Captain Jack Aubrey’s fine new frigate has just called in at Alexandria. the sailors have been at sea for 6 weeks, and now want liberty. of course, being horny young men, they head for the local brothels-and upon their return, Dr. Maturin holds sick bay.
Captain Jack Aubrey is furious-he cannot afford to have his men out of action-so, Dr. Maturin-what do you do? Most of the lads are already complaining about painful urination-what is the conversation at the wardroom table likely to be like?
Of course, Aubrey himself is after a comely egyptian girl-what happens if HE comes down with a dose? Will that get back to wife Sophie? and how would it affect jack’s chances for promotion?
Lads just have a bit of copper wire inserted into their urethra and then a flame is applied to the end, heating the wire through and burning out the infection.
No big deal. These are sailors, not nancy little girls. 
They also injected your urethra with Mercury hence the expression “one night with Venus gets you Six months with Mercury”. I don’t know if it killed you or cured you.
You realize that, every thirtieth page or so when Dr. Maturin is contemplating his sick list and after the list of those wounded in action or more exotically damaged adds ‘and the usual poxes’, he’s talking about just that situation?
From “A Sea of Words”
Because syphilis was almost an occupational hazard of sailors,
Navy Surgeons stocked various mercury salts to treat it.
Most victims required prolonged therapy with oral mercury preparations,
such as calomel or Maturin’s “blue pill” (mercuric chloride, also
known as corrosive sublimate) and with unguents made with the latter.
All mercuricals were cathartic and diaphoretic, providing clear
routes for the elimination of the contagious factor responsible for
the affliction. However, it seems unlikely that such treatments could have
eradicated the syphilis organism.
Blue pill, blue ointment are, I think, mercury compounds.
From here
And Jack did catch VD at one point, when Molly was screwing the army guy IIRC.