Bacteria that cause UTI are divided into two main classes: gram-negative and gram-positive bacteria.

Gram-negative bacteria have an outer cell membrane while gram-positive bacteria don’t. A simple test with a violet color dye (called gram stain) is used to determine the type of the bacteria when looked at under a microscope. The bacteria with a membrane repel the gram stain and remain pink, and therefore are called gram-negative. On the other hand, gram-positive bacteria are lacking the membrane, and therefore easily accumulate the dye under the microscope, and appear violet.

This membrane is what makes it harder to treat infections caused by gram-negative bacteria. On top of it, the gram-negative bacteria also share an increased resistance to antibiotics and are more toxic to the host than gram-positive bacteria

Some examples of gram-negative bacteria that cause urinary tract infections include:

• Escherichia coli (or E. coli)–cause most uncomplicated cystitis and pyelonephritis cases.
• Klebsiella pneumonia–notorious for causing bloodstream infections.
• Pseudomonas aeruginosa–cause hospital-acquired UTIs that also could lead to dangerous sepsis.

A subgroup of gram-negative bacteria that produce extended-spectrum beta-lactamases (ESBL) enzymes deserves special mention. This enzyme allows the bacteria to resist most beta-lactam antibiotics, including penicillins, cephalosporins, and the monobactam aztreonam. Unfortunately, infections with ESBL-producing organisms are very hard to treat. The most common ESBL-producing bacteria are some strains of E. coli and Klebsiella pneumoniae. Patients in hospitals or nursing home settings are at an increased risk to contract an ESBL-producing bacteria.

Some examples of gram-positive bacteria causing UTI are:

• Staphylococcus saprophyticus (S. saprophyticus)
• Group B Streptococcus (GBS)
• Aerococcus
• Enterococcus

Who gets what bacteria?

When examining UTI bacteria types, we need to keep in mind that different patients (kids, young women, pregnant females, males, or the elderly) are unequally susceptible to different bacteria types.  Also, depending on how you acquired your UTI (for example due to bladder stones or a catheter in a hospital setting) will determine which bacteria are most likely to be at fault. Moreover, in certain settings, the urinary tract can be infected by multiple bugs at the same time — referred to as “polymicrobial infection” in the medical world. Moreover, some bacteria might colonize a bladder without even causing a UTI.

E. coli UTI

The commonest bacteria isolated from the urinary tract of 75%- 80% of young, sexually active, non-pregnant women with an uncomplicated UTI are E. coli bacteria. This is a gram-negative bacterium prone to developing resistance to antibiotics.  

E. coli presides in abundance in our lower intestines and therefore could be found in human excrements. While E. coli are harmless and even helpful (they participate in the production of vitamin K) in your intestines, they could be extremely dangerous when misplaced.

Unfortunately, it’s relatively easy for E.coli to ascend from your anus upward in the direction of your vagina and urethra to cause a UTI. That’s why we also call  E.coli an opportunistic bacteria.

Opportunistic bacteria take advantage of an opportunity that is not normally available, such as a host with a weakened immune system or an altered microbiota (for example, a disrupted gut or vaginal microbiota) and rapidly grow in those circumstances.

Therefore, if your gut or vaginal flora are in a state of imbalance, you’ll be more susceptible to an attack by an opportunistic bacteria. On the other hand, when your microbiome is in a state of healthy balance, the bacteria won’t have a chance for uncontrolled growth.

Proteus mirabilis

Proteus mirabilis is a gram-negative bacterium and favors patients with long-term catheters. Catheter-associated urinary tract infections (CAUTI) caused by Proteus mirabilis are very difficult to treat due to their ability to form biofilms and develop drug resistance. When a catheter is inserted, it could damage the mucosal layer of the urethra, which disrupts the natural barrier and allows bacterial colonization. Moreover, the catheter tube is like a highway for bacteria that makes it easier for them to enter the bladder as well as establish their biofilm colonies on its surface.

