Nose swabs reveal bacteria that cause ear infections, helping to target treatments

• Amoxicillin is the right medication for more than 94 percent of children with ear infections.

• A rapid nasal diagnostic test may reduce unnecessary antibiotic use while individualizing care for ear infections.

• COVID-19 infections can occur at the same time as ear infections.

Dr. Holly Frost often wondered if the antibiotics she prescribed the children she treated for ear infections were effective, or even called for.

Now well into her research that seeks to improve the clinical care of young children with acute otitis media (ear infections), the pediatrician is confident she is zeroing in on the answers.

Her study is revealing that the popular childhood medication amoxicillin does work best for most ear infections, that nasal swabs that can be done in any doctor’s office can indicate which of three common bacteria is causing the ear infection, and that the COVID-19 coronavirus can be present at the same time as an ear infection.

All this is helpful because ear infections are the most common childhood infection requiring antibiotics. More than 8.7 million children in the United States get ear infections annually, and more than 60 percent of all children can expect to have the bothersome illness by the time they are 3 years old.

The number of antibiotic prescriptions to treat these infections – more than 10 million annually – is staggering, Dr. Frost said. And nearly a quarter of children will have three or more ear infections by age 3.

Yet today’s standard treatment for ear infections has been in place for decades and many children – up to 40% – are receiving broad-spectrum antibiotics that are associated with higher rates of side effects she said.

In her prospective, longitudinal study of 300 children, Dr. Frost is examining how often amoxicillin fails to clear up ear infections in children ages 6-34 months old, and whether nose swabs using rapid diagnostic tests correlate to how children do with treatment. She also wondered whether COVID-19 and ear infections might be present at the same time.

“Three bacteria are behind most ear infections: S. pneumoniae, H. influenzae, and M. catarrhalis. The need for an antibiotic, and the optimal antibiotic, differs by the bacteria,” Dr. Frost said. And while 85 percent of ear infections will go away without an antibiotic, 95 percent of children are given a prescription, according to the study. Many times, these are broad-spectrum antibiotics that act against a wide range of disease-causing bacteria.

There are consequences of children receiving too many or the wrong antibiotics, Dr. Frost noted, including later antibiotic resistance, adverse drug events, developing chronic diseases later in life, and diarrhea infections, as well as the costs of the medications.

The preliminary study data suggest that amoxicillin works for nearly 95 percent of children with ear infections, with no need for broader-spectrum antibiotics.

“The failure rate when using amoxicillin and the recurrent rate of infection is very low,” Dr. Frost said. “If, for example, we prescribe amoxicillin, but the bacteria is not typical for that treatment, it probably doesn’t matter. Amoxicillin will most likely work.”

Dr. Frost was pleased to learn that rapid polymerase chain reaction tests, commonly known as PCR tests, using a nasal swab in a doctor’s office are effective at teasing out which bacteria is likely causing the ear infection.

“We know, for example, that if the bacteria is not in the nose, it’s likely not in the ear,” Dr. Frost said. “This demonstrates how we can potentially individualize care by pairing the type of bacteria to the best treatment, which sometimes means not prescribing an antibiotic and allowing the ear infection to clear up on its own.” Parents are still given guidance on relieving pain with Tylenol and ibuprofen.

The bacteria present in a child’s nose can also help doctors choose the best antibiotic for that particular patient.

“We know that each type of bacteria has a different chance of getting better without an antibiotic. For example, most kids with S. pneumoniae are likely to benefit from an antibiotic, whereas most kids with M. catarrhalis will get better without one,” Dr. Frost said.

“We believe the majority of kids getting antibiotics today to treat ear infections don’t need them at all. Which is likely why we see low failure rates and recurrent infections with amoxicillin, because kids didn’t need the treatment in the first place,” she said.

Because the COVID-19 pandemic sprang up during her study, Dr. Frost said she wondered if ear infection symptoms and outcomes would be the same between children with and without COVID-19.

The result: COVID-19 can be present at the same time as an ear infection, meaning that providers should not use a diagnosis of an ear infection to rule out COVID-19, she said. Most of the children who tested positive for COVID-19 infections attended daycare.

Detailed analysis of the study data, planned for the summer of 2022, will give more detail on the potential for the long-term health impact of targeted treatments for ear infections and the potential for cost savings, according to Dr. Frost. These savings could come from fewer lost school days for children and work days for parents, and by cutting back on unnecessary antibiotic expenses.

The savings on drug costs, as well as minimizing side effects from medications, should more than compensate for the additional costs of providing the rapid diagnostic tests in doctors’ offices, she said.

“The ultimate goal is to individualize care for ear infections so we can assure that every child is receiving the best care and has the best possible outcome.”

Project Information:


Holly Frost, MD


Denver Health Foundation, University of Colorado

Funded Research:

NO TEARS: Nasopharyngeal organism testing to improve outcomes for children with ear infections