Acid-fast bacteria and Gram-variable / atypical bacteria

Genus Mycobacterium

Mycobacterium is a major high G+C, non–endospore-forming pathogen, , a genus whose species have cell walls packed with waxy lipids called mycolic acids—long molecules with 60 to 90 carbon atoms. This unusual cell wall structure gives mycobacteria several distinctive traits: they grow very slowly because producing so much mycolic acid takes time; they resist lysis after being phagocytized and can even survive and grow inside cells; they tolerate drying extremely well and can remain infectious in dried aerosols for up to eight months; and they are difficult to stain and naturally resistant to many detergents and antimicrobial drugs. Because they do not stain reliably with the Gram method, the acid-fast stain was developed specifically to visualize them. Although about 75 mycobacterial species exist, human disease is mainly caused by M. tuberculosis and M. leprae, which are responsible for tuberculosis and leprosy. Other species, such as M. avium-intracellulare and M. ulcerans, are also increasingly associated with emerging infections.

M. tuberculosis

Tuberculosis (TB), once known as consumption, is a respiratory disease caused by Mycobacterium tuberculosis. The bacterium is an acid-fast, slow-growing bacillus with a waxy cell wall containing mycolic acid, which makes it resistant to drying, many antimicrobial drugs, digestion by phagocytes, and common staining procedures. Infection typically occurs through inhalation of respiratory droplets from infected individuals.

Once in the lungs, macrophages engulf the bacteria but cannot destroy them, allowing M. tuberculosis to replicate inside the cells until they burst. Immune cells then wall off the infection, forming a tubercle within two to three months. Collagen fibers surround the area, and the center may undergo caseous necrosis, forming a cheese-like lesion. In many individuals, infection becomes dormant and may persist for years.

Reactivation can occur, especially in people with weakened immune systems due to HIV infection, malnutrition, drug or alcohol abuse, or old age. Reactivated TB causes progressive lung damage and symptoms including a persistent cough, fatigue, weight loss, fever, chest pain, and sometimes coughing up blood. Bacteria may spread through blood and lymph to organs such as the liver, kidneys, bones, and brain, causing disseminated TB.

Diagnosis involves a tuberculin skin test and chest X-rays that reveal tubercles. Treatment requires long-term combination therapy due to the organism’s slow growth and intracellular location, typically including isoniazid and rifampin with additional drugs for several months. Drug-resistant strains are a growing problem. MDR-TB resists isoniazid and rifampin, while XDR-TB also resists fluoroquinolones and at least one injectable antimicrobial. Rare cases of totally drug-resistant TB have been reported.

Prevention includes early detection, treatment of active cases, mask use to limit droplet spread, and vaccination with BCG where TB is common. Although TB cases declined significantly after public health interventions, global disease remains severe, with millions infected and high mortality worldwide.

 M. leprae

Mycobacterium leprae is the causative agent of leprosy, also known as Hansen’s disease, named after Gerhard Hansen who first identified the organism in 1873. Although it is classified as a high–G+C Gram-positive bacillus, the large amount of mycolic acid in its cell wall prevents it from staining purple with the Gram stain, so an acid-fast stain must be used instead. M. leprae grows best at about 30°C, which explains its preference for cooler areas of the human body, such as peripheral nerve endings and skin on the fingers, toes, lips, and earlobes. The bacterium cannot be cultured in cell-free laboratory media, a limitation that has delayed research, but armadillos—whose body temperature naturally matches the organism’s growth preference—serve as the only other known host and have become an important model for studying the disease.

Leprosy presents in two very different forms depending on the strength of the patient’s cell-mediated immune response. Individuals with strong cellular immunity develop tuberculoid leprosy, a nonprogressive form in which infected cells are destroyed before the bacteria can multiply extensively. This form is characterized by patches of skin that lose sensation due to nerve damage. In contrast, patients with weak cell-mediated immunity develop lepromatous leprosy, the more severe and disfiguring form of the disease. In these patients, M. leprae multiplies freely in skin and nerve cells, gradually destroying tissues and causing the loss of facial features, digits, and other structures. Historically, the severe disfigurement and fear of contagion led to social isolation and the forced quarantine of affected individuals.

