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.

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 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.

Opportunistic infections caused by Feline Leukemia Virus and Feline immunodeficiency virus retroviral infections can be treated with Lymphocyte T-Cell Immune Modulator.

Since opportunistic infections can cause severe disease, much emphasis is placed on measures to prevent infection. Such a strategy usually includes restoration of the immune system as soon as possible, avoiding exposures to infectious agents, and using antimicrobial medications ("prophylactic medications") directed against specific infections.

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.

There are several populations that have a higher risk for contracting coccidioidomycosis and developing the advanced disseminated version of the disease. Populations with exposure to the airborne arthroconidia working in agriculture and construction have a higher risk. Outbreaks have also been linked to earthquakes, windstorms and military training exercises where the ground is disturbed. Historically an infection is more likely to occur in males than females, although this could be attributed to occupation rather than gender specific. Women who are pregnant and immediately postpartum are at a high risk of infection and dissemination. There is also an association between stage of pregnancy and severity of the disease, with third trimester women being more likely to develop dissemination. Presumably this is related to highly elevated hormonal levels, which stimulate growth and maturation of spherules and subsequent release of endospores. Certain ethnic populations are more susceptible to disseminated coccioidomycosis. The risk of dissemination is 175 times greater in Filipinos and 10 times greater in African Americans than non-Hispanic whites. Individuals with a weakened immune system are also more susceptible to the disease. In particular, individuals with HIV and diseases that impair T-cell function. Individuals with pre-existing conditions such as diabetes are also at a higher risk. Age also affects the severity of the disease, with more than one third of deaths being in the 65-84 age group.

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.”

The prognosis of nocardiosis is highly variable. The state of the host's health, site, duration, and severity of the infection all play parts in determining the prognosis. As of now, skin and soft tissue infections have a 100% cure rate, and pleuropulmonary infections have a 90% cure rate with appropriate therapy. The cure rate falls to 63% with those infected with dissemented nocardiosis, with only half of those surviving infections that cause brain abscess. Additionally, 44% of people who are infected in the spinal cord/brain die, increasing to 85% if that person has an already weakened immune system. Unfortunately, there is not a preventative to nocardiosis. The only recommendation is to protect open wounds to limit access.

"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).

Individuals with a weak immune system are most at risk. This includes individuals taking immunosuppressive medication, cancer patients, HIV patients, premature babies with very low birth weight, the elderly, etc.

People who are at an increased risk of acquiring particular fungal infections in general may also be at an increased risk of developing fungal meningitis, as the infection may in some cases spread to the CNS. People residing in the Midwestern United States, and Southwestern United States and Mexico are at an increased risk of infection with "Histoplasma" and "Coccidioides", respectively.

If left untreated, miliary tuberculosis is almost always fatal. Although most cases of miliary tuberculosis are treatable, the mortality rate among children with miliary tuberculosis remains 15 to 20% and for adults 25 to 30%. One of the main causes for these high mortality rates includes late detection of disease caused by non-specific symptoms. Non-specific symptoms include: coughing, weight loss, or organ dysfunction. These symptoms may be implicated in numerous disorders, thus delaying diagnosis. Misdiagnosis with tuberculosis meningitis is also a common occurrence when patients are tested for tuberculosis, since the two forms of tuberculosis have high rates of co-occurrence.

Normally found in soil, these organisms cause occasional sporadic disease in humans and animals throughout the world. Another well publicized find is that of Nocardia as an oral microflora. Nocardia spp. have been reported in the normal gingiva and periodontal pockets along with other species such as "Actinomyces", "Arthromyces" and "Streptomyces" spp.

The usual mode of transmission is inhalation of organisms suspended in dust. Another very common method is that by traumatic introduction, especially in the jaw. This leads to the entrance of Nocardia into the blood stream and the propagation of its pathogenic effects. Transmission by direct inoculation through puncture wounds or abrasions is less common. Generally, nocardial infection requires some degree of immune suppression.

A weakened immune system is a general indicator of someone who is more susceptible to nocardiosis, such as someone who already has a disease that weakens their immune system. Additionally, those with low T-cell counts or other complications involving T-cells can expect to have a higher chance of becoming infected. Besides those with weak immune systems, a local traumatic inoculation can cause nocardiosis, specifically the cutaneous, lymphocutaneous, and subcutaneous forms of the disease.

