There are only a few intravenous antibiotic options to treat the superbug-related infections.
Scientists have found that superbugs - antibiotic-resistant bacteria - can make it more difficult to treat a common but severe kidney infection.
Pyelonephritis - infection of the kidney usually caused by E coli bacteria and which can start as a urinary tract infection - causes fever, back pain and vomiting.
About half of people infected require hospitalisation, researchers said. If not treated with effective antibiotics, it can cause sepsis and death.
In the study by University of California, Los Angeles (UCLA), based on data from 10 large hospital emergency departments in the US, almost 12 per cent of people diagnosed with pyelonephritis had infections resistant to the standard class of antibiotic used in treatment - fluoroquinolone.
That is up from 4 per cent in a similar study conducted a decade ago. In some cities, and among some people with certain risk factors - such as international travel or recent hospitalisation or treatment with an antibiotic -fluoroquinolone resistance rates exceeded 20 per cent.
The study documents the emergence of infections caused by a specific strain of E coli that is resistant to additional types of antibiotics, severely limiting treatment options.
That strain, dubbed ESBL (extended-spectrum beta-lactamases) for the antibiotic-destroying enzymes it produces, was not detected in the previous study.
The enzymes were first detected in 1979 and are most often found in developing nations.
Currently, there are only a few intravenous antibiotic options to treat ESBL-related infections, and no oral antibiotics that are consistently effective.
"This is a very real example of the threat posed by the emergence of new antibiotic-resistant strains of bacteria, which greatly complicates treatment of infection," said David Talan, professor at UCLA.
The study included 453 people diagnosed with kidney infection.
Participants were diagnosed between July 2013 and December 2014 in 10 emergency departments at large hospitals.
Researchers found that the rates of ESBL-related infections varied from 0 per cent to more than 20 per cent, depending on the location of the emergency room and patient risk factors.
About one in three people infected with ESBL-producing E coli had no traditional risk factors for antibiotic resistance, suggesting the bacterial strain is now endemic in the US and healthy people are also at risk, researchers said.
About three of every four people infected with ESBL-producing E coli were initially treated with antibiotics ineffective against that particular strain of bacteria, placing them at risk for poor outcomes.
The study was published in the journal of Emerging Infectious Diseases.