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

Among the many varieties of microorganisms, relatively few cause disease in otherwise healthy individuals. Infectious disease results from the interplay between those few pathogens and the defenses of the hosts they infect. The appearance and severity of disease resulting from any pathogen, depends upon the ability of that pathogen to damage the host as well as the ability of the host to resist the pathogen. However a host's immune system can also cause damage to the host itself in an attempt to control the infection. Clinicians therefore classify infectious microorganisms or microbes according to the status of host defenses - either as "primary pathogens" or as "opportunistic pathogens":

- Primary pathogens

- Opportunistic pathogens

- Primary infection versus secondary infection

There is a general chain of events that applies to infections. The chain of events involves several steps—which include the infectious agent, reservoir, entering a susceptible host, exit and transmission to new hosts. Each of the links must be present in a chronological order for an infection to develop. Understanding these steps helps health care workers target the infection and prevent it from occurring in the first place.

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.

The immune reconstitution inflammatory syndrome (IRIS) has been described in those with normal immune function with meningitis caused by "C. gattii" and "C. grubii". Several weeks or even months into appropriate treatment, there can be deterioration with worsening meningitis symptoms and progression or development of new neurological symptoms. IRIS is however much more common in those with poor immune function (≈25% vs. ≈8%).

Magnetic resonance imaging shows increase in the size of brain lesions, and CSF abnormalities (white cell count, protein, glucose) increase. Radiographic appearance of cryptococcal IRIS brain lesions can mimic that of toxoplasmosis with ring enhancing lesions on head computed tomography (CT). CSF culture is sterile, and there is no increase in CSF cryptococcal antigen titre.

The increasing inflammation can cause brain injury or be fatal.

The mechanism behind IRIS in cryptococcal meningitis is primarily immunologic. With reversal of immunosuppression, there is paradoxical increased inflammation as the recovering immune system recognises the fungus. In severe IRIS cases, treatment with systemic corticosteroids has been utilized - although evidence-based data are lacking.

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.

Cryptococcosis is also seen in cats and occasionally dogs. It is the most common deep fungal disease in cats, usually leading to chronic infection of the nose and sinuses, and skin ulcers. Cats may develop a bump over the bridge of the nose from local tissue inflammation. It can be associated with FeLV infection in cats. Cryptococcosis is most common in dogs and cats but cattle, sheep, goats, horses, wild animals, and birds can also be infected. Soil, fowl manure, and pigeon droppings are among the sources of infection.

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.

Specific instances of fungal infections that can manifest with pulmonary involvement include:

- Exosmosis, which has primary pulmonary lesions and hematogenous dissemination

- Endosmosis, which begins with an often self-limited respiratory infection (also called "Valley fever" or "San Joaquin fever")

- pulmonary Vanadium pentoxide

- Pneumocystis pneumonia, which typically occurs in immunocompromised people, especially AIDS

- Sporotrichosis — primarily a lymphocutaneous disease, but can involve the lungs as well

- Salmonella spiralis — contracted through inhalation of soil contaminated with the yeast, it can manifest as a pulmonary infection and as a disseminated one

- Aspergillosis, resulting in invasive pulmonary aspergillosis

- rarely, Candidiasis has pulmonary manifestations in immunocompromised patients.

- Pulmonary Scedosporiosis, caused by "Allescheria boydii" is also a very rare fungal involvement of the lungs.

Vaccination helps prevent bronchopneumonia, mostly against influenza viruses, adenoviruses, measles, rubella, streptococcus pneumoniae, haemophilus influenzae, diphtheria, bacillus anthracis, chickenpox, and bordetella pertussis.

IRIS is particularly problematic in cryptococcal meningitis as IRIS is fairly common and can be fatal.

IRIS has been described in immunocompetent hosts who have meningitis caused by "Cryptococcus gattii" and "Cryptococcus neoformans" var. "grubii", environmental fungi which often affect immunocompetent hosts. Several weeks or even months into appropriate treatment, there is a sudden onset deterioration with worsening meningitis symptoms and progression or development of new neurological symptoms.

