A study conducted on 452 patients revealed that the genotype responsible for higher IL-10 expression makes HIV infected people more susceptible to tuberculosis infection. Another study on HIV-TB co-infected patients also concluded that higher level of IL-10 and IL-22 makes TB patient more susceptible to Immune reconstitution inflammatory syndrome (IRIS). It is also seen that HIV co-infection with tuberculosis also reduces concentration of immunopathogenic matrix metalloproteinase (MMPs) leading to reduced inflammatory immunopathology.

HIV-infected children less than 12 years of age also develop disseminated MAC. Some age adjustment is necessary when clinicians interpret CD4+ T-lymphocyte counts in children less than 2 years of age. Diagnosis, therapy, and prophylaxis should follow recommendations similar to those for adolescents and adults.

CAP is common worldwide, and a major cause of death in all age groups. In children, most deaths (over two million a year) occur in newborn period. According to a World Health Organization estimate, one in three newborn deaths are from pneumonia. Mortality decreases with age until late adulthood, with the elderly at risk for CAP and its associated mortality.

More CAP cases occur during the winter than at other times of the year. CAP is more common in males than females, and more common in black people than Caucasians. Patients with underlying illnesses (such as Alzheimer's disease, cystic fibrosis, COPD, tobacco smoking, alcoholism or immune-system problems) have an increased risk of developing pneumonia.

A full spectrum of microorganisms is responsible for CAP in adults, and patients with certain risk factors are more susceptible to infections of certain groups of microorganisms. Identifying people at risk for infection by these organisms aids in appropriate treatment.

Many less-common organisms can cause CAP in adults, and are identified from specific risk factors or treatment failure for common causes.

MAI is common in immunocompromised individuals, including senior citizens and those with HIV/AIDS or cystic fibrosis. Bronchiectasis, the bronchial condition which causes unnatural enlargement of the bronchial tubes, is commonly found with MAI infection. Whether the bronchiectasis leads to the MAC infection or is the result of it is not always known.

The "Mycobacterium avium complex" (MAC) includes common atypical bacteria, i.e. nontuberculous mycobacteria (NTM), found in the environment which can infect people with HIV and low CD4 cell count (below 100/microliter); mode of infection is usually inhalation or ingestion.

MAC causes disseminated disease in up to 40% of people with human immunodeficiency virus (HIV) in the United States, producing fever, sweats, weight loss, and anemia. Disseminated MAC characteristically affects people with advanced HIV disease and peripheral CD4+ T-lymphocyte counts less than 100 cells/uL. Effective prevention and therapy of MAC has the potential to contribute substantially to improved quality of life and duration of survival for HIV-infected persons.

A number of factors make people more susceptible to TB infections. The most important risk factor globally is HIV; 13% of all people with TB are infected by the virus. This is a particular problem in sub-Saharan Africa, where rates of HIV are high. Of people without HIV who are infected with tuberculosis, about 5–10% develop active disease during their lifetimes; in contrast, 30% of those coinfected with HIV develop the active disease.

Tuberculosis is closely linked to both overcrowding and malnutrition, making it one of the principal diseases of poverty. Those at high risk thus include: people who inject illicit drugs, inhabitants and employees of locales where vulnerable people gather (e.g. prisons and homeless shelters), medically underprivileged and resource-poor communities, high-risk ethnic minorities, children in close contact with high-risk category patients, and health-care providers serving these patients.

Chronic lung disease is another significant risk factor. Silicosis increases the risk about 30-fold. Those who smoke cigarettes have nearly twice the risk of TB compared to nonsmokers.

Other disease states can also increase the risk of developing tuberculosis. These include alcoholism and diabetes mellitus (three-fold increase).

Certain medications, such as corticosteroids and infliximab (an anti-αTNF monoclonal antibody), are becoming increasingly important risk factors, especially in the developed world.

Genetic susceptibility also exists, for which the overall importance remains undefined.

When HIV-negative children take isoniazid after they have been exposed to tuberculosis, their risk to contract tuberculosis is reduced. A Cochrane review investigated whether giving isoniazid to HIV-positive children can help to prevent this vulnerable group from getting tuberculosis. They included three trials conducted in South Africa and Botswana and found that isoniazid given to all children diagnosed with HIV may reduce the risk of active tuberculosis and death in children who are not on antiretroviral treatment. For children taking antiretroviral medication, no clear benefit was detected.

