It is entirely possible that the bacteria in her urine is resistant to the antibiotic her doctor is prescribing. This has happened to me many times.
Has he done a culture and sensitivity test to see what will work? If not she should insist on it. It's about the only way to determine what will work.
See the following for more information:
http://www.americanpregnancy.org/pregnancycomplications/utiduringpreg.html
http://www.webmd.com/baby/guide/pregnancy-urinary-tract-infection
http://www.babycenter.com/0_urinary-tract-infections-during-pregnancy_9403.bc