Medical Policy

This document addresses metagenomic sequencing of infectious pathogens in the outpatient setting. Metagenomic testing, which employs next generation sequencing (NGS), analyzes microbial DNA from a clinical sample without reliance on traditional culture or targeted molecular tests. Clinical metagenomic testing is used for comprehensive detection of all pathogens in a single test.

This document does not address targeted or multiplex (panel-based) nucleic acid tests (NAAT) or metagenomic sequencing of infectious diseases in the inpatient setting.

Investigational and Not Medically Necessary:

Metagenomic sequencing for infectious diseases in the outpatient setting is considered investigational and not medically necessary for all indications.

Summary

Metagenomic next-generation sequencing (mNGS) analyzes microbial DNA and RNA directly from clinical samples. While analytical validity is recognized, clinical utility requires evidence that use of this testing improves net health outcomes or materially better clinical decision-making and provides benefits at least equivalent to standard testing. As of late 2025, available data are largely inpatient or peri-operative and therefore have limited external validity for ambulatory care. The currently available published evidence addressing outpatient use of such tests do not show improvements in recovery time, return visits, or antibiotic exposure.

Discussion

Operational and Interpretive Challenges

The clinical implementation of mNGS in the outpatient setting is hampered by significant operational and interpretive constraints. A primary difficulty lies in distinguishing clinically relevant pathogens from colonization or environmental contamination, particularly in non-sterile sites (for example, urine, wounds). The high sensitivity of mNGS frequently detects microbial DNA that may not represent active infection; this poses a significant risk to antimicrobial stewardship by potentially leading to unnecessary therapy and associated patient harms when commensals are reported. Furthermore, mNGS assays may not have the sensitivity of dedicated single microbiologic tests for specific targets and can miss causative pathogens, particularly fungi and mycobacteria (Kaur, 2025). Real-world turnaround times, often spanning 2 to 4 business days including shipping, may also blunt the impact on time-sensitive outpatient decisions.

Urinary Tract Infections (UTIs)

Evidence regarding mNGS for UTIs consistently demonstrates higher microbial detection rates compared to standard urine culture; however, it has not established superior clinical outcomes or patient-relevant benefits in the outpatient setting. The existing published prospective randomized controlled trials (RCTs) remain weak and methodologically flawed. An early (n=44), unblinded study for acute cystitis failed to demonstrate improved symptom resolution when treatment was guided by mNGS (McDonald, 2017). A subsequent RCT evaluating mNGS for preoperative antibiotic prophylaxis reported a reduction in post-surgical UTIs (Liss, 2023). However, a 35% attrition rate, lack of blinding, and uncertain clinical significance limit inference to routine outpatient care. Current guidance for complicated UTI emphasizes culture-based diagnosis and does not recommend mNGS for routine outpatient management (Ackerman, 2025; IDSA, 2025).

Peri-Prosthetic Joint Infection (PJI) and Orthopedic Infections

In the context of orthopedic infections, mNGS demonstrates high analytical sensitivity, but its impact on improving health outcomes remains unproven. While meta-analyses confirm higher pooled sensitivity for mNGS (94%) compared to culture (70%), they also reveal lower specificity for mNGS (89%) compared to culture (95%) (Hantouly, 2023). This lower specificity increases the risk of false positives due to contamination, complicating management decisions. The literature lacks prospective studies demonstrating that mNGS-guided therapy leads to improved health outcomes (for example, reduced reinfection rates). Furthermore, available data derive largely from operative or inpatient settings, not ambulatory evaluation, and IDSA guidance for PJI has not incorporated mNGS into standard diagnostic pathways (IDSA, 2025). Similarly, while one study associated positive mNGS results with persistent fracture non-union (Goswami, 2022), it did not evaluate whether interventions based on these results improved union rates compared to standard care. Findings align with earlier arthroplasty studies that detected organisms beyond culture without achieving outcome gains (Rao, 2019; Ivy, 2018).

Plasma-Based Metagenomic Sequencing (Cell-Free DNA)

The clinical impact of plasma-based microbial cell-free DNA (mcfDNA) tests (for example, the Karius test) remains modest and highly context-dependent, with recent evidence confirming very limited utility in the outpatient setting. A large retrospective analysis of 1000 real-world cases across adult and pediatric patients found that the test had no clinical impact in 82% of cases, a positive impact in 16%, and a negative impact in 2% (Kaur, 2025). The lack of impact was primarily due to results not being acted upon, results confirming a known diagnosis without changing management, or the test missing the causative pathogen. While the study identified specific indications associated with higher positive impact in adults (e.g., culture-negative endocarditis), it found that immunocompromised status alone was not associated with improved utility. Implications of this study are further limited by its retrospective design, variable timing of testing relative to suspicion of infection, heterogeneous inclusion criteria with insufficient power to perform subgroup analysis. The results of this single-center study conducted at a very large academic institution might not be achieved in less resource-intensive settings. The authors concluded that future prospective studies are needed to better define the role of this testing (Kaur, 2025).