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.

It is not practical to test or decontaminate most sites that may be contaminated with "H. capsulatum", but the following sources list environments where histoplasmosis is common, and precautions to reduce a person's risk of exposure, in the three parts of the world where the disease is prevalent. Precautions common to all geographical locations would be to avoid accumulations of bird or bat droppings.

The US National Institute for Occupational Safety and Health (NIOSH) provides information on work practices and personal protective equipment that may reduce the risk of infection. This document is available in English and Spanish.

Authors at the University of Nigeria have published a review which includes information on locations in which histoplasmosis has been found in Africa (in chicken runs, bats and the caves bats infest, and in soil), and a thorough reference list including English, French, and Spanish language references.

Prognosis depends on the pathogen responsible for the infection and risk group. Overall mortality for "Candida" meningitis is 10-20%, 31% for patients with HIV, and 11% in neurosurgical cases (when treated). Prognosis for "Aspergillus" and coccidioidal infections is poor.

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.

"Histoplasmosis capsulatum" is found throughout the world. It is endemic in certain areas of the United States, particularly in states bordering the Ohio River valley and the lower Mississippi River. The humidity and acidity patterns of soil are associated with endemicity. Bird and bat droppings in soil promote growth of "Histoplasma". Contact with such soil aerosolizes the microconidia, which can infect humans. It is also common in caves in southern and East Africa. Positive histoplasmin skin tests occur in as many as 90% of the people living in areas where "H. capsulatum" is common, such as the eastern and central United States.

In Canada, the St. Lawrence River Valley is the site of the most frequent infections, with 20-30 percent of the population testing positive.

In India, the Gangetic West Bengal is the site of most frequent infections, with 9.4 percent of the population testing positive. "Histoplasma capsulatum capsulatum" was isolated from the local soil proving endemicity of histoplasmosis in West Bengal.

Preventing Valley fever is challenging because it is difficult to avoid breathing in the fungus should it be present, however, the public health effect of the disease is essential to understand in areas where the fungus is endemic. Enhancing surveillance of Coccidiodomycosis is key to preparedness in the medical field in addition to improving diagnostics for early infections. Currently there are no completely effective preventive measures available for people who live or travel through Valley Fever -endemic areas. Recommended preventive measures include avoiding airborne dust or dirt, but this does not guarantee protection against infection. People in certain occupations may be advised to wear face masks. The use of air filtration indoors is also helpful, in addition to keeping skin injuries clean and covered to avoid skin infection.

In 1998-2011, there were 111,117 cases of coccidioidomycosis in the U.S. that were logged into the National Notifiable Diseases Surveillance System (NNDSS). Since many U.S. states do not require reporting of coccidioidomycosis, the actual numbers can be higher. The United States' Centers for Disease Control and Prevention (CDC) called the disease a "silent epidemic" and acknowledged that there is no proven anticoccidioidal vaccine available. Studies done in the past show that the cost benefit of a vaccine is most notable among infants, teens, and immigrant adults, with negative cost-benefit results among older age groups.

Raising both surveillance and awareness of the disease while medical researchers are developing a human vaccine can positively contribute towards prevention efforts. Research demonstrates that patients from endemic areas who are aware of the disease are most likely to request diagnostic testing for coccidioidomycosis. Presently, Meridian Bioscience manufactures the so-called "EIA test" to diagnose the Valley fever, which however is known for producing a fair quantity of false positives. Currently, recommended prevention measures can include type-of-exposure-based respirator protection for persons engaged in agriculture, construction and others working outdoors in endemic areas. Dust control measures such as planting grass and wetting the soil, and also limiting exposure to dust storms are advisable for residential areas in endemic regions.

Aspergillosis is the name given to a wide variety of diseases caused by infection by fungi of the genus "Aspergillus". The majority of cases occur in people with underlying illnesses such as tuberculosis or chronic obstructive pulmonary disease (COPD), but with otherwise healthy immune systems. Most commonly, aspergillosis occurs in the form of chronic pulmonary aspergillosis (CPA), aspergilloma or allergic bronchopulmonary aspergillosis (ABPA). Some forms are intertwined; for example ABPA and simple aspergilloma can progress to CPA.

