Klebsiella pneumoniae and UTI: Causes, Testing, and Treatment

What is Klebsiella pneumoniae?

Klebsiella pneumoniae is a bacterium that can cause infections in different parts of the body. According to Bray and Zafar, K. pneumoniae is commonly found in the gut microbiomes of humans and animals, where it is typically harmless, and roughly one in six healthy adults carries it in the gut¹. Podschun and colleagues also found it in the environment, including soil, surface water, and plants². CDC surveillance identifies it as the second most common cause of catheter-associated urinary tract infections in hospitals, after Escherichia coli³.

K. pneumoniae belongs to the Enterobacterales, a large group of gram-negative bacteria that also includes E. coli. It is rod-shaped and can grow with or without oxygen. The StatPearls clinical review notes that it cannot move on its own, lacking the whip-like tails many gut bacteria use to swim⁴. It is also wrapped in a thick outer coating called a capsule⁵.

What causes a Klebsiella pneumoniae UTI?

Klebsiella pneumoniae commonly lives in the gastrointestinal tract, which can serve as a reservoir for infection of the urinary tract¹⁴. The bacteria can be introduced in different ways, but one way is that it travels from the perianal region to the urethra and then moves up to the bladder, one of the routes taken by other UTI-causing bacteria. Once in the urinary tract, features including the capsule and fimbriae help the bacteria evade the immune system and attach to the cells lining the bladder, as described by Flores-Mireles and colleagues⁶. Certain people are at higher risk of a UTI caused byK. pneumoniae than others.

• Medical devices: People who use urinary medical devices, such as urinary catheters, ureteral stents, and nephrostomy tubes, have a higher risk of a UTI caused by K. pneumoniae. These devices bypass the body's normal defenses and give bacteria a surface to attach to and travel along. Tambyah and colleagues describe how bacteria can reach the bladder along the outside of the catheter, from the skin around the urethra, or through the inside of the tubing⁷.
• Healthcare and hospital exposure: K. pneumoniae is a leading cause of nosocomial, or hospital-acquired, infections. Spending time in a hospital or a long-term care facility increases the chance someone may be exposed to the bacteria⁴⁸.
• Prior antibiotic use: Antibiotic use, particularly broad-spectrum antibiotics, can disrupt the body's microbiome by reducing protective bacteria. This allows potentially harmful bacteria likeK. pneumoniae to overgrow⁴⁸.
• Other factors: As with UTIs caused by other bacteria, older age, female sex, immunocompromising conditions, diabetes, sexual activity, and structural or functional abnormalities of the urinary tract can increase the risk of a K. pneumoniae UTI⁶⁸.

Risks and complications of K. pneumoniae

K. pneumoniae UTIs carry certain risks and may cause complications, especially in people with multiple underlying medical conditions. This is due to a set of features that help it invade the urinary tract, evade the immune system, and establish infection.

Polysaccharide capsule

The capsule is the bacterium's most important tool for causing infection⁴. Because it encases the bacterium, the capsule blocks immune cells from detecting and destroying it. It also acts as a decoy for the body's natural antibacterial proteins, binding them so that fewer reach the bacterial surface⁵.

Fimbriae

Klebsiella pneumoniae also has fimbriae and adhesins. Fimbriae are short, hair-like appendages that extend from the bacterial surface through the capsule. At the tip of each fimbria is an adhesin, which determines what part of the host cell the bacterium attaches to⁵. Fimbriae and adhesins also let K. pneumoniae stick to non-living surfaces such as catheter material. That attachment is the first step in biofilm formation: once anchored, the bacteria multiply, stick to one another, and produce a protective layer around the growing community⁹.

Biofilms

Klebsiella pneumoniae is known to form biofilms: communities of bacteria attached to a surface and encased in a self-produced, slime-like layer. The layer blocks immune cells and reduces the amount of antibiotic able to reach the bacteria. This helps the bacteria survive even when the right antibiotic is taken, which can lead to relapse after treatment ends. Guerra and colleagues explain that biofilms matter especially in infections involving medical devices, including urinary catheters, where bacteria that attach and persist can be harder to clear⁹.

