdiagnosis resulting in inappropriate treatment while postponing treatment for the true condition. Such a situation could lead to incorrect, unnecessary, or no treatment, subsequent testing, and delay of correct diagnosis and treatment.

Follow-up typically occurs in the days and weeks after diagnosis decision and initiation of treatment.

Study Selection Criteria

Methodologically credible studies were selected using the following principles:

• The study population represents the population of interest. Eligibility and selection are described.
• The test is compared with a credible reference standard.
• If the test is intended to replace or be an adjunct to an existing test; it should also be compared with that test.
• Studies should report sensitivity, specificity, and predictive values. Studies that completely report true- and false-positive results are ideal. Studies reporting other measures (eg, ROC, AUROC, c-statistic, likelihood ratios) may be included but are less informative.
  • Reported on a validation cohort that was independent of the development cohort.
• Studies should also report reclassification of diagnostic or risk category.

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this policy and alternative sources exist. This policy focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

Huang et al. (2018) published a systematic review and meta-analysis of a multiplex PCR system for the rapid diagnosis of respiratory virus infections.^22, Authors summarized diagnostic accuracy evidence on the detection of viral respiratory infections for BioFire FilmArray RP (Film Array), Nanosphere Verigene RV+ test, and Hologic Gen-Probe Prodesse assays. The study reviewed 20 studies with 5510 patient samples. Multiplex PCRs were found to have high diagnostic accuracy with AUROC > 0.98 for all reviewed viruses expected adenovirus (AUROC 0.89). All 3 reviewed multiplex PCR systems were shown to be highly accurate.

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Review of Evidence

Several studies of various respiratory viral panels have demonstrated the multiplex assay detected clinically important viral infections in a single genomic test and thus, may be useful for detecting causative agents for respiratory tract disorders.^23,24,25,

Randomized Controlled Trials

Andrews et al. (2017) published a quasi-randomized study assessing the impact of multiplex PCR on length of stay and turnaround time compared with routine, laboratory-based testing in the treatment of patients aged ≥ 16 years presenting with influenza-like illness or upper or lower respiratory tract infection.^26, (See Table 10 for study characteristics.) Patients were selected at inpatient and outpatient clinics in 3 areas of a hospital. FilmArray RP PCR systems were used. Of eligible patients (N=606), 545 (89.9%) were divided into a control arm (n=211) and an intervention arm (n=334). While PCR testing was not associated with a reduction in length of stay, turnaround time was reduced. (See Table 11 for detailed results.) Limitations of the study included design and patient allocation (patients were allocated to the intervention arm on even days). Additionally, the patients considered in the study were not noted to be high-risk individuals as defined above, only those with pertinent symptoms.

The parallel-group, open-label RCT by Brendish et al.(2017) evaluated the routine use of molecular point-of-care testing (POCT) for respiratory viruses in adults presenting to a hospital with acute respiratory illness ^27,. (See Table 10 for study characteristics.) In a large U.K. hospital, over 2 winter seasons, investigators enrolled adults within 24 hours of presenting to the emergency department or acute medical unit with acute respiratory illness or fever > 37.5°C, or both. A total of 720 patients were randomized (1:1) to either molecular POCT for respiratory viruses (FilmArray Respiratory Panel; n = 362) or routine care (n = 358), which included diagnosis based on clinical judgment and testing by laboratory PCR at the clinical team’s discretion. All patients in the POCT group were tested for respiratory viruses; 158 (45%) of 354 patients in the control group were tested. Because patients presenting with symptoms are often put on antibiotics before tests can be run, the results of the POCTs were unable to influence the outcome in many patients; therefore, a subgroup analysis was necessary for those who were only given antibiotics after test results were available. The results of the analysis showed antibiotics were prescribed for 61 (51%) of 120 patients in the POCT group and for 107 (64%) of 167 in the control group (difference = -13.2%; 95% CI, -24.8% to -1.7%; p =.0289). Mean test turnaround time for POCT was 2.3 hours (SD = 1.4) versus 37.1 hours (SD = 21.5) in the control group. The percentage of patients prescribed a neuraminidase inhibitor who tested positive for influenza was significantly higher for the POCT group than the control group (82% vs. 47%), and it was significantly lower for the percentage who tested negative for influenza (18% vs. 53%). In addition, the time to first dose was 8.8 hours (SD = 15.3) for POCT and 21.0 hours (SD = 28.7) for the control group. (See Table 11 for more results.) Blinding of the clinical teams to which group a patient had been randomized to was not possible because the purpose of the study was to inform the clinical team of POCT results. In addition, the limit of the study to the winter months means the findings cannot be extrapolated to the rest of the year.

Table 10. Summary of Key RCT Characteristics

Study; Trial	Countries	Sites	Dates	Participants	Interventions
					Active	Comparator
Andrews et al. (2017)a 26,	United Kingdom	1	Jan-Jul 2015	Patients with influenza-like illness/upper RTI +/- lower RTI N = 454	FilmArray POC testing (even days of month) n = 334	Routine, laboratory-based RP PCR testing +/- atypical serology (odd days)n = 211
Brendish et al. (2017) 27,	United Kingdom	1	Jan 2015-Apr 2016 and Oct 2015-Apr, 2016b	Adults who could be recruited within 24 h of triage in ED or arrival at acute medical unit with acute respiratory illness or fever >37.5°C for ≤7 d N = 720	POCT n = 362	Diagnosis based on clinical judgment and PCR testing at clinical team’s discretionn = 358

ARTI: acute respiratory tract infection; ED: emergency department; PCR: polymerase chain reaction; POCT: point of care testing (using FilmArray Respiratory Panel); RCT: randomized controlled trial; RP: respiratory panel; RTI: respiratory tract infection
^a Quasi-randomized study
^b The dates do not make sense because they overlap, likely due to an error in the article. Another place in the article says the “winter seasons in 2014-15 and 2015-16.”

Table 11. Summary of Key RCT Results

Study	Test Efficacy	Length of Stay	Antimicrobic Use Duration	All-Cause Mortalitya	Readmissionb
Andrews et al.(2017) 26,		Median (IQR)	Median (IQR)
Active	24%	98.6 h (48.1–218.4)	6.0 d (4.0–7.0)	4%	19%
Comparator	20%	79.6 h (41.9–188.9)	6.8 d (5.0–7.3)	4%	20%
Estimated intervention effect	NR	NR	Absolute difference in natural logarithm of duration: -0.08 (95% CI: -0.22–0.054)	aOR: 0.9 (95% CI: 0.3–2.2)	OR: 0.9 (95% CI: 0.6–1.4)
Adjusted p-value	NR	NR	0.23	0.79	0.70
Brendish et al. (2017) 27,		Mean (SD)	Mean (SD)
Active	NR	5.7 d (6.3)	7.2 d (5.1)	3%	13%
Comparator	NR	6.8 d (7.7)	7.7 d (4.9)	5%	16%
Difference (95% CI)	NR	-1.1 d (-2.2 to -0.3)	-0.4 (-1.2–0.4)c	-2.0% (-4.7%–0.6%)	-3.0% (-8.3%–2.0%)
OR (95% CI)	NR	NR	0.95 (0.85–1.05)d	0.54 (0.3–1.2)	0.78 (0.5–1.2)
p-value	NR	0.04	0.32	0.15	0.28

CI: confidence interval;IQR: interquartile range; NR: not reported; OR: odds ratio; RCT: randomized controlled trial; SD: standard deviation.
^a 30 days post-enrollment.
^b Within 30 days of study participation.
^c Mean risk difference.
^d Unadjusted odds ratio.