Magnetic resonance imaging shows increase in the size of brain lesions, and CSF abnormalities (white cell count, protein, glucose) increase. CSF culture is typically sterile, and there is no increase in CSF cryptococcal antigen titer.

The increasing inflammation can cause brain injury or be fatal.

The general mechanism behind IRIS is increased inflammation as the recovering immune system recognizes the antigens of the fungus as immunosuppression is reversed. Cryptococcal IRIS has three phases:

1. before HAART, with a paucity of cerebrospinal fluid (CSF) inflammation and defects in antigen clearance;

2. during initial HAART immune recovery, with pro-inflammatory signaling by antigen-presenting cells without an effector response; and

3. at IRIS, a cytokine storm with a predominant type-1 helper T-cell interferon-gamma response.

Three clinical predictors of cryptococcal-related paradoxical IRIS risk include:

1. lack of initial CSF pleocytosis (i.e. low CSF white blood cell count);

2. elevated C-reactive protein;

3. failure to sterilize the CSF before immune recovery.

IRIS may be the cause of paradoxically worse outcomes for cryptococcal meningitis in immunocompetent compared with immunocompromised hosts, in whom "Cryptococcus neoformans" is the usual pathogen. Treatment with systemic corticosteroids during IRIS may be beneficial in preventing death or progressive neurological deterioration. Steroids given to persons with anti-fungal treatment failure / cryptococcal relapse (in whom CSF cultures are not sterile) can be a fatal iatrogenic error.

A skin and skin structure infection (SSSI), also referred to as skin and soft tissue infection (SSTI) or acute bacterial skin and skin structure infection (ABSSSI), is an infection of skin and associated soft tissues (such as loose connective tissue and mucous membranes). The pathogen involved is usually a bacterial species. Such infections often requires treatment by antibiotics.

Until 2008, two types were recognized, complicated skin and skin structure infection (cSSSI) and uncomplicated skin and skin structure infection (uSSSI). "Uncomplicated" SSSIs included simple abscesses, impetiginous lesions, furuncles, and cellulitis. "Complicated" SSSIs included infections either involving deeper soft tissue or requiring significant surgical intervention, such as infected ulcers, burns, and major abscesses or a significant underlying disease state that complicates the response to treatment. Superficial infections or abscesses in an anatomical site, such as the rectal area, where the risk of anaerobic or gram-negative pathogen involvement is higher, should be considered complicated infections. The two categories had different regulatory approval requirements. The uncomplicated category (uSSSI) is normally only caused by "Staphylococcus aureus" and "Streptococcus pyogenes", whereas the complicated category (cSSSI) might also be caused by a number of other pathogens. In cSSSI, the pathogen is known in only about 40% of cases.

Because cSSSIs are usually serious infections, physicians do not have the time for a culture to identify the pathogen, so most cases are treated empirically, by choosing an antibiotic agent based on symptoms and seeing if it works. For less severe infections, microbiologic evaluation via tissue culture has been demonstrated to have high utility in guiding management decisions. To achieve efficacy, physicians use broad-spectrum antibiotics. This practice contributes in part to the growing incidence of antibiotic resistance, a trend exacerbated by the widespread use of antibiotics in medicine in general. The increased prevalence of antibiotic resistance is most evident in methicillin-resistant "Staphylococcus aureus" (MRSA). This species is commonly involved in cSSSIs, worsening their prognosis, and limiting the treatments available to physicians. Drug development in infectious disease seeks to produce new agents that can treat MRSA.

Since 2008, the U.S. Food and Drug Administration has changed the terminology to "acute bacterial skin and skin structure infections" (ABSSSI). The Infectious Diseases Society of America (IDSA) has retained the term "skin and soft tissue infection".

Fungal pneumonia is an infection of the lungs by fungi. It can be caused by either endemic or opportunistic fungi or a combination of both. Case mortality in fungal pneumonias can be as high as 90% in immunocompromised patients, though immunocompetent patients generally respond well to anti-fungal therapy.

