Anaerobes can be isolated from most types of upper respiratory tract and head and neck and infection and are especially common in chronic ones. These include tonsillar, peritonsillar and retropharyngeal abscesses, chronic otitis media, sinusitis and mastoiditis, eye ocular) infections, all deep neck space infections, parotitis, sialadenitis, thyroiditis, odontogenic infections, and postsurgical and nonsurgical head and neck wounds and abscesses., The predominant organisms are of oropharyngeal flora origin and include AGNB, "Fusobacterium" and Peptostreptococcus spp.

Anaerobes involve almost all dental infections. These include dental abscesses, endodontal pulpitis and periodontal (gingivitis and periodontitis) infections, and perimandibular space infection. Pulpitis can lead to abscess formation and eventually spread to the mandible and other neck spaces. In addition to strict anaerobic bacteria, microaerophilic streptococci and "Streptococcus salivarius" can also be present.

"Fusobacterium" spp. and anaerobic spirochetes are often the cause of acute necrotizing ulcerative gingivitis (or Vincent's angina) which is a distinct form of ulcerative gingivitis.

Deep neck infections that develop as a consequence of oral, dental and pharyngeal infections are generally polymicrobial in nature. These include extension of retropharyngeal cellulitis or abscess, mediastinitis following esophagus perforation, and dental or periodontal abscess.

Secondary peritonitis and intra-abdominal abscesses including splenic and hepatic abscesses generally occur because of the entry of enteric micro-organisms into the peritoneal cavity through a defect in the wall of the intestine or other viscus as a result of obstruction, infarction or direct trauma. Perforated appendicitis, diverticulitis, inflammatory bowel disease with perforation and gastrointestinal surgery are often associated with polymicrobial infections caused by aerobic and anaerobic bacteria, where the number of isolates can average 12 (two-thirds are generally anaerobes). The most common aerobic and facultative bacteria are "Escherichia coli", "Streptococcus" spp. (including Enterococcus spp.), and the most frequently isolated anaerobic bacteria are the "B. fragilis" group, "Peptostreptococcus" spp., and "Clostridium" spp.

Abdominal infections are characteristically biphasic: an initial stages of generalized peritonitis associated with "Escherichia coli" sepsis, and a later stages, in which intra abdominal abscesses harboring anaerobic bacteria ( including "B. fragilis" group ) emerge.

The clinical manifestations of secondary peritonitis are a reflection of the underlying disease process. Fever, diffuse abdominal pain, nausea and vomiting are common. Physical examination generally show signs of peritoneal inflammation, isuch as rebound tenderness, abdominal wall rigidity and decrease in bowel sounds. These early findings may be followed by signs and symptoms of shock.

Biliary tract infection is usually caused by "E. coli, Klebsiella" and "Enterococcus" spp. Anaerobes (mostly "B. fragilis" group, and rarely "C. perfringens") can be recovered in complicated infections associated with carcinoma, recurrent infection, obstruction, bile tract surgery or manipulation.

Laboratory studies show elevated blood leukocyte count and predominance of polymorphonuclear forms. Radiographs studies may show free air in the peritoneal cavity, evidence of ileus or obstruction and obliteration of the psoas shadow. Diagnostic ultrasound, gallium and CT scanning may detect appendiceal or other intra-abdominal abscesses. Polymicrobial postoperative wound infections can occur.

Treatment of mixed aerobic and anaerobic abdominal infections requires the utilization of antimicrobials effective against both components of the infection as well as surgical correction and drainage of pus. Single and easily accessible abscesses can be drained percutaneously.

An opportunistic infection is an infection caused by pathogens (bacteria, viruses, fungi, or protozoa) that take advantage of an opportunity not normally available, such as a host with a weakened immune system, an altered microbiota (such as a disrupted gut flora), or breached integumentary barriers. Many of these pathogens do not cause disease in a healthy host that has a normal immune system. However, a compromised immune system, a penetrating injury, or a lack of competition from normal commensals presents an opportunity for the pathogen to infect.

