Health service shortfalls are often blamed for high disease rates in slums, but service problems are not the only reason poor neighborhoods fare worse than wealthy ones. Infectious diseases can differ at a basic biological level between rich and poor locales, and these differences can cripple vaccines intended to fight them.

My colleagues and I have seen these effects with rheumatic heart disease in poor parts of Brazil. This ailment has virtually disappeared from high-income countries, where antibiotics are readily available, but it is a major cause of heart trouble in less affluent nations, and it is often fatal. The disease is caused by repeated throat infections from group A streptococcal, or GAS, bacteria. When the body's immune system attacks these microbes, some proteins in heart valve cells that look similar to the bacterial proteins get attacked as well.

A vaccine against GAS could thwart such infections. But the bacteria are difficult targets. There are more than 120 different strains of these bacteria, and a typical sore throat from these pathogens can be caused by any number of these strains. Each has a different version of a gene that codes for M protein, a molecule that is a key part of the bacterium's outer membrane. To make an experimental vaccine, researchers included M proteins from 26 common strains to try to ensure immunity. Yet when scientists looked at non-European and non–North American patients with GAS infections, the 26 types appeared much less often or not at all. While these strains were frequent in high-income countries, where the vaccine was developed, they were rarities elsewhere, where the vaccine would be less effective.

Biological differences occur even within the same city. My research team compared GAS strains from children in slums and in wealthy neighborhoods in Salvador, Brazil. The collection of strains in a community is given a number called a diversity index. The greater the number of strains with different M protein genes, the higher the index. The diversity index of GAS strains of well-to-do children—they attended a private clinic and could afford private insurance—was close to that reported from high-income countries, around 0.90. But the index for slum children was higher, about 0.96. There was another distinction: the two most common strains in high-income countries accounted for 36 percent of GAS samples in wealthier Brazilian children but only for 19 percent of samples from two slum clinics. If this experimental vaccine were to be administered to the children in Salvador, it would be far less effective in the slums.

The higher diversity of GAS strains in slums may be the result of bacteria changing by trading genes back and forth. Trades may be easier when extreme human crowding exists, which means more frequent contact among different bacterial cells and more gene-trading chances. Strain diversification may increase the chances of a bad immune reaction against the heart.

Germ-level disparity has also been recognized as a potential problem with current widely used vaccines against cervical cancer. These injections target strains of cancer-causing human papillomavirus, or HPV. Research has indicated that a portion of African-American women living in some parts of the southeastern U.S. have different HPV strain infections, however. We do not know if these racial and geographical differences in virus types will ultimately affect vaccine effectiveness. What we do know now is that it is not just access to a clinic that determines what therapies work but also differences among disease-driving germs—distinctions created by the social environment.