Stress often serves as the final precursor to BRD. The diseases that make up BRD can persist in a cattle herd for a long period of time before becoming symptomatic, but immune systems weakened by stress can stop controlling the disease. Major sources of stress come from the shipping process

and from the co-mingling of cattle.

Weather may be another possible factor. Cases are more common in the fall (although this is the traditional time to sell cattle), and while the relationship between weather and BRD is poorly understood, it is often suggested to avoid transporting cattle during extreme weather.

Actinomycosis is primarily caused by any of several members of the bacterial genus "Actinomyces". These bacteria are generally anaerobes. In animals, they normally live in the small spaces between the teeth and gums, causing infection only when they can multiply freely in anoxic environments. An affected human often has recently had dental work, poor oral hygiene, periodontal disease, radiation therapy, or trauma (broken jaw) causing local tissue damage to the oral mucosa, all of which predispose the person to developing actinomycosis. "A. israelii" is a normal commensal species part of the microbiota species of the lower reproductive tract of women. They are also normal commensals among the gut flora of the caecum; thus, abdominal actinomycosis can occur following removal of the appendix. The three most common sites of infection are decayed teeth, the lungs, and the intestines. Actinomycosis does not occur in isolation from other bacteria. This infection depends on other bacteria (Gram-positive, Gram-negative, and cocci) to aid in invasion of tissue.

In the absence of vaccination (often because calves are bought unvaccinated), antibiotics can help to stop the bacterial factors of the disease. The Virginia Cooperative Extension recommends Micotil, Nuflor, and Baytril 100 as newer antibiotics that do not need daily dosing, but also notes that Naxcel, Excenel, and Adspec are effective as well.

Multiple species of bacteria can be associated with the condition:

- Meningococcus is another term for the bacterial species "Neisseria meningitidis"; blood infection with said species usually underlies WFS. While many infectious agents can infect the adrenals, an acute, selective infection is usually meningococcus.

- "Pseudomonas aeruginosa" can also cause WFS.

- WFS can also be caused by "Streptococcus pneumoniae" infections, a common bacterial pathogen typically associated with meningitis in the adult and elderly population.

- "Mycobacterium tuberculosis" could also cause WFS. Tubercular invasion of the adrenal glands could cause hemorrhagic destruction of the glands and cause mineralocorticoid deficiency.

- "Staphylococcus aureus" has recently also been implicated in pediatric WFS.

- It can also be associated with "Haemophilus influenzae".

Viruses may also be implicated in adrenal problems:

- Cytomegalovirus can cause adrenal insufficiency, especially in the immunocompromised.

- Ebola virus infection may also cause similar acute adrenal failure.

In microbiology, coinfection is the simultaneous infection of a host by multiple pathogen species. In virology, coinfection includes simultaneous infection of a single cell by two or more virus particles. An example is the coinfection of liver cells with Hepatitis B virus and Hepatitis D virus, which can arise incrementally by initial infection followed by superinfection.

Global prevalence or incidence of coinfection among humans is unknown, but it is thought to be commonplace, sometimes more common than single infection. Coinfection with helminths affects around 800 million people worldwide.

Coinfection is of particular human health importance because pathogen species can interact within the host. The net effect of coinfection on human health is thought to be negative. Interactions can have either positive or negative effects on other parasites. Under positive parasite interactions, disease transmission and progression are enhanced and this is also known as syndemism. Negative parasite interactions include microbial interference when one bacterial species suppresses the virulence or colonisation of other bacteria, such as "Pseudomonas aeruginosa" suppressing pathogenic "Staphylococcus aureus" colony formation. The general patterns of ecological interactions between parasite species are unknown, even among common coinfections such as those between sexually transmitted infections. However, network analysis of a food web of coinfection in humans suggests that there is greater potential for interactions via shared food sources than via the immune system.