A hospital-acquired infection (HAI), also known as a nosocomial infection, is an infection that is acquired in a hospital or other health care facility. To emphasize both hospital and nonhospital settings, it is sometimes instead called a health care–associated infection (HAI or HCAI). Such an infection can be acquired in hospital, nursing home, rehabilitation facility, outpatient clinic, or other clinical settings. Infection is spread to the susceptible patient in the clinical setting by various means. Health care staff can spread infection, in addition to contaminated equipment, bed linens, or air droplets. The infection can originate from the outside environment, another infected patient, staff that may be infected, or in some cases, the source of the infection cannot be determined. In some cases the microorganism originates from the patient's own skin microbiota, becoming opportunistic after surgery or other procedures that compromise the protective skin barrier. Though the patient may have contracted the infection from their own skin, the infection is still considered nosocomial since it develops in the health care setting.

In the United States, the Centers for Disease Control and Prevention estimated roughly 1.7 million hospital-associated infections, from all types of microorganisms, including bacteria and fungi combined, cause or contribute to 99,000 deaths each year. In Europe, where hospital surveys have been conducted, the category of gram-negative infections are estimated to account for two-thirds of the 25,000 deaths each year. Nosocomial infections can cause severe pneumonia and infections of the urinary tract, bloodstream and other parts of the body. Many types are difficult to treat with antibiotics. In addition, antibiotic resistance can complicate treatment.

Symptoms are similar to tuberculosis (TB), and include fever, fatigue, and weight loss. Pulmonary involvement is similar to TB, while diarrhea and abdominal pain are associated with gastrointestinal involvement.

"Mycobacterium avium-intracellulare" infection (MAI) is an atypical mycobacterial infection, i.e. one with nontuberculous mycobacteria or NTM, caused by "Mycobacterium avium" complex ("MAC"), which is made of three mycobacteria species, "M. avium", "M. intracellulare", and "M. chimaera". This infection causes respiratory illness in birds, pigs, and humans, especially in immunocompromised people. In the later stages of AIDS it can be very severe. It usually first presents as a persistent cough. It is typically treated with a series of three antibiotics for a period of at least six months.

"M. avium", "M. intracellulare", and "M. chimaera" are each saprotrophic organisms present in soil and water; entry into hosts is usually via the gastrointestinal tract, but also can be via the lungs.

MAC infections can cause fevers, diarrhea, malabsorption, as well as loss of appetite and weight loss, and can disseminate to the bone marrow. Therapy for MAI is typically resistant to standard mycobacterial therapies.

Antimicrobial resistance (AMR) is the ability of a microbe to resist the effects of medication previously used to treat them. The term includes the more specific "antibiotic resistance", which applies only to bacteria becoming resistant to antibiotics. Resistant microbes are more difficult to treat, requiring alternative medications or higher doses, both of which may be more expensive or more toxic. Microbes resistant to multiple antimicrobials are called multidrug resistant (MDR); or sometimes superbugs.

Resistance arises through one of three mechanisms: natural resistance in certain types of bacteria, genetic mutation, or by one species acquiring resistance from another. All classes of microbes can develop resistance: fungi develop antifungal resistance, viruses develop antiviral resistance, protozoa develop antiprotozoal resistance, and bacteria develop antibiotic resistance. Resistance can appear spontaneously because of random mutations; or more commonly following gradual buildup over time.

Preventive measures include only using antibiotics when needed, thereby stopping misuse of antibiotics or antimicrobials. Narrow-spectrum antibiotics are preferred over broad-spectrum antibiotics when possible, as effectively and accurately targeting specific organisms is less likely to cause resistance. For people who take these medications at home, education about proper use is essential. Health care providers can minimize spread of resistant infections by use of proper sanitation and hygiene, including handwashing and disinfecting between patients, and should encourage the same of the patient, visitors, and family members.

