HOW CAN WE ANALYZE INFECTIOUS DISEASES?
Most of the time when people become sick, it clears quickly and we say they have been cured. We often do not know how they became sick and how lasting the effects are. For example, people who have a fever rarely know the exact origin of their illness. They rarely even know whether it is a virus or caused by bacteria, or whether there may be long-term consequences to their illness.
Understanding the cause of illness is not often thought to be important, given that most illnesses are transient. In some cases, however, the effects are more lasting. Assays currently exist to diagnose many common viruses, such as rhinoviruses, influenza, adenoviruses, respiratory syncytial viruses, and to identify various types of bacteria, including subspecies that may be particularly pathogenic. The new sequencing technologies not only allow us to identify “all known human viruses” but also the potential for subtypes as well as the identification of new ones. This is important for several reasons. First, we can identify the exact cause early. Diseases such as mononucleosis often are diagnosed only when the illness has refused to go away—in fact, the diagnosis is often made well after others have been infected! Early and precise diagnosis can be extremely valuable for the prevention of epidemics. For example, early detection of serious pathogens such as those causing severe acute respiratory syndrome (SARS), avian influenza (“bird flu”), H1N1, and Ebola virus will be extremely beneficial to the population as a whole. In other cases, detailed analyses can help find the causes of diseases that remain mysterious much longer than they should. A recent case of encephalitis in a critically ill child was solved by sequencing of the child’s cerebrospinal fluid; the illness was found to be due to a group of bacteria called Leptospira. Treatment with antibiotics cured the child. In the future, this type of diagnosis should become routine, if not in a primary clinic, then, at least in rapid follow-up clinical testing.
An important benefit of capturing this information is the possibility of determining long-term effects of diseases. There are clear links between serious illness during pregnancy and autism and other diseases, but we do not know which diseases lead to which effects. Type 1 diabetes is believed to be associate with a pathogen infection. Are some viruses more likely than others to cause this disease? If so, which viruses? This information will be be extremely valuable for how we predict risk for particular diseases. For example, an expectant mother with a particular viral or bacterial infection might have her child monitored later for diabetes or autism to enable early intervention.
Finally, another benefit of performing detailed analyses of viruses/bacteria and hosts is to understand their spread. Viruses and bacteria tend to mutate at high frequency and accumulate genetic changes (which is how they often escape the immune system). By analyzing pathogen genomic sequences, it is possible to delineate their spread through their unique changes as well as identify the origin of infection and its pattern of transmission. For example, a recent methicillin-resistant Staphylococcus aureus (MRSA) infection outbreak in the United Kingdom was analyzed by genome sequencing of the MRSA strains and subsequently traced to a specific caregiver who had contact with the earliest MRSA-infected patients. This individual could then be isolated to prevent further spread of MRSA. Similarly, on a broader scale, the origin of the recent Ebola outbreak could be traced to its original location, as well as to the likely individual of origin by sequencing the viral genomes and following the pattern of genetic changes. Such information can be useful in evaluating the virulence of pathogens, identifying contacts of those with deadly pathogens, and attempting to quarantine potentially infected individuals.