Laryngitis that continues for more than three weeks is considered chronic. If laryngeal symptoms last for more than three weeks, a referral should be made for further examination, including direct laryngoscopy. The prognosis for chronic laryngitis varies depending on the cause of the laryngitis.

Treatment is often supportive in nature, and depends on the severity and type of laryngitis (acute or chronic). General measures to relieve symptoms of laryngitis include behaviour modification, hydration and humidification.

Vocal hygiene (care of the voice) is very important to relieve symptoms of laryngitis. Vocal hygiene involves measures such as

- Resting the voice

- Drinking sufficient amounts of water

- Reducing caffeine and alcohol intake

- Stopping smoking

- Limiting throat clearing

Voice hygiene programs are given by speech-language pathologists. These programs typically include the following components:

- Addressing amount and type of voice use

- Reducing behaviours that are damaging to the vocal folds

- Increasing hydration

- Adjusting lifestyle (for example, limiting caffeine and managing medical conditions)

Some cases of pharyngitis are caused by fungal infection such as Candida albicans causing oral thrush.

Pharyngitis may also be caused by mechanical, chemical or thermal irritation, for example cold air or acid reflux. Some medications may produce pharyngitis such as pramipexole and antipsychotics.

There is low or very-low quality evidence that probiotics may be better than placebo in preventing acute URTIs. Vaccination against influenza viruses, adenoviruses, measles, rubella, "Streptococcus pneumoniae", "Haemophilus influenzae", diphtheria, "Bacillus anthracis", and "Bordetella pertussis" may prevent them from infecting the URT or reduce the severity of the infection.

In terms of pathophysiology, rhino virus infection resembles the immune response. The viruses do not cause damage to the cells of the upper respiratory tract but rather cause changes in the tight junctions of epithelial cells. This allows the virus to gain access to tissues under the epithelial cells and initiate the innate and adaptive immune responses.

Up to 15% of acute pharyngitis cases may be caused by bacteria, most commonly "Streptococcus pyogenes", a group A streptococcus in streptococcal pharyngitis ("strep throat"). Other bacterial causes are "Streptococcus pneumoniae", "Haemophilus influenzae", "Corynebacterium diphtheriae", "Bordetella pertussis", and "Bacillus anthracis".

Sexually transmitted infections have emerged as causes of oral and pharyngeal infections.

This affliction is a common cause of throat irritation. Normally the stomach produces acid in the stomach which is neutralized in the small intestine. To prevent acid from flowing backwards, the lower part of the swallowing tube (esophagus) has a valve which closes after food passes through. In some individuals, this valve becomes incompetent and acid goes up into the esophagus. Reflux episodes often occur at night and one may develop a bitter taste in the mouth. The throat can be severely irritated when acid touches the vocal cords and can lead to spasms of coughing. To prevent throat irritation from reflux, one should lose weight, stop smoking, avoid coffee beverages and sleep with the head elevated.

Viruses are common causes of the common cold. Less often, bacteria may also cause pharyngitis. Both of these organisms enter the body via the nose or mouth as aerosolized particles when someone sneezes or coughs. Because many germs are contagious, one can even acquire them from touching utensils, toys, personal care products or door knobs. The most common viruses that causes throat irritation include the common cold virus, influenza, infectious mononucleosis, measles and croup. Most bacteria and viruses usually induce throat irritation during the winter or autumn.

The symptoms of strep throat usually improve within three to five days, irrespective of treatment. Treatment with antibiotics reduces the risk of complications and transmission; children may return to school 24 hours after antibiotics are administered. The risk of complications in adults is low. In children, acute rheumatic fever is rare in most of the developed world. It is, however, the leading cause of acquired heart disease in India, sub-Saharan Africa and some parts of Australia.

Complications arising from streptococcal throat infections include:

- Acute rheumatic fever

- Scarlet fever

- Streptococcal toxic shock syndrome

- Glomerulonephritis

- PANDAS syndrome

- Peritonsillar abscess

- Cervical lymphadenitis

- Mastoiditis

The economic cost of the disease in the United States in children is approximately $350 million annually.

Lower respiratory infectious disease is the fifth-leading cause of death and the combined leading infectious cause of death, being responsible for 2·74 million deaths worldwide. This is generally similar to estimates in the 2010 Global Burden of Disease study.

This total only accounts for "Streptococcus pneumoniae" and "Haemophilus Influenzae" infections and does not account for atypical or nosocomial causes of lower respiratory disease, therefore underestimating total disease burden.

