Bacterial and viral infections can both cause the same kinds of symptoms. It can be difficult to distinguish which is the cause of a specific infection. It's important to distinguish, because viral infections cannot be cured by antibiotics.

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.

Diagnosis is made with isolation of "Pasteurella multocida" in a normally sterile site (blood, pus, or cerebrospinal fluid).

As the infection is usually transmitted into humans through animal bites, antibiotics usually treat the infection, but medical attention should be sought if the wound is severely swelling. Pasteurellosis is usually treated with high-dose penicillin if severe. Either tetracycline or chloramphenicol provides an alternative in beta-lactam-intolerant patients. However, it is most important to treat the wound.

Fever and sickness behavior and other signs of infection are often taken to be due to them. However, they are evolved physiological and behavioral responses of the host to clear itself of the infection. Instead of incurring the costs of deploying these evolved responses to infections, the body opts to tolerate an infection as an alternative to seeking to control or remove the infecting pathogen.

Subclinical infections are important since they allow infections to spread from a reserve of carriers. They also can cause clinical problems unrelated to the direct issue of infection. For example, in the case of urinary tract infections in women, this infection may cause preterm delivery if the person becomes pregnant without proper treatment.

Some studies reported up to 80% of patients with irritable bowel syndrome (IBS) have SIBO (using the hydrogen breath test). Subsequent studies demonstrated statistically significant reduction in IBS symptoms following therapy for SIBO.

There is a lack of consensus however, regarding the suggested link between IBS and SIBO. Other authors concluded that the abnormal breath results so common in IBS patients do not suggest SIBO, and state that "abnormal fermentation timing and dynamics of the breath test findings support a role for abnormal intestinal bacterial distribution in IBS." There is general consensus that breath tests are abnormal in IBS; however, the disagreement lies in whether this is representative of SIBO. More research is needed to clarifiy this possible link.

Certain people are more predisposed to the development of bacterial overgrowth because of certain risk factors. These factors can be grouped into three categories: (1) disordered motility or movement of the small bowel or anatomical changes that lead to stasis, (2) disorders in the immune system and (3) conditions that cause more bacteria from the colon to enter the small bowel.

Problems with motility may either be diffuse, or localized to particular areas. Diseases like scleroderma and possibly celiac disease cause diffuse slowing of the bowel, leading to increased bacterial concentrations. More commonly, the small bowel may have anatomical problems, such as out-pouchings known as diverticula that can cause bacteria to accumulate. After surgery involving the stomach and duodenum (most commonly with Billroth II antrectomy), a "blind loop" may be formed, leading to stasis of flow of intestinal contents. This can cause overgrowth, and is termed "blind loop syndrome".

Disorders of the immune system can cause bacterial overgrowth. Chronic pancreatitis, or inflammation of the pancreas can cause bacterial overgrowth through mechanisms linked to this. The use of immunosuppressant medications to treat other conditions can cause this, as evidenced from animal models. Other causes include inherited immunodeficiency conditions, such as common variable immunodeficiency, IgA deficiency, and hypogammaglobulinemia.

Finally, abnormal connections between the bacteria-rich colon and the small bowel can increase the bacterial load in the small bowel. Patients with Crohn's disease or other diseases of the ileum may require surgery that removes the ileocecal valve connecting the small and large bowel; this leads to an increased reflux of bacteria into the small bowel. After bariatric surgery for obesity, connections between the stomach and the ileum can be formed, which may increase bacterial load in the small bowel.

Proton pump inhibitors, a class of medication that are used to reduce stomach acid, is associated with an increased risk of developing SIBO.

In recent years, several proposed links between SIBO and other disorders have been made. However, the usual methodology of these studies involves the use of breath testing as an indirect investigation for SIBO. Breath testing has been criticized by some authors for being an imperfect test for SIBO, with multiple known false positives.

