The newborn`s exposure to the maternal vaginal bacterial flora which contains aerobic and anaerobic bacterial flora can lead to the development of anaerobic bacterial infection. These infections include cellulitis of the site of fetal monitoring (caused by "Bacterodes" spp.), bacteremia, aspiration pneumonia (caused by "Bacterodes" spp.), conjunctivitis (caused by clostridia,) omphalitis (caused by mixed flora), and infant botulism. Clostridial species may play a role in necrotizing enterocolitis. Management of these infection necessitates treating of the underlying condition(s) when present, and administration of proper antimicrobial therapy

Condition predisposing to anaerobic infections include: exposure of a sterile body location to a high inoculum of indigenous bacteria of mucous membrane flora origin, inadequate blood supply and tissue necrosis which lower the oxidation and reduction potential which support the growth of anaerobes. Conditions which can lower the blood supply and can predispose to anaerobic infection are: trauma, foreign body, malignancy, surgery, edema, shock, colitis and vascular disease. Other predisposing conditions include splenectomy, neutropenia, immunosuppression, hypogammaglobinemia, leukemia, collagen vascular disease and cytotoxic drugs and diabetes mellitus. A preexisting infection caused by aerobic or facultative organisms can alter the local tissue conditions and make them more favorable for the growth of anaerobes. Impairment in defense mechanisms due to anaerobic conditions can also favor anaerobic infection. These include production of leukotoxins (by "Fusobacterium" spp.), phagocytosis intracellular killing impairments (often caused by encapsulated anaerobes and by succinic acid ( produced by "Bacteroides" spp.), chemotaxis inhibition (by "Fusobacterium, Prevotella" and "Porphyromonas" spp.), and proteases degradation of serum proteins (by Bacteroides spp.) and production of leukotoxins (by "Fusobacterium" spp.).

The hallmarks of anaerobic infection include suppuration, establishment of an abscess, thrombophlebitis and gangrenous destruction of tissue with gas generation. Anaerobic bacteria are very commonly recovered in chronic infections, and are often found following the failure of therapy with antimicrobials that are ineffective against them, such as trimethoprim–sulfamethoxazole (co-trimoxazole), aminoglycosides, and the earlier quinolones.

Some infections are more likely to be caused by anaerobic bacteria, and they should be suspected in most instances. These infections include brain abscess, oral or dental infections, human or animal bites, aspiration pneumonia and lung abscesses, amnionitis, endometritis, septic abortions, tubo-ovarian abscess, peritonitis and abdominal abscesses following viscus perforation, abscesses in and around the oral and rectal areas, pus-forming necrotizing infections of soft tissue or muscle and postsurgical infections that emerge following procedures on the oral or gastrointestinal tract or female pelvic area. Some solid malignant tumors, ( colonic, uterine and bronchogenic, and head and neck necrotic tumors, are more likely to become secondarily infected with anaerobes. The lack of oxygen within the tumor that are proximal to the endogenous adjacent mucosal flora can predispose such infections.

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

The Centers for Disease Control and Prevention (CDC) estimated roughly 1.7 million hospital-associated infections, from all types of bacteria combined, cause or contribute to 99,000 deaths each year. Other estimates indicate 10%, or 2 million, patients a year become infected, with the annual cost ranging from $4.5 billion to $11 billion. In the USA, the most frequent type of infection hospitalwide is urinary tract infection (36%), followed by surgical site infection (20%), and bloodstream infection and pneumonia (both 11%).

In 2012 the Health Protection Agency reported the prevalence rate of HAIs in England was 6.4% in 2011, against a rate of 8.2% in 2006. With respiratory tract, urinary tract and surgical site infections the most common types of HAI reported.

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.

Bacteria with resistance to antibiotics predate medical use of antibiotics by humans. However, widespread antibiotic use has made more bacteria resistant through the process of evolutionary pressure.

Reasons for the widespread use of antibiotics in human medicine include:

- increasing global availability over time since the 1950s

- uncontrolled sale in many low or middle income countries, where they can be obtained over the counter without a prescription, potentially resulting in antibiotics being used when not indicated. This may result in emergence of resistance in any remaining bacteria.