Besides typical UTI, this bacteria could also cause a dangerous, symptom-less bacteriuria, especially in the elderly and in patients with type-2 diabetes, which could lead to life-threatening urosepsis. Additionally, P. mirabilis infections can cause the formation of urinary stones (urolithiasis).

P.mirabilis are often found in the gastrointestinal tract but we still don’t know much about the role of this bacterium in the gut microbiome. It is also not clear if P.mirabilis make their way to the urinary tract by ascending from the gastrointestinal tract. In fact, some clinical studies point out that this infection could be transmitted from person-to-person, especially in a hospital setting. This is supported by evidence that some patients with P. mirabilis UTI have the same strain of P. mirabilis in their stool, while others have no P. mirabilis in their stools.

Pseudomonas aeruginosa

P. aeruginosa is a gram-negative bacterium and is one of the organisms most commonly responsible for catheter-associated UTIs and infections in immuno-suppressed patients. At the same time, P. aeruginosa is one of the least researched bacteria, meaning that hospitals lack an understanding of how to prevent and treat infections caused by these organisms. Unfortunately, P. aeruginosa UTIs are notoriously hard to treat. Not only does this bacterium possess a variety of virulent mechanisms helping it to spread and withstand antibiotics, but it also quickly forms biofilms on the surface of catheters further avoiding antibiotic attacks.

Klebsiella pneumoniae

Klebsiella pneumoniae (K. pneumoniae) is particularly known to cause UTI and sepsis in newborns as well as hospital-acquired urinary tract infections in adults. This gram-negative bacterium is also notorious for developing antibiotic resistance, including to carbapenem antibiotics.

K. pneumoniae bacteria naturally reside in humans, but the rate at which these bacteria are found depends on a variety of factors. For example, carrier rates of K. pneumoniae in the community are significantly higher in certain parts of the world, as well as in a hospital setting. Specifically, patients of Asian ethnicity have an increased risk for intestinal colonization with this bacterium. Some studies estimate stool carrier rates of K. pneumoniae in healthy adults range from 19% in Japan to 88% in Malaysia.

Staphylococcus saprophyticus

Staphylococcus saprophyticus (or S. saprophyticus) cause 10-15% of UTI cases and are gram-positive bacteria. About 40% of S. saprophyticus UTIs occur in young, sexually-active women.

S. saprophyticus shares many clinical features of urinary tract infection caused by Escherichia coli, but this bacteria have some very unusual characteristics.  For example, they are normally found in the urinary tract of predominantly girls and young women during late summer and early fall seasons. Post-menopausal women are rarely diagnosed with a UTI caused by this bacterium, and this bacteria decreases its appearance in winter and spring.

While S. saprophyticus infection is rare in males, it could affect elderly or hospitalized men.

On the bright side, S. saprophyticus UTI is less likely to cause bacteremia (blood infection) and is generally susceptible to most antibiotics, including penicillin.

Staphylococcus aureus

Unlike S. saprophyticus, S. aureus UTI usually affects individuals with a urinary catheter and pregnant women. In addition, the majority of S. aureus superstrains are resistant to Methicillin.

Enterococci

Enterococci are Gram-positive, lactic acid bacteria that can survive and grow with or without oxygen as well as bear temperatures ranging from 10–45°C and pH of 4.6 to 9. A urinary catheter is a major risk factor with enterococci accounting for about 15 to 30% of CAUTIs. Enterococci are also the third leading cause of UTIs acquired in hospital settings.

The poor immunity and incomplete bladder emptying in diabetics also increase the risk for enterococcal UTIs. These bacteria can spread to the bloodstream as well as contribute to prostate inflammation in about 10% of diabetic men.

Unfortunately, Enterococcal superstrains are becoming more and more resistant to antibiotics. In particular, E. faecalis forms resilient biofilms, making it notoriously difficult for the antibiotics to penetrate these films and kill the superbug.

