This endearing childhood nursery masks a darker reality that most young children would cringe at if they discovered the origin of this rhyme as a ditty about the Black Death. Most people know two things about the Black Death.
It was a fourteenth-century pandemic that decimated anywhere between one-third and one-half of the European population.
Flea-bitten rats, carried by ships, spread the disease which came to be identified as the bubonic plague.
None of these assertions is entirely true. The death toll of the disease varied from region to region with many places experiencing a great percentage of their population lost whereas some regions hardly saw any. The second fact constitutes a very alive and ongoing debate not only in the historic but also scientific communities. And it is that second assertion which provides the focal point of this post.
What was the Black Death? Today, most people traditionally regard the bacillus Yersinia pestis (bubonic plague) as the cause of the Black Death, though many contest this theory. Others point to symptoms, the rat as a vector, and other factors to indicate that the plague was potentially not bubonic. Identification of the Black Death as bubonic rather than say, pneumonic, typically comes from those who understand the symptoms of modern-day victims.  Others believe that typhus or anthrax may have been the culprit.
One factor concerns symptoms. According to the fourteenth-century Italian Marchione di Coppo Stefani, people who contracted the Black Death showed “a bubo in the groin, where the thigh meets the trunk; or a small swelling under the armpit; sudden fever; spitting blood and saliva (and no one who spit blood survived it).”  The spitting of blood indicates the pneumonic plague, a much more fatal version of the bubonic plague, and one that could be passed human-to-human rather than through the infection of fleas. Once one caught the disease, his or her chances of survival were probably slim, especially if the person dwelled in an urban area with poor sanitation and was young or old.
Interestingly but perhaps not unexpected, medieval chroniclers believed the causes of the Black Death to be from more “otherworldly” sources. In several available sources, many firmly believed that either God or the heavens were sending down the Black Death as a form of punishment for mankind’s misdeeds. Petrarch contends that “[e]ither it is the wrath of God, for certainly I would think out misdeeds deserve it, or it just the harsh assault of the stars in their perpetually changing conjunctions.”  Gabriele de’ Mussi agrees that those “of Genoa and Venice are compelled to make God’s chastisement manifest. 
Yet another cause for debate centers around the common-held belief that ship-carried rats transmitted the disease. Some people maintain that the Black Death was carried via other means instead of rats. Some plague deniers claim the lack of references to rats in contemporary sources indicates that it could not have been the plague.  Harvard University professor Michael McCormick counters this argument by attributing the lack of contemporary accounts of massive piles of dead rats to simple disinterest of such creatures to chroniclers of the time.  Furthermore, he states that the ancients lacked a distinct word for the word “rat”, and as a result, rats become synonymous with mice.  A fellow blogger agrees with this, questioning whether contemporaries would notice a decrease of rats if they failed to understand the transmission of the disease in the first place.  In other words, who really cared enough to comment on it?
As for transmission, history traditionally has it that the Black Death arrived from the east on rats that ‘jumped ship’ and landed at port cities in Italy. Then either the rats or humans spread the disease westward via trade and encounters with other people. This simplistic version has a strong ring of truth to it, but one cannot forget that rats, attracted to grain as they are, feasibly hitched rides on trade carts or other wheeled transportation.  Thus, the common misconception that rats only traveled by sea expands to include land transmission as well.
A point I had never considered prior to researching this topic was that there existed other potential vectors. When I presented this paper at a conference for the Midwest World History Association in 2011, a session spectator indicated that cats and other smaller animals also transmitted the plague. Michelle Zeigler identifies the four types of plague transmission as coming from flea bites, inhalation of respiratory droplets, blood-to-blood contact, and ingestion, all causing various forms of plague.  Therefore, it may be safe to say that the Black Death, spread from the Eurasian landmass, was comprised of a few different diseases spread via land, sea, and air rather than the spoon-fed misconceptions of rats, fleas, and ships.
 David Routt. “The Economic Impact of the Black Death.” EH.Net Encyclopedia, edited by Robert Whaples. July 20, 2008. http://eh.net/encyclopedia/article/Routt.Black.Death; Robert Lerner. “Fleas: Some Scratchy Issues Concerning the Black Death.” The Journal of the Historical Society 8 (2008): 205-228, 205.
 Marchione di Coppo Stefani. “Rubric 643: Concerning A Mortality In The City Of Florence In Which Many People Died.” (1370s-1380s). From Cronaca florentina. Rerum Italicarum Scriptores, Vol. 30., ed. by Niccolo Rodolico. Castello: 1903-13. http://www2.iath.virginia.edu/osheim/marchione.html
 Francesco Petrarcha. “Ad Seipsum.” (1349). From the Epistola Metrica I, 14: lines 1-55. Trans. by Jonathan Usher at the University of Edinburgh.
 Gabriele de’ Mussi. “On the Plague.” (1348). From George Deaux, The Black Death 1347. New York: Weybright and Tailey, 1969.
 Lerner, 211.
 Michael McCormick. “Rats, Communications, and Plague: Toward an Ecological History.” Journal of Interdisciplinary History 34, no. 1 (2003): 1-25, 4.
 Ibid. 4
 Michele Zeigler. “Cats, Camels, and the Plague.” On Heavenfield: Exploring Early Medieval Britain and Ireland. http://hefenfelth.wordpress.com/2008/07/19/cats-camels-and-the-plague/ (accessed 18 August 2012).
 McCormick, 13-14.
Other Sources Referenced:
Donald, Graeme. “Plague’s Progress.” In Lies, Damned Lies, and History: A Catalogue of Historical Errors and Misunderstandings. Stroud, Gloucestershire: The History Press, 2009. pp. 87-93.
Michelle Zeigler’s wonderful blog on not only the Black Death but also the Justinian plague and the most recent one
Medievalists.net up-to-date listing of Black Death resources
This post was strongly derived from a paper I wrote last year on the socioeconomic impacts of the Black Death in Europe and the Middle East as a way to explain the decline of the East and rise of the West. For either the full paper or the bibliography, feel free to email me at email@example.com.