Other causes include:

- Antibiotic use in livestock feed at low doses for growth promotion is an accepted practice in many industrialized countries and is known to lead to increased levels of resistance.

- Releasing large quantities of antibiotics into the environment during pharmaceutical manufacturing through inadequate wastewater treatment increases the risk that antibiotic-resistant strains will develop and spread.

- It is uncertain whether antibacterials in soaps and other products contribute to antibiotic resistance, but antibacterial soaps are discouraged for other reasons.

The World Health Organization concluded that inappropriate use of antibiotics in animal husbandry is an underlying contributor to the emergence and spread of antibiotic-resistant germs, and that the use of antibiotics as growth promoters in animal feeds should be restricted. The World Organisation for Animal Health has added to the Terrestrial Animal Health Code a series of guidelines with recommendations to its members for the creation and harmonization of national antimicrobial resistance surveillance and monitoring programs, monitoring of the quantities of antibiotics used in animal husbandry, and recommendations to ensure the proper and prudent use of antibiotic substances. Another guideline is to implement methodologies that help to establish associated risk factors and assess the risk of antibiotic resistance.

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.

When properly diagnosed, the mortality of Lemierre's syndrome is about 4.6%. Since this disease is not well known and often remains undiagnosed, mortality might be much higher.

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.

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.

Gram-negative toe web infection is a relatively common infection. It is commonly found on people who are engaged in athletic activities while wearing closed-toe or tight fitting shoes. It grows in a moist environment. Gram-negative is mixed bacterial infection with the following organisms:

- Moraxella

- Alcaligenes

- Acinetobacter

- Pseudomonas

- Proteus

- Erwinia

This mixing of infection and organisms may also cause a mild secondary infection of tinea pedis.

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.

Humans contract "Blastocystis" infection by drinking water or eating food contaminated with feces from an infected human or animal. "Blastocystis" infection can be spread from animals to humans, from humans to other humans, from humans to animals, and from animals to animals. Risk factors for infection have been reported as following:

- International travel: Travel to less developed countries has been cited in development of symptomatic Blastocystis infection. A 1986 study in the United States found that all individuals symptomatically infected with "Blastocystis" reported recent travel history to less developed countries. In the same study, all hospital employees working in New York who were screened for "Blastocystis" were found to have asymptomatic infections.

- Military service: Several studies have identified high rates of infection in military personnel. An early account described infection of British troops in Egypt in 1916 who recovered following treatment with emetine. A 1990 study published in "Military Medicine" from Lackland AFB in Texas concluded symptomatic infection was more common in foreign nationals, children, and immunocompromised individuals. A 2002 study published in "Military Medicine" of army personnel in Thailand identified a 44% infection rate. Infection rates were highest in privates who had served the longest at the army base. A follow-up study found a significant correlation between infection and symptoms, and identified the most likely cause as contaminated water. A 2007 newspaper article suggested the infection rate of US military personnel returning from the Gulf War was 50%, quoting the head of Oregon State University's Biomedicine department.

- Consumption of Untreated Water (well water): Many studies have linked "Blastocystis" infection with contaminated drinking water. A 1993 study of children infected symptomatically with "Blastocystis" in Pittsburgh indicated that 75% of them had a history of drinking well water or travel in less developed countries. Two studies in Thailand linked "Blastocystis" infection in military personnel and families to drinking of unboiled and untreated water. A book published in 2006 noted that in an Oregon community, infections are more common in winter months during heavy rains. A research study published in 1980 reported bacterial contamination of well water in the same community during heavy rainfall. A 2007 study from China specifically linked infection with "Blastocystis sp. subtype 3" with drinking untreated water. Recreational contact with untreated water, for example though boating, has also been identified as a risk factor. Studies have shown that "Blastocystis" survives sewage treatment plants in both the United Kingdom and Malaysia. "Blastocystis" cysts have been shown to be resistant to chlorination as a treatment method and are among the most resistant cysts to ozone treatment.

- Contaminated Food: Contamination of leafy vegetables has been implicated as a potential source for transmission of "Blastocystis" infection, as well as other gastrointestinal protozoa. A Chinese study identified infection with "Blastocystis sp. subtype 1" as specifically associated with eating foods grown in untreated water.