The U.S. Centers for Disease Control and Prevention (CDC) publishes a journal "Emerging Infectious Diseases" that identifies the following factors contributing to disease emergence:

- Microbial adaption; e.g. genetic drift and genetic shift in Influenza A

- Changing human susceptibility; e.g. mass immunocompromisation with HIV/AIDS

- Climate and weather; e.g. diseases with zoonotic vectors such as West Nile Disease (transmitted by mosquitoes) are moving further from the tropics as the climate warms

- Change in human demographics and trade; e.g. rapid travel enabled SARS to rapidly propagate around the globe

- Economic development; e.g. use of antibiotics to increase meat yield of farmed cows leads to antibiotic resistance

- Breakdown of public health; e.g. the current situation in Zimbabwe

- Poverty and social inequality; e.g. tuberculosis is primarily a problem in low-income areas

- War and famine

- Bioterrorism; e.g. 2001 Anthrax attacks

- Dam and irrigation system construction; e.g. malaria and other mosquito borne diseases

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.

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.

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.

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.

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

Methicillin-resistant Staphylococcus aureus (MRSA) evolved from Methicillin-susceptible Staphylococcus aureus (MSSA) otherwise known as common "S. aureus". Many people are natural carriers of "S. aureus", without being affected in any way. MSSA was treatable with the antibiotic methicillin until it acquired the gene for antibiotic resistance. Though genetic mapping of various strains of MRSA, scientists have found that MSSA acquired the mecA gene in the 1960s, which accounts for its pathogenicity, before this it had a predominantly commensal relationship with humans. It is theorized that when this "S. aureus" strain that had acquired the mecA gene was introduced into hospitals, it came into contact with other hospital bacteria that had already been exposed to high levels of antibiotics. When exposed to such high levels of antibiotics, the hospital bacteria suddenly found themselves in an environment that had a high level of selection for antibiotic resistance, and thus resistance to multiple antibiotics formed within these hospital populations. When "S. aureus" came into contact with these populations, the multiple genes that code for antibiotic resistance to different drugs were then acquired by MRSA, making it nearly impossible to control. It is thought that MSSA acquired the resistance gene through the horizontal gene transfer, a method in which genetic information can be passed within a generation, and spread rapidly through its own population as was illustrated in multiple studies. Horizontal gene transfer speeds the process of genetic transfer since there is no need to wait an entire generation time for gene to be passed on. Since most antibiotics do not work on MRSA, physicians have to turn to alternative methods based in Darwinian medicine. However prevention is the most preferred method of avoiding antibiotic resistance. By reducing unnecessary antibiotic use in human and animal populations, antibiotics resistance can be slowed.

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

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.

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.

Infection in the newborn is accompanied by a strong immune response and is correlated with the need for prolonged mechanical ventilation.

Infection with "U. urealyticum" in pregnancy and birth can be complicated by chorioamnionitis, stillbirth, premature birth, and, in the perinatal period, pneumonia, bronchopulmonary dysplasia and meningitis. "U. urealyticum" has been found to be present in amniotic fluid in women who have had a premature birth with intact fetal membranes.

"U. urealyticum" has been noted as one of the infectious causes of sterile pyuria. It increases the morbidity as a cause of neonatal infections. It is associated with premature birth, preterm rupture of membranes, preterm labor, cesarean section, placental inflammation, congenital pneumonia, bacteremia, meningitis, fetal lung injury and death of infant. "Ureaplasma urealyticum" is associated with miscarriage.

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.

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.

It had also been associated with a number of diseases in humans, including nonspecific urethritis, and infertility.

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".

"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.

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.

Rotavirus, norovirus, adenovirus, and astrovirus are known to cause viral gastroenteritis. Rotavirus is the most common cause of gastroenteritis in children, and produces similar rates in both the developed and developing world. Viruses cause about 70% of episodes of infectious diarrhea in the pediatric age group. Rotavirus is a less common cause in adults due to acquired immunity. Norovirus is the cause in about 18% of all cases.

Norovirus is the leading cause of gastroenteritis among adults in America, causing greater than 90% of outbreaks. These localized epidemics typically occur when groups of people spend time in close physical proximity to each other, such as on cruise ships, in hospitals, or in restaurants. People may remain infectious even after their diarrhea has ended. Norovirus is the cause of about 10% of cases in children.