Bubonic plague

The bubonic plague — commonly called the Black Death and clinically Yersinia pestis (COMIC: Black Death White Life) — was a devastating disease which originated in the Middle Ages. It was spread by rats and fleas due to the poor sanitation of that age. (TV: The Visitation)

13th century
The entity known as the Pied Piper fed on the fear of the plague in Hamelin in 1283 and 1284. (TV: The Day of the Clown)

14th century
Ashildr fell victim to the Black Death in 1348. Her immune system coped and she got better, in no small part due to having been rendered effectively immortal since the 9th century due to an implanted Mire repair kit, but her children Essie, Johann, and Rue died. (PROSE: The Triple Knife, TV: The Woman Who Lived)

In 1479, Duroc, also known as Death, appeared during a bubonic plague outbreak in Cardiff until Faith stopped it before it could claim its thirteenth victim and enter the universe permanently. (TV: Dead Man Walking)

16th century
When a colony of Saturnyn came to Venice in 1580, they claimed that there was an outbreak of plague, allowing them to isolate Venice. (TV: The Vampires of Venice)

William Shakespeare's son was a victim. It was grief over his death that brought Shakespeare to his lowest emotional ebb, allowing the Carrionites to manipulate him. (TV: The Shakespeare Code)

17th century
Barnaby's parents were killed by bubonic plague. (GAME: The Gunpowder Plot)

In 1666, escaped Terileptil convicts created a deliberately more virulent variant on the black death in order to infect rats with it so as to spread it to humans. The Fifth Doctor defeated them, eliminating the storage of viruses in the Great Fire of London, which was unintentionally set whilst fighting the Terileptils. (TV: The Visitation)

Another outbreak appeared to have occurred in a village in 1669. In fact, it was an instance of Macro-viruses. (COMIC: Black Death White Life)

19th century
Memories of the plague persisted as far as the 19th century and any unexplained death was attributed to the plague or, in more bizarre cases, the legendary Plague Warriors. (PROSE: Plague of the Cybermen)

21st century
When the Cardiff Space-Time Rift became more active after it was opened by the Rift Manipulator, at least one female victim of the Bubonic plague came through into a hospital in 2008. She died shortly after, in isolation, but not before her presence at the hospital caused an outbreak of the plague. (TV: End of Days)

The Hotel Historia had rooms contaminated with the Black Death. The Doctor was displeased with them. (COMIC: Hotel Historia)