The purpose of the limitations tables (Tables 12 and 13) is to display notable limitations identified in each study. This information is synthesized as a summary of the body of evidence following each table and provides the conclusions on the sufficiency of evidence supporting the position statement.

Table 12. Study Design and Conduct Limitations

Study	Selectiona	Blindingb	Delivery of Testc	Selective Reportingd	Data Completenesse	Statisticalf
Andrews et al. (2017) 26,	2. Patients allocated to study arms based on even vs. odd days of the week; patient groups unbalanced in favor of FilmArray group
Brendish et al. (2017)27,		1. Patients and data collectors not blinded

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment.
^a Selection key: 1. Selection not described; 2. Selection not random or consecutive (ie, convenience).
^b Blinding key: 1. Not blinded to results of reference or other comparator tests.
^c Test Delivery key: 1. Timing of delivery of index or reference test not described; 2. Timing of index and comparator tests not same; 3. Procedure for interpreting tests not described; 4. Expertise of evaluators not described.
^d Selective Reporting key: 1. Not registered; 2. Evidence of selective reporting; 3. Evidence of selective publication.
^e Data Completeness key: 1. Inadequate description of indeterminate and missing samples; 2. High number of samples excluded; 3. High loss to follow-up or missing data.
^f Statistical key: 1. Confidence intervals and/or p values not reported; 2. Comparison with other tests not reported.

Table 13. Study Relevance Limitations

Study	Populationa	Interventionb	Comparatorc	Outcomesd	Duration of Follow-Upe
Andrews et al. (2017)26,	4. Patients were not noted to be high-risk
Brendish et al. (2017)27,				3. Sensitivity and specificity not reported (study was on clinical utility)

The study limitations stated in this table are those notable in the current review; this is not a comprehensive limitations assessment.
^a Population key: 1. Intended use population unclear; 2. Clinical context is unclear; 3. Study population is unclear; 4. Study population not representative of intended use.
^b Intervention key: 1. Classification thresholds not defined; 2. Version used unclear; 3. Not intervention of interest.
^c Comparator key: 1. Classification thresholds not defined; 2. Not compared to credible reference standard; 3. Not compared to other tests in use for same purpose.
^d Outcomes key: 1. Study does not directly assess a key health outcome; 2. Evidence chain or decision model not explicated; 3. Key clinical validity outcomes not reported (sensitivity, specificity and predictive values); 4. Reclassification of diagnostic or risk categories not reported; 5. Adverse events of the test not described (excluding minor discomforts and inconvenience of venipuncture or noninvasive tests).
^e Follow-Up key: 1. Follow-up duration not sufficient with respect to natural history of disease (true-positives, true-negatives, false-positives, false-negatives cannot be determined).
Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from RCTs.

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

Section Summary: Respiratory Pathogen Panels

The evidence for the clinical validity or clinical utility of respiratory pathogen panels in diagnosing respiratory infections includes a systematic review and 2 RCTs. The systematic review reported that all 3 reviewed multiplex PCR systems were highly accurate. The clinical utility demonstrated by the RCTs showed benefits to the respiratory panel in test results turnaround time, time to receive treatment, and length of hospital stay. Significant differences were not seen in antibiotic prescription, readmission, or mortality.

Summary of Evidence

For individuals who have signs and/or symptoms of meningitis and/or encephalitis who receive a nucleic acid-based central nervous system pathogen panel, the evidence includes a systematic review and a pivotal prospective study. Relevant outcomes include test accuracy and validity, other test performance measures, medication use, symptoms, and change in disease status. Access to a rapid method that can simultaneously test for multiple pathogens may lead to the faster initiation of more effective treatment and conservation of cerebrospinal fluid. The available central nervous system panel is highly specific for the included organisms, but the sensitivity for each pathogen is not well-characterized. More than 15% of positives in the largest clinical validity study were false-positives. A negative panel result does not exclude infection due to pathogens not included in the panel. The evidence is insufficient to determine the effects of the technology on health outcomes.

For individuals who have signs and/or symptoms of gastroenteritis who receive nucleic acid-based gastrointestinal pathogen panel, the evidence includes prospective and retrospective evaluations of the tests’ sensitivity and specificity and prospective studies on utility. Relevant outcomes include test accuracy and validity, other test performance measures, medication use, symptoms, and change in disease status. The evidence suggests that gastrointestinal pathogen panels are likely to identify both bacterial and viral pathogens with high sensitivity, compared with standard methods. Access to a rapid method for etiologic diagnosis of gastrointestinal infections may lead to more effective early treatment and infection-control measures. However, in most instances, when a specific pathogen is suspected, individual tests could be ordered. There may be a subset of patients with an unusual presentation who would warrant testing for a panel of pathogens at once, but that subset has not been well defined. The evidence is insufficient to determine the effects of the technology on health outcomes.

For individuals who have signs and/or symptoms of respiratory infection who receive a nucleic acid-based respiratory pathogen panel, the evidence includes a systematic review and 2 randomized controlled trials (RCTs). Relevant outcomes include test accuracy and validity, other test performance measures, medication use, symptoms, and change in disease status. The systematic review reported that all 3 reviewed multiplex polymerase chain reaction systems were highly accurate. One RCT and 1 quasi-RCT evaluated utility of a respiratory panel and found benefits in time-to-treat and length of hospital stay; in addition, 1 subanalysis found fewer antibiotics being prescribed for patients diagnosed with the panel. The panel did not significantly affect duration of antibiotic use, readmission, or mortality rates. The evidence is sufficient to determine the effects of the technology on health outcomes.

SUPPLEMENTAL INFORMATION

Practice Guidelines and Position Statements

Numerous guidelines have been identified concerning the use of nucleic acid amplification tests (NAATs) for the diagnosis of the pathogens discussed in this review. Table 14 provides an index of NAAT recommendation by Virus/Infection.

