Escherichia coli and UTI: Risk Factors, Diagnostic Testing, and Treatment Options

What is Escherichia coli?

Escherichia coli, generally referred to as E. coli, is a type of bacteria that is the most common cause of urinary tract infections, accounting for approximately 80–90% of UTIs¹. It is a Gram-negative bacterium that can be found in the human intestinal tract as a commensal species of the microbiome, meaning that it typically doesn’t cause harm. There are also strains of E. coli that can be found in livestock or in the environment. These strains don’t always find their way into humans.

When an E. coli strain causes a urinary tract infection, it is considered uropathogenic E. coli (UPEC). These strains may have certain traits that other strains do not, which can make them particularly good at causing UTIs. These traits, called virulence factors, are biological “tools” that help the bacteria attach to the bladder wall, evade the immune system, and cause infection.

Common virulence factors in UPEC¹:

What causes an E. coli UTI?

When E. coli is in urine, it most often finds its way to the urinary tract by migrating from the gastrointestinal tract to the urethra to ascend to the bladder. Once there, the bacteria multiply and cause infection. While anyone can get a UTI caused by E. coli, there are certain factors known to increase a person’s risk.

• Female anatomy: People assigned female at birth have a shorter urethra that sits closer to the perianal region, which provides a shorter path for E. coli from the gut to reach the bladder. This is a major reason why women are much more likely to get a UTI as compared to men.
• Sexual activity: Sexual activity increases the risk of getting a UTI because of the potential for different bacteria to be introduced into the urinary tract. Certain sexual practices or behaviors can increase the risk of infection, such as using spermicide or diaphragms, anal intercourse, and more.
• Age: Both younger children as well as older adults are at higher risk of UPEC. Older adults (usually 60+) are specifically at a higher risk for infections caused by biofilm-forming E. coli².
• History of UTIs: A history of UTIs is one of the strongest predictors of recurrence. Most recurrences involve the same E. coli strain that persists in the gut.
• Other factors: Diabetes, catheter use, pregnancy, peri/post-menopause, structural or functional issues of the urinary tract, and hospitalization among others can also increase your risk of getting an E. coli UTI.

Risks and Complications

As one of the most common causes of UTIs, the distinct risks and complications that come with uropathogenic E. coli strains have received a large amount of research attention. The most important are outlined here.

E. coli Biofilms

E. coli is one of the many bacteria that can create biofilms, a type of covering that protects the bacteria from the host’s immune system and antibiotics while also helping the bacteria persist in the urinary tract. Structured communities of E. coli stick to surfaces and wrap themselves in a “slimy” covering called an extracellular matrix. This matrix shields the bacteria, making them up to 1,000 times more resistant to antibiotics and immune defenses than free-floating cells. A 2026 study found that 43.2% of E. coli isolates from UTI patients were biofilm producers². It is thought that biofilms can play a role in recurrent UTIs.

E. coli and intracellular bacterial communities (IBCs)

E. coli may also form what are called intracellular bacterial communities (IBCs). UPEC strains form IBCs by invading the cells that line the urinary tract, aggregating into a biofilm-like pod that can contain thousands of organisms. Because they are inside the human cells, the immune system doesn’t find the bacteria, allowing them to persist. Antibiotics have more difficulty reaching the necessary concentration inside of the cells of the urinary tract to be effective against IBCs – providing the bacteria protection from antibiotics outside of antibiotic resistance.

If the bacteria reach deeper cells making up the lining of the urinary tract, they may establish quiescent intracellular reservoirs (QIRs). QIRs are essentially dormant IBCs, meaning that the bacteria are not actively multiplying. As these deeper cells mature and become the new lining of the urinary tract, the QIRs may reactivate and form IBCs. When the human cells containing the IBCs are damaged or naturally sloughed off as they die, the bacteria that had been living in the cell are released into the urine where they can begin the cycle anew. This is another major reason as to why a person may experience recurrent, persistent, or chronic UTIs caused by E. coli. Advanced molecular diagnostic tests, like the BIOTIA-ID Urine Test, can provide strain-level identification of E. coli to help inform your provider about the likelihood that IBCs may be at play.

Antibiotic resistance and E. coli

E. coli is treated with antibiotics because it is a type of bacteria. However, not all antibiotics may work to treat all strains of E. coli. Studies show high resistance rates to common, older antibiotics like ampicillin and trimethoprim-sulfamethoxazole, especially among biofilm-forming strains³. This means that if you are prescribed one of these medications and your UTI is caused by a resistant E. coli strain, the medication may not work.

Extended-spectrum beta-lactamase (ESBL)-producing E. coli strains are a growing concern. Extended-spectrum beta-lactamases are a type of enzyme that inactivate penicillins, cephalosporins, and aztreonam before they can act. The genes for these enzymes often live on mobile plasmids which can be shared between different E. coli strains and other species of bacteria. ESBL strains of E. coli often carry co-resistance for fluoroquinolones and trimethoprim-sulfamethoxazole, narrowing treatment to last-resort antibiotics.