Antibiotic resistance and K. pneumoniae

Antibiotic resistance is a major concern with K. pneumoniae because some strains produce enzymes, or develop other mechanisms, that make commonly used antibiotics less effective. For example, ESBL-producing strains can resist many penicillins and cephalosporins, while carbapenem-resistant strains may also resist the carbapenems normally reserved for more difficult infections. This narrows treatment options and makes infections harder to treat, as detailed in the IDSA treatment guidance and a review by Castanheira and colleagues¹⁰¹¹.

Some of K. pneumoniae's resistance is not acquired at all; it is built into the species. EUCAST lists essentially all K. pneumoniae as naturally resistant to ampicillin and amoxicillin¹². This is one reason a K. pneumoniae UTI cannot be treated the same way as a UTI caused by E. coli, the most common cause of UTIs.

ESBL-producing Klebsiella pneumoniae

ESBL stands for extended-spectrum beta-lactamase. Beta-lactamases are enzymes that bacteria produce to break down beta-lactam antibiotics, the family that includes penicillins and cephalosporins. Ordinary beta-lactamases inactivate a narrow set of these drugs. Extended-spectrum beta-lactamases inactivate a much wider range, including many newer cephalosporins. Importantly, ESBLs do not break down carbapenems, which is why carbapenems remain reliable against ESBL-producing strains and are held in reserve for serious infections¹¹.

ESBL genes are typically carried on plasmids, mobile pieces of DNA that bacteria can pass to one another, which is part of why ESBL-producing bacteria spread efficiently in healthcare settings¹¹.

For a patient, an “ESBL-positive” result on a urine culture means the Klebsiella causing the infection is likely to be resistant not just to one antibiotic but to a whole family of them. It does not necessarily mean the infection is untreatable. It does mean that several commonly prescribed oral antibiotics are off the table and that treating the infection may require intravenous antibiotics if it has moved beyond the bladder¹⁰.

K. pneumoniae and urosepsis

UTIs caused by K. pneumoniae can become more serious when the infection extends beyond the bladder into the kidneys, or when bacteria enter the bloodstream. If the body's response to the infection becomes severe enough to affect how other organs work, the result is urosepsis, a life-threatening condition that requires immediate medical care. In these cases, accurate identification of the bacteria causing the infection, along with its resistance profile, is essential to selecting the right intravenous antibiotic.

How is Klebsiella pneumoniae detected?

Standard urine culture

Standard urine culture remains one of the most used methods for diagnosing bacterial UTIs. A urine sample is placed onto a petri dish with specific nutrients and incubated to see if any bacteria form colonies. If there is growth, laboratory identification methods can determine the species, and antimicrobial susceptibility testing can help determine which antibiotics are likely to be effective.

Although urine culture is useful for identifying live bacteria and performing susceptibility testing, it has limitations. A systematic review by Szlachta-McGinn and colleagues found that conventional culture may detect fewer organisms than molecular methods and can be less sensitive for identifying bacteria present in urine samples, particularly when multiple organisms are present¹³.

PCR

Polymerase chain reaction, or PCR, works by making millions of copies of a DNA sequence specific to a given pathogen, so that even small amounts become detectable. Because it looks for pathogen DNA, PCR can identify organisms included in the test panel quickly, without requiring bacterial growth. K. pneumoniae is often included on PCR panels.

PCR is a targeted method: it can only detect pathogens and resistance markers it was specifically designed to identify, so anything outside the panel will not appear in the results¹³. Some panels also look for antibiotic resistance genes, though those results require careful interpretation. Washington State Department of Health guidance notes that PCR panels usually cannot tell which organism a detected resistance gene came from, a recognized limitation when more than one organism is present¹⁴.

Next-generation sequencing for UTI

Next-generation sequencing (NGS) can analyze microbial DNA directly from a urine sample without requiring the organisms to grow in culture first. Two types are commonly used in infectious disease diagnostics: 16S rRNA sequencing and clinical metagenomic sequencing.

