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Manual of Clinical Microbiology


Fluorescence microscopy

Bacti pathogenesis

Clinical bacteria GNC microscope
Clinical bacteria for which the gram stain is not applicable for various reasons.

Borrelia sp.

" Pathogenesis: Borrelia is transmitted by tick or louse bites. The relapsing-fever borreliae cause recurrent febrile bacteremias separated by remissions during which the borreliae are sequestered in tissues; each resurgence involves a change in cell surface antigens. Lyme disease may have different manifestations at different times; recurrences and late sequelae may appear for many years. The pathogenesis of borrelial diseases is not understood."http://gsbs.utmb.edu/microbook/ch035.htm

"Borrelia recurrentis (louse borne) and B hermsii and B turicatae (tick borne) cause relapsing fevers: influenza-like febrile diseases that follow a relapsing and remitting course. Myocarditis is a rare sequela. Borrelia burgdorferi, causes Lyme disease, a multisystem, relapsing febrile disease with a rash and manifestations such as arthritis, carditis, and neuritis. " http://gsbs.utmb.edu/microbook/ch035.htm

"The clinical diagnosis is confirmed by serology and also by microscopic visualization of the organism in blood of relapsing fever patients. ""The tick-borne relapsing fevers and Lyme disease are zoonoses with rodents as the major reservoir; incidence and distribution depend mainly on the biology of the tick vectors. Louseborne relapsing fever has no animal reservoir and causes epidemics in crowded, unsanitary populations."" Like Leptospira, Borrelia is a flexible, spiral-shaped, gram-negative spirochete with internal flagella. Borrelia species are differentiated primarily on the basis of vectors and DNA homology." http://gsbs.utmb.edu/microbook/ch035.htm

The CDC reports there were just under 13,000 cases of Lyme disease in the US in 1999. And a small decline to about 11,000 cases in 2000.

Borrelia burgdorferi

specific information, http://www.wadsworth.org/databank/borreli.htm

Bartonella sp. cause Cat scratch fever, Oroya fever, bacillary angiomatosis, etc.

Unraveling Mysteries Associated with Cat-Scratch Disease, Bacillary Angiomatosis, and Related Syndromes: http://www.cdc.gov/ncidod/eid/vol1no1/regnery.htm

Image of cat scratch lesion on thumb from CDC's Public Health Image Library: http://phil.cdc.gov/public/1269.htm

Cat-scratch disease lesion on thumb

Encephalitis Associated with Cat Scratch Disease: http://www.cdc.gov/mmwr/preview/mmwrhtml/00033958.htm

"Emergence of Bartonella quintana Infection among Homeless Persons": http://www.cdc.gov/ncidod/eid/vol2no2/jackson.htm

Nomenclature of Bartonella: http://www.bacterio.cict.fr/b/bartonella.html

Molecular Approaches to the Identification of Unculturable Infectious Agents: http://www.cdc.gov/ncidod/eid/vol2no3/gao.htm

Persistent Infection of Pets within a Household with Three Bartonella Species: http://www.cdc.gov/ncidod/eid/vol4no2/kordick.htm

Preventing Zoonotic Diseases in Immunocompromised Persons: The Role of Physicians and Veterinarians: http://www.cdc.gov/ncidod/eid/vol5no1/grant.htm

Cat scratch disease images, Bristol Biomedical archive: http://www.brisbio.ac.uk/ROADS/subject-listing/catscratchdisease.html

"Bartonella is a genus of aerobic gram-negative bacilli. Four of the 10 species identified cause the majority of Bartonella diseases in humans: Bartonella bacilliformis, B. elizabethae, B. henselae, and B. quintana. In the United States, the most common clinical syndrome caused by Bartonella is cat-scratch disease. Approximately 22,000 cases are reported each year. Although a clinical profile of cat-scratch disease was described in 1950, the primary pathogen was not identified until 43 years later. That pathogen, formerly assigned to the genus Rochalimaea, is now designated as B. henselae." http://www.hosppract.com/issues/1998/12/celout.htm

"Bartonella species also cause bacillary angiomatosis, an unusual clinical syndrome involving vascular proliferative lesions of the skin and other organs."