The disease progresses slowly, often taking years before clinical signs appear, and death is usually due not to the mycobacterium itself but to secondary infections of open lesions. Although lepromatous leprosy is more virulent, global prevalence has declined dramatically—from about 12 million cases annually in the early 1990s to fewer than 200,000 cases reported in 2014. Transmission occurs through prolonged person-to-person contact, likely via inhalation of respiratory droplets from individuals with lepromatous disease, whose nasal secretions contain high numbers of bacteria. Because transmission is inefficient and modern treatment is effective, quarantine is no longer necessary.

Diagnosis is based on characteristic symptoms, such as areas of numb skin in tuberculoid leprosy or extensive tissue damage in lepromatous cases. Confirmation can be achieved with a positive leprosy skin test—similar to the tuberculin test—or by observing acid-fast rods in tissue samples or nasal secretions. Like Mycobacterium tuberculosis, M. leprae rapidly develops resistance if treated with a single antimicrobial drug, so therapy requires long-term multidrug treatment, commonly including clofazimine, rifampin, and dapsone, usually for at least twelve months, though some individuals require lifelong therapy. Clofazimine is no longer sold in the United States but remains widely used worldwide.

Although the BCG vaccine provides partial protection against leprosy, prevention is mainly achieved by limiting exposure to infected individuals and administering prophylactic antimicrobials after confirmed exposure. The World Health Organization aims to reduce global prevalence to fewer than one case per 10,000 people in all endemic regions, a level expected to interrupt human transmission altogether and move the world closer to eliminating leprosy.

N. asteroides

Nocardia asteroides is a soil-dwelling bacterium found in environments rich in organic matter and is responsible for about 90% of infections caused by its genus. It acts as an opportunistic pathogen, infecting the lungs, skin, or central nervous system depending on how it enters the body—through inhalation, contaminated wounds, or spread via the bloodstream. Lung infections typically cause pneumonia with symptoms such as cough, fever, and shortness of breath, while skin infections can lead to mycetoma, a chronic, painless condition marked by swelling, pus, and draining sores. Diagnosis is usually made by observing long, acid-fast, filament-like cells in samples such as sputum, skin scrapings, pus, or cerebrospinal fluid. Treatment generally requires six weeks of antimicrobial therapy, with sulfonamides being the preferred drugs, though outcomes are worse in immunocompromised patients with widespread disease. Prevention mainly involves minimizing contact with contaminated soil, particularly for individuals with weakened immune systems.

Chlamydias

Chlamydias are small, obligate intracellular bacteria classified in the phylum Chlamydiae. They are non-motile, lack cell walls, and multiply only within host cell vesicles. Their unique life cycle alternates between infectious, environmentally resistant elementary bodies (EBs) and metabolically active, intracellular reticulate bodies (RBs). Chlamydias are energy parasites, relying on host ATP, and survive by preventing lysosome-phagosome fusion.

Chlamydia trachomatis is a human-specific pathogen that infects mucous membranes of the urogenital tract and the eyes. Pathogenicity results from cell destruction and the inflammatory response, which can cause blindness, sterility, and sexual dysfunction. Sexually transmitted strains cause urethritis, lymphogranuloma venereum (LGV), and pelvic inflammatory disease (PID) in women. Most genital infections in women are asymptomatic, while men often develop urethritis. Trachoma strains infect conjunctival cells, leading to scarring, inward-turned eyelashes, corneal damage, and eventual blindness. Transmission occurs via sexual contact, birth canal passage, contaminated hands, fomites, or flies. Diagnosis uses detection of intracellular bacteria through Giemsa staining, culture in susceptible cells, or nucleic acid amplification with fluorescent antibody confirmation. Treatment includes doxycycline or erythromycin for 21 days, with azithromycin cream used for ocular infections. Prevention relies on abstinence, monogamy, condom use, and prompt treatment of infections.