Other, non-invasive manifestations include fungal sinusitis (both allergic in nature and with established fungal balls), otomycosis (ear infection), keratitis (eye infection) and onychomycosis (nail infection). In most instances these are less severe, and curable with effective antifungal treatment.

People with deficient immune systems—such as patients undergoing hematopoietic stem cell transplantation, chemotherapy for leukaemia, or AIDS—are at risk of more disseminated disease. Acute invasive aspergillosis occurs when the immune system fails to prevent "Aspergillus" spores from entering the bloodstream via the lungs. Without the body mounting an effective immune response, fungal cells are free to disseminate throughout the body and can infect major organs such as the heart and kidneys.

The most frequently identified pathogen is "Aspergillus fumigatus"—a ubiquitous organism that is capable of living under extensive environmental stress. It is estimated that most humans inhale thousands of "Aspergillus" spores daily, but they do not affect most people’s health due to effective immune responses. Taken together, the major chronic, invasive and allergic forms of aspergillosis account for around 600,000 deaths annually worldwide.

Lobar pneumonia is a form of pneumonia that affects a large and continuous area of the lobe of a lung.

It is one of the two anatomic classifications of pneumonia (the other being bronchopneumonia).

The standard treatment recommended by the WHO is with isoniazid and rifampicin for six months, as well as ethambutol and pyrazinamide for the first two months. If there is evidence of meningitis, then treatment is extended to twelve months. The U.S. guidelines recommend nine months' treatment. "Common medication side effects a patient may have such as inflammation of the liver if a patient is taking pyrazinamide, rifampin, and isoniazid. A patient may also have drug resistance to medication, relapse, respiratory failure, and adult respiratory distress syndrome."

Albeit relatively rare in humans, aspergillosis is a common and dangerous infection in birds, particularly in pet parrots. Mallards and other ducks are particularly susceptible, as they will often resort to poor food sources during bad weather. Captive raptors, such as falcons and hawks, are susceptible to this disease if they are kept in poor conditions and especially if they are fed pigeons, which are often carriers of "asper". It can be acute in chicks, but chronic in mature birds.

Aspergillosis has been the culprit in several rapid die-offs among waterfowl. From 8 December until 14 December 2006, over 2,000 Mallards died in the Burley, Idaho area of the USA, an agricultural community approximately 150 miles southeast of Boise. Mouldy waste grain from the farmland and feedlots in the area is the suspected source. A similar aspergillosis outbreak caused by mouldy grain killed 500 Mallards in Iowa, USA, in 2005.

While there is no connection between aspergillosis and the H5N1 strain of avian influenza (commonly called "bird flu"), rapid die-offs caused by aspergillosis can spark fears of bird flu outbreaks. Laboratory analysis is the only way to distinguish bird flu from aspergillosis.

In dogs, aspergillosis is an uncommon disease typically affecting only the nasal passages (nasal aspergillosis). This is much more common in dolicocephalic breeds. It can also spread to the rest of the body; this is termed disseminated aspergillosis and is rare, usually affecting individuals with underlying immune disorders.

Bats recovering from white-nose syndrome (WNS) may be the first natural occurrence of IRIS, in a report released by the USGS. WNS is typified by a cutaneous infection of the fungus "Pseudogymnoascus destructans" during hibernation, when the immune system is naturally suppressed to conserve energy through the winter. This study suggests that bats undergoing an intense inflammation at the site of infection after a return to euthermia is a form of IRIS.

An individual may only develop signs of an infection after a period of subclinical infection, a duration that is called the incubation period. This is the case, for example, for subclinical sexually transmitted diseases such as AIDS and genital warts. Individuals with such subclinical infections, and those that never develop overt illness, creates a reserve of individuals that can transmit an infectious agent to infect other individuals. Because such cases of infections do not come to clinical attention, health statistics can often fail to measure the true prevalence of an infection in a population, and this prevents the accurate modeling of its infectious transmission.