Table 14. Index of NAAT Recommendations by Virus/Infection

Microorganism	Guidelines Recommending the Use of NAATs (Location)	Guidelines Not Recommending the Use of NAATsa (Location)
Bartonella hensalae	NIH (2.1.1), IDSA (3.1), AAP (5.1)	NA
Candida Species	CDC (1.5.1)b	IDSA (3.1, 3.7), AAP (5.1)
CNS Pathogen Panel	IDSA (3.2, 3.3)	NA
Chlamydia pneumonia	CDC (1.5.3), IDSA (3.1c)	AAP (5.1)
Chlamydia trachomatis	CDC (1.5.2,c 1.6c), IDSA (3.1), AAP (5.1)	NA
Clostridium difficile	NIH (2.1.2), AAP (5.1)	IDSA (3.1, 3.4)
Cytomagolovirus	CDC (1.1), NIH (2.1.3), IDSA (3.1,c 3.3)	AAP (5.1)
Enterovirus	IDSA (3.1), AAP (5.1)	NA
Gardnerella vaginalis	AAP (5.1)	CDC (1.5.4), IDSA (3.1)
GI Pathogen Panel	CDC (1.4c), IDSA (3.5), ACG (6.1)	NA
Hepatitis B	NIH (2.1.4), IDSA (3.1), AAP (5.1)	NA
Hepatitis C	CDC (1.5.5c), NIH (2.1.5), IDSA (3.1), AAP (5.1)	NA
Herpes Simplex Virus	CDC (1.5.6c), NIH (2.1.6), IDSA (3.1,c 3.3), AAP (5.1)	NA
Human Herpesvirus 6	IDSA (3.1,c 3.3)	AAP (5.1)
Human Papillomavirus	CDC (1.5.8c), AAP (5.1)	NA
HIV 1	CDC (1.5.7c), IDSA (3.1), AAP (5.1)	NA
Influenza virus	IDSA (3.1c), AAP (5.1)	NA
Legionella pneumophila	IDSA (3.1), AAP (5.1)	NA
Meningitis	NA	IDSA (3.6)
Mycobacteria Species	CDC (1.8), NIH (2.1.7), IDSA (3.1, 3.3)	AAP (5.1)
Mycoplasma pneumoniae	CDC (1.2c), IDSA (3.3), AAP (5.1)	NA
Neisseria gonorrhoeae	CDC (1.6c), IDSA (3.1), AAP (5.1)	NA
Respiratory Panel	None Identified	NA
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)	IDSA (3.8)	NA
Staphylococcus aureus	IDSA (3.1), AAP (5.1)	NA
Streptococcus, Group A	IDSA (3.1)	AAP (5.1)
Streptococcus, Group B	CDC (1.7), AAP (5.2)	IDSA (3.1), AAP (5.1)
Trichomonas vaginalis	CDC (1.5.9), IDSA (3.1),c AAP (5.1)	NA
Vancomycin-resistant enterococcus	AST (4.1)	IDSA (3.1), AAP (5.1)
Zika	CDC (1.3), IDSA (3.1), AAP (5.1)	NA

AAP: American Academy of Pediatrics; ACG: American College of Gastroenterology; AST: American Society of Transplantation; CDC: Centers for Disease Control and Prevention; IDSA: Infectious Disease Society of America; NA: not applicable (none found);
NAAT: nucleic acid amplification test; NIH: National Institutes of Health.
^a Guidelines Not Recommending includes not only guidelines that recommend again NAATs but also those that were neutral on the use of NAATs.
^b CDC recommends culture for first-line identification of Candida species; it recommends NAAT for complicated infections and for second-line diagnosis.
^c Indicates guidelines in which the issuing body specifically recommends that U.S. Food and Drug Administration (FDA)-cleared NAATs be used.

A. Centers for Disease Control and Prevention

The Centers for Disease Control and Prevention (CDC) has published 10 recommendations and statements regarding the use of NAATs to diagnose the viruses and infections discussed in this policy since 2009.

1.1 In 2019, the CDC published guidance for laboratory testing for Cytomagolovirus (CMV), the guideline stated that the standard laboratory test for congenital CMV is polymerase chain reaction (PCR) on saliva, with confirmation via urine test to avoid false-positive results from ingesting breast milk from CMV seropositive mothers. Serologic tests were recommended for persons > 12 months of age.^28,

1.2 In 2018, the CDC published diagnostic methods for mycoplasma pneumoniae.^29, They cited NAAT as a method of diagnosis, along with culture or serology.

1.3 In 2017, the CDC published updated interim guidance for the diagnosis, evaluation, and management of infants with possible congenital Zika virus infection.^30, It recommended:

• Asymptomatic pregnant women with ongoing possible Zika virus exposure (residing in or frequently traveling to an area with risk for Zika virus transmission) should be offered a Zika virus nucleic acid test (NAT) as part of routine obstetric care; and
• For infants with possible Zika virus infection, “if cerebrospinal fluid (CSF) is obtained for other purposes, NAT and IgM antibody testing should be performed on CSF because CSF was the only sample that tested positive in some infants with congenital Zika virus syndrome.”

1.5 In 2015, the following recommendations were made for the use of NAATs in diagnosing sexually transmitted diseases^33,

1.5.1 For Candida Species:

• "PCR testing for yeast is not FDA-cleared; culture for yeast remains the gold standard for diagnosis."

• "NAATs for chlamydia and gonorrhea are recommended because of their high sensitivity and specificity; a specific diagnosis can potentially reduce complications, re-infection, and transmission."
• "Pregnant women found to have chlamydial infection should have a test-of-cure to document chlamydial eradication (preferably by nucleic acid amplification testing [NAAT]) 3–4 weeks after treatment and then retested within 3 months. Screening during the first trimester might prevent the adverse effects of chlamydia during pregnancy, but evidence for such screening is lacking."
• "NAAT performed on rectal specimens is the preferred approach to testing."
• For follow-up, "the use of chlamydial NAATs at <3 weeks after completion of therapy is not recommended because the continued presence of nonviable organisms can lead to false-positive results."

• NAAT is recommended as an alternative to tissue culture, which “is the definitive standard diagnostic test for chlamydial pneumonia… NAATs are not FDA-cleared for the detection of chlamydia from nasopharyngeal specimens, and clinical laboratories must verify the procedure according to CLIA regulations.”

• Although PCR has been researched “for the detection of various organisms associated with BV [bacterial vaginosis],” its clinical utility has not yet been established.

• NAATs are recommended for screening pregnant women with known risk factors; NAAT “is necessary to confirm the diagnosis of current HCV infection.”
• In addition, “testing for HCV infection should include use of an FDA-cleared test for antibody to HCV…followed by NAAT to detect HCV RNA for those with a positive antibody result.”

• “Cell culture and PCR are the preferred HSV tests for persons who seek medical treatment for genital ulcers or other mucocutaneous lesions;” and
• “PCR is the test of choice for diagnosing HSV infections affecting the central nervous system and systemic infections.”

• The use of NAAT is not mentioned; serologic tests are recommended for detecting antibodies against HIV-1 and by virologic tests that detect HIV antigens or RNA.

• There are several FDA-cleared HPV tests that detect viral nucleic acid or messenger RNA; however, there are currently no algorithms for HPV 16/18/45 testing in the clinical guidelines;
• The “use of non-oncogenic tests is not recommended;” and
• “HPV assays should be FDA-cleared and used only for the appropriate indications” and should not be performed if the patient is “deciding whether to vaccinate against HPV;” while “conducting STD screening in women or men at risk for STDs;” when “providing care to persons with genital warts or their partners;” when “conducting screening for cervical cancer as a stand-alone test;” when “testing women aged <30 years as part of routine cervical cancer screening;” or when “testing oral or anal specimens.”

• NAAT is recommended for detecting vaginalis in women due to its high sensitivity and specificity. The APTIMA T. vaginalis assay (Hologic Gen-Probe, San Diego, CA) is FDA-cleared to detect T. vaginalis from vaginal, endocervical, or urine specimens for women.
• In 1 study, “[f]or vaginalis diagnosis in men, the sensitivity of self-collected penile-meatal swabs was higher than that of urine.” However, there is currently no FDA-cleared test for men.