Strep throat is caused by group A beta-hemolytic streptococcus (GAS or S. pyogenes). Other bacteria such as non–group A beta-hemolytic streptococci and fusobacterium may also cause pharyngitis. It is spread by direct, close contact with an infected person; thus crowding, as may be found in the military and schools, increases the rate of transmission. Dried bacteria in dust are not infectious, although moist bacteria on toothbrushes or similar items can persist for up to fifteen days. Contaminated food can result in outbreaks, but this is rare. Of children with no signs or symptoms, 12% carry GAS in their pharynx, and, after treatment, approximately 15% of those remain positive, and are true "carriers".

Lower respiratory tract infections place a considerable strain on the health budget and are generally more serious than upper respiratory infections.

A 2014 systematic review of clinical trials does not support using routine rapid viral testing to decrease antibiotic use for children in emergency departments. It is unclear if rapid viral testing in the emergency department for children with acute febrile respiratory infections reduces the rates of antibiotic use, blood testing, or urine testing. The relative risk reduction of chest x-ray utilization in children screened with rapid viral testing is 77% compared with controls. In 2013 researchers developed a breath tester that can promptly diagnose lung infections.

The lower respiratory tract consists of the trachea (wind pipe), bronchial tubes, the bronchioles, and the lungs.

Lower respiratory tract infections are generally more serious than upper respiratory infections. LRIs are the leading cause of death among all infectious diseases. The two most common LRIs are bronchitis and pneumonia. Influenza affects both the upper and lower respiratory tracts, but more dangerous strains such as the highly pernicious H5N1 tend to bind to receptors deep in the lungs.

In the case of infectious rhinitis, vaccination against influenza viruses, adenoviruses, measles, rubella, "Streptococcus pneumoniae", "Haemophilus influenzae", diphtheria, "Bacillus anthracis", and "Bordetella pertussis" may help prevent it.

Rhinitis is commonly caused by a viral or bacterial infection, including the common cold, which is caused by Rhinoviruses, Coronaviruses, and influenza viruses, others caused by adenoviruses, human parainfluenza viruses, human respiratory syncytial virus, enteroviruses other than rhinoviruses, metapneumovirus, and measles virus, or bacterial sinusitis, which is commonly caused by "Streptococcus pneumoniae", "Haemophilus influenzae", and "Moraxella catarrhalis". Symptoms of the common cold include rhinorrhea, sneezing, sore throat (pharyngitis), cough, congestion, and slight headache.

Acute infectious thyroiditis is very rare, with it only accounting for about 0.1–0.7% of all thyroiditis. Large hospitals tend to only see two cases of AIT annually. For the few cases of AIT that are seen the statistics seem to show a pattern. AIT is found in children and young adults between the ages of 20 and 40. The occurrence of the disease in people between 20 and 40 is only about 8% with the other 92% being in children. Men and women are each just as likely to get the disease. If left untreated, there is a 12% mortality rate.

Transmission may occur via consumption of contaminated water, or when people share personal objects. In places with wet and dry seasons, water quality typically worsens during the wet season, and this correlates with the time of outbreaks. In areas of the world with four seasons, infections are more common in the winter. Bottle-feeding of babies with improperly sanitized bottles is a significant cause on a global scale. Transmission rates are also related to poor hygiene, especially among children, in crowded households, and in those with pre-existing poor nutritional status. After developing tolerance, adults may carry certain organisms without exhibiting signs or symptoms, and thus act as natural reservoirs of contagion. While some agents (such as "Shigella") only occur in primates, others may occur in a wide variety of animals (such as "Giardia").

A variety of causes may lead to dacrocystitis. Most notably, obstruction of the nasolacrimal duct leads to stasis of the nasolacrimal fluid, which predisposes to infection. Staphylococcus aureus is a common bacterial pathogen causing infectious dacrocystitis. Sometimes, especially in women, stones may develop in the lacrimal gland, causing recurrent bouts of dacrocystitis; this condition is called "acute dacryocystic retention syndrome."

Also due to pneumococcus, infection due to surrounding structure such as paranasal sinuses.