If you've been placed on an antibiotic and are still experiencing symptoms or your symptoms quickly return after stopping, it is worth talking to your provider about recurrent UTIs.

Urosepsis and E. coli

In rare cases, an E. coli UTI can spread to the bloodstream, causing a life-threatening condition called urosepsis. Researchers are actively studying the genetic and protein markers that make certain E. coli strains more likely to cause severe infections³. This research may one day help doctors identify high-risk UPEC strains earlier allowing for more aggressive treatment.

How is E. coli detected in urine?

There are several ways to determine whether a UTI is caused by E. coli, but not all of them are the same. For certain patients, especially those who experience recurrent UTIs or at risk of complications from UTIs, the type of test used may matter.

Urine culture

E. coli is most often diagnosed through standard urine culture. Your urine sample is placed on a petri dish in the lab and observed for several days. If E. coli is present in the urine, it will grow into visible colonies and be confirmed through additional testing. However, standard urine culture fails to identify E. coli in 20-30% of cases, particularly when there is low bacterial count in the urine⁴. This is called a culture-negative E. coli UTI, which should be confirmed by another diagnostic testing method such as PCR or next-generation sequencing.

Depending on what type of testing your provider ordered and/or the practices of the specific laboratory your sample was sent to, another type of test may be run if E. coli colonies grew in urine culture. Called antimicrobial susceptibility testing, the colonies that grew on the plate will be grown in the presence of different antibiotics to determine which ones may work against the specific strain causing your symptoms. Results are reported as Susceptible (S), Intermediate (I), or Resistant (R). This guides your provider in choosing the safest and most effective antibiotic for your infection.

PCR

Another diagnostic test that can detect E. coli is polymerase chain reaction, more commonly known as PCR. This test looks for a specific fragment of DNA that is unique to E. coli. These tests are highly sensitive, meaning very little DNA is required to be in a sample to return a positive result. Because of this, contamination can be a concern. Always ensure you follow proper sample collection instructions.

Next-generation sequencing for UTIs

Next-generation sequencing (NGS) is another type of test that can be used to diagnose UPEC. Biotia specializes in a more comprehensive form of next-generation sequencing called clinical metagenomics. This test type looks at all of the DNA present in a urine sample instead of just a particular fragment. This allows for strain-level detection of bacteria and fungi, providing insight into important traits about the organisms such as whether it is likely to form biofilms and IBCs or may be resistant to certain antibiotics.

The BIOTIA-ID Urine Test detects E. coli and 43 other pathogens known to cause UTIs as well as a broad panel of antimicrobial resistance markers. While standard urine culture is sufficient for a good portion of E. coli UTIs, if you continually get E. coli UTIs, frequently receive negative urine culture results but are still experiencing UTI symptoms, or are at risk of complications due to underlying medical conditions, testing with Biotia may provide a more accurate diagnosis and help your provider select which treatment might work best.

How is an E. coli UTI treated?

An E. coli UTI, like other bacterial infections, is treated with antibiotics. Your provider will use the results of your test(s) to choose a medication that is most likely to be effective. They will also take into consideration your current symptoms, medical history, as well as local resistance rates to determine the best treatment option. Not just any antibiotic will work which highlights the importance of getting an understanding of both what is causing your UTI as well as if antibiotic resistance is at play.

Common antibiotics that may be prescribed to treat a UTI caused by uropathogenic E. coli include²:

• Ciprofloxacin or other fluoroquinolones
• Nitrofurantoin (Macrobid)
• Trimethoprim-sulfamethoxazole (Bactrim)
• Fosfomycin (a single-dose option)

UTIs caused by ESBL-producing E. coli may require last-resort antibiotic choices, like carbapenems. Carbapenems, a class of broad-spectrum antibiotics, previously had to be administered intravenously. In 2026, the U.S. Food and Drug Administration approved a new drug called Utebzi, the first ever oral carbapenem therapy in the United States. This new approval will reduce barriers for patients with antibiotic resistant infections, including those with UTIs.

Important: Make sure to take the full course of antibiotics exactly as prescribed, even if you start feeling better. Stopping early can allow surviving bacteria to multiply and potentially develop resistance. Additionally, do not take antibiotics that were prescribed for a different illness.

The bottom line

UTIs caused by Escherichia coli are the most common type of urinary tract infection. E. coli can also form biofilms, which protect bacteria from the immune system and antibiotics. Separately, there are E. coli strains that are known to be resistant to certain antibiotics. While standard diagnostics tend to accurately identify E. coli, advanced diagnostic testing may help people experiencing recurrent, persistent, or chronic UTI symptoms or who may be at high-risk of complications from getting a UTI. If you’re unsure whether advanced diagnostic testing may be right for you, contact your healthcare provider or meet with a UTI-specialized provider from our telehealth partner Clinova Solutions.