While subject to debate, the idea of secondary infections or viral reactivation in the setting of CFS/FM remains important to many providers, perhaps because empiric treatments sometimes seem to help.
As long as antibiotics are used chronically for acne and long term prophylaxis for herpes is acceptable, it is probably within the bounds of reasonable medicine for an individual physician to empirically prescribe an antimicrobial for their patient with CFS or FM.
If such a decision is made, it should be done with caution, monitoring both for positive effects and for potential adverse effects.
Potential situations include the use of antivirals or atypical antibiotics when a specific organism is suspected such as mycoplasma, Chlamydia, Lyme, herpes viruses, etc.