Progression from TB infection to overt TB disease occurs when the bacilli overcome the immune system defenses and begin to multiply. In primary TB disease (some 1–5% of cases), this occurs soon after the initial infection. However, in the majority of cases, a latent infection occurs with no obvious symptoms. These dormant bacilli produce active tuberculosis in 5–10% of these latent cases, often many years after infection.

The risk of reactivation increases with immunosuppression, such as that caused by infection with HIV. In people coinfected with "M. tuberculosis" and HIV, the risk of reactivation increases to 10% per year. Studies using DNA fingerprinting of "M. tuberculosis" strains have shown reinfection contributes more substantially to recurrent TB than previously thought, with estimates that it might account for more than 50% of reactivated cases in areas where TB is common. The chance of death from a case of tuberculosis is about 4% as of 2008, down from 8% in 1995.

For infecting organisms to survive and repeat the infection cycle in other hosts, they (or their progeny) must leave an existing reservoir and cause infection elsewhere. Infection transmission can take place via many potential routes:

- Droplet contact, also known as the "respiratory route", and the resultant infection can be termed airborne disease. If an infected person coughs or sneezes on another person the microorganisms, suspended in warm, moist droplets, may enter the body through the nose, mouth or eye surfaces.

- Fecal-oral transmission, wherein foodstuffs or water become contaminated (by people not washing their hands before preparing food, or untreated sewage being released into a drinking water supply) and the people who eat and drink them become infected. Common fecal-oral transmitted pathogens include "Vibrio cholerae", "Giardia" species, rotaviruses, "Entameba histolytica", "Escherichia coli", and tape worms. Most of these pathogens cause gastroenteritis.

- Sexual transmission, with the resulting disease being called sexually transmitted disease

- Oral transmission, Diseases that are transmitted primarily by oral means may be caught through direct oral contact such as kissing, or by indirect contact such as by sharing a drinking glass or a cigarette.

- Transmission by direct contact, Some diseases that are transmissible by direct contact include athlete's foot, impetigo and warts

- Vehicle Transmission, transmission by an inanimate reservoir (food, water, soil).

- Vertical transmission, directly from the mother to an embryo, fetus or baby during pregnancy or childbirth. It can occur when the mother gets an infection as an intercurrent disease in pregnancy.

- Iatrogenic transmission, due to medical procedures such as injection or transplantation of infected material.

- Vector-borne transmission, transmitted by a vector, which is an organism that does not cause disease itself but that transmits infection by conveying pathogens from one host to another.

The relationship between "virulence versus transmissibility" is complex; if a disease is rapidly fatal, the host may die before the microbe can be passed along to another host.

A number of studies have reported associations between pathogen load in an area and human behavior. Higher pathogen load is associated with decreased size of ethnic and religious groups in an area. This may be due high pathogen load favoring avoidance of other groups, which may reduce pathogen transmission, or a high pathogen load preventing the creation of large settlements and armies that enforce a common culture. Higher pathogen load is also associated with more restricted sexual behavior, which may reduce pathogen transmission. It also associated with higher preferences for health and attractiveness in mates. Higher fertility rates and shorter or less parental care per child is another association that may be a compensation for the higher mortality rate. There is also an association with polygyny which may be due to higher pathogen load, making selecting males with a high genetic resistance increasingly important. Higher pathogen load is also associated with more collectivism and less individualism, which may limit contacts with outside groups and infections. There are alternative explanations for at least some of the associations although some of these explanations may in turn ultimately be due to pathogen load. Thus, polygny may also be due to a lower male:female ratio in these areas but this may ultimately be due to male infants having increased mortality from infectious diseases. Another example is that poor socioeconomic factors may ultimately in part be due to high pathogen load preventing economic development.

The 2007 guideline “Official American Thoracic Society (ATS) and Infectious Diseases Society of America (IDSA) statement: diagnosis, treatment, and prevention of non-tuberculosis mycobacterial diseases”, notes that M. fortuitum isolates are usually susceptible to multiple oral antimicrobial agents, including the macrolides and quinolones, doxycycline and minocycline, and sulfonamides. Isolates of this mycobacterium are susceptible to the beta-lactam antibiotics, belonging to the carbopenam subgroup, such as Imipenem. Imipenem is a broad spectrum antibiotic produced by the bacteria Streptomyces cattleya. Ondansetron HCL (Zofran) is an antiemetic often given to offset the nausea and vomiting that are a common side effect of Imipenem. Severe infections require IV treatment combined with oral antibiotics for a prolonged period, up to several months. The guideline recommends “for serious skin, bone, and soft tissue M fortuitum disease, a minimum of 4 months of therapy with at least two agents with in vitro activity against the clinical isolate is necessary to provide a high likelihood of cure. Surgery is generally indicated with extensive disease, abscess formation, or where drug therapy is difficult.”