Urinary Tract Infection caused by Group B Streptococcus

Group B Streptococcus (GBS) is a Gram-positive chain-forming bacterium that commonly dwells in the lower gut and female reproductive tract without causing any symptoms. Statistics show that the bug causes only about 1–2% of all UTIs.

Advanced age and pregnancy are the main risk factors for contracting a UTI caused by this organism. In fact, GBS UTIs can be fatal in the elderly population. Those with poor immunity–such as in those suffering from cancer and diabetes, and pre-existing abnormalities of the urinary tract such as chronic kidney disease or stones in the kidneys–are subject to additional risk factors for contracting a GBS UTI.

When it comes to pregnancy, although GBS often doesn’t cause any symptoms in women, its presence in urine and/or the vagina can pose serious threats for both the mother and the child. Most importantly, if there is a transfer of GBS from the mother to the baby during labor and delivery, the infection could spread to the child ’s bloodstream, which can be life-threatening. Given the high risk of GBS complications in the baby, the Centers for Disease Control recommend universal screening of all females at 35-37 weeks of pregnancy. If a woman tests positive for GBS, preventive IV antibiotics are recommended during labor and delivery.

UTI caused by multiple disease-causing bacteria  (Polymicrobial UTI)

A polymicrobial UTI is an infection caused by more than one bacteria type. Polymicrobial UTIs are often hospital-acquired and more frequently associated with urinary catheters. Pseudomonas aeruginosa is more often associated with polymicrobial than with monomicrobial infections, whereas Escherichia coli is more common in monomicrobial infections.

Groups at risk:

• The elderly
• Immune-compromised people, such as those with cancer, diabetes, or infected with HIV
• Those with indwelling catheters

Other Rare, Emerging UTI Bugs

• Aerococcus: a gram-positive cluster-forming bug that can cause life-threatening bladder, kidney, and blood infection if not addressed promptly.
• Corynebacterium urealyticum: a gram-positive bacterium that causes long-standing inflammation of the bladder and kidneys along with the formation of giant kidney stones.
• Actinobaculum schaalii: Possibly a gram-positive bug, resistant to first-line antibiotics used for treating UTI.
• Gardnerella vaginalis: Found in women with BV, can infect the bladder and kidneys.

Different tests for different bacteria

What tests can be helpful if infected?

The initial test to screen for a UTI in clinical practice is a urine dipstick. The dipstick testing uses chemical strips to detect the presence of compounds named nitrites, or an enzyme called leukocyte esterase (LE) in a clean-catch urine sample. Both are potential pointers of UTI. LE reveals white blood cells in the urine, which are a likely indicator of UTI.

If the dipstick testing is positive, the doctors may then order a urine culture to confirm the results. In practice, a urine culture is usually done in women suspected of having a complicated UTI or in whom the initial treatment has failed. Urine culture is, however, the benchmark test that identifies all types of UTIs. So, why is the dipstick test not regarded as the gold standard for diagnosing a UTI?

The Pitfalls of Urine Dipstick

Although clinicians most often use urine dipstick to screen for a UTI initially, the test has certain drawbacks. For instance, this test can miss UTIs in pregnant women and the elderly. In fact, during pregnancy, the diagnosis of UTI doesn’t rely on finding nitrites or pus cells. But urine is labeled as containing evidence of “UTI” if a clean-catch sample shows 105 bacteria per milliliters of urine.

In addition, the urine of the elderly is most likely to be infected by gram-positive bugs that lack the capability of converting nitrates to nitrites or testing positive for LE. Thus, nitrite and LE tests fall short of picking up all kinds of bacteria.

The Drawbacks of Urine Culture

It might be surprising to know that although considered a gold standard, even the urine culture may be falsely negative in up to 20% of women who have classic symptoms of UTI. In these cases, culture-independent tests that rely on molecular methods may be effective at identifying bacteria that will grow only in the presence of certain nutrients.