• NAATs are superior other available diagnostic tests in “overall sensitivity, specificity, and ease of specimen transport;”
• The use of “NAAT to detect chlamydia and gonorrhea except in cases of child sexual assault involving boys and rectal and oropharyngeal infections in prepubescent girls” is supported by evidence; and
• Only NAATs that have been cleared by the FDA for detection of C. trachomatis and N. gonorrhoeae “as screening or diagnostic tests because they have been evaluated in patients with and without symptoms” should be used.

• The use of NAATs with the addition of an enrichment broth to the sample increases NAAT sensitivity for GBS to 92.5%-100.0%;
• However, “data on the currently available assays do not support their use in replacement of antenatal culture or risk-based assessment of women with unknown GBS status on admission for labor;” and
• Because of the additional time needed to enrich samples, NAAT with enrichment is “not feasible for intrapartum testing, and the sensitivity of assays in the absence of enrichment is not adequate in comparison to culture.”

B. National Institute of Health et al

2.1 In 2019, the NIH, CDC, and HIV Medicine Association of the IDSA published guidelines for the prevention and treatment of opportunistic infections in adults and adolescents with HIV.^35, NAATs are discussed in the following situations:

2.1.1 Bartonella species

• For patients with suspected bacillary angiomatosis, serologic tests are the standard of care for diagnosing Bartonella infection. There are PCR “methods that have been developed for identification and speciation of Bartonella but are not widely available.”

• Routine testing with PCR is necessary for patients with diarrhea who have “recently received or are currently receiving antibiotics or cancer chemotherapy, those who have been hospitalized in the past 4 to 6 week, those who reside in a long-term care facility, those with CD4 counts <200 cells/mm³, those taking acid-suppressive medication, and those with moderate-to-severe community-acquired diarrhea.”

• For patients with suspected cytomegalovirus disease, “viremia can be deterred by PCR” and “a positive result is highly suggestive that CMV is the cause of end-organ disease. However, PCR assays are not standardized; therefore, sensitivity, specificity, and interassay comparability are not clearly delineated.”

• The CDC, the United States Preventive Services Task Force, and the AASLD recommend that patients with HIV infection should be tested for hepatitis B; however, NAATs are not recommended for initial testing in patients with HIV.

• Patients with HIV are recommended to undergo routine hepatitis C screening, initially “performed using the most sensitive immunoassays licensed for detection of antibody to HCV in blood.” The use of NAATs are not mentioned for initial testing in patients with HIV.

• “HSV DNA PCR… is the preferred method for diagnosis of mucocutaneous HSV lesions caused by HSV.”

• “It is recommended that for all patients with suspected pulmonary TB, an NAA test be performed on at least one specimen.”
• “Rapid diagnosis is essential in patients with HIV given the risk of rapid clinical progression of TB among patients with advanced immunodeficiency. NAA tests provide rapid diagnosis of TB.”
• “NAA tests have at least two uses among patients with suspected HIV-related TB. First, NAA assays, if positive, are highly predictive of TB disease when performed on AFB smear-positive specimens…. Second, NAA tests are more sensitive than AFB smear, being positive in 50% to 80% of smear-negative, culture-positive specimens and up to 90% when three NAA tests are performed. Therefore, it is recommended that for all patients with suspected pulmonary TB, a NAA test be performed on at least one specimen.”

Since 2008, the IDSA has partnered with various societies to publish 9 recommendations regarding the use of NAATs to diagnose the viruses and infections discussed in this policy.

3.1 In 2018, the IDSA and the American Society for Microbiology published a guide on the diagnosis of infectious diseases^36,. NAATs were recommended diagnostic procedures for Enterovirus, Hepatitis C, Hepatitis B, Cytomegalovirus, Herpes Simplex Virus, Human Herpesvirus 6, HIV, Influenza Virus, and Zika Virus. NAATs were not recommended diagnostic procedures for Bacterial vaginosis. In addition to providing guidance on diagnosing these diseases, the guidelines also provided recommendations on testing for other conditions by testing for common etiologic agents. Table 15 describes the conditions for which IDSA recommends NAATs for diagnosing etiologic agents.

Table 15. IDSA Recommended Conditions for Use of NAATs in Identifying Etiologic Agents of Other Conditions*

Etiologic Agents	Recommended Conditions for Use of NAATs in Diagnosis when Specific Etiologic Agents is Suspected
Bartonella spp	Bloodstream infections
Chlamydia pneumoniae	Bronchiolitis, Bronchitis, and Pertussis; Community-Acquired Pneumonia
Chlamydia trachomatis	Periocular structure infections/ Conjunctivitis, Orbital and Periorbital Cellulitis, and Lacrimal and Eyelid Infections; Proctitis; Epididymitis and Orchitis; Pathogens Associated with Cervicitis/Urethritis; Pathogens Associated with Pelvic Inflammatory Disease and Endometritis
Clostridium difficile	Gastroenteritis, Infectious, and Toxin-Induced Diarrhea
Cytomegalovirus	Pericarditis and Myocarditisa; Encephalitis; Pneumonia in the Immunocompromised Host; Esophagitis; Gastroenteritis, Infectious, and Toxin-Induced Diarrhea; Burn Wound Infectionsb
Enterovirus	Meningitis; Encephalitis; Brochiolitis, Bronchitis, and Pertussis; Community-Acquired Pneumonia; Gastroenteritis, Infectious, and Toxin-Induced Diarrhea
Herpes Simplex Virus	Meningitis; Encephalitis; Immunocompromised Host; Esophagitis; Proctitis; Pathogens Associated with Cervicitis/Urethritis; Burn Wound Infectionb; Periocular structure infections/ Conjunctivitis, Orbital and Periorbital Cellulitis, and Lacrimal and Eyelid Infections; Periocular Structure Infections/Keratitis; Pharyngitis; Genital Lesions
HIV	Pericarditis and Myocarditis; Meningitisc; Pharyngitisc
Human Herpesvirus 6	Encephalitis
Influenza	Encephalitis; Bronchiolitis, Bronchitis, and Pertussis; Community-Acquired Pneumonia; Hospital-Acquired Pneumonia and Ventilator-Associated Pneumonia; Pulmonary Infections in Cystic Fibrosis;
Legionella spp	Community-Acquired Pneumonia; Hospital-Acquired Pneumonia and Ventilator-Associated Pneumonia; Infections of the Pleural Space; Surgical Site Infections
Mycobacteria Species- both Tuberculosis and NTM	Community-Acquired Pneumonia; Infections of the Pleural Space; Osteomyelitis
Neisseria gonorrhoeae	Pharyngitis; Proctitis; Native Joint Infection and Bursitis; Epididymitis and Orchitis; Pathogens Associated with Cervicitis/Urethritis; Pathogens Associated with Pelvic Inflammatory Disease and Endometritis
Staphylococcus aureus	Burn Wound Infections for MRSA and S. aureus only, Trauma-Associated Cutaneous Infections; Surgical Site Infections
Streptococcus, Group A	Pharyngitis
Trichomonas vaginalis	Pathogens Associated with Cervicitis/Urethritis; Pathogens Associated with Pelvic Inflammatory Disease and Endometritis

* The IDSA provided recommendations for many situations in which NAATs are recommended for diagnosing certain etiologic agents commonly seen with the listed conditions noted under the Recommended Conditions for Use of NAATs in Diagnosis Column.
HIV: human immunodeficiency virus; IDSA: Infectious Disease Society of America;MSRA: methicillin-resistant Staphylococcus aureus; NAAT: nucleic acid amplification test: NTM: nontuberculous mycobacteria.
^a Recommended as first choice if available;
^b Where applicable and laboratory-validated;
^c The guidelines caution that NAAT is not 100% sensitive in individuals with established HIV infection due to viral suppression; therefore, if NAAT is used, subsequent serologic testing is recommended.

