Urine dipstick tests

Dipstick tests are used to detect nitrites (bacteria convert urinary nitrates to nitrites) and leukocyte esterase (an enzyme produced by neutrophils, which presumptively associates pyuria with an UTI). They are advantageous in being simple and quick to use.

These tests have several disadvantages, including low sensitivity. False negative nitrite tests are common due to insufficient bladder incubation time for converting nitrate to nitrite, reduced urinary excretion of nitrate, and the failure of certain pathogens, particularly Enterococcus faecalis, to convert nitrate to nitrite.

Microscopic urinalysis

Flow cytometry can be used for the initial screening of urine samples. Depending on the sample, the concentration of bacteria required for a positive result may range from 40 to 1000/µL.

The advantages of urine flow cytometry are that it is standardized, less expensive when compared to urine culture, and the results are rapid. The disadvantages are that flow cytometry is only a screen for bacteriuria; also, it does not provide either species identification or antimicrobial susceptibility testing (AST).

Urine Gram-staining

The analysis of Gram-stained urine samples can be used as a screening technique for UTI. The sensitivity depends on whether the sample has been centrifuged or not. While the urine Gram-stain test provides quick information on the nature of the urinary pathogen, it is disadvantageous in that it is labor intensive and the sensitivity is poor. It is reliable only when the bacterial concentration in urine is >105 colony forming units per milliliter (CFU/mL).

MALDI-TOF mass spectrometry

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was initially approved for pathogen identification in UTIs, wherein the urine sample is cultured, the bacteria isolated, and a colony from the culture plate then analyzed. For the direct analysis of urine, several initial sample preparation steps are essential. These include the removal of cellular debris, leukocytes, and mucus, and the collection of bacteria. Best results are obtained when there is a high bacterial count (>105CFU/mL) and Gram-negative bacteria are involved. The main disadvantage is the inability to perform AST, for which conventional methods will still be required.

Fluorescence in situ hybridization (FISH)

The target for bacterial detection in FISH is the 16S ribosomal RNA (rRNA), which is an integral constituent of bacterial genomes and is present in abundant quantities in the bacterial cell. Detection depends on the availability of specific probes. Rapid FISH assays are available that can give results within 20 minutes with high sensitivity and specificity. The main disadvantage is the inability to perform AST, for which conventional methods will still be required.

Multiplex PCR

Multiplex PCR assays are increasingly being used in the clinical laboratory for the rapid detection and identification of uropathogens. The advantage is the ability to identify organisms that are not detected by routine culturing because they are considered fastidious. The disadvantage with currently available multiplex PCR assays is that they do not provide comprehensive or definitive phenotypic information about antibiotic susceptibility.