"Mycobacterium fortuitum" is a fast-growing species that can cause infections. The term "fast growing" is a reference to a growth rate of 3 or 4 days, when compared to other Mycobacteria that may take weeks to grow out on laboratory media. Pulmonary infections of "M. fortuitum" are uncommon, but "Mycobacterium fortuitum" can cause local skin disease, osteomyelitis (inflammation of the bone), joint infections and infections of the eye after trauma. "Mycobacterium fortuitum" has a worldwide distribution and can be found in natural and processed water, sewage, and dirt.

Bacteria classified as Mycobacteria, include the causative agents for tuberculosis and leprosy. Mycobacteria are sometimes referred to as “acid-fast bacteria,” a term referencing their response to a laboratory staining technique. This simply means that when microscopic slides of these bacteria are rinsed with an acidic solution, they retain a red dye. "Mycobacterium fortuitum" is one of the many species of nontuberculosis mycobacteria (NTM) that are commonly found in the environment. These are not involved in tuberculosis. This does not mean, however, that they will not cause an infection in the right circumstances.

"M. fortuitum" infection can be a nosocomial (hospital acquired) disease. Surgical sites may become infected after the wound is exposed directly or indirectly to contaminated tap water. Other possible sources of "M. fortuitum" infection include implanted devices such as catheters, injection site abscesses, and contaminated endoscopes. Recent publication on Rapidly Growing Mycobacteria (RGM) is available provides the following aspects of RGM: (i) its sources, predisposing factors, clinical manifestations, and concomitant fungal infections; (ii) the risks of misdiagnoses in the management of RGM infections in dermatological settings; (iii) the diagnoses and outcomes of treatment responses in common and uncommon infections in immunocompromised and immunocompetent patients; (iv) conventional versus current molecular methods for the detection of RGM; (v) the basic principles of a promising MALDI-TOF MS, sampling protocol for cutaneous or subcutaneous lesions and its potential for the precise differentiation of "M. fortuitum", "M. chelonae", and "M. abscessus"; and (vi) improvements in RGM infection management as described in the recent 2011 Clinical and

Laboratory Standards Institute (CLSI) guidelines, including interpretation criteria of molecular methods and antimicrobial drug panels and their break points [minimum inhibitory concentrations (MICs)], which have been highlighted for the initiation of antimicrobial therapy (Kothavade RJ et al., 2012).

In most cases, the prognosis of mucormycosis is poor and has varied mortality rates depending on its form and severity. In the rhinocerebral form, the mortality rate is between 30% and 70%, whereas disseminated mucormycosis presents with the highest mortality rate in an otherwise healthy patient, with a mortality rate of up to 90%. Patients with AIDS have a mortality rate of almost 100%. Possible complications of mucormycosis include the partial loss of neurological function, blindness and clotting of brain or lung vessels.

Mucormycosis is a very rare infection, and as such, it is hard to note histories of patients and incidence of the infection. However, one American oncology center revealed that mucormycosis was found in 0.7% of autopsies and roughly 20 patients per every 100,000 admissions to that center. In the United States, mucormycosis was most commonly found in rhinocerebral form, almost always with hyperglycemia and metabolic acidosis (e.g. DKA). In most cases the patient is immunocompromised, although rare cases have occurred in which the subject was not; these are usually due to a traumatic inoculation of fungal spores. Internationally, mucormycosis was found in 1% of patients with acute leukemia in an Italian review.

MAP is capable of causing Johne's-like symptoms in humans, though difficulty in testing for MAP infection presents a diagnostic hurdle.

Clinical similarities are seen between Johne's disease in ruminants and inflammatory bowel disease in humans, and because of this, some researchers contend the organism is a cause of Crohn's disease. However, epidemiologic studies have provided variable results; in certain studies, the organism (or an immune response directed against it) has been much more frequently found in patients with Crohn's disease than asymptomatic people.

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.

Mendelian susceptibility to mycobacterial disease, also called familial disseminated atypical mycobacterial infection, is a rare genetic disease characterized by susceptibility to mycobacteria and Salmonella infection outside of the intestinal tract.