Chlamydophila pneumoniae causes approximately 10% of community-acquired pneumonia and 5% of bronchitis and sinusitis cases in the U.S. Its pathogenicity stems from intracellular replication in respiratory epithelial cells, leading to mild respiratory symptoms such as malaise and chronic cough. Severe pneumonia is less common. Diagnosis relies on fluorescent antibody detection, and treatment involves azithromycin or doxycycline for 14 days. Prevention is challenging because the bacterium spreads via respiratory droplets.

Chlamydophila psittaci causes ornithosis (parrot fever), a zoonotic disease transmitted from birds to humans via inhalation of aerosolized feces or respiratory secretions, ingestion, or direct contact. Pathogenicity is mediated by intracellular replication and host immune response, leading to flu-like symptoms and occasionally severe pneumonia. Mortality can reach 20% without treatment. Diagnosis requires serological testing, and tetracycline or azithromycin for one week is effective. Prevention includes protective clothing, quarantine and treatment of imported birds, and proper husbandry; no vaccine exists.

Rickettsias

Rickettsias are extremely small Gram-negative bacteria that function as obligate intracellular parasites. Because they produce only minimal peptidoglycan, they appear almost wall-less, and their tiny size—only about 0.3 by 1.0 micrometers—initially led researchers to believe they were viruses. Later studies revealed that they contain DNA and RNA, ribosomes, Krebs cycle enzymes, and reproduce through binary fission, demonstrating that they are true bacterial cells. Despite having genes for essential metabolic functions, rickettsias must live within host cells, likely because their cytoplasmic membranes are unusually permeable and allow important cofactors such as NAD⁺ to leak out unless they remain in the nutrient-rich cytoplasm of a host. Based on rRNA sequences, they are classified within the class Alphaproteobacteria of the Proteobacteria phylum. Four genera—Rickettsia, Orientia, Ehrlichia, and Anaplasma—are responsible for most human disease.

The genus Rickettsia consists of aerobic, nonmotile, intracellular parasites that live within the cytosol of host cells. They are surrounded by a poorly organized slime layer and possess LPS with endotoxin activity. Because they are unstable and die quickly outside host cells, they depend on arthropod vectors not only for transmission but also as reservoirs. Once phagocytosed, they escape the endocytic vesicle by releasing enzymes that digest its membrane. Clinically, rickettsial infections fall into two major groups: the spotted fever group and the typhus group. Rocky Mountain spotted fever, caused by Rickettsia rickettsii, is the best-known spotted fever disease. The typhus group includes Rickettsia prowazekii, Rickettsia typhi, and Orientia tsutsugamushi, each responsible for a different form of typhus.

Rickettsia prowazekii causes epidemic or louse-borne typhus and is transmitted by the human body louse, Pediculus humanus. The bacteria inhabit the louse’s gut and are passed in its feces during feeding; scratching introduces them into the bite wound. After entering the body, the organisms infect and multiply within endothelial cells of blood vessels, spreading through the bloodstream and causing bacteremia. Unlike most other rickettsias, R. prowazekii has humans as its primary host and multiplies until the host cell bursts. Epidemic typhus is associated with overcrowded, unhygienic conditions that allow lice to thrive and is currently found most commonly in parts of Central and South America, Africa, and northern China. Symptoms include high fever, profound lethargy, and a persistent rash; in severe cases, poor circulation may lead to the loss of digits or limbs, and mortality is high in untreated elderly patients. Diagnosis is based on the clinical picture following exposure to lice. The disease may reappear years later in a milder form known as Brill–Zinsser disease. Treatment relies on doxycycline or chloramphenicol, while prevention focuses on good hygiene, lice control, and vaccination of high-risk groups.