- Daycare facilities: A Canadian study identified an outbreak of "Blastocystis" associated with daycare attendance. Prior studies have identified outbreaks of similar protozoal infections in daycares.

- Geography: Infection rates vary geographically, and variants which produce symptoms may be less common in industrialized countries. For example, a low incidence of "Blastocystis" infection has been reported in Japan. A study of individuals infected with "Blastocystis" in Japan found that many (43%, 23/54) carried "Blastocystis sp. subtype 2", which was found to produce no symptoms in 93% (21/23) of patients studied, in contrast to other variants which were less common but produced symptoms in 50% of Japanese individuals. Studies in urban areas of industrialized countries have found "Blastocystis" infection associated with a low incidence of symptoms. In contrast, studies in developing countries generally show "Blastocystis" to be associated with symptoms. In the United States, a higher incidence of "Blastocystis" infection has been reported in California and West Coast states.

- Prevalence over Time: A 1989 study of the prevalence of "Blastocystis" in the United States found an infection rate of 2.6% in samples submitted from all 48 states. The study was part of the CDC's MMWR Report. A more recent study, in 2006, found an infection rate of 23% in samples submitted from all 48 states. However, the more recent study was performed by a private laboratory located in the Western US, and emphasized samples from Western states, which have previously been reported to have a higher infection rate.

Research studies have suggested the following items are not risk factors for contracting "Blastocystis" infection:

- Consumption of municipal water near water plant (not a risk factor): One study showed that municipal water was free of "Blastocystis", even when drawn from a polluted source. However, samples taken far away from the treatment plant showed cysts. The researchers suggested that aging pipes may permit intrusion of contaminated water into the distribution system.

- Human-to-Human transmission among adults (not a risk factor): Some research suggests that direct human-to-human transmission is less common even in households and between married partners. One study showed different members of the same household carried different subtypes of Blastocystis.

Although previously considered a mere nuisance infection, untreated bacterial vaginosis may cause complications, such as increased susceptibility to sexually transmitted infections including HIV and pregnancy complications.

It has been shown that HIV-infected women with bacterial vaginosis (BV) are more likely to transmit HIV to their sexual partners than those without BV. Diagnostic criteria for BV have also been associated with a female genital tract factor that induces expression of HIV.

There is evidence of an association between BV and increased rates of sexually transmitted infections such as HIV/AIDS. BV is associated with up to a six-fold increase in HIV shedding. There is also a correlation between the absence of vaginal lactobacilli and infection by Neisseria gonorrhea and Chlamydia trachomatis. BV is a risk factor for viral shedding and herpes simplex virus type 2 infection. BV may increase the risk of infection with or reactivation of human papillomavirus (HPV).

In addition, bacterial vaginosis an intercurrent disease in pregnancy may increase the risk of pregnancy complications, most notably premature birth or miscarriage.

Pregnant women with BV have a higher risk of chorioamnionitis, miscarriage, preterm birth, premature rupture of membranes, and postpartum endometritis. BV is associated with gynecological and obstetric complications. Data suggest an association between BV, tubal factor infertility, and pelvic inflammatory disease. Women with BV who are treated with in vitro fertilization have a lower implantation rate and higher rates of early pregnancy loss.

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.

Experimental infection in immunocompetent and immunocompromised mice has produced intestinal inflammation, altered bowel habits, lethargy and death. Chronic diarrhea has been reported in non-human higher primates.

Sixty percent of mothers of preterm infants are infected with cytomegalovirus (CMV). Infection is asymptomatic in most instances but 9% to 12% of postnatally infected low birth weight, preterm infants have severe, sepsis-like infection. CMV infection duration can be long and result in pneumonitis in association with fibrosis. CMV infection in infants has an unexpected effect on the white blood cells of the immune system causing them to prematurely age. This leads to a reduced immune response similar to that found in the elderly.

Early onset sepsis can occur in the first week of life. It usually is apparent on the first day after birth. This type of infection is usually acquired before the birth of the infant. Premature rupture of membranes and other obstetrical complications can add to the risk of early-onset sepsis. If the amniotic membrane has been ruptured greater than 18 hours before delivery the infant may be at more risk for this complication. Prematurity, low birth weight, chorioamnionitis, maternal urinary tract infection and/or maternal fever are complications that increase the risk for early-onset sepsis. Early onset sepsis is indicated by serious respiratory symptoms. The infant usually suffers from pneumonia, hypothermia, or shock. The mortality rate is 30 to 50%.