NAATs for diagnosing Candida species, Gardnerella vaginalis, Streptococcus Group B, and Vancomycin-resistant enterococcus as etiologic agents were not recommended.

3.2 In 2017, the IDSA published clinical practice guidelines for the management of healthcare-associated ventriculitis and meningitis.^37, When making diagnostic recommendations, the IDSA notes cultures as the standard of care in diagnosing healthcare-associated ventriculitis and meningitis, but that “nucleic acid amplification tests, such as PCR, on CSF may both increase the ability to identify a pathogen and decrease the time to making a specific diagnosis (weak, low).” (Strength of recommendation and quality of evidence established using the GRADE [Grading of Recommendations Assessment, Development and Evaluation] methodology.^37,)

3.3 In 2008, the IDSA published clinical practice guidelines for the management of encephalitis.^38, The following recommendations were made:

• “Biopsy of specific tissues for culture, antigen detection, nucleic acid amplification tests (such as PCR), and histopathologic examination should be performed in an attempt to establish an etiologic diagnosis of encephalitis (A-III).” (Strength of recommendation level “A indicates good evidence to support recommendation for use.” Quality of evidence level III indicates “evidence from opinions of respected authorities based on clinical experience, descriptive studies, or reports of expert committees.”^39,)
• “Nucleic acid amplification tests (such as PCR) of body fluids outside of the CNS may be helpful in establishing the etiology in some patients with encephalitis (B-III).” (Strength of recommendation level B indicates “moderate evidence to support recommendation.” Quality of evidence level III indicates “evidence from opinions of respected authorities based on clinical experience, descriptive studies, or reports of expert committees.”^39,)
• “Nucleic acid amplification tests (such as PCR) should be performed on CSF specimens to identify certain etiologic agents in patients with encephalitis (A-III). Although a positive test result is helpful in diagnosing infection caused by a specific pathogen, a negative result cannot be used as definitive evidence against the diagnosis.”
• The use of NAATs was recommended for diagnosing CMV, HSV-1 and -2, Human herpesvirus 6, Bartonella henselae, Mycoplasma pneumoniae, and Mycobacterium tuberculosis.

• “The best-performing method (ie, in use positive and negative predictive value) for detecting patients at increased risk for clinically significant C. difficile [CDI] infection” is use of a “stool toxin test as part of a multistep algorithm…rather than NAAT along for all specimens received in the clinical laboratory when there are no preagreed institutional criteria for patient stool submission.”
• “The most sensitive method of diagnosis of CDI in stool specimens from patients likely to have CDI based on clinical symptoms” is use of “a NAAT alone or a multistep algorithm for testing…rather than a toxin test alone when there are preagreed institutional criteria for patient stool submission.”

• In situations where enteric fever or bacteremia is suspected, “culture-independent, including panel-based multiplex molecular diagnostics from stool and blood specimens, and when indicated, culture-dependent diagnostic testing should be performed” (GRADE: strong, moderate).
• In testing for Clostridium difficile in patients >2 years of age, “a single diarrheal stool specimen is recommended for detection of toxin or toxigenic C. difficile strain (eg, nucleic acid amplification testing)” (GRADE: strong, low).
• NAATs are not recommended for diagnosing Cytomegalovirus.
• It was also noted that “clinical consideration should be included in the interpretation of results of multiple-pathogen nucleic acid amplification tests because these assays detect DNA and not necessarily viable organisms” (GRADE: strong, low).

3.7 In 2016, the IDSA published updated clinical practice guidelines for managing candidiasis.^42, The guideline noted many limitations of PCR testing. No formal recommendation was made, but the guidelines did state that “the role of PCR in testing samples other than blood is not established.”

3.8 In 2020, the IDSA established a panel composed of 8 members including frontline clinicians, infectious diseases specialists and clinical microbiologists who were members of the IDSA, American Society for Microbiology (ASM), Society for Healthcare Epidemiology of America (SHEA), and the Pediatric Infectious Diseases Society (PIDS). Panel members represented the disciplines of adult and pediatric infectious diseases, medical microbiology, as well as nephrology and gastroenterology. The panel created a COVID-19 Diagnosis guideline using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach for evidence assessment; and, given the need for rapid response to an urgent public health crisis, the methodological approach was modified according to the GIN/McMaster checklist for development of rapid recommendations. The panel published recommendations for COVID-19 Diagnosis in an online format, as when substantive new information becomes available the recommendations will require frequent updating.^43, The current recommendations (published May 6, 2020) support SARS-CoV-2 nucleic acid testing for the following groups:

• all symptomatic individuals suspected of having COVID-19;
• asymptomatic individuals with known or suspected contact with a COVID-19 case;
• asymptomatic individuals without known exposure when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform administration of immunosuppressive therapy.

• collecting nasopharyngeal, or mid-turbinate or nasal swabs rather than oropharyngeal swabs or saliva alone for SARS-CoV-2 RNA testing in symptomatic individuals with upper respiratory tract infection (URTI) or influenza like illness (ILI) suspected of having COVID-19 (conditional recommendation, very low certainty of evidence).
• nasal and mid-turbinate (MT) swab specimens may be collected for SARS-CoV-2 RNA testing by either patients or healthcare providers, in symptomatic individuals with upper respiratory tract infection (URTI) or influenza like illness (ILI) suspected of having COVID-19 (conditional recommendation, low certainty of evidence).
• a strategy of initially obtaining an upper respiratory tract sample (e.g., nasopharyngeal swab) rather than a lower respiratory sample for SARS-CoV-2 RNA testing in hospitalized patients with suspected COVID-19 lower respiratory tract infection. If the initial upper respiratory sample result is negative, and the suspicion for disease remains high, the IDSA panel suggests collecting a lower respiratory tract sample (e.g., sputum, bronchoalveolar lavage fluid, tracheal aspirate) rather than collecting another upper respiratory sample (conditional recommendations, very low certainty of evidence)
• performing a single viral RNA test and not repeating testing in symptomatic individuals with a low clinical suspicion of COVID-19 (conditional recommendation, low certainty of evidence).
• repeating viral RNA testing when the initial test is negative (versus performing a single test) in symptomatic individuals with an intermediate or high clinical suspicion of COVID-19 (conditional recommendation, low certainty of evidence).

D. American Society of Transplantation

4.1 In 2019, the American Society of Transplantation Infectious Diseases Community of Practice published guidelines which addressed vancomycin-resistant enterococci infections in solid organ transplant patients.^44, The guidelines noted the cost-effectiveness and accuracy of “emerging molecular diagnostics for VRE colonization, including multiplexed PCR performed after culture on selective media,” compared with culture alone.

