Chances are very high that there were germs involved. Some of them can make us sick, by causing infections, so doctors and scientists work hard to learn as much as they can about them. Water suppliers need to understand germs, too, because it is their job to keep drinking water safe.
Pathogens are germs that cause disease.
Pathos is Greek for suffering, and -gen is a suffix meaning producer, also from Greek. Common types of germs are bacteria, viruses, fungi, and protozoa.