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.

Lemierre's syndrome is currently rare, but was more common in the early 20th century before the discovery of penicillin. The reduced use of antibiotics for sore throats may have increased the risk of this disease, with 19 cases in 1997 and 34 cases in 1999 reported in the UK. The incidence rate is currently 0.8 cases per million in the general population, leading it to be termed the "forgotten disease". The disease is known to affect healthy young adults. The disease is becoming less rare with many cases being reported, however it is still known as "the forgotten disease" as many doctors are unaware of its existence, therefore often not even diagnosed which might considerably change the above-mentioned statistics. The mortality rate was 90% prior to antibiotic therapy, but is now generally quoted as 15% once this illness is correctly diagnosed and cured with proper medical treatment, although one series of cases reported mortality as low as 6.4%.

The elderly and those with a weakened immune system are especially vulnerable to contracting cellulitis. Diabetics are more susceptible to cellulitis than the general population because of impairment of the immune system; they are especially prone to cellulitis in the feet, because the disease causes impairment of blood circulation in the legs, leading to diabetic foot or foot ulcers. Poor control of blood glucose levels allows bacteria to grow more rapidly in the affected tissue, and facilitates rapid progression if the infection enters the bloodstream. Neural degeneration in diabetes means these ulcers may not be painful, thus often become infected. Those who have suffered poliomyelitis are also prone because of circulatory problems, especially in the legs.

Immunosuppressive drugs, and other illnesses or infections that weaken the immune system, are also factors that make infection more likely. Chickenpox and shingles often result in blisters that break open, providing a gap in the skin through which bacteria can enter. Lymphedema, which causes swelling on the arms and/or legs, can also put an individual at risk.

Diseases that affect blood circulation in the legs and feet, such as chronic venous insufficiency and varicose veins, are also risk factors for cellulitis.

Cellulitis is also common among dense populations sharing hygiene facilities and common living quarters, such as military installations, college dormitories, nursing homes, oil platforms, and homeless shelters.

In the United States and other developed countries, the incidence of mastoiditis is quite low, around 0.004%, although it is higher in developing countries. The condition most commonly affects children aged from two to thirteen months, when ear infections most commonly occur. Males and females are equally affected.

Healthy vaginal microbiota consists of species which neither cause symptoms or infections, nor negatively affect pregnancy. It is dominated mainly by Lactobacillus species. BV is defined by the disequilibrium in the vaginal microbiota, with decline in the number of lactobacilli. While the infection involves a number of bacteria, it is believed that most infections start with Gardnerella vaginalis creating a biofilm, which allows other opportunistic bacteria to thrive.

One of the main risks for developing BV is douching, which alters the vaginal flora and predisposes women to developing BV. Douching is strongly discouraged by the U.S. Department of Health and Human Services and various medical authorities, for this and other reasons.

BV is a risk factor for pelvic inflammatory disease, HIV, sexually transmitted infections (STIs), and reproductive and obstetric disorders or negative outcomes. It is possible for sexually inactive persons to develop bacterial vaginosis.

Bacterial vaginosis may sometimes affect women after menopause. Also, subclinical iron deficiency may correlate with bacterial vaginosis in early pregnancy. A longitudinal study published in February 2006, in the "American Journal of Obstetrics and Gynecology", showed a link between psychosocial stress and bacterial vaginosis persisted even when other risk factors were taken into account. Exposure to the spermicide nonoxynol-9 does not affect the risk of developing bacterial vaginosis.

Having a female partner increases the risk of BV by 60%. The bacteria associated with BV have been isolated from male genitalia. BV microbiota has been found in the penis, coronal sulcus, and male urethra, in the male partners of infected females. Partners who have not been circumcised may act as a ‘reservoir’ increasing the likelihood of acquiring an infection after sexual intercourse. Another mode of transmission of the BV-associated microbiota is to a female sexual partner via skin-to-skin transfer. BV may be transmitted via the perineal enteric bacteria from the microbiota of the female and male genitalia.