To tackle your problems each in turn:
organisms and antibiotics are in the region of 40-50 values... If this is not too much for a dropdown is probably near the limit
The most direct, simple solution is to switch from a dropdown to a combobox with autocomplete. I assume this form is at least relatively important and users likely go through selecting things pretty often, so you get to kill two birds with one stone using a combobox:
Power-users no longer have to rely on autocomplete through their browsers implementation of dropdowns, and can now either just type the organism/antibiotic they want, or type a few characters and complete automatically.
While your naked dropdown will still be around 40-50 values, the second a user inputs any character into the box they will be presented with a much smaller subset of suggestions, effectively cutting down the selection space by a large margin (which you can tweak by configuring autocomplete settings accordingly).
The susceptibility list on the contrary only has 3 values, so it seems better suited for a radiogroup
Do you foresee the susceptibility list growing to more than 3 values in the future? If not, it may indeed be better suited for a radiogroup.
However, it looks like you're using Bootstrap, which provides a more user-friendly buttongroup class, which would provide toggleable buttons that better conform to the rest of your form than radios would. You could easily in-place replace the susceptibility dropdown with a three-button button group. Bonus: it's one less click (and far less eye-scanning) than clicking a dropdown and a value within it!
It is not clear enough that you can add the same organism multiple times with a different antibiotic (and this is probably the most important bit)
You can take lots of approaches here to make this more visible, but each of them boil down to structure in the form. If your goal is to let users know they can add the same organism multiple times with different antibiotics, here's some example actions you can take (and probably use to come up with your own idea):
Reorganizing the form to indent the antibiotic field or otherwise imply it is some sub-field of a parent organism value would let users know that an organism can react with an antibiotic in many ways.
Redesigning the form into some all-parent structure (think: a view of [organism] + [antibiotic] = [susceptibility], rather than [organism],[antibiotic],[susceptibility]) would let the user know the options are combinations to some means, rather than just properties of an organism.
If users frequently (or should frequently) add multiple rows of the same organism with varied antibiotics, you could let them know it's okay by pre-filling the organism field with its previous value. If this is not immediately obvious, you can make it even more obvious by marking fields correct (opposite of the usual invalid class you see on forms) as you give each a value, and applying that "correct" class to the pre-filled organism field, even when it shares a value with existing rows.
Rather than having a form, you could allow in-place editing of fields on click in the actual table, allowing users to click in an empty row to create one, or click in the values of existing rows to edit them. Doing this would put the content entered in a more tabular form mentally, which might be the necessary bump to make users realize these are all combinations that don't have to be unique on a single column (like organism).
You have lots of whitespace left of the form Cancel/Save buttons which, if you wanted to just be blunt, could be used for helpful banner hints, such as "Hey, you can add the same organism multiple times with a different antibiotic!"