2004 "holistic" treatment guidelines (most recent?): http://www.guidelines.gov/summary/su...793&string=hiv
HIV Resistance Testing
Because drug-resistant virus can be transmitted from one person to another, patients presenting during or shortly after primary infection should be tested for transmitted drug resistance (B-II). A resistance test at this stage is likely to detect the resistance pattern of the infecting virus strain. The results of early resistance assays may be useful in guiding therapy, even if treatment is deferred for many years (B-III). With time, however, resistant virus will be overgrown by wild-type virus, and resistance tests will be less sensitive in detecting acquired resistance. A baseline resistance test for a patient with chronic infection is helpful only if it yields positive results: the absence of resistance does not mean that the patient does not harbor drug-resistant virus. Resistance testing should be offered to antiretroviral-naive subjects (those who have never taken any antiretroviral medications) who are initiating therapy and who have been infected for less than 2 years and perhaps longer. It is often difficult to ascertain how long a person has been infected, and consideration should be given to testing when the duration is uncertain and the expected regional prevalence of resistance is greater than 5% (B-II). Resistance testing should be done for patients experiencing virological failure to guide changes in antiretroviral therapy, and resistance testing should always be done during pregnancy (A-II).
2008 antiretroviral treatment recommendations: http://www.guidelines.gov/summary/su...+AND+treatment
As you already pointed out, there is a big difference between treating bacterial and viral infections. Where in bacterial infection a single antibiotic may be effective, for HIV at least 3 antivirals in various combinations are used.
It is impossible to predict which way the viruses or bacteria will mutate, we are dependent on the heuristic method to determine which infectious agent is predominant in the infected individual and what medications are effective AND tolerated by the infected individual.
Basic Scientists tend to look down on Physicians, many Physicians ignore critical thinking processes as they are forced to look at the whole person(patient).