The high bacterial strain specificity of phage therapy may make it necessary for clinics to make different cocktails for treatment of the same infection or disease because the bacterial components of such diseases may differ from region to region or even person to person.
In addition, due to the specificity of individual phages, for a high chance of success, a mixture of phages is often applied. This means that 'banks' containing many different phages must be kept and regularly updated with new phages.
Further, bacteria can evolve different receptors either before or during treatment; this can prevent the phages from completely eradicating the bacteria.
The need for banks of phages makes regulatory testing for safety harder and more expensive. Such a process would make it difficult for large-scale production of phage therapy. Additionally, patent issues (specifically on living organisms) may complicate distribution for pharmaceutical companies wishing to have exclusive rights over their "invention", making it unlikely that a for-profit corporation will invest capital in the widespread application of this technology.
As has been known for at least thirty years, mycobacteria such as Mycobacterium tuberculosis have specific bacteriophages.[39] No lytic phage has yet been discovered for Clostridium difficile, which is responsible for many nosocomial diseases, but some temperate phages (integrated in the genome) are known for this species, which opens encouraging avenues.
To work, the virus has to reach the site of the bacteria, and viruses do not necessarily reach the same places that antibiotics can reach.
Funding for phage therapy research and clinical trials is generally insufficient and difficult to obtain, since it is a lengthy and complex process to patent bacteriophage products. Scientists comment that 'the biggest hurdle is regulatory', whereas an official view is that individual phages would need proof individually because it would be too complicated to do as a combination, with many variables. Due to the specificity of phages, phage therapy would be most effective with a cocktail injection, which is generally rejected by the U.S. Food and Drug Administration (FDA). Researchers and observers predict that for phage therapy to be successful the FDA must change its regulatory stance on combination drug cocktails. Public awareness and education about phage therapy are generally limited to scientific or independent research rather than mainstream media.
The negative public perception of viruses may also play a role in the reluctance to embrace phage therapy.