Rickettsia typhi causes murine, or endemic, typhus, so named because rodents serve as the primary reservoir. Transmission occurs through the rat flea Xenopsylla cheopis and the cat flea Ctenocephalides felis, which also feed on animals such as opossums and raccoons. About twelve days after being bitten by an infected flea, patients typically develop sudden fever, severe headache, chills, muscle pain, and nausea. Less than half develop a rash, which is usually confined to the abdomen and chest. The untreated illness lasts about three weeks and is rarely fatal, and people who recover generally acquire long-lasting immunity. Murine typhus occurs worldwide except in Antarctica and is most commonly reported in the southern United States. Diagnosis is based on symptoms and known flea exposure, with confirmation by immunofluorescent staining. Doxycycline is the standard treatment. Prevention depends on avoiding flea bites, using repellents, and wearing protective clothing, as no vaccine is available

Mycoplasma

Mycoplasmas are unique bacteria in the genera Mycoplasma and Ureaplasma. They lack cell walls, cytochromes, and the enzymes of the Krebs cycle, making them pleomorphic and resistant to beta-lactam antibiotics. Their membranes contain sterols, providing structural stability. Mycoplasmas are the smallest free-living microbes, capable of independent growth, and they require host-derived nutrients such as cholesterol, amino acids, and nucleotides.

Mycoplasma pneumoniae is a strictly human pathogen that colonizes the respiratory tract. Its pathogenicity relies on adhesive proteins that attach to cilia on epithelial cells, stopping ciliary motion and causing cell death. This disrupts mucus clearance and allows secondary bacterial colonization. Clinically, it causes primary atypical pneumonia, or “walking pneumonia,” with mild fever, headache, malaise, sore throat, and persistent unproductive cough. Transmission occurs via nasal secretions, mainly among children aged 5–15 and in close-contact settings. Diagnosis is challenging due to slow growth in culture (2–6 weeks) and small colony size; hemagglutination, ELISA, or indirect fluorescent antibody tests are often used. Treatment includes macrolides, doxycycline, or fluoroquinolones, while prevention focuses on hygiene and limiting aerosol spread; no vaccine exists.

Other pathogenic mycoplasmas include M. hominis, M. genitalium, and Ureaplasma urealyticum, which colonize the urinary and genital tracts. M. genitalium and U. urealyticum cause nongonococcal urethritis, while M. hominis can lead to pelvic inflammatory disease in women. Pathogenicity is linked to mucosal colonization and induction of local inflammation. Transmission is primarily sexual, and prevalence is high in sexually active adults (15% for M. hominis and 70% for Ureaplasma). Diagnosis relies on molecular or serological tests, and treatment involves macrolides or tetracyclines for M. genitalium and Ureaplasma, with clindamycin used for M. hominis. Prevention includes abstinence, monogamy, and proper condom use.

Actinomyces

Actinomyces is a genus of bacteria characterized by hypha-like cells, giving them a filamentous appearance. Despite their name, which means “ray fungus,” Actinomyces are bacteria, not fungi. They are Gram-positive and non–acid-fast. Colonies of Actinomyces can form visible concretions known as “sulfur granules,” which are yellow due to calcium phosphate, not sulfur.

Actinomyces are normal members of the human microbiota, inhabiting mucous membranes of the mouth, gastrointestinal tract, urinary tract, and female genital tract. However, they can become opportunistic pathogens, causing actinomycosis when they enter breaks in mucous membranes, often due to trauma, surgery, or other infections. Actinomycosis is characterized by multiple abscesses connected by channels in the skin or mucous membranes and can also contribute to dental caries.

Epidemiologically, infections are relatively rare and typically occur in individuals with compromised mucosal barriers. Diagnosing actinomycosis is challenging because its symptoms resemble those of other infections, and detection must distinguish true infection from normal colonization. Diagnosis often involves microscopic examination of crushed “sulfur granules” to identify filamentous cells.

Treatment requires surgical removal of infected tissue combined with prolonged penicillin therapy, typically lasting 4–12 months. Preventive measures include maintaining good oral hygiene and using prophylactic antibiotics when mucous membranes are breached during surgery or trauma. 

Coxiella

Coxiella burnetii is an extremely small, aerobic, obligate intracellular bacterium that grows within the acidic environment of phagolysosomes. Its reliance on host cytoplasm and small size initially led researchers to mistake it for a virus. However, it is a Gram-negative bacterium with functional ribosomes, RNA, DNA, and Krebs cycle enzymes. Coxiella forms a stable, spore-like infective body that allows survival under harsh environmental conditions, including desiccation and heat, for years.

