Remember this is not cut and dried. Sometimes an opportunistic pathogen can be a frank pathogen in a different body site or with one tiny change in the microbe's genes that gives it a new virulence factor. Microbes have many many related species and very few cause infectious disease. Gene mutations and gene mixing between microbes coupled with selective pressure . I've organized the infectious diseases into types of microbes first and then by structural characteristics .
Structure is the key to function .
Use all you've learned about structure, metabolism, genetics, control methods and the immune system to understand disease and how to conquer it. Pathogenic bacteria like to live in the particular conditions found in the human body. Mesophilic, neutrophilic, either microaerophilic or even anaerobic . Bacteria that prefer or require other conditions won't cause infection. Strict aerobes are not pathogens.