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By Liz Szabo, USA TODAY

For the first time, American researchers have found evidence that the bacteria that cause whooping cough are becoming resistant to vaccines, a new study shows.

Vaccine-resistant whooping cough has previously been documented in Japan, France and Finland, according to the report, published Thursday in The New England Journal of Medicine.

Public health officials have been particularly concerned about whooping cough, also known as pertussis, because of recent outbreaks. Last year, the USA suffered the largest whooping cough outbreak since 1955, with nearly 42,000 reported cases and 18 fatalities, according to the Centers for Disease Control and Prevention. Most deaths were in children, particularly babies under 3 months old. Newborns like these are too young to be fully vaccinated, and their tiny airways can quickly swell shut.

Those cases are a fraction of the damage caused by whooping cough in the pre-vaccine era. In the 1930s, doctors reported more than 250,000 cases a year, according to the CDC.

In the new study, genetic tests showed signs of resistance in 11 of 12 children hospitalized for whooping cough in Philadelphia in 2011 and 2012. The bacteria infecting 11 of these children lacked a key protein included in the pertussis vaccine, which helps stimulate immunity to the disease.

While most of the hospitalized children were newborns, one was 9 and another 14.

The prospect of vaccine-resistant whooping cough is real concern, says Michael Osterholm, director of the University of Minnesota's Center for Infectious Disease Research and Policy.

Tuberculosis, which was considered to be defeated by antibiotics, also has emerged as a serious problem, as the number of cases of antibiotic-resistant tuberculosis has grown, says William Schaffner, a professor at the Vanderbilt University School of Medicine.

Those cases "may foretell a growing problem," Schaffner says. While there has been little research on resistant whooping cough in the USA, "This report will open up the issue," Schaffner says.

Public health leaders still urge people to get vaccinated against whooping cough, in spite of any limitations in the vaccine. In addition to vaccinating children, the CDC now recommends whooping cough shots for new parents and anyone else who comes in contact with infants.

Recent studies suggest that resistant forms of whooping cough can spread from person to person, according to the Minnesota research center. Another study, published Jan. 31 in Emerging Infectious Diseases, found that this new form of whooping cough is equally dangerous as the more common variety.

American scientists have been closely examining reasons for the resurgence in whooping cough. Some outbreaks arise because of children who are unvaccinated, or undervaccinated.

Scientists also have found that the protection offered by the whooping cough vaccine fades more quickly than previously thought.

So even fully vaccinated children - who have received all five doses recommended by age 4 to 6 - could still be vulnerable to the disease by age 10, according to a September study in The New England Journal of Medicine.

Part of the difficulty in producing a better whooping cough vaccine stems from the fact that researchers know relatively little about the bacteria itself, at least compared with germs such as measles, Schaffner says. Doctors don't know why, for example, even people "naturally" infected with whooping cough may become reinfected a decade or so later. In comparison, people who catch measles or chickenpox don't typically get those infections again.