Terminal alliance - Jim C. Hines

The Krakau came to invite Earth into an alliance of sentient species, only to find that plague had turned humanity into shambling, near-unstoppable animals. A century later a bioweapon wipes out the Krakau command crew and reverts the rest of the humans to their feral state - only Marion 'Mops' Adamopoulos and her Shipboard Hygiene and Sanitation team on board the Earth Mercenary Corps Ship Pufferfish are left with their minds intact. They stumble onto a conspiracy born from the truth of what happened on Earth all those years ago.