Humans don't constantly produce antibodies for a pathogen when the pathogen has been gone for a while. They just store the 'recipe' for making the particular antibody in memory T cells.
If the antigens that the virus contains mutate enough to not work for the antibodies an immune person has developed. Then the process starts over and the immune system will ...
"I think, though am not at all sure, that pathogens need to invade cells to be dangerous."
True in the case of viruses and some bacteria.
Hiding within the cells of the host is the intracellular pathogenesis.
But other "tricks" are possible. Four examples:
surface proteins that "catch" antibodies
fast mutation of ...
You could inoculate your sample in a selective medium or an enrichment medium to kill off the unwanted species. Of course, you will need to do a literature search to find the optimum medium for the species of your interest.
Another option is to streak plates like so. With successive 'generations' of streaks, the inoculum gets diluted, so that you ultimately ...
The black RPE contributes to the "normal" color of the eye fundus in photos of the retina. Albinism is a condition of absence of black pigment, and then you can see the eye fundus without pigment. Compare the two images below