Rising drug resistance is caused mainly by use of antimicrobials in humans and other animals, and spread of resistant strains between the two. Antibiotics increase selective pressure in bacterial populations, causing vulnerable bacteria to die; this increases the percentage of resistant bacteria which continue growing. With resistance to antibiotics becoming more common there is greater need for alternative treatments. Calls for new antibiotic therapies have been issued, but new drug development is becoming rarer.

Antimicrobial resistance is on the rise. Estimates are that 700,000 to several million deaths result per year. Each year in the United States, at least 2 million people become infected with bacteria that are resistant to antibiotics and at least 23,000 people die as a result. There are public calls for global collective action to address the threat include proposals for international treaties on antimicrobial resistance. Worldwide antibiotic resistance is not fully mapped, but poorer countries with weak healthcare systems are more affected.

Immunodeficiency or immunosuppression can be caused by:

- Malnutrition

- Fatigue

- Recurrent infections

- Immunosuppressing agents for organ transplant recipients

- Advanced HIV infection

- Chemotherapy for cancer

- Genetic predisposition

- Skin damage

- Antibiotic treatment leading to disruption of the physiological microbiome, thus allowing some microorganisms to outcompete others and become pathogenic (e.g. disruption of intestinal flora may lead to "Clostridium difficile" infection

- Medical procedures

- Pregnancy

- Ageing

- Leukopenia (i.e. neutropenia and lymphocytopenia)

The lack of or the disruption of normal vaginal flora allows the proliferation of opportunistic microorganisms and will cause the opportunistic infection - bacterial vaginosis.

A subclinical infection (sometimes called a preinfection) is an infection that, being , is nearly or completely asymptomatic (no signs or symptoms). A subclinically infected person is thus an asymptomatic carrier of a microbe, intestinal parasite, or virus that usually is a pathogen causing illness, at least in some individuals. Many pathogens spread by being silently carried in this way by some of their host population. Such infections occur both in humans and nonhuman animals. An example of an asymptomatic infection is a mild common cold that is not noticed by the infected individual. Since subclinical infections often occur without eventual overt sign, their existence is only identified by microbiological culture or DNA techniques such as polymerase chain reaction.

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.

Indwelling catheters have recently been identified with hospital acquired infections. Procedures using Intravascular Antimicrobial Lock Therapy can reduce infections that are unexposed to blood-borne antibiotics. Introducing antibiotics, including ethanol, into the catheter (without flushing it into the bloodstream) reduces the formation of biofilms.

Contact transmission is divided into two subgroups: direct-contact transmission and indirect-contact transmission.

The signs and symptoms of Lemierre's syndrome vary, but usually start with a sore throat, fever, and general body weakness. These are followed by extreme lethargy, spiked fevers, rigors, swollen cervical lymph nodes, and a swollen, tender or painful neck. Often there is abdominal pain, diarrhea, nausea and vomiting during this phase. These signs and symptoms usually occur several days to 2 weeks after the initial symptoms.

Symptoms of pulmonary involvement can be shortness of breath, cough and painful breathing (pleuritic chest pain). Rarely, blood is coughed up. Painful or inflamed joints can occur when the joints are involved.

Septic shock can also arise. This presents with low blood pressure, increased heart rate, decreased urine output and an increased rate of breathing. Some cases will also present with meningitis, which will typically manifest as neck stiffness, headache and sensitivity of the eyes to light.

Liver enlargement and spleen enlargement can be found, but are not always associated with liver or spleen abscesses.