Pathogenicity stems from its ability to invade and replicate inside host phagolysosomes, evading immune defenses while resisting harsh intracellular conditions. This intracellular lifestyle enables both acute and chronic infections. Acute infection often results in Q fever, characterized by high fever, severe headache, chills, myalgia, and mild pneumonia. Chronic infection can develop months to years later, sometimes leading to life-threatening endocarditis and inflammation of the lungs and liver.

Epidemiology: C. burnetii has a wide range of mammalian and avian hosts. Farm animals and pets are the main reservoirs. Humans are usually infected by inhaling airborne infective bodies from dried tick feces, animal urine, feces, or placentas. Infection through ticks or contaminated milk is less common, and sexual transmission is rare. Most infections are asymptomatic. Q fever occurs worldwide, particularly among ranchers, veterinarians, and food handlers.

Diagnosis, Treatment, and Prevention: Q fever is diagnosed through serological testing. Treatment of chronic Q fever is challenging because antibiotics must penetrate the acidic phagolysosome; doxycycline, often combined with a fluoroquinolone, is commonly used for long-term therapy. An effective vaccine exists but is not available in the United States. Prevention relies on avoiding inhalation of contaminated dust from animal or barnyard waste and practicing safe handling of livestock.

Treponema

Treponema is a genus of human pathogenic spirochetes, with Treponema pallidum pallidum being the causative agent of syphilis. The bacterium is extremely thin and helical, making it hard to visualize with standard microscopy. It is highly sensitive to environmental conditions and survives only in human hosts. Pathogenicity is linked to its ability to adhere to host cells via surface proteins and to produce enzymes like hyaluronidase, which help it penetrate intercellular spaces. It also has a protective glycocalyx that reduces phagocytosis. Syphilis progresses through primary, secondary, latent, and tertiary stages. Primary infection forms a painless chancre rich in spirochetes, which disseminate via the bloodstream. Secondary syphilis involves systemic spread, causing rash, fever, malaise, and lymphadenopathy. In the latent phase, the bacteria persist in tissues without symptoms. Tertiary syphilis results from immune-mediated tissue damage rather than direct bacterial activity, causing gummas, cardiovascular, and neurological complications. Congenital syphilis occurs when the spirochetes cross the placenta, potentially causing fetal death or organ malformations. Other Treponema species, like T. pallidum endemicum, T. pallidum pertenue, and T. carateum, cause nonvenereal diseases (bejel, yaws, and pinta), which are primarily localized skin and bone infections in children.

Borrelia

Borrelia species are Gram-negative spirochetes causing Lyme disease and relapsing fever. Borrelia burgdorferi is transmitted by Ixodes ticks and causes Lyme disease. Its pathogenicity involves evading the immune system, partly by lacking iron-dependent enzymes and using manganese instead, which reduces host-mediated oxidative killing. It adheres to connective tissue and vascular endothelium, triggering inflammation that contributes to arthritis, neurological symptoms, and cardiac dysfunction. Relapsing fever, caused by Borrelia recurrentis (louse-borne) or tick-borne species, is marked by recurrent fevers due to antigenic variation of surface proteins. This allows Borrelia to repeatedly evade the immune system, causing cycles of septicemia and fever. The bacteria’s presence in blood during febrile episodes facilitates diagnosis via blood smears, while serology confirms Lyme disease. Treatment is doxycycline or penicillin, and prevention focuses on avoiding vectors, using repellents, and maintaining hygiene.

Leptospira

Leptospira species, particularly Leptospira interrogans, are thin, highly motile, aerobic spirochetes causing leptospirosis. Pathogenicity stems from their ability to penetrate intact mucous membranes or small skin abrasions, disseminate via the bloodstream, and damage endothelial cells lining small blood vessels. This can lead to hemorrhage, liver and kidney dysfunction, and systemic inflammation. The bacteria colonize renal tubules, from where they are excreted in urine, sustaining environmental contamination and zoonotic transmission. Humans typically acquire infection through direct contact with animal urine or indirectly through contaminated water or soil. Diagnosis relies on antibody detection, and treatment is intravenous penicillin. Prevention includes rodent control, avoiding contaminated environments, and vaccinating domestic animals.