In the developed world "Campylobacter jejuni" is the primary cause of bacterial gastroenteritis, with half of these cases associated with exposure to poultry. In children, bacteria are the cause in about 15% of cases, with the most common types being "Escherichia coli", "Salmonella", "Shigella", and "Campylobacter" species. If food becomes contaminated with bacteria and remains at room temperature for a period of several hours, the bacteria multiply and increase the risk of infection in those who consume the food. Some foods commonly associated with illness include raw or undercooked meat, poultry, seafood, and eggs; raw sprouts; unpasteurized milk and soft cheeses; and fruit and vegetable juices. In the developing world, especially sub-Saharan Africa and Asia, cholera is a common cause of gastroenteritis. This infection is usually transmitted by contaminated water or food.

Toxigenic "Clostridium difficile" is an important cause of diarrhea that occurs more often in the elderly. Infants can carry these bacteria without developing symptoms. It is a common cause of diarrhea in those who are hospitalized and is frequently associated with antibiotic use. "Staphylococcus aureus" infectious diarrhea may also occur in those who have used antibiotics. Acute "traveler's diarrhea" is usually a type of bacterial gastroenteritis, while the persistent form is usually parasitic. Acid-suppressing medication appears to increase the risk of significant infection after exposure to a number of organisms, including "Clostridium difficile", "Salmonella", and "Campylobacter" species. The risk is greater in those taking proton pump inhibitors than with H2 antagonists.

About 60 percent of initial attacks of dacryocystitis will recur. Individuals with a poorly functioning immune system (immunocompromised) may develop orbital cellulitis, which may lead to optic neuritis, proptosis, motility abnormalities, or blindness.

No specific treatment is available, but antibiotics can be used to prevent secondary infections.

Vaccines are available (ATCvet codes: for the inactivated vaccine, for the live vaccine; plus various combinations).

Biosecurity protocols including adequate isolation, disinfection are important in controlling the spread of the disease.

Chemical pneumonitis is inflammation of the lung caused by aspirating or inhaling irritants. It is sometimes called a "chemical pneumonia", though it is not infectious. There are two general types of chemical pneumonitis: acute and chronic.

Irritants capable of causing chemical pneumonitis include vomitus, barium used in gastro-intestinal imaging, chlorine gas (among other pulmonary agents), ingested gasoline or other petroleum distillates, ingested or skin absorbed pesticides, gases from electroplating, smoke and others. It may also be caused by the use of inhalants.

Mendelson's syndrome is a type of chemical pneumonitis.

Mineral oil should not be given internally to young children, pets, or anyone with a cough, hiatus hernia, or nocturnal reflux, because it can cause complications such as lipoid pneumonia. Due to its low density, it is easily aspirated into the lungs, where it cannot be removed by the body. In children, if aspirated, the oil can work to prevent normal breathing, resulting in death of brain cells and permanent paralysis and/or retardation

Avian infectious bronchitis (IB) is an acute and highly contagious respiratory disease of chickens. The disease is caused by avian infectious bronchitis virus (IBV), a coronavirus, and characterized by respiratory signs including gasping, coughing, sneezing, tracheal rales, and nasal discharge. In young chickens, severe respiratory distress may occur. In layers, respiratory distress, nephritis, decrease in egg production, and loss of internal (watery egg white) and external (fragile, soft, irregular or rough shells, shell-less) egg quality are reported.

Causes of hemorrhagic cystitis include chemotherapy (e.g. cyclophosphamide, Ifosfamide), radiation, or infection. Ifosfamide is the most common cause of hemorrhagic cystitis. Radiation-induced hemorrhagic cystitis develops in similar or smaller patient numbers when compared to cyclophosphamide-induced cases.

Adenovirus (particularly serotypes 11 and 21 of subgroup B) is the most common cause of acute viral hemorrhagic cystitis in children, though it can result from BK virus as well. A chemical hemorrhagic cystitis can develop when vaginal products are inadvertently placed in the urethra. Gentian violet douching to treat candidiasis has resulted in hemorrhagic cystitis when the drug was misplaced in the urethra, but this hemorrhagic cystitis resolved spontaneously with cessation of treatment. Accidental urethral placement of contraceptive suppositories has also caused hemorrhagic cystitis in several patients. The bladder irritation was thought to be caused by the spermicidal detergent nonoxynol-9. In the acute setting, the bladder can be copiously irrigated with alkalinized normal saline to minimize bladder irritation.

Although hemorrhagic cystitis post-transplantation/bone marrow transplantation is not technically infectious, a short discussion is in order for completeness. Patients undergoing therapy to suppress the immune system are at risk for hemorrhagic cystitis due to either the direct effects of chemotherapy or activation of dormant viruses in the kidney, ureter, or bladder.