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. If not treated with effective antibiotics, it can cause sepsis and death, researchers said.
In the study led by researchers at University of California, Los Angeles (UCLA) based on data from 10 large hospital emergency departments around the US, almost 12 per cent of people diagnosed with pyelonephritis had infections resistant to the standard class of antibiotic used in treatment - fluoroquinolone.
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.
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The study also documented 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 for the antibiotic-destroying enzymes it produces (extended-spectrum beta-lactamases), was not detected in the previous study.
The enzymes were first detected in 1979 and are most often found in developing nations, researchers said.
"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 Dr David Talan, the study's lead author.
The study included 453 people diagnosed with kidney infection. The participants were diagnosed between July 2013 and December 2014 in 10 emergency departments at large hospitals.
Talan and his colleagues recommended the development of new medications and new guidelines calling for treatment with different types and combinations of antibiotics
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