Evidence specifically evaluating mcfDNA in the outpatient environment demonstrates lower utility than in the inpatient setting. A retrospective study evaluated 150 individuals in an outpatient rheumatology practice where testing was used primarily to evaluate atypical rheumatic disease presentations or distinguish flare from infection (Jenkins, 2025). While 16% of tests were positive, only 25% of those (6/150, or 4% of the total cohort) were deemed clinically relevant and altered the final diagnosis and treatment. The false-negative rate was 4%. While the authors suggested negative results provided reassurance before initiating immunosuppression in select cases, the study concluded the data did not support universal testing in this setting due to the low rate of actionable positive findings (Jenkins, 2025).

Studies evaluating mcfDNA for evaluation of Fever of Unknown Origin (FUO) show mixed results and highlight concerns regarding applicability to non-specific presentations. A retrospective study of 176 individuals referred for evaluation of FUO (65% inpatient) found that mcfDNA-NGS contributed to a positive diagnostic impact in 30% of cases with an infectious etiology, primarily through earlier diagnosis (Ranganath, 2025). However, the study found that FUO without localization was associated with a significantly decreased likelihood of positive testing, suggesting low yield in non-specific presentations common in ambulatory care. Furthermore, the assay failed to detect infections identified by standard methods and was often negative in cases of localized infections or those caused by RNA viruses (Ranganath, 2025). Earlier cohorts also demonstrated a low or mixed clinical impact, with limited management changes (Hogan, 2020; Weiss, 2023).

Other Applications

Evidence for other outpatient indications, such as chronic wound infection, prostatitis, or onychomycosis, remains insufficient. Published studies are often retrospective, with a limited number of individuals studied, or lack of appropriate comparators, and rarely report patient-important outcomes. No trial has demonstrated that sequencing-directed management improves outpatient clinical endpoints compared to established pathways. Routine outpatient use is not supported.

Regulatory and Coverage Context

The regulatory and coverage context do not support routine outpatient use. Following a federal court ruling, the FDA withdrew its 2024 Laboratory Developed Test (LDT) rule in September 2025 (FDA, 2025). Consequently, these assays remain Clinical Laboratory Improvement Amendments (CLIA) -regulated LDTs, and there are still no FDA-cleared mNGS indications for infectious disease. CMS has no National Coverage Determination (NCD) for infectious-disease multi-gene sequencing (mNGS), and Local Coverage Determinations (LCDs) for infectious panels explicitly exclude mNGS (CMS, 2025).

Approximately 10.2 million physician office visits per year have infectious or parasitic diseases as the primary diagnosis (CDC, 2023). In 2018, there were 3.4 million emergency department visits that had infectious and parasitic diseases as the primary diagnosis. The most common principal diagnoses among these infectious disease hospitalizations were pneumonia, urinary tract infections (UTI) and unspecified septicemia (Kennedy, 2019).

Microbial culture is a conventional method for identification of infectious agents. This technique is limited by the relatively long time required to culture organisms, the difficulty growing many microorganisms in culture, and the need for invasive procedures to obtain samples of deep-seated infection. Newer approaches to identification of microbial agents use DNA sequencing technology, including polymerase chain reaction (PCR) techniques. A limitation of ‘first-generation sequencing technology’, including PCR, is that only one sequencing can be analyzed at one time and thus the DNA from a biological sample needs to be divided into fragments to test for multiple agents. Moreover, unlike culture tests, PCR methods are unable to test for drug/antibiotic susceptibility. Molecular diagnostic and targeted nucleic acid detection tests (NATs) reference methods that detect DNA or RNA specific infectious organisms (for example, bacteria, viruses) as a means of diagnosis. Multiplex (or panel-based) nucleic acid amplification tests (NATs) combine multiple individual NATs into a single test, thereby allowing clinicians to test for an array of potential pathogens that may cause a clinical syndrome at the same time.

Metagenomic sequencing has been proposed as a method to diagnose infection by comparing genetic material found in a patient's sample to a database of thousands of bacteria, viruses, and other pathogens. Metagenomics is a molecular tool used to analyze DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures. Metagenomic sequencing employs NGS testing, also referred to as massively parallel sequencing or high-throughput sequencing. Metagenomic NGS technology allows sequencing for multiple agents in parallel without the physical separation of samples into pieces. Millions or billions of sequencing reactions can occur and be analyzed simultaneously. NGS thus allows for the comprehensive identification of the species of bacteria and fungi in an infectious disease sample without culturing the organisms. Metagenomic NGS has the potential to provide a direct, unbiased analysis of the microbial composition of clinical samples without reliance on traditional culture or targeted molecular tests, and has the capacity to identify a broad range of pathogens in a single test.