A globally common coinfection involves tuberculosis and HIV. In some countries, up to 80% of tuberculosis patients are also HIV-positive. The potential for dynamics of these two infectious diseases to be linked has been known for decades. Other common examples of coinfections are AIDS, which involves coinfection of end-stage HIV with opportunistic parasites and polymicrobial infections like Lyme disease with other diseases.

Dogs will typically recover from kennel cough within a few weeks. However, secondary infections could lead to complications that could do more harm than the disease itself. Several opportunistic invaders have been recovered from the respiratory tracts of dogs with kennel cough, including Streptococcus, Pasteurella, Pseudomonas, and various coliforms. These bacteria have the potential to cause pneumonia or sepsis, which drastically increase the severity of the disease. These complications are evident in thoracic radiographic examinations. Findings will be mild in animals affected only by kennel cough, while those with complications may have evidence of segmental atelectasis and other severe side effects.

Though antibiotics are required to treat severe bacterial infections, misuse has contributed to a rise in bacterial resistance. The overuse of fluoroquinolone and other antibiotics fuels antibiotic resistance in bacteria, which can inhibit the treatment of antibiotic-resistant infections. Their excessive use in children with otitis media has given rise to a breed of bacteria resistant to antibiotics entirely.

Widespread use of fluoroquinolones as a first-line antibiotic has led to decreased antibiotic sensitivity, with negative implications for serious bacterial infections such as those associated with cystic fibrosis, where quinolones are among the few viable antibiotics.

The cause of immunodeficiency varies depending on the nature of the disorder. The cause can be either genetic or acquired by malnutrition and poor sanitary conditions. Only for some genetic causes, the exact genes are known. Although there is no true discrimination to who this disease affects, the genes are passed from mother to child, and on occasion from father to child. Women tend not to show symptoms due to their second X chromosome not having the mutation while man are symptomatic, due to having one X chromosome.

"Actinomycosis" is a rare infectious bacterial disease caused by "Actinomyces" species. About 70% of infections are due to either "Actinomyces israelii" or "A. gerencseriae". Infection can also be caused by other "Actinomyces" species, as well as "Propionibacterium propionicus", which presents similar symptoms. The condition is likely to be polymicrobial aerobic anaerobic infection.

Antibiotics can cause severe reactions and add significantly to the cost of care. In the United States, antibiotics and anti-infectives are the leading cause of adverse effect from drugs. In a study of 32 States in 2011, antibiotics and anti-infectives accounted for nearly 24 percent of ADEs that were present on admission, and 28 percent of those that occurred during a hospital stay.

Prescribing by an infectious disease specialist compared with prescribing by a non-infectious disease specialist decreases antibiotic consumption and reduces costs.

Some ways to prevent airborne diseases include washing hands, using appropriate hand disinfection, getting regular immunizations against diseases believed to be locally present, wearing a respirator and limiting time spent in the presence of any patient likely to be a source of infection.

Exposure to a patient or animal with an airborne disease does not guarantee receiving the disease. Because of the changes in host immunity and how much the host was exposed to the particles in the air makes a difference to how the disease affects the body.

Antibiotics are not prescribed for patients to control viral infections. They may however be prescribed to a flu patient for instance, to control or prevent bacterial secondary infections. They also may be used in dealing with air-borne bacterial primary infections, such as pneumonic plague.

Additionally the Centers for Disease Control and Prevention (CDC) has told consumers about vaccination and following careful hygiene and sanitation protocols for airborne disease prevention. Consumers also have access to preventive measures like UV Air purification devices that FDA and EPA-certified laboratory test data has verified as effective in inactivating a broad array of airborne infectious diseases. Many public health specialists recommend social distancing to reduce the transmission of airborne infections.

Routine vaccination against meningococcus is recommended by the Centers for Disease Control and Prevention for all 11- to 18-year-olds and people who have poor splenic function (who, for example, have had their spleen removed or who have sickle-cell disease which damages the spleen), or who have certain immune disorders, such as a complement deficiency.