A healthy person lives in harmony with the microbial flora that helps protect its host from invasion by pathogens, usually defined as microorganisms that have the capacity to cause disease. The microbial flora is mostly bacteria and fungi and includes normal resident flora, which is present consistently and which promptly reestablishes itself if disturbed, and transient flora, which may colonize the host for hours to weeks but does not permanently establish itself. Organisms that are normal flora can occasionally cause disease, especially when defenses are disrupted.
Laboratory tests may identify organisms directly (eg, visually, using a microscope, growing the organism in culture) or indirectly (eg, identifying antibodies to the organism). General types of tests include
Arbovirus (arthropod-borne virus) is defined as any virus that is transmitted to humans and/or other vertebrates by certain species of blood-feeding arthropods, mostly insects (flies and mosquitoes) and arachnids (ticks). Arbovirus is a descriptive term based on transmission by vectors with particular characteristics. It is not part of the International Committee on Taxonomy of Viruses classification of viruses (ie, it is not a species, genus, or family), which is based on the nature and structure of the viral genome.
Bacteria are microorganisms that have circular double-stranded DNA and (except for mycoplasmas) cell walls. Most bacteria live extracellularly, but some preferentially reside and replicate intracellularly. Obligate intracellular pathogens are able to grow, reproduce, and cause disease only within the cells of the host. Examples of these pathogens include Chlamydiae, Chlamydophila species, and rickettsiae. Facultative intracellular pathogens are able to live and reproduce either inside or outside of host cells. Examples of these pathogens include Salmonella typhi, Brucella species, Francisella tularensis, Neisseria gonorrhoeae, N. meningitidis, Legionella and Listeria species, and Mycobacterium tuberculosis.
Three species of Chlamydia cause human disease, including sexually transmitted infections and respiratory infections. Diagnosis depends on species; culture, nucleic acid amplification tests (NAATs), or serologic tests may be done. Treatment is with doxycycline for nonpregnant people and with azithromycin for pregnant women.
COVID-19 is an acute, sometimes severe, respiratory illness caused by the novel coronavirus SARS-CoV-2. Prevention is by vaccination and infection control precautions (eg, face masks, handwashing, social distancing, isolation of infected individuals). Diagnosis is by antigen or PCR (polymerase chain reaction) testing of upper or lower respiratory secretions. Treatment is with supportive care, antiviral drugs, or corticosteroids.
Enteroviruses, along with rhinoviruses (see Common Cold) and human parechoviruses, are a genus of picornaviruses (pico, or small, RNA viruses). All enteroviruses are antigenically heterogeneous and have wide geographic distribution.
Free-living amebas are protozoa that live independently in soil or water and do not require a human or animal host. They rarely cause disease, in contrast to the parasitic ameba Entamoeba histolytica, which is a common cause of intestinal infection ( amebiasis). Pathogenic free-living amebas are of the genera Acanthamoeba, Balamuthia, Naegleria, and Sappinia.
Fungi are eukaryotic organisms that exist as yeast, molds, or both forms. Yeasts consist of solitary cells that reproduce by budding. Molds occur in filaments, also known as hyphae, which extend by apical elongation. Dimorphic fungi grow as mold in the environment and as yeast cells or spherules (sac-like cells that are the reproductive form of the fungus) in vivo.
Gram-negative bacilli are responsible for numerous diseases. Some are commensal organisms present among normal intestinal flora. These commensal organisms plus others from animal or environmental reservoirs may cause disease.
Enterococci are gram-positive, facultative anaerobic organisms. Enterococcus faecalis and E. faecium cause a variety of infections, including endocarditis, urinary tract infections, prostatitis, intra-abdominal infection, cellulitis, and wound infection as well as concurrent bacteremia.
Anthrax is caused by the gram-positive Bacillus anthracis, which are toxin-producing, encapsulated, facultative anaerobic organisms. Anthrax, an often fatal disease of animals, is transmitted to humans by contact with infected animals or their products. In humans, infection is typically acquired through the skin. Inhalation infection is less common; oropharyngeal, meningeal, and gastrointestinal infections are rare. For inhalation and gastrointestinal infections, nonspecific local symptoms are typically followed in several days by severe systemic illness, shock, and often death. Empiric treatment is with fluoroquinolones or doxycycline. A vaccine is available.
