Systems, devices, methods, and software are provided that are suitable for use in the creation, implementation, use and/or refinement of treatment protocols. The software is configured for use in a client-server environment where the server communicates with client devices such as PDAs, laptops, tablets, or desktop computers. The software is directed to programming for basing an assessment of risk of bacterial infection in a subject on the presence, or lack, of viral illness in that subject. The diagnosis of viral illness is made through the use of results obtained from an enterovirus polymerase chain reaction test or a direct fluorescent assay test for respiratory viruses. Such test data, in conjunction with `time to positivity` data for urine, blood, cerebrospinal fluid, or other cultures, is then processed by the software to assess the individual risk of occurrence of various conditions, such as bacterial infection, in a particular subject.