E. American Academy of Pediatrics

5.1 The current edition of the AAP Red Book describes the diagnostic and treatment options of many infectious diseases in the pediatric population.^45, Their recommendations for appropriate diagnostic tests for the viruses and infections discussed in this policy are detailed in Table 16.

Table 16. Redbook Diagnostic Test Recommendations for the Pediatric Population

Infection	Diagnostic Test Recommendation
Bartonella henselae	IFA NAAT (PCR)
Candida Species	Clinical Evaluation Microscopy
Chlamydia pneumoniae	Serologic antigen test PCRs- “can provide a specific diagnosis but are not available in most clinical laboratories”
Chlamydia trachomatis	NAATs are recommended for C trachomatis urogenitial infections and in postpubescent individuals. They are not recommended for diagnosis C trachomatis conjunctivitis or pneumonia or in the evaluation of prepubescent children for possible sexual assault.
Clostridium difficile	Anaerobic cultures of wound exudate and blood should be performed.
Cytomegalovirus	Saliva PCR is the preferred diagnostic tool for screening.
Enterovirus	Reverse-transcriptase PCR and culture from a variety of specimens
Gardnerella vaginalis	Microscopy Numerous NAATs have been recommended when microscopy is unavailable
Hepatitis B	Serologic antigen tests NAATs
Hepatitis C	IgG antibody enzyme immunoassays NAATs
Herpes Simplex Virus	Cell culture NAATs- diagnostic method of choice for neonates with CNS infections, older children, and adults with HSE
Human Herpesvirus 6	Few developed assays are available commercially and do not differentiate between new, past, and reactivated infection. Therefore, these tests “have limited utility in clinical practice:” Serologic tests; PCR- the assays are not sensitive in younger children.
HIV 1	HIV DNA PCR- “preferred test to diagnose HIV-1 subtype B infection in infants and children younger than 18mo; HIV RNA PCR- “preferred test to identify non-B subtype HIV-1 infections… DNA PCR is generally preferred because of greater clinical experience with that assay.”
Human Papillomavirus	“Detection of HPV infection is based on detection of viral nucleic acid or capsid protein.”
Influenza Virus	“RT-PCR, viral culture tests, and rapid influenza molecular assays offer potential for high sensitivity as well as specificity and are recommended as the tests of choice.”
Legionella pneumophila	BCYE Media Legionella antigen in urine Direct IFA Genus-specific PCR reaction-based assays
Meningitis	Cultures of blood and CSF NAATs- “useful in patients who receive antimicrobial therapy before cultures are obtained.”
Mycobacteria Species	M tuberculosis disease: Chest radiography and physical examination While several NAATs are cleared by the FDA, “further research is needed before NAATs can be recommended routinely for the diagnosis of tuberculosis in children,” Nontuberculous Mycobacteria: “definite diagnosis of NTM disease requires isolation of the organism.”
Mycoplasma pneumonia	“PCR tests for M pneumoniae are available commercially and increasing replacing other tests, because PCR tests performed on respiratory tract specimens have sensitivity and specifically between 80% and 100%, yield positive results earlier in the course of illness than serologic tests, and are rapid.”
Neisseria gonorrhoeae	“NAATs are far superior in overall performance compared with other N gonorrhoeae culture and nonculture diagnostic methods to test genital and nongenital specimens, but performance varies by NAAT type.”
Staphylococcus aureus	“NAATS are approved for detection and identification of S aureus, including MRSA, in positive blood cultures.”
Streptococcus, Group A	“Children with pharyngitis and obvious viral symptoms should not be tested or treated for GAS infection. Laboratory confirmation is required for cases in children without viral symptoms… culture on sheep blood agar can confirm GAS infection.”
Streptococcus, Group B	“Gram-positive cocci in pairs or short chains by gram stain of body fluids that typically are sterile provide presumptive evidence of infection.”
Trichomonas vaginalis	Microscopy NAATs are “the most sensitive mean of diagnosing T vaginalis infection and is encouraged for detection in females and males.”
Vancomycin-resistant enterococcus	“Diagnosis is established by culture of usually sterile body fluids with appropriate biochemical testing and serologic analysis for definitive identification.”
Zika	NAATs Trioplex real-time PCR assay Serologic testing

BCYE: buffered charcoal yeast extract; CNS: central nervous sytem; CSF: cerebrospinal fluid; FDA: Food and Drug Administration; HIV: human immunodeficiency virus; HPV: human papillomavirus; HSE: herpes simplex encephalitis;
IFA: indirect fluorescent antibody; MSRA: methicillin-resistant Staphylococcus aureus; NAAT: nucleic acid amplification test; NTM: nontuberculous mycobacteria; PCR: polymerase chain reaction.

5.2 In 2019, the AAP published guidelines on managing infants at risk for GBS.^46, It recommends antenatal vaginal-rectal culture performed by using a broth enrichment “followed by GBS identification by using traditional microbiologic methods or by NAAT-based methods.” However, point-of-care NAAT-based screening should not be the primary method of determining maternal colonization status due to reported variable sensitivity as compared with traditional culture, as well as “because most NAAT-based testing cannot be used to determine the antibiotic susceptibility of colonizing GBS isolates among women with a penicillin allergy.”

F. American College of Gastroenterology

6.1 In 2016, the American College of Gastroenterology published clinical guidelines on the diagnosis, treatment, and prevention of acute diarrheal infections in adults.^47, It recommended that, given that “traditional methods of diagnosis (bacterial culture, microscopy with and without special stains and immunofluorescence, and antigen testing) fail to reveal the etiology of the majority of cases of acute diarrheal infection,… the use of FDA-approved culture-independent methods of diagnosis can be recommended at least as an adjunct to traditional methods. (Strong recommendation, low level of evidence).” These are described in the rationale as multiplex molecular testing.

U.S. Preventive Services Task Force Recommendations

Not applicable.

Ongoing and Unpublished Clinical Trials

Some currently ongoing trials that might influence this review are listed in Table 17.

Table 17. Summary of Key Trials

NCT No.	Trial Name	Planned Enrollment	Completion Date
Ongoing
NCT03809117	A Randomized Controlled Trial of Biofire Film Array Gastrointestinal Panel Compared to Usual Care for Evaluation of Acute Infectious Diarrhea in the Emergency Department	176	Nov 2019
NCT03551340	Impact of the Introduction of Gasto-intestinal Panel by PCR on the Treatment of Patients with Gastroenteritis	210	Mar 2020
NCT03895281	Clinical Evaluation of the FilmArray® Meningitis/Encephalitis (ME) Panel	150	Apr 2020
NCT03452826	Combined Use of a Respiratory Broad Panel MULTIplex PCR and Procalcitonin to Reduce Antibiotics Exposure in Patients With Severe Community-Acquired Pneumonia: a Multicentre, Parallel-group, Open-label, Randomized Controlled Trial (MULTI-CAP)	450	Aug 2020
NCT03362970	Improvements Through the Use of a Rapid Multiplex PCR Enteric Pathogen Detection Kit in Children With Hematochezia	60	Dec 2020
NCT03840603	PROARRAY: Impact on PCT+ FilmArray RP2 Plus Use in LRTI Suspicion in Emergency Department	444	Jan 2021
NCT04372004	Comparison of the Efficacy of Rapid Tests to Identify COVID-19 Infection (CATCh COVID-19) (CATCH COVID-19)	100	June 2021

