(covers information from several alternate timelines)
A foreign body, foreign substance, foreign organism or contaminant was any material or creature which originated from somewhere other than the space it occupied. The term was often used in medical terminology to describe an infection, such as a parasite, or an object, such as a splinter, originating outside the body of an organism. By the 24th century, replicator bio-filters automatically screened out contaminants, such as viruses. (DS9: "Babel")
In 2263 of the alternate reality, the diagnostic wrap identified a foreign substance in the body of an USS Enterprise crewman that Doctor Leonard McCoy scanned. (Star Trek Beyond)
In 2268, after a thorough examination of the child survivors from the Starnes Exploration Party, Dr. Leonard McCoy was unable to find any foreign biochemical substances in their systems which would account for their lack of grief over their parents' deaths. (TOS: "And the Children Shall Lead")
In 2367, Dr. Beverly Crusher theorized that the presence of a foreign body inside Susanna Leijten could explain why a T-cell stimulator was ineffective in halting her transformation. (TNG: "Identity Crisis")
Later that year, she described the Odan symbiont as a foreign organism inside William T. Riker's body, saying that immunosuppressants would only alleviate his symptoms of rejection, not cure them. (TNG: "The Host")
In 2375, The Doctor suggesting making USS Voyager unpalatable to the telepathic pitcher plant, allowing them to escape. He reasoned that it would work because "any living organism, no matter how large, will attempt to expel a foreign body." (VOY: "Bliss")