Other signs and symptoms that may occur:

- Headache (unrelated to meningitis)

- Memory loss

- Muscle pain

- Jaundice

- Decreased ability to open the jaw

- Crepitations are sometimes heard over the lungs

- Pericardial friction rubs as a sign of pericarditis (rare)

- Cranial nerve paralysis and Horner's syndrome (both rare)

In most cases AIT is characterized by onset of pain, firmness, tenderness, redness or swelling in the anterior aspect of the neck. Patients will also present with a sudden fever, dysphagia and dysphonia. Symptoms may be present from 1 to 180 days, with most symptoms lasting an average of about 18 days. The main issue associated with the diagnosis of AIT is differentiating it from other more commonly seen forms of thyroid conditions. Pain, fever and swelling are often much more severe and continue to get worse in patients who have AIT compared to those with other thyroid conditions. Patients who are suspected of having AIT often undergo tests to detect for elevated levels of white blood cells as well as an ultrasound to reveal unilobular swelling. Depending on the age and immune status of the patient more invasive procedures may be performed such as fine needle aspiration of the neck mass to facilitate a diagnosis.

In cases where the infection is thought to be associated with a sinus fistula it is often necessary to confirm the presence of the fistula through surgery or laryngoscopic examination. While invasive procedures can often tell definitively whether or not a fistula is present, new studies are working on the use of computed tomography as a useful method to visualize and detect the presence of a sinus fistula.

The typical signs and symptoms of cellulitis is an area which is red, hot, and painful. The photos shown here of are of mild to moderate cases, and are not representative of earlier stages of the condition.

Gram-negative toe web infection is a cutaneous condition that often begins with dermatophytosis.

Researchers have published conflicting reports concerning whether "Blastocystis" causes symptoms in humans, with one of the earliest reports in 1916. The incidence of reports associated with symptoms began to increase in 1984, with physicians from Saudi Arabia reporting symptoms in humans and US physicians reporting symptoms in individuals with travel to less developed countries. A lively debate ensued in the early 1990s, with some physicians objecting to publication of reports that "Blastocystis" caused disease. Some researchers believe the debate has been resolved by finding of multiple species of "Blastocystis" that can infect humans, with some causing symptoms and others being harmless (see Genetics and Symptoms).

A few of most commonly reported symptoms are:

- abdominal pain

- itching, usually anal itching

- constipation

- diarrhea

- watery or loose stools

- weight loss

- fatigue

- flatulence

Some less commonly reported symptoms include:

- Skin rash

- Headache, depression

- Arthritic symptoms and joint pain

- Intestinal inflammation

Common symptoms include increased vaginal discharge that usually smells like fish. The discharge is often white or gray in color. There may be burning with urination. Occasionally, there may be no symptoms.

The discharge coats the walls of the vagina, and is usually without significant irritation, pain, or erythema (redness), although mild itching can sometimes occur. By contrast, the normal vaginal discharge will vary in consistency and amount throughout the menstrual cycle and is at its clearest at ovulation—about two weeks before the period starts. Some practitioners claim that BV can be asymptomatic in almost half of affected women, though others argue that this is often a misdiagnosis.

The most commonly reported symptoms in conjunction with infection with "D. fragilis" include abdominal pain (69%) and diarrhea (61%). Diarrhea may be intermittent and may not be present in all cases. It is often chronic, lasting over two weeks. The degree of symptoms may vary from asymptomatic to severe, and can include weight loss, vomiting, fever, and involvement of other digestive organs.

Symptoms may be more severe in children. Additional symptoms reported have included:

1. Weight loss

2. Fatigue

3. Nausea and vomiting

4. Fever

5. Urticaria (skin rash)

6. Pruritus (itchiness)

7. Biliary infection

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.

Cellulitis is caused by a type of bacteria entering the skin, usually by way of a cut, abrasion, or break in the skin. This break does not need to be visible. Group A "Streptococcus" and "Staphylococcus" are the most common of these bacteria, which are part of the normal flora of the skin, but normally cause no actual infection while on the skin's outer surface.

About 80% of cases of Ludwig's angina, or cellulitis of the submandibular space, are caused by dental infections. Mixed infections, due to both aerobes and anaerobes, are commonly associated with this type of cellulitis. Typically, this includes alpha-hemolytic streptococci, staphylococci, and bacteroides groups.

