Previously, we learned that the dose and genetic properties of a pathogen one is exposed to can affect the risk and severity of disease. But these genetic properties which proteins a pathogen expresses, and even the dose that is available for transmission are shaped by evolution. In this session, we will discuss several examples of pathogen evolution, that is, changes in pathogen populations over time that arise due to the action of natural selection. For evolution by natural selection to occur, two things are required: the organisms must have genetic variation and there must be differential reproductive success of different genetic types. In the case of pathogens, both conditions are very often met. Bacteria and viruses reproduce in a matter of hours to a few days, and every round of reproduction results in genetic mutations that provide ample genetic variation. Bacteria have evolved many mechanisms that enhance this genetic variation, by allowing transfer of DNA between even distantly related species, such as plasmid transfer and DNA transformation. Viruses don’t have these mechanisms, as far as we know, but they do often have very high mutation rates, leading to the generation of highly diverse populations of virus even during one infection. Natural selection on microbes takes many forms as well. Any property that makes a pathogen reproduce faster within a host and outrun the immune system will be favored, though there is some limit to this, because growing too fast may kill the host, leading to the end of the infection. Sometimes, it’s useful to think of the pathogen as racing to reproduce faster than the host‘s immune response can ramp up. But it’s a race where winning too decisively can be harmful in the long run, as dead hosts don’t usually transmit infection. Let’s see two examples of this kind of evolution. Myxoma virus is a virus that infects European rabbits, causing a disease called myxomatosis. In the 1950s, myxoma virus was imported to Australia, where rabbits were crop pests, in the hopes of using it as a bio-control agent to kill off rabbit populations. Frank Fenner, who is famous for his role in eradicating smallpox, was a young scientist then and realized that this was a grand evolutionary experiment. At the start, he put aside some stocks of the virus so he could have some virus that had not had a chance to evolve in the Australian rabbits. He also gathered some wild rabbits and kept them in captivity, where they would not be exposed to myxomatosis. In this way, he had some unevolved rabbits that could be used as a test for evolutionary changes in the myxoma virus, and unevolved virus that could be used to test for changes in the rabbits. Evolution in both rabbits and virus happened very fast. When the virus was first introduced, almost all strains killed over 99 percent of the rabbits infected. Over time, the lethality declined, though not to zero. Why? It‘s believed that strains that kept their hosts alive longer produced more secondary cases than those that killed off their hosts too quickly. But some virulence was necessary to the perpetuation of the virus, which was spread by direct contact with lesions on the skin of a rabbit, or by biting insects. A strain that was too unaggressive would be unable to reach high enough levels in the rabbit and get to the surface for transmission before being cleared by the immune system. Thus it seems that an intermediate level of virulence was optimal for the transmission success of this virus. The host, too, evolved. After all, rabbits reproduce rapidly, so natural selection can work fast on them, too. The most susceptible rabbits were killed off before they could reproduce, so they left few or no offspring. Rabbits with more genetic resistance did better, leaving more descendants who inherited the genetic resistance from their parents. Over time, the lethality of the unevolved virus declined as the host evolved resistance. Another example comes from human immunodeficiency virus, or HIV. As we saw in a previous session, the virus transmits more efficiently from an infected to a susceptible person when the amount of virus in the blood, and correspondingly in genital secretions, is high. Studies have shown that the viral load in an infected person is determined in part by genetic properties of the HIV virus that infects them. Different strains tend to produce higher or lower viral loads in each of the people they infect. If all else were equal, selection would favor viral loads to be as high as possible, and viral load would evolve upward indefinitely until some limit was reached where it could not be higher. But, in fact, all else is not equal. Higher viral load is associated with faster progression of the infected person towards AIDS and death. These data show the survival curves of persons with different HIV viral loads. Those with the highest viral loads died several years earlier on average than those with lower viral loads. Thus, like myxoma, HIV faces a tradeoff. Strains that are too aggressive maintain high viral loads and are more transmissible, but kill the host faster, while those that are less aggressive keep the host alive longer, but have a lower chance of transmitting each month, or in each sexual act. Evolutionary theory predicts that the average viral load under these conditions will evolve toward a level that balances these, producing the largest number of secondary cases over time. Quantitatively, the predicted mean steady state viral load, depending on some details of the assumptions, is between 10,000 and 100,000. This is consistent with what we observe in modern HIV cases. Growing quickly to outrun the immune system is not the only trait that is selected for in pathogens. Our immune systems respond to specific components of each infectious agent called antigens. Therefore, strains that can change or shed the major antigens can gain an advantage, as long as the change doesn't have too much of an impact on their ability to infect the host. This is particularly apparent when we use a vaccine that selectively targets certain strains of a pathogen but not others. Mass administration of such vaccines can create very strong selective pressures in the population as a whole. One such vaccine is a vaccine against Streptococcus pneumoniae, or pneumococcus, and is called the pneumococcal conjugate vaccine. The first such vaccine licensed, PCV7, included seven of the over 90 serotypes of pneumococcus. As this graph shows, declines in disease in small kids in the United States, from the serotypes included in the vaccine, were partially offset by increases in disease from other types, most notably 19A. Since 2010, the U.S. has been using PCV13, an updated vaccine that includes serotype 19A. The population of pneumococci continues to evolve, with the most recent studies showing a rise of those serotypes not included in PCV13. Fortunately, those remaining sereotypes tend to have a low propensity to cause disease, so although they are present in children's respiratory tracts, they are less of a public health concern than the ones they replaced. I've saved for last perhaps the best-known example of how pathogens evolve in response to selection. That is antimicrobial resistance, which is caused largely by the use of antimicrobial drugs for treatment of infections, and also by their overuse and misuse, for example, to treat viral infections for which they are not effective. This graph shows the relationship between penicillin use in different European countries, and the prevalence of penicillin resistance in Streptococcus pneumoniae in those countries. It is striking that France uses about four times as much penicillin per capita as the Netherlands just next door. The more intense selection pressure in France in 2000 was reflected in much higher rates of penicillin resistance. In this segment, we have considered some of the ways that pathogen populations change genetically in response to selection pressure. This is evolution in action, a process we can observe, because microbes reproduce so quickly, going through many generations in the periods in which we observe them. Whether the selection comes from the pressure to grow and transmit, or to escape our immune responses, or to escape antimicrobial treatment, pathogens usually evolve quickly in response.
