Mercantilism or the rise of commerce, brought not only wealth to the cities, but also disease. A physicians with a modicum of knowledge would stay in the cities where they received substantial wages and privileges. Catering predominately to the wealthy formal medicine was practiced and governed by the church; illness was divine retribution.
Knowledge of medicine from ancient text remained for the most part in the hands of the church with each monastery having an infirmary. Cultivating their own herbal remedies to treat some monasteries functioned as hospitals for the old, the disabled and traveling pilgrims.
Knowledge of herbal remedies lay not only with the church but also with women who performed practical medicine for their village. Some methods often combined Pagan cures or invoked spells. Naturally, these practices were frowned upon by the church, but calling upon the Christian God saints would remedy that.
Where the two practices collided meant religious persecution as being in league with the devil which meant execution.
From a compendium of medieval diseases, these were the most common for our period:
Dysentery (the “bloody flux”)
An infection caused either by bacteria or amoebas, spread through contamination of food and water by infected fecal matter.
Symptoms: (Bacillary) After 1-6 days incubation, watery stools, fever, cramps, dehydration. In advanced stages, bloody stools, meningitis, conjunctivitis, and arthritis. (Amebic) Acute form: watery, bloody stools, cramps, fever, weakness. Chronic form: intermittent diarrhea, mild abdominal discomfort.
Result: Generally weakened condition.
Note: Endemic in medieval armies and pretty common in cities. Infantile diarrhea was a leading cause of death for infants. After the Black Death, many urban areas instituted public health reforms to improve sanitation and prevent these enteric fevers.
Ergotism (“St. Anthony's fire,” “holy fire,” “evil fire,” “devil's fire,” “saints' fire”)
Poisoning from a fungal infection of grain, especially rye.
Symptoms: (Convulsive) Degeneration of the nervous system causes anxiety, vertigo, aural/visual hallucinations, and the sensation of being bitten or burned; stupor, convulsions, and psychosis. (Gangrenous) Constriction of the blood vessels causes reddening and blistering of skin, then blackening, with itching and burning, and finally necrosis.
Result: 40% mortality. Lingering symptoms, including mental impairment, among survivors.
Note: Ergotism was known as a rural disease, particularly of marshy areas, and one that followed crop damage or famine; especially after a severe winter and a rainy spring. Children are more susceptible because of their smaller body weight. Because England did not rely on rye as much as populations on the continent, it suffered fewer cases of the convulsive type.
An acute, extremely contagious viral infection of the upper respiratory tract, spread by inhalation.
Symptoms: After 1-2 days, a sudden onset of chills and fever, headache, backache, muscular aches, and general malaise; weakness, prostration, nausea, eye pain, mental confusion. After 1-5 days the respiratory symptoms become more prominent: dry or sore throat, cough, runny nose. Serious complications include bronchitis and bacterial pneumonia.
Results: A few months, maximum, of resistance to repeated infection.
Note: Flu was not a major worry in the 14th century but became a scourge in the 15th. Because flu is very contagious it often forms epidemics, generally occurring in the winter or early spring.
As you may have noted, the onset of dysentery is nearly a given while encamped for periods longer than a week. This would affect both sides, as the besiegers had no proper sanitation and the besieged having to cope with the extra population gathered behind its walls. Naturally, a good army would have an abundance of clergy to help heal the body and soul.
Repeated crop failure would bring on conditions of famine, but also be a source for additional disease for the stricken fields. Certainly ruinous for the local noble and whose adversaries would see this a divine intervention.
A severe winter would increase the chances of influenza. Keep in mind when designing event tables, many situations were a natural flow of “cause and effect”. So a brilliant harvest and well stocked for the winter period, a region would have less problem with influenza.