After a bout of the flu, lingering germs can wreak havoc on the weakened immune system. These pathogens are not influenza organisms but, rather, bacteria such as Streptococcus pneumoniae, a microbe that normally lies dormant in the nose or throat of children but migrates on a path cleared by the flu to the middle ear where it causes an infection called acute otitis. There are more than 24 million cases of middle ear infections—which can cause pain, fever, vomiting and appetite loss—diagnosed each year in the U.S.

"Secondary bacterial infections cause much of the sickness and about 25 percent of all deaths during the flu season, and 50 to 95 percent of deaths during pandemics of influenza," says Jonathan McCullers, an infectious disease specialist at St. Jude Children's Research Hospital and co-author of a study that suggests a new way of treating such conditions. "Eliminating these secondary infections could dramatically reduce the sickness and death rates among susceptible populations such as infants and the elderly."

McCullers and Vincent Fischetti, co-heads of the Laboratory of Bacterial Pathogenesis and Immunology at the Rockefeller University, provide evidence that the enzyme lysin can be tailored to kill specific secondary pathogens before they pounce on compromised immune systems. Fischetti notes that this technology could potentially be used to prevent pandemics during an avian or other flu outbreak by destroying secondary germs that might attack when the immune system is compromised. "If we can go in and, during a pandemic, treat individuals that are either susceptible to flu—the elderly or young children—or basically everybody during that period of time and decolonize them," he says, "we have a better chance of saving a lot of lives."

The researchers used lysin, a protein antibody typically produced by a virus after it has infected and hijacked a host cell's machinery to replicate. Once several copies of the virus exist, it manufactures lysin, which punches holes in the cell wall allowing it to escape. "You can't use antibiotics to eliminate a carrier," or germs that lay dormant in the body, explains Fischetti, "otherwise you run into a lot more serious resistance problems."

After injecting colonies of S. pneumoniae into the noses of mice, the scientists infected some of them with an influenza virus and the others were given a harmless solution. Sixty-three percent of the influenza-infected mice developed the flu and then also contracted middle ear infections. Those mice that did not get infected with the flu also avoided the secondary bacterial illness, despite carrying the bacteria. The researchers repeated the experiment, but this time they nasally administered lysin to one of the groups after introducing the bacteria. The results, published in PLoS Pathogens: after fighting off the flu, 80 percent of the mice that did not receive lysin developed acute otitis. None of the mice given lysin were stricken with ear infections.

"In my mind, it's a no-brainer experiment," says Fischetti. "If the [S. pneumoniae] organisms are there, they have the potential of causing disease; if they're not there, they can't cause disease. Basically what we're doing is removing them very specifically, without disturbing the mucus membrane organisms."

Fischetti notes that his research team has developed lysin complexes that target bacteria, which cause illnesses such as strep throat, pneumonia and meningitis and are typically treated with increasingly ineffective antibiotics. In addition, he says that one lysin in his arsenal targets the bacterial agent anthrax, inhalation of which can lead to cold and flulike symptoms followed by shortness of breath, muscle aches and, in some cases, death. "We've shown in animal models that if you give an animal anthrax and then intravenous anthrax enzyme," Fischetti says, "you can cure 90 percent of the animals."

He expects to begin human lysin trials within three years and says the drug could be available as a nasal spray for public use in six or seven years.