Frequently asked questions

If symptoms persist after treatment, follow-up testing (no earlier than 48 hours after stopping antimicrobials) is recommended. Our 2% reporting threshold can occasionally miss low-abundance pathogens that, once the dominant pathogen is treated, may thrive and cause recurring symptoms. This is particularly important for patients with chronic or recurrent UTIs, where treatment may provide only temporary relief. Follow-up testing helps ensure accurate diagnosis and better treatment planning.

In most cases, the primary pathogen will be the dominant organism detected by NGS, however certain organisms are considered pathogenic at any abundance level.

Yes, it’s better to continue biofilm disruptors before the test. They help break up biofilms, making it easier to capture bacteria, especially in bladder infections. Although still considered experimental, patients using biofilm disruptors often show better recovery rates.

While NGS can occasionally detect Chlamydia trachomatis and Neisseria gonorrhoeae in blood, blood is not an appropriate sample type for diagnosing sexually transmitted infections (STIs). NGS is not validated for the detection of other STIs from blood samples. Direct sampling from the site of infection (e.g., urine, urethral, cervical, or vaginal swabs) is recommended for accurate identification.

Yes, NGS can detect a wide range of fungal species, including molds such as Stachybotrys chartarum (black mold), as long as fungal DNA is present in the clinical sample. NGS does not rely on the viability of the organism, making it possible to identify both fastidious and non-culturable fungi that may be missed by traditional methods. Detection of environmental molds like Stachybotrys is rare in human clinical samples but may occur, particularly in cases involving respiratory specimens or immunocompromised patients.

Yes, a list of antimicrobials for consideration is provided for each species detected, based on references such as the Sanford Guide and Johns Hopkins ABX Guide. For common pathogens, local antibiograms should be consulted to account for regional resistance patterns and guide optimal antimicrobial selection.

NGS is more sensitive than conventional culture, detecting multiple organisms in a specimen, including those suppressed by antimicrobial therapy or that are non-viable. Because NGS does not rely on organism growth, results may not always fully correlate with culture, particularly for fastidious or biofilm-associated pathogens. Based on a study by Dr. Javad Parvizi, our technology has 96% concordance with culture in terms of species identification.

A biofilm is a community of bacterial and fungal species embedded within a protective extracellular matrix, making them resistant to antibiotics and inaccessible to the immune system. Because biofilms involve multiple organisms, single-antibiotic therapies are often ineffective. The CDC estimates that 65–80% of chronic infections involve biofilm formation. Traditional cultures frequently fail to detect biofilms, whereas NGS can identify all organisms present, enabling more effective, targeted treatment.

MicroGenDX provides antimicrobials for consideration for each species detected. These antimicrobial options are based on the Sanford Guide to Antimicrobial Therapy, the Johns Hopkins ABX Guide, and related research. When a more typical bacterium like E. coli is detected that is easily grown in the microbiology lab, your local antibiogram, which tracks local resistance patterns, should be referenced—though this will only apply to 20–25 microbial species that are easily grown in culture.

MicroGenDX does not directly assess bacterial viability. Dead or non-viable bacterial DNA typically degrades within 24 hours in the host environment, while DNA from viable bacteria remains stable longer. Samples that are refrigerated or frozen help preserve DNA integrity. Species that meet the threshold for DNA reads are reported; if insufficient reads are obtained, the species is not detected. Due to the rapid degradation of DNA in dead bacterial cells it becomes extremely challenging for the technology to reach the threshold of DNA reads. If we don’t achieve enough DNA reads we can not detect the species. If the bacterial species is listed in our report it has met our criteria for DNA reads.