Several metagenomic sequencing tests for diagnosing microbial infection are commercially available and are offered in CLIA-certified laboratories. The MicroGenDx test (MicroGen Diagnostics LLC, Lubbock, TX) is marketed for diagnosing microbial infections in a variety of specialties including urology (e.g., urinary tract infections, prostate infections), ENT (e.g., sinus infection diagnosis), wound care (e.g., wound infection diagnosis), orthopedics (e.g., post-operative infection diagnosis) and podiatry (e.g., nail fungus diagnosis). Microbial DNA is extracted from patient samples (e.g., cell swabs, tissue samples, urine samples) using NGS DNA sequencing techniques and analyzed using molecular diagnostic methods. Test result reports, returned within 3-5 days, contain information about all of the microbes and fungi detected in the sample and any antibiotic resistance genes that were identified. In 2022, MicroGen Diagnostics, along with Evvy, launched a metagenomic-based vaginal infection test kit. Tests are processed in the MicroGen laboratory.

The Karius Test (Karius Inc, Redwood City, CA), which involves NGS of cell-free DNA is being marketed for detecting pathogens in culture-negative infections including sepsis and endocarditis, identifying microorganisms involved in invasive fungal infections, targeting antimicrobial therapy and monitoring immunocompromised patients susceptible to infection. The Karius test has been evaluated in the inpatient setting, including testing individuals who met sepsis alert criteria and testing immunocompromised individuals with unknown infections. However, no published studies were identified on the outpatient applications of the test.  In May 2024, Karius Test received FDA Breakthrough Device designation for immunocompromised patients with suspected lung infections; however, a formal 510 (k) clearance for the device has not been issued (Karius Inc, 2024).

There are other metagenomic sequencing tests for evaluating microbes, including ThermoFisher Scientific’s Ion 16S™ Metagenomics Kit and the Illumina whole genome microbial NGS sequencing test. Both of these tests appear to be intended for research purposes at this time; no studies were identified on outpatient applications of the tests. Johns Hopkins and other centers offer cerebrospinal fluid metagenomic sequencing as a clinical laboratory-developed test, with the health system receiving proprietary laboratory analyses code in 2022 (CMS, 2022). Mayo Clinic has its own code related to its own cerebrospinal fluid metagenomic sequencing laboratory-developed test  (CMS, 2024). Both remain laboratory-developed tests without United States Food and Drug Administration clearance.

Clinical metagenomics: The comprehensive analysis of all nucleic acid material present within a clinical sample to recover clinically relevant microbial information such as potential pathogens.

Next-generation sequencing: A laboratory test that allows rapid sequencing of large numbers of segments of DNA, up to and including entire genomes.

Pathogen: Bacteria, viruses or other microorganism that can cause disease.

The following codes for treatments and procedures applicable to this document are included below for informational purposes. Inclusion or exclusion of a procedure, diagnosis or device code(s) does not constitute or imply member coverage or provider reimbursement policy. Please refer to the member's contract benefits in effect at the time of service to determine coverage or non-coverage of these services as it applies to an individual member.

When services are Investigational and Not Medically Necessary:For the following procedure codes; or when the code describes a procedure indicated in the Position Statement section as investigational and not medically necessary.

Peer Reviewed Publications:

1. Goswami K, Tipton C, Clarkson S, et al. Fracture-associated microbiome and persistent nonunion: next-generation sequencing reveals new findings. J Orthop Trauma. 2022; 36(Suppl 2):S40-S46.
2. Hantouly AT, Alzobi O, Toubasi AA, et al. Higher sensitivity and accuracy of synovial next-generation sequencing in comparison to culture in diagnosing periprosthetic joint infection: a systematic review and meta-analysis. Knee Surg Sports Traumatol Arthrosc. 2023; 31(9):3672-3683.  
3. Hogan CA, Yang S, Garner OB, et al. Clinical impact of metagenomic next-generation sequencing of plasma cell-free DNA for the diagnosis of infectious diseases: a multicenter retrospective cohort study. Clin Infect Dis. 2021; 72(2):239-245. 
4. Ivy MI, Thoendel MJ, Jeraldo PR, et al. Direct detection and identification of prosthetic joint infection pathogens in synovial fluid by metagenomic shotgun sequencing. J Clin Microbiol. 2018; 56(9):e00402-18.
5. Kaur I, Shaw B, Multani A, et al. Real-world clinical impact of plasma cell-free DNA metagenomic next-generation sequencing assay. Infect Control Hosp Epidemiol. 2025; 46(5):504-511.
6. Kennedy JL, Haberling DL, Huang CC, et al. Infectious disease hospitalizations: United States, 2001 to 2014. Chest. 2019; 156(2):255-268.
7. Jenkins RA, Samec MJ, Arment CA, et al. Use of metagenomic microbial plasma cell-free dna next-generation sequencing assay in outpatient rheumatology practice. J Rheumatol. 2025; 52(8):823-828.
8. Liss MA, Reveles KR, Tipton CD, et al. Comparative effectiveness randomized clinical trial using next-generation microbial sequencing to direct prophylactic antibiotic choice before urologic stone lithotripsy using an interprofessional model. Eur Urol Open Sci. 2023; 57:74-83.
9. McDonald M, Kameh D, Johnson ME, et al. A head-to-head comparative phase II study of standard urine culture and sensitivity versus DNA next-generation sequencing testing for urinary tract infections. Rev Urol. 2017; 19(4):213-220.
10. Rao AJ, MacLean IS, Naylor AJ, et al. Next-generation sequencing for diagnosis of infection: is more sensitive really better? J Shoulder Elbow Surg. 2020; 29(1):20-26.
11. Ranganath N, Bisono Garcia B, Vaillant J, et al. From chart biopsy to liquid biopsy: evaluating the diagnostic yield and clinical impact of plasma microbial cell-free DNA next-generation sequencing in the management of fever of unknown origin. Open Forum Infect Dis. 2025; 12(2):ofaf038.
12. Simner PJ, Miller HB, Breitwieser FP, et al. Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics. J Clin Microbiol. 2018; 56(9):e00472-18.
13. Tarabichi M, Shohat N, Goswami K, et al. Can next-generation sequencing play a role in detecting pathogens in synovial fluid? Bone Joint J. 2018; 100-B(2):127-133.
14. Weiss ZF, Pyden AD, Jhaveri TA, et al. The diagnostic and clinical utility of microbial cell-free DNA sequencing in a real-world setting. Diagn Microbiol Infect Dis. 2023; 107(2):116004.

Government Agency, Medical Society, and Other Authoritative Publications:

1. Ackerman AL, Bradley M, D’Anci KE, et al. Updates to recurrent uncomplicated urinary tract infections in women: AUA/CUA/SUFU guideline (2025). J Urol. 2025 Sep 4; Epub ahead of print.
2. Centers for Disease Control and Prevention (CDC). National Center for Health Statistics: Infectious Disease. Last updated December 17, 2024. Available at: https://www.cdc.gov/nchs/fastats/infectious-disease.htm. Accessed on September 19, 2024.
3. Centers for Medicare & Medicaid Services. CMS Manual System: Pub 100-04 Medicare Claims Processing, Transmittal 12721. Quarterly Update for Issued July 18, 2024. https://www.cms.gov/files/document/r12721cp.pdf. Accessed October 6, 2025.
4. Centers for Medicare & Medicaid Services. CMS Manual System: Pub 100-04 Medicare Claims Processing, Transmittal 11398. Issued May 4, 2022. https://www.cms.gov/files/document/r11398cp.pdf. Accessed October 6, 2025.
5. Centers for Medicare & Medicaid Services (CMS). LCD - MolDX: molecular syndromic panels for infectious disease pathogen identification testing (L39044). Updated June 16, 2025. https://www.cms.gov/medicare-coverage-database/view/lcd.aspx?lcdid=39044. Accessed October 6, 2025.
6. Infectious Diseases Society of America. Complicated urinary tract infections (cUTI): clinical guidelines for treatment and management. May 12, 2025. Available at: https://www.idsociety.org/practice-guideline/complicated-urinary-tract-infections. Accessed October 6, 2025.
7. U.S. Food and Drug Administration (FDA). Laboratory developed tests. https://www.fda.gov/medical-devices/in-vitro-diagnostics/laboratory-developed-tests Updated September 19, 2025. Accessed October 6, 2025.

1. Karius. Karius test receives FDA breakthrough device designation to aid in the diagnosis of infectious disease. Published May 16, 2024. https://kariusdx.com/resources/press-releases/karius-test-r-receives-fda-breakthrough-device-designation-to-aid-in-the-diagnosis-of-infectious-disease. Accessed October 6, 2025.
2. Urology Care Foundation of the American Urological Association (AUA). Urinary Tract Infections in Adults. Last updated October 2025. Available at: https://www.urologyhealth.org/urologic-conditions/urinary-tract-infections-in-adults. Accessed on September 19, 2024.

Evvy
Karius Test
MicroGenDx

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