NCT: national clinical trial.]
________________________________________________________________________________________

Horizon BCBSNJ Medical Policy Development Process:

This Horizon BCBSNJ Medical Policy (the “Medical Policy”) has been developed by Horizon BCBSNJ’s Medical Policy Committee (the “Committee”) consistent with generally accepted standards of medical practice, and reflects Horizon BCBSNJ’s view of the subject health care services, supplies or procedures, and in what circumstances they are deemed to be medically necessary or experimental/ investigational in nature. This Medical Policy also considers whether and to what degree the subject health care services, supplies or procedures are clinically appropriate, in terms of type, frequency, extent, site and duration and if they are considered effective for the illnesses, injuries or diseases discussed. Where relevant, this Medical Policy considers whether the subject health care services, supplies or procedures are being requested primarily for the convenience of the covered person or the health care provider. It may also consider whether the services, supplies or procedures are more costly than an alternative service or sequence of services, supplies or procedures that are at least as likely to produce equivalent therapeutic or diagnostic results as to the diagnosis or treatment of the relevant illness, injury or disease. In reaching its conclusion regarding what it considers to be the generally accepted standards of medical practice, the Committee reviews and considers the following: all credible scientific evidence published in peer-reviewed medical literature generally recognized by the relevant medical community, physician and health care provider specialty society recommendations, the views of physicians and health care providers practicing in relevant clinical areas (including, but not limited to, the prevailing opinion within the appropriate specialty) and any other relevant factor as determined by applicable State and Federal laws and regulations.

___________________________________________________________________________________________________________________________

Index:
Identification of Microorganisms Using Nucleic Acid Probes
Direct Probe Technique, Identification of Microorganisms Using
Amplified Probe Technique, Identification of Microorganisms Using
Quantification Technique, Identification of Microorganisms Using
Nucleic Acid Probe Technique, Identification of Microorganisms Using
DNA Probe Technique, Identification of Microorganisms Using
RNA Probe Technique, Identification of Microorganisms Using
Probe Technique, Identification of Microorganisms Using

References:
1. He T, Kaplan S, Kamboj M, et al. Laboratory Diagnosis of Central Nervous System Infection. Curr Infect Dis Rep. Nov 2016; 18(11): 35. PMID 27686677

2. Tansarli GS, Chapin KC. Diagnostic test accuracy of the BioFire(R) FilmArray(R) meningitis/encephalitis panel: a systematic review and meta-analysis. Clin Microbiol Infect. Mar 2020; 26(3): 281-290. PMID 31760115

3. Leber AL, Everhart K, Balada-Llasat JM, et al. Multicenter Evaluation of BioFire FilmArray Meningitis/Encephalitis Panel for Detection of Bacteria, Viruses, and Yeast in Cerebrospinal Fluid Specimens. J Clin Microbiol. Sep 2016; 54(9): 2251-61. PMID 27335149

4. Graf EH, Farquharson MV, Cardenas AM. Comparative evaluation of the FilmArray meningitis/encephalitis molecular panel in a pediatric population. Diagn Microbiol Infect Dis. Jan 2017; 87(1): 92-94. PMID 27771208

5. Hanson KE, Slechta ES, Killpack JA, et al. Preclinical Assessment of a Fully Automated Multiplex PCR Panel for Detection of Central Nervous System Pathogens. J Clin Microbiol. Mar 2016; 54(3): 785-7. PMID 26719436

6. Gastrointestinal Tract Infections. https://www.uib.cat/depart/dba/microbiologia/ADSenfcomI/material_archivos/infeccion%20gastrointestinal.pdf. Accessed January 17, 2020.

7. Bintsis T. Foodborne pathogens. AIMS Microbiol. 2017; 3(3): 529-563. PMID 31294175

8. Sattar SBA, Singh S. Bacterial Gastroenteritis. [Updated 2019 Mar 8]. In: StatPearls [Internet]. Treasure Island, FL: StatPearls Publishing; 2019 Jan. https://www.ncbi.nlm.nih.gov/books/NBK513295/. Accessed January 17, 2020.

9. Burden of Norovirus Illness in the U.S. Centers for Disease Control and Prevention. https://www.cdc.gov/norovirus/trends-outbreaks/burden-US.html. Last reviewed June 1, 2018. Accessed January 21, 2020.

10. Centers for Medicare & Medicaid Coverage. Local Coverage Determination (LCD): Foodborne Gastrointestinal Panels Identified by Multiplex Nucleic Acid Amplification (NAATs) (L37709). CMS.gov. https://www.cms.gov/medicare-coverage-database/details/lcd-details.aspx?LCDId=37709&ver=13&Date=10%2f31%2f2019&DocID=L37709&bc=iAAAABAAAAAA&. Revised October 31, 2019. Accessed January 21, 2020.

11. Beckmann C, Heininger U, Marti H, et al. Gastrointestinal pathogens detected by multiplex nucleic acid amplification testing in stools of pediatric patients and patients returning from the tropics. Infection. Dec 2014; 42(6): 961-70. PMID 25015433

12. Borst A, Box AT, Fluit AC. False-positive results and contamination in nucleic acid amplification assays: suggestions for a prevent and destroy strategy. Eur J Clin Microbiol Infect Dis. Apr 2004; 23(4): 289-99. PMID 15015033

13. Evaluation of Automatic Class III Designation for FilmArray Meningitis/Encephalitis (ME) Panel Decision Summary. U.S. Food and Drug Administration. https://www.accessdata.fda.gov/cdrh_docs/reviews/K063765.pdf. Accessed January 9, 2020.

14. Evaluation of automatic class III designation (de novo) for xTAG gastrointestinal pathogen panel (GPP) decision summary. Food and Drug Administration. https://www.accessdata.fda.gov/cdrh_docs/reviews/K121454.pdf. Accessed January 9, 2020.

15. Claas EC, Burnham CA, Mazzulli T, et al. Performance of the xTAG(R) gastrointestinal pathogen panel, a multiplex molecular assay for simultaneous detection of bacterial, viral, and parasitic causes of infectious gastroenteritis. J Microbiol Biotechnol. 2013; 23(7): 1041-5. PMID 23711521

16. Buchan BW, Olson WJ, Pezewski M, et al. Clinical evaluation of a real-time PCR assay for identification of Salmonella, Shigella, Campylobacter (Campylobacter jejuni and C. coli), and shiga toxin-producing Escherichia coli isolates in stool specimens. J Clin Microbiol. Dec 2013; 51(12): 4001-7. PMID 24048539

17. Al-Talib H, Latif B, Mohd-Zain Z. Pentaplex PCR assay for detection of hemorrhagic bacteria from stool samples. J Clin Microbiol. Sep 2014; 52(9): 3244-9. PMID 24958797

18. Jiang Y, Fang L, Shi X, et al. Simultaneous detection of five enteric viruses associated with gastroenteritis by use of a PCR assay: a single real-time multiplex reaction and its clinical application. J Clin Microbiol. Apr 2014; 52(4): 1266-8. PMID 24478418

19. Freeman K, Mistry H, Tsertsvadze A, et al. Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis. Health Technol Assess. Apr 2017; 21(23): 1-188. PMID 28619124