Predisposing conditions for cellulitis include insect or spider bite, blistering, animal bite, tattoos, pruritic (itchy) skin rash, recent surgery, athlete's foot, dry skin, eczema, injecting drugs (especially subcutaneous or intramuscular injection or where an attempted intravenous injection "misses" or blows the vein), pregnancy, diabetes, and obesity, which can affect circulation, as well as burns and boils, though debate exists as to whether minor foot lesions contribute. Occurrences of cellulitis may also be associated with the rare condition hidradenitis suppurativa or dissecting cellulitis.

The appearance of the skin assists a doctor in determining a diagnosis. A doctor may also suggest blood tests, a wound culture, or other tests to help rule out a blood clot deep in the veins of the legs. Cellulitis in the lower leg is characterized by signs and symptoms similar to those of a deep vein thrombosis, such as warmth, pain, and swelling (inflammation).

This reddened skin or rash may signal a deeper, more serious infection of the inner layers of skin. Once below the skin, the bacteria can spread rapidly, entering the lymph nodes and the bloodstream and spreading throughout the body. This can result in influenza-like symptoms with a high temperature and sweating or feeling very cold with shaking, as the sufferer cannot get warm.

In rare cases, the infection can spread to the deep layer of tissue called the fascial lining. Necrotizing fasciitis, also called by the media "flesh-eating bacteria", is an example of a deep-layer infection. It is a medical emergency.

A amoebic liver abscess is a type of liver abscess caused by amebiasis. It is the involvement of liver tissue by trophozoites of the organism "Entamoeba histolytica" and of is abscess due to necrosis.

The WHO defines antimicrobial resistance as a microorganism's resistance to an antimicrobial drug that was once able to treat an infection by that microorganism.

A person cannot become resistant to antibiotics. Resistance is a property of the microbe, not a person or other organism infected by a microbe.

Bacterial vaginosis (BV) is a disease of the vagina caused by excessive growth of bacteria. Common symptoms include increased vaginal discharge that often smells like fish. The discharge is usually white or gray in color. Burning with urination may occur. Itching is uncommon. Occasionally, there may be no symptoms. Having BV approximately doubles the risk of infection by a number of other sexually transmitted infections, including HIV/AIDS. It also increases the risk of early delivery among pregnant women.

BV is caused by an imbalance of the naturally occurring bacteria in the vagina. There is a change in the most common type of bacteria and a hundred to thousandfold increase in total numbers of bacteria present. Typically, bacteria other than "Lactobacilli" become more common. Risk factors include douching, new or multiple sex partners, antibiotics, and using an intrauterine device, among others. However, it is not considered a sexually transmitted infection. Diagnosis is suspected based on the symptoms, and may be verified by testing the vaginal discharge and finding a higher than normal vaginal pH, and large numbers of bacteria. BV is often confused with a vaginal yeast infection or infection with Trichomonas.

Usually treatment is with an antibiotic, such as clindamycin or metronidazole. These medications may also be used in the second or third trimesters of pregnancy. However, the condition often recurs following treatment. Probiotics may help prevent re-occurrence. It is unclear if the use of probiotics or antibiotics affects pregnancy outcomes.

BV is the most common vaginal infection in women of reproductive age. The percentage of women affected at any given time varies between 5% and 70%. BV is most common in parts of Africa and least common in Asia and Europe. In the United States about 30% of women between the ages of 14 and 49 are affected. Rates vary considerably between ethnic groups within a country. While BV like symptoms have been described for much of recorded history, the first clearly documented case occurred in 1894.

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 young children, the only symptom of a urinary tract infection (UTI) may be a fever. Because of the lack of more obvious symptoms, when females under the age of two or uncircumcised males less than a year exhibit a fever, a culture of the urine is recommended by many medical associations. Infants may feed poorly, vomit, sleep more, or show signs of jaundice. In older children, new onset urinary incontinence (loss of bladder control) may occur.