In an endemic herd, only a minority of the animals develops clinical signs; most animals either eliminate the infection or become asymptomatic carriers. The mortality rate is about 1%, but up to 50% of the animals in the herd can be asymptomatically infected, resulting in losses in production. Once the symptoms appear, paratuberculosis is progressive and affected animals eventually die. The percentage of asymptomatic carriers that develop overt disease is unknown.

Despite the thyroid gland being extremely resistant to infection, it is still susceptible to infection by various bacteria. The cause can be almost any bacterium. "Staphylococcus aureus", "Streptococcus pyogenes", "Staphylococcus epidermidis", and "Streptococcus pneumoniae" in descending order are the organisms most commonly isolated from acute thyroiditis cases in children. Other aerobic organisms are "Klebsiella sp", "Haemophilus influenza", "Streptococcus viridans", "Eikenella corrodens", "Enterobacteriaceae", and "salmonella sp".

Occurrences of AIT are most common in patients with prior thyroid disease such as Hashimoto's thyroiditis or thyroid cancer. The most common cause of infection in children is a congenital abnormality such as pyriform sinus fistula. In most cases, the infection originates in the piriform sinus and spreads to the thyroid via the fistula. In many reported cases of AIT the infection occurs following an upper respiratory tract infection. One study found that of the reported cases of AIT, 66% occurred after an acute illness involving the upper respiratory tract. Although the rates of infection are still very low, cases of AIT have been on the rise in recent years due to the higher occurrence of immune-compromised patients.

Other causes of AIT are commonly due to contamination from an outside source and are included below.

- Repeated fine needle aspirates

- Perforation of esophagus

- Regional infection

Most household disinfectants will inactivate FHV-1. The virus can survive up to 18 hours in a damp environment, but less in a dry environment and only shortly as an aerosol.

Tuberculosis, pneumonia, inhaled foreign bodies, allergic bronchopulmonary aspergillosis and bronchial tumours are the major acquired causes of bronchiectasis. Infective causes associated with bronchiectasis include infections caused by the Staphylococcus, Klebsiella, or Bordetella pertussis, the causative agent of whooping cough and nontuberculous mycobacteria.

Aspiration of ammonia and other toxic gases, pulmonary aspiration, alcoholism, heroin (drug use), various allergies all appear to be linked to the development of bronchiectasis.

Various immunological and lifestyle factors have also been linked to the development of bronchiectasis:

- Childhood Acquired Immune Deficiency Syndrome (AIDS), which predisposes patients to a variety of pulmonary ailments, such as pneumonia and other opportunistic infections.

- Inflammatory bowel disease, especially ulcerative colitis. It can occur in Crohn's disease as well, but does so less frequently. Bronchiectasis in this situation usually stems from various allergic responses to inhaled fungal spores. A Hiatal hernia can cause Bronchiectasis when the stomach acid that is aspirated into the lungs causes tissue damage.

- People with rheumatoid arthritis who smoke appear to have a tenfold increased rate of the disease. Still, it is unclear as to whether or not cigarette smoke is a specific primary cause of bronchiectasis.

- Case reports of Hashimoto's thyroiditis and bronchiectasis occurring in the same persons have been published.

No cause is identified in up to 50% of non-cystic-fibrosis related bronchiectasis.

There is a vaccine for FHV-1 available (ATCvet code: , plus various combination vaccines), but although it limits or weakens the severity of the disease and may reduce viral shedding, it does not prevent infection with FVR. Studies have shown a duration of immunity of this vaccine to be at least three years. The use of serology to demonstrate circulating antibodies to FHV-1 has been shown to have a positive predictive value for indicating protection from this disease.

Buruli ulcer commonly affects poor people in remote rural areas with limited access to health care. The disease can affect all age groups, although children under the age of 15 years (range 2–14 years) are predominantly affected. There are no sex differences in the distribution of cases among children. Among adults, some studies have reported higher rates among women than males (Debacker "et al." accepted for publication). No racial or socio-economic group is exempt from the disease. Most ulcers occur on the extremities; lesions on the lower extremities are almost twice as common as those on the upper extremities. Ulcers on the head and trunk accounted for less than 8% of cases in one large series.

Otomycosis is treated by debridment followed with topical azole antifungals, and symptomatically managed with oral antihistamines. Per a study in Iran 10cc acetic acid 2% plus 90 cc of isopropyl alcohol 70% was effective.

Bacterial infections of the orbit have long been associated with a risk of catastrophic local

sequelae and intracranial spread.

The natural course of the disease, as documented by Gamble (1933), in the pre-antibiotic era,

resulted in death in 17% of patients and permanent blindness in 20%.