"Despite the name, not all patients with cat-scratch disease have been scratched by a cat. A few have been bitten by a cat; about 30% do not recall either scratches or bites. Just how B. henselae is transmitted from cats to humans remains uncertain, but it may involve traumatic inoculation of infected fleas' feces. " "Most cat-scratch disease is transmitted from cats less than one year old, particularly kittens with fleas."http://www.hosppract.com/issues/1998/12/celout.htm

"Laboratory confirmation of the diagnosis can be provided by indirect fluorescent antibody (IFA) testing for Bartonella. A titer greater than 1:64 indicates infection. The IFA test screens for three Bartonella species associated with human disease: B. henselae, B. quintana, and B. elizabethae. It does not distinguish between them, since there is considerable cross-reactivity between species. The IFA test is available from the U.S. Centers for Disease Control and Prevention." http://www.hosppract.com/issues/1998/12/celout.htm

" Culture of the organism remains very difficult, in part because culture specimens often are obtained late in the disease, when few organisms are present. The organism is also extremely fastidious. It requires specific culture media, usually fresh blood plates, and it must be incubated for several weeks at 5% CO2." http://www.hosppract.com/issues/1998/12/celout.htm


Chlamydia are obligate intracellular pathogens. While many believe chlamydial infections to be esoteric and or rare, the numbers tell a different story. CDC reported cumulative incidence for all types of chlamydial infections for 1999 and for 2000 at just over 500,000 cases per year.

"Diagnosis: The clinical presentation is often diagnostic; the diagnosis may be confirmed by serology (complement fixation or microimmunofluorescence tests) on sera and/or tears."

"Tetracycline and erythromycin are the drugs of choice. Penicillin is not effective. Chlamydiae are obligate intracellular bacteria. They lack several metabolic and biosynthetic pathways and depend on the host cell for intermediates, including ATP. Chlamydiae exist as two stages: (1) infectious particles called elementary bodies and (2) intracytoplasmic, reproductive forms called reticulate bodies. The chlamydiae consist of three species, C trachomatis, C psittaci, and C pneumoniae. The first two contain many serovars based on differences in cell wall and outer membrane proteins. Chlamydia pneumoniae contains one serovar the TWAR organism. "

"Ocular Infections: Chlamydia trachomatis causes trachoma and inclusion conjunctivitis. Trachoma is characterized by the development of follicles and inflamed conjunctivae. The cornea may become cloudy and vascularized; repeated infections are a common cause of blindness. Inclusion conjunctivitis is a milder inflammatory conjunctival infection with purulent discharge."

"Genital Infections: Some C trachomatis strains cause genital infections, including nongonococcal urethritis in men and acute salpingitis and cervicitis in women. Other strains cause lymphogranuloma venereum, a venereal disease with genital lesions and regional lymph node involvement (buboes)."

"Respiratory Infections: Chlamydia psittaci usually causes an influenzalike illness called psittacosis. Chlamydia pneumoniae (TWAR organism) causes atypical pneumonitis in humans." http://gsbs.utmb.edu/microbook/ch039.htm

University of Bristol, UK, Bristol Biomedical Image Archive, http://www.brisbio.ac.uk/, enter term "chlamydia." Currently ten images of chlamydia. All are very high quality.

Calymmatobacterium granulomatis(gnr)
"This microorganism causes granuloma inguinale, a venereal disease with local tissue destruction in the genital, inguinal, and perianal region."
""Calymmatobacterium granulomatis causes granuloma inguinale. This infection typically is localized in the genital region. It spreads to adjacent areas, and the regional lymph nodes also may be inflamed. Persistent granulomatous lesions tend to ulcerate, destroying skin and subcutaneous tissue."
"Calymmatobacterium granulomatis is a Gram-negative, nonmotile rod. The capsule that surrounds the bacterial cell appears similar to that of Klebsiella. Addition of egg yolk and incubation in a CO2 atmosphere are required for growth on artificial media."
"Calymmatobacterium granulomatis is normally present in the gut flora and may be transmitted to the genital area by autoinoculation or sexual contact. After penetrating the skin the bacteria induce an inflammatory reaction, which may lead to destruction of the infected tissue. Within the inflammatory foci C granulomatis is found mainly intracellularly."
"Microscopic evidence of intracellular Gram-negative encapsulated rods in ulcerative skin wounds of the genitoinguinal region is highly indicative for granuloma inguinale. Since experience with C granulomatis is lacking in most laboratories, cultural diagnosis probably will fail. Eventually, the yolk sac of 5-day-old chicken embryos can be inoculated directly with the infected material." "Infection can be prevented by cleanliness or by avoiding sexual contacts with infected persons. Antibiotics active against intracellular bacteria, such as tetracycline or erythromycin, are effective in treatment.http://gsbs.utmb.edu/microbook/ch016.htm


