Bacteria, fungus, and viruses can cause HAIs. Bacteria alone cause about 90 percent of these cases. Many people have compromised immune systems during their hospital stay, so they’re more likely to contract an infection. Some of the common bacteria that are responsible for HAIs are:Bacteria, fungi, and viruses spread mainly through person-to-person contact. This includes unclean hands, and medical instruments such as catheters, respiratory machines, and other hospital tools. HAI cases also increase when there’s excessive and improper use of antibiotics. This can lead to bacteria that are resistant to multiple antibiotics.