It differs from pathogen to pathogen. Some get in though the airways (mouth, nose, throat, lungs etc), some through the digestive tract, some through breaks in the skin. Things like bacteria are often harmless when they are on our skin or inside our guts, but can be very harmful if they can get into the blood. Some things like viruses can attach to molecules on the outside of cells that they “like” to infect, and from there get inside the cell. In general, micro-organisms don’t actively seek out targets, they just get swept along until they end up in the right place to cause problems. Medicines, on the other hand, are designed to get absorbed into the blood (or injected there directly). From there, they spread throughout the body. They are designed to only work where they need to, but will still be present throughout the body
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