Eight types of herpesviruses infect humans ( All.see table Herpesviruses That Infect Humans). After initial infection, all herpesviruses remain latent within specific host cells and may subsequently reactivate. Clinical syndromes due to primary infection can vary significantly from those caused by reactivation of these viruses. Herpesviruses do not survive long outside a host; thus, transmission usually requires intimate contact. In people with latent infection, the virus can reactivate without causing symptoms; in such cases, asymptomatic shedding occurs and people can transmit infection.
Human immunodeficiency virus (HIV) infection results from 1 of 2 similar retroviruses (HIV-1 and HIV-2) that destroy CD4+ lymphocytes and impair cell-mediated immunity, increasing risk of certain infections and cancers. Initial infection may cause nonspecific febrile illness. Risk of subsequent manifestations—related to immunodeficiency—is proportional to the level of CD4+ lymphocyte depletion. HIV can directly damage the brain, gonads, kidneys, and heart, causing cognitive impairment, hypogonadism, renal insufficiency, and cardiomyopathy. Manifestations range from asymptomatic carriage to acquired immune deficiency syndrome (AIDS), which is defined by the presence of an AIDS-defining illness (serious opportunistic infections or cancers) or a CD4 count of 200/mcL. HIV infection can be diagnosed by antibody, nucleic acid (HIV RNA), or antigen (p24) testing. Screening should be routinely offered to all adults and adolescents. Treatment aims to suppress HIV replication by using combinations of ≥ 2 drugs that inhibit HIV enzymes; treatment can restore immune function in most patients if suppression of replication is sustained.
Protozoa is a loose term for certain nucleated, unicellular organisms (eukaryotes) that lack a cell wall and are neither animals, plants, nor fungi. The most important intestinal protozoan pathogens that cause enteric infections in humans include
Tuberculosis is a chronic, progressive mycobacterial infection, often with an asymptomatic latent period following initial infection. Tuberculosis most commonly affects the lungs. Symptoms include productive cough, fever, weight loss, and malaise. Diagnosis is most often by sputum smear and culture and, when available, by nucleic acid amplification tests. Treatment is with multiple antimicrobial drugs given for at least 4 months.
Angiostrongyliasis is infection with larvae of worms of the genus Angiostrongylus. Depending on the infecting species, abdominal symptoms (Angiostrongylus costaricensis) or neural involvement with eosinophilic meningitis (A. cantonensis) result. Diagnosis is suspected by history and presence of eosinophilia in cerebrospinal fluid (CSF) and/or blood. Anthelmintics are either ineffective or deleterious.
Mpox (monkeypox)is caused by the monkeypox virus, an orthopoxvirus structurally related to the smallpox virus. Patients present with a vesicular or pustular rash that may be painful and often with fever, malaise, and lymphadenopathy. Diagnosis is by polymerase chain reaction (PCR). Treatment is generally supportive and potentially with antiviral drugs. Prevention involves vaccination.
Viral infections commonly affect the upper or lower respiratory tract. Although respiratory infections can be classified by the causative virus (eg, influenza), they are generally classified clinically according to syndrome (eg, the common cold, bronchiolitis, croup, pneumonia). Although specific pathogens commonly cause characteristic clinical manifestations (eg, rhinovirus typically causes the common cold, respiratory syncytial virus [RSV] typically causes bronchiolitis), each can cause many of the viral respiratory syndromes.
Rickettsial diseases (rickettsioses) and related diseases (anaplasmosis, ehrlichiosis, Q fever, scrub typhus) are caused by a group of gram-negative, obligately intracellular coccobacilli. All, except for Coxiella burnetii, have an arthropod vector. Symptoms usually include sudden-onset fever with severe headache, malaise, prostration, and, in most cases, a characteristic rash. Diagnosis is clinical, confirmed by immunofluorescence assay or polymerase chain reaction (PCR). First-line treatment is with doxycycline, a tetracycline.
Sexually transmitted infection (STI) refers to infection with a pathogen that is transmitted through blood, semen, vaginal fluids, or other body fluids during oral, anal, or genital sex with an infected partner. Sexually transmitted disease (STD) refers to a recognizable disease state that has developed from an STI ( 1). STIs can be caused by a number of microorganisms that vary widely in size, life cycle, susceptibility to available treatments and the diseases and symptoms they cause.
Bejel, pinta, and yaws (endemic treponematoses) are chronic, tropical, nonvenereal spirochetal infections spread by body contact. Symptoms of bejel are mucous membrane and cutaneous lesions, followed by bone and skin gummas. Yaws causes periostitis and dermal lesions. Pinta lesions are confined to the dermis. Diagnosis is clinical and epidemiologic. Treatment is with azithromycin.