20. Cybulski RJ, Bateman AC, Bourassa L, et al. Clinical Impact of a Multiplex Gastrointestinal Polymerase Chain Reaction Panel in Patients With Acute Gastroenteritis. Clin Infect Dis. Nov 13 2018; 67(11): 1688-1696. PMID 29697761

21. Beal SG, Tremblay EE, Toffel S, et al. A Gastrointestinal PCR Panel Improves Clinical Management and Lowers Health Care Costs. J Clin Microbiol. Jan 2018; 56(1). PMID 29093106

22. Huang HS, Tsai CL, Chang J, et al. Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis. Clin Microbiol Infect. Oct 2018; 24(10): 1055-1063. PMID 29208560

23. Mansuy JM, Mengelle C, Da Silva I, et al. Performance of a rapid molecular multiplex assay for the detection of influenza and picornaviruses. Scand J Infect Dis. Dec 2012; 44(12): 963-8. PMID 22830610

24. Dabisch-Ruthe M, Vollmer T, Adams O, et al. Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay. BMC Infect Dis. Jul 24 2012; 12: 163. PMID 22828244

25. Pierce VM, Hodinka RL. Comparison of the GenMark Diagnostics eSensor respiratory viral panel to real-time PCR for detection of respiratory viruses in children. J Clin Microbiol. Nov 2012; 50(11): 3458-65. PMID 22875893

26. Andrews D, Chetty Y, Cooper BS, et al. Multiplex PCR point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use. BMC Infect Dis. Oct 10 2017; 17(1): 671. PMID 29017451

27. Brendish NJ, Malachira AK, Armstrong L, et al. Routine molecular point-of-care testing for respiratory viruses in adults presenting to hospital with acute respiratory illness (ResPOC): a pragmatic, open-label, randomised controlled trial. Lancet Respir Med. May 2017; 5(5): 401-411. PMID 28392237

28. Cytomegalovirus (CMV) and Congenital CMV Infection: Laboratory Testing. Centers for Disease Control and Prevention. https://www.cdc.gov/cmv/clinical/lab-tests.html. Page last reviewed May 31, 2019. Accessed January 21, 2020.

29. Center for Disease Control and Prevention. Mycoplasma pneumoniae Infections: Diagnostic Methods. https://www.cdc.gov/pneumonia/atypical/mycoplasma/hcp/diagnostic-methods.html. Accessed January 21, 2020.

30. Adebanjo T, Godfred-Cato S, Viens L, et al. Update: Interim Guidance for the Diagnosis, Evaluation, and Management of Infants with Possible Congenital Zika Virus Infection - United States, October 2017. MMWR Morb Mortal Wkly Rep. Oct 20 2017; 66(41): 1089-1099. PMID 29049277

31. MacCannell T, Umscheil CA, Agarwal RK, et al. Guideline for the Prevention and Control of Norovirus Gastroenteritis Outbreaks in Healthcare Settings. CDC. Updated 2/15/17. https://www.cdc.gov/infectioncontrol/pdf/guidelines/norovirus-guidelines.pdf. Accessed January 10, 2020.

32. Hall AJ, Vinje J, Lopman B, et al. Updated Norovirus Outbreak Management and Disease Prevention Guidelines. CDC MMWR. Published 3/4/11. https://www.cdc.gov/mmwr/pdf/rr/rr6003.pdf. Accessed January 10, 2020.

33. Workowski KA, Bolan GA, Workowski KA, et al. Sexually transmitted diseases treatment guidelines, 2015. MMWR Recomm Rep. Jun 05 2015; 64(RR-03): 1-137. PMID 26042815

34. Verani JR, McGee L, Schrag SJ. Prevention of perinatal group B streptococcal disease--revised guidelines from CDC, 2010. MMWR Recomm Rep. Nov 19 2010; 59(RR-10): 1-36. PMID 21088663

35. 2019 NIH Guidelines for the Prevention and Treatment of Opportunistic Infections in Adults and Adolescents with HIV. Published October 22, 2019. https://aidsinfo.nih.gov/contentfiles/lvguidelines/adult_oi.pdf. Accessed on January 21, 2020.

36. Miller JM, Binnicker MJ, Campbell S, et al. A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. Aug 31 2018; 67(6): e1-e94. PMID 29955859

37. Tunkel AR, Hasbun R, Bhimraj A, et al. 2017 Infectious Diseases Society of America's Clinical Practice Guidelines for Healthcare-Associated Ventriculitis and Meningitis. Clin Infect Dis. Mar 15 2017; 64(6): e34-e65. PMID 28203777

38. Tunkel AR, Glaser CA, Bloch KC, et al. The management of encephalitis: clinical practice guidelines by the Infectious Diseases Society of America. Clin Infect Dis. Aug 01 2008; 47(3): 303-27. PMID 18582201

39. Lee DH, Vielemeyer O. Analysis of overall level of evidence behind Infectious Diseases Society of America practice guidelines. Arch Intern Med. Jan 10 2011; 171(1): 18-22. PMID 21220656

40. McDonald LC, Gerding DN, Johnson S, et al. Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis. Mar 19 2018; 66(7): e1-e48. PMID 29462280

41. Shane AL, Mody RK, Crump JA, et al. 2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea. Clin Infect Dis. Nov 29 2017; 65(12): e45-e80. PMID 29053792

42. Pappas PG, Kauffman CA, Andes DR, et al. Clinical Practice Guideline for the Management of Candidiasis: 2016 Update by the Infectious Diseases Society of America. Clin Infect Dis. Feb 15 2016; 62(4): e1-50. PMID 26679628

43. Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19. Published May 6, 2020. https://www.idsociety.org/practice-guideline/covid-19-guideline-diagnostics/. Accessed on May 27, 2020.

44. Nellore A, Huprikar S. Vancomycin-resistant Enterococcus in solid organ transplant recipients: Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice. Clin Transplant. Sep 2019; 33(9): e13549. PMID 30913322

45. Kimberlin DW, Brady MT, Jackson, MA, et al. Redbook 2018. Am Acad Peds.

46. Puopolo KM, Lynfield R, Cummings JJ, et al. Management of Infants at Risk for Group B Streptococcal Disease. Pediatrics. Aug 2019; 144(2). PMID 31285392

47. Riddle MS, DuPont HL, Connor BA. ACG Clinical Guideline: Diagnosis, Treatment, and Prevention of Acute Diarrheal Infections in Adults. Am J Gastroenterol. May 2016; 111(5): 602-22. PMID 27068718

48. Centers for Medicare & Medicade Services Current Emergencies 2020: Coronavirus Disease 2019. Last reviewed May 26, 2020. https://www.cms.gov/About-CMS/Agency-Information/Emergency/EPRO/Current-Emergencies/Current-Emergencies-page. Accessed May 27, 2020.

Codes:
(The list of codes is not intended to be all-inclusive and is included below for informational purposes only. Inclusion or exclusion of a procedure, diagnosis, drug or device code(s) does not constitute or imply authorization, certification, approval, offer of coverage or guarantee of payment.)

CPT*

87471 - 87661 (except 87505, 87506 and 87507)
87797
87798
87799
0098U
0099U
0100U
0115U
0151U
0202U