Leptospira interrogans causes leptospirosis, a usually mild febrile illness that may result in liver or kidney failure. Leptospira is a flexible, spiral-shaped, Gram-negative spirochete with internal flagella. Leptospira interrogans has many serovars based on cell surface antigens. Pathogenesis: Leptospira enters the host through mucosa and broken skin, resulting in bacteremia. The spirochetes multiply in organs, most commonly the central nervous system, kidneys, and liver. They are cleared by the immune response from the blood and most tissues but persist and multiply for some time in the kidney tubules. Infective bacteria are shed in the urine. The mechanism of tissue damage is not known. Serum antibodies are responsible for host resistance. Epidemiology: Leptospirosis is a worldwide zoonosis affecting many wild and domestic animals. Humans acquire the infection by contact with the urine of infected animals. Human-to-human transmission is extremely rare." http://gsbs.utmb.edu/microbook/ch035.htm

"Diagnosis: Clinical diagnosis is usually confirmed by serology. Isolation of spirochetes is possible, but it is time-consuming and requires special media. Control: Animal vaccination and eradication of rodents are important. Treatment with tetracycline and penicillin G is effective. No human vaccine is available." http://gsbs.utmb.edu/microbook/ch035.htm

PHIL ID# 138 Title: Scanning electron micrograph of Leptospira Content Provider(s): CDC/NCID/Rob Weyant Provider E-Mail: --- Creation Date: 1998 Description: Scanning electron micrograph of Leptospira bacteria on 0.1 µm polycarbonate filter Source Library: Photo Credit: CDC/NCID/HIP/Janice Carrhttp://phil.cdc.gov/public/138.htm

Leptospira EM

PHIL ID# 1619 Leptospira bacteria, FA stain of liver impression smear. Content Provider(s): CDC/Mildred M. Galton http://phil.cdc.gov/public/1619.htm

Leptospira FA

PHIL ID# 1346 Title: Leptospira bacteria in liver impression smear. FA stain. Content Provider(s): CDC/Mildred Galton http://phil.cdc.gov/public/1346.htm

Leptospira FA

Technical information on Leptospirosis: http://www.cdc.gov/ncidod/dbmd/diseaseinfo/leptospirosis_t.htm

" The Centers for Disease Control and Prevention in Atlanta, Georgia, has preliminary evidence that the cause of acute febrile illness among participants in the Eco-Challenge Sabah 2000 Expedition Race held in Malaysian Borneo, August 20 to September 3, 2000, is an infection called leptospirosis." http://www.cdc.gov/travel/other/lepto-malaysia.htm

Mycobacterium, in general, is characterized by the presence of long chain fatty acids called glycolic acids in the cell wall. This property accounts for the effectiveness of the Ziehl-Nielsen stain which is used to visualize acid-fast bacilli, AFB. Acid-fast bacilli retain carbol-fuchsin red dye after washing with decolorizer, which is an acid, an alcohol, or both. The organisms are very slow growing inhabitants of soil with doubling times of 18-24 hours. Culture identification and sensitivity results take 4-8 weeks using traditional methods. Newer Bactec procedures can take as little as 5-12 days for identification.

Mycobacterium tuberculosis" Tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis and is responsible for more than three million deaths per year. More than eight million new cases of TB are diagnosed each year (worldwide), and almost two billion people are latently infected with the tubercle bacillus."

More specific information about M tuberculosis from Wadsworth Medical Center, http://www.wadsworth.org/databank/mycotubr.htm

PHIL ID# 837 Title: Histopathology of tuberculosis, endometrium. Ziehl-Neelsen stain. Content Provider(s): CDC/Dr. Edwin P. Ewing, Jr. Provider E-Mail: epe1@cdc.gov Creation Date: 1993 Description: Acid-fast Mycobacterium tuberculosis bacillus is visible within granuloma. Source Library: PHIL http://phil.cdc.gov/public/837.htm

M tuberculosis in endometrium

The University of Wisconsin online Textbook of Microbiology: http://www.bact.wisc.edu/MicrotextBook/disease/tuberculosis.html

WebPath online, AFB stain of Mycobacterium tuberculosis: http://medstat.med.utah.edu/WebPath/INFEHTML/INFEC033.html

WebPath online, auramine fluorescence microscopy of Mycobacterium tuberculosis: http://medstat.med.utah.edu/WebPath/INFEHTML/INFEC034.html

Mycobacterium tuberculosis

The CDC reported a total of 12,517 new cases of TB in 1999.

PHIL ID# 28 Title: Histopathology of tuberculosis, placenta Content Provider(s): CDC/Dr. Edwin P. Ewing, Jr. Provider E-Mail: epe1@cdc.gov Creation Date: 1994 Description: Histopathology of placenta thrombus with inflammatory cells and acid-fast bacilli of Mycobacterium tuberculosis (Ziehl-Neelsen stain). Source Library: CDC-PHIL http://phil.cdc.gov/public/28.htm

M tuberculosis in placenta

Mycobacterium leprae
Hansen's disease; leprosy,
"A bacillus, Mycobacterium leprae, that multiplies very slowly and mainly affects the skin, nerves, and mucous membranes