Thanks for your post.
Your patient clearly has a lot of transmitted drug resistance. In such cases, we'd usually obtain a combined phenotype+genotype. In your patient's case, the principle reason is to get confirmation of susceptibility to any nucleosides and protease inhibitors. Given the number of mutations present, my confidence in only genotypic information is lower than in cases with limited resistance. NNRTI options are compromised, and with both the 181 and 103 mutations, TMC 125 is compromised.
I have a patient with a very similar resistance pattern- in this case, phenotypic data suggested susceptibility to tenofovir and darunavir- both of which could be partnered with raltegravir or maraviroc (this of course, requires separate resistance testing).
The issue of performing a second resistance test is somewhat limited by the potential of genetic drift and the additional costs, but accepting these issues, I'd find that having the data is often helpful (if only confirmatory).
I hope this is helpful, let us know what you decide and how your patient does after initiation of treatment.