Introduction to Microorganism Spotlights

Welcome to our UTI Knowledge Center! Here you will find links to individual posts for each bacteria, yeast, and organism in the Guidance® UTI assay. These spotlights aim to answer common questions about each organism. Each spotlight post has several sections describing key features of the microorganism. Continue reading below to learn about each section.

Gram-stain

Gram staining is a process of applying dyes to cultured bacteria. The dye tells microbiologists about the organism’s cell wall.[1]  Some antibiotics work by attacking the bacterial cell wall. Gram stain result can help with determining appropriate treatment.  For example, Vancomycin is only effective against “gram-positive” bacteria.

Bacteria with a thick cell wall stain purple and are called “gram-positive”. Bacteria with a thin cell wall surrounded by a membrane stain pink. These are called “gram-negative”. A few special cases of bacteria that do not stain in a consistent way and are called “gram-variable”. Some bacteria lack a cell wall so the Gram stain result is “not applicable” for those bacteria.

Morphology

Morphology, or shape, helps visually identify bacteria.[2]  Common bacterial morphologies are: 1) “coccus” (round), 2) “bacillus” (rods), and 3) “spiral”. Some bacteria have an intermediate shape between round and rod-shaped, called “coccobacillus”. Bacteria that lack a cell wall may appear in a variety of shapes.

For coccus-shaped bacteria (plural “cocci”), their arrangement is also helpful. For example, Staphylococci grow in an arrangement resembling a cluster of grapes. However, Streptococci grow in long chains.

Growth Requirements

Like all living things, different microorganisms have different needs for their growth. Microorganisms can be divided into two main categories based on those needs. Those that grow readily in a wide range of conditions are called “non-fastidious”. These organisms are the most studied and best-recognized clinically. That’s because they easily grow in standard clinical microbiological laboratory conditions.

Others, called “fastidious” organisms, have very specific requirements. Fastidious organisms are not as well studied because they require specialized culture conditions. They may need nutritionally supplemented media or extended growth times. Some require an environment with little to no oxygen in the air. These “fastidious” organisms usually can’t grow in standard diagnostic clinical urine cultures.[3–12]

Oxygen requirements for microorganisms can be divided into six general categories:[13,14]

1. “Obligate aerobe” (only survives in environments rich in oxygen)
2. “Facultative anaerobe” (preferentially uses oxygen for cellular respiration but is also capable of fermentation in the absence of oxygen)
3. “Microaerophile” (performs only cellular respiration using oxygen, yet is harmed by the high oxygen concentration at ambient atmospheric conditions… a “Goldilocks” requirement)
4. “Aerotolerant anaerobe” (performs only fermentation, which does not require oxygen, but is not harmed by high oxygen concentrations at ambient atmospheric conditions)
5. “Capnophile” (requires more CO₂ than is present at ambient atmospheric conditions to grow)
6. “Obligate anaerobe” (only grows in environments free from oxygen)

Nitrate Reduction

The urine dipstick, a common point-of-care test for urinary tract infections (UTIs), checks for nitrites in the urine. Many organisms (marked “no” in this section*) aren’t capable of metabolizing nitrates in the urine to produce nitrites. A dipstick test for nitrites will result in a false-negative in these cases.[15]

*This information was compiled according to the Biocyc Database of genomes [16] and the Bacterial Diversity Database of Analytical Profile Index (API) test results.[17]

Urease

Urease is an enzyme responsible for hydrolyzing urea into ammonia and carbonic acid. Bacterial urease activity is associated with complications[18] including:

• Urinary stone formation
• Urinary catheter encrustation or blocking
• Hyperammonemia
• Pyelonephritis

Organisms marked “yes” in this section may be considered a risk for such complications.

*This information was compiled according to the Biocyc Database of genomes [16] and the Bacterial Diversity Database of Analytical Profile Index (API) test results.[17]

Biofilm Formation

Biofilms frequently form on urinary catheters and other indwelling medical devices. They often involve multiple bacteria and/or yeasts. Organisms in these polymicrobial biofilms cooperate to increase growth and antimicrobial resistance.[19]

Pathogenicity

Clinically relevant, potentially disease-causing microorganisms present within human tissues can generally be classified into 3 pathogenicity categories [14]:

1. “Pathogen” (causes disease when present in host tissue)
2. “Colonizer” (resides in host tissues and may or may not cause disease)
3. “Pathobiont” (resides in host tissues and generally benefits the host, but may cause disease under certain conditions)

Clinical Relevance in UTI

This section summarizes the role of the microorganism in urinary tract infections.  The evidence in this section comes from peer-reviewed publications.

Treatment

Evidence of Efficacy (Checkmarks):
This section lists which antibiotics from the Guidance® UTI test can be effective for treating the organism.  These recommendations appear as checkmarks on Guidance UTI result reports.

Sources are 1) the Clinical and Laboratory Standards Institute (CLSI),[20] and 2) the United States Food and Drug Administration (FDA)[21]:

• M100: Performance Standards for Antimicrobial Susceptibility Testing,
• M43-A: Methods for Antimicrobial Susceptibility Testing for Human Mycoplasmas, 1st Edition (corrected 2015)
• M45: Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria, 3rd Edition (corrected 2017)
• M27M44S: Performance Standards for Antifungal Susceptibility Testing of Yeasts, 3rd Edition (2022)

The CLSI and FDA guidance documents do not provide guidance for the treatment of A. schaalii,    A. omnicolens, or G. vaginalis. Instead, primary peer-reviewed literature references are provided.