TEST LIMITATIONS
General
Negative results do not rule out the presence of potential uropathogens.The analytical sensitivity of this test depends on sample processing and next-generation sequencing methods and sample composition, including the cellularity of the sample and the concentration of all microorganisms present. Analytical sensitivity is assessed using internal controls that are added to each sample. Sequencing data for internal controls are quantified, and samples with internal control values below the validated minimum may have reduced analytical sensitivity or contain inhibitors and are reported as ‘Reduced Analytical Sensitivity’. Consider urine culture or nucleic acid amplification tests when detection of uropathogens at low abundance is required and follow current testing guidelines. False-positive results are possible due to specimen contamination or cross-reactivity among closely related microorganisms. The presence of bacterial or fungal nucleic acids does not imply microorganisms causing urinary tract infection. Bacterial or fungal nucleic acid may persist after microorganisms are no longer viable. Results need to be interpreted in conjunction with the clinical history, results of other laboratory tests, epidemiologic information, and other available data. Confirmation of positive results by an alternate method may be indicated in select cases.

Semi-Quantitative Detection
Quantification of potential bacterial and fungal uropathogens by next-generation sequencing (GE/mL) correlates but does not always predict quantification by culture. Live microorganisms are required for detection by culture. Molecular methods, such as next-generation sequencing, can also detect non-viable microorganisms and free microbial DNA. Therefore, GE/mL may be less predictive of culture-based quantification (CFU/mL) in some patients, including those who received antibiotic treatment prior to sample collection. Consider urine culture if quantification at low abundance or by traditional means (CFU/mL) is required.

Genetic Markers for Antibiotic Resistance
This test detects genetic markers that are known to confer antibiotic resistance in eight common uropathogens. However, results do not establish that a given genetic marker is identified in a bacterium. Genetic markers are only reported when one or more bacterium is detected in which that genetic marker is known to confer antibiotic resistance. In the case of Staphylococcus aureus, reporting of mecA and/or mecC is qualified when coagulase-negative Staphylococcus species are detected that have been reported to carry mecA and/or mecC (i.e., Staph. capitis, Staph. caprae, Staph. cohnii, Staph. fleurettii, Staph. kloosii, Staph. lentus, Staph. pasteuri, Staph. petrasii, Staph. pseudintermedius, Staph. schleiferi, Staph. sciuri, Staph. vitulinus, Staph. xylosus). This test does not detect resistance conferred by mutations in chromosomal genes or the presence of efflux pumps and does not differentiate between chromosomally and plasmid-encoded markers for antibiotic resistance. Antibiotic resistance can occur via multiple mechanisms, not all of which are known. Detection of a genetic marker for antibiotic resistance does not always predict phenotypic resistance. For example, genes may not be expressed, expressed at low levels, not be functional, or additional factors may be required for phenotypic resistance. Conversely, lack of detection of a genetic marker does not exclude the presence of other resistance mechanisms and does not indicate antibiotic susceptibility. The reported antibiotic resistance genes may confer resistance to other antibiotics in addition to the twelve antibiotics reported by this test. Not all OXA alleles confer resistance to cephalosporins (Cefalexin, Ceftriaxone) and carbapenems (Imipenem and Meropenem). This test is not intended for epidemiological and infection control purposes or to monitor treatment response. Phenotypic susceptibility testing is preferred.