16S rRNA sequencing is a targeted method: it reads one bacterial gene, so it detects bacteria but not fungi or viruses. Most 16S tests read only short segments of that gene, which makes species-level identification difficult and provides no information on antimicrobial resistance.

Clinical metagenomic sequencing, also called shotgun metagenomic sequencing, reads all the genetic material in a sample rather than one gene. A DNA-based metagenomic test can detect bacteria, fungi, parasites, and DNA viruses. Because it reads whole genomes rather than a single marker gene, it generally identifies organisms to the species level and sometimes to the strain level.

Because shotgun metagenomic sequencing can detect a broad range of microorganisms at the same time, it can identify organisms that are difficult to detect in urine culture. This makes it particularly useful in complex or polymicrobial UTIs, which are more common in hospital settings and among patients using urinary medical devices.

Because clinical metagenomic testing reads all of the microbial DNA in a sample rather than selected regions, it can also report which antimicrobial resistance genes are present. With this additional information, a provider can make a more informed decision about which antibiotic treatment may work for a patient's specific infection.

The BIOTIA-ID Urine Test

Biotia's UTI test, the BIOTIA-ID Urine Test, uses clinical metagenomics to identify 44 key UTI-causing bacterial and fungal pathogens, includingKlebsiella pneumoniae. It also reports antimicrobial resistance genes, including the ESBL and carbapenemase genes most relevant to K. pneumoniae. Resistance results should always be interpreted by a healthcare professional in the context of the patient's clinical picture.

The BIOTIA-ID Urine Test is available for patients and providers across the United States for both at-home and in-person collection. For patients accessing the test through Biotia's test-to-treat service, they will have the opportunity to connect with a UTI specialist from Clinova Solutions, Biotia's telehealth partner.

How do you treat K. pneumoniae in urine?

Treatment of a K. pneumoniae UTI depends on the location and severity of the infection, the patient's previous antibiotic exposure, and the bacteria's resistance profile. Treatment may differ between uncomplicated bladder infections and more serious infections such as pyelonephritis or complicated UTIs. For strains that are mostly susceptible to antibiotics, several options may be considered depending on the site of infection. Importantly, IDSA guidance recommends using antibiotic susceptibility testing or resistance profiling to tailor treatment decisions¹⁰.

When an ESBL-producing strain is identified, treatment depends on whether the infection is classified as uncomplicated cystitis, complicated cystitis, or pyelonephritis. Some oral antibiotics may be appropriate for uncomplicated infections, while carbapenems administered intravenously and other agents may be considered for more serious infections, depending on susceptibility results and the patient's clinical condition¹⁰.

Treatment becomes more challenging when a UTI is caused by carbapenem-resistant Klebsiella pneumoniae. These strains are typically resistant to most classes of antibiotics. Treatment depends on the specific resistance mechanisms present, including the type of carbapenemase produced. Newer beta-lactam/beta-lactamase inhibitor combinations and other targeted antibiotics may be used depending on the resistance profile¹⁰. Because K. pneumoniae can carry more than one resistance mechanism, identifying both the organism and its resistance profile can help clinicians select antibiotics that are more likely to be effective.

The bottom line

Klebsiella pneumoniae is an important cause of complicated and healthcare-associated UTIs. Its ability to attach to host cells and medical devices, form biofilms, evade immune defenses, and acquire antibiotic resistance can make these infections harder to treat than UTIs caused by other pathogens.

Standard urine culture remains widely used for detecting K. pneumoniae and performing antimicrobial susceptibility testing in routine cases. For people experiencing recurrent, complicated, device-associated, or hospital-associated UTIs, clinical metagenomic tests can provide additional information about which organisms are present and profile antimicrobial resistance to help inform optimal treatment.

Bacteria found in urine without symptoms may represent asymptomatic bacteriuria, which the IDSA guideline says should be interpreted in clinical context rather than treated automatically¹⁵.