Mariana,
There are at least two possible explanations that come to mind:
(1) You are indeed seeing the appearance of bacteria resistant to the
phage. This is simple to demonstrate. Do a plaque assay with a high
enough phage titer to give complete lysis of the bacterial lawn. Are
there ant colonies of bacteria in the field of complete lysis? if so,
it indicates that the culture contains resistant cells.
(2) Perhaps you are getting a large number of replication-defective
phages, which lowers the overall pfu titer. This is not uncommon with
certain viruses, such as vesicular stomatitis virus. As this virus is
propageted in vitro, defective interfering particles are generated
which powers virus titers. This is a little more difficult to prove.
Jay Mone'
