All pathogenic bacteria, by definition, live inside the human body, because that is the method by which they cause disease. A pathogen is anything that causes disease in its host; without the host, disease is not possible, as disease is a pattern of harmful activity within the host.
Large amounts of bacteria live within the human body. Most are harmless, some are beneficial, and some are pathogenic. All three groups often live within the same bodily locations. For example, the human gastrointestinal tract is especially rich in bacteria, including species that are usually thought of as pathogenic, such as E. coli.
Not all strains of E. coli cause food poisoning, and in fact, most are harmless. It is only when the body becomes out of balance due to a chronic condition, such as malnutrition, that pathogenic bacteria are able to gain a foothold and overrun harmless or beneficial bacteria in these areas of the body. In other cases, pathogenic bacteria deliberately invade parts of the body that are normally bacteria-free, as with bacterial meningitis.
Bacteria in general are an extremely resilient and wide-ranging group of organisms. They live in almost every conceivable environment, and they are ubiquitous in water systems and soil all over the Earth. Pathogenic bacteria are not always clearly separate from other, non-pathogenic bacterial groups, except in their pattern of causing sickness and harm to their hosts. Pathogenic bacteria carry virulence genes, but sometimes pathogens and non-pathogens are closely related, behave the same way and live in the same environments. For example, the bacteria that cause cholera only differ from harmless strains by carrying a few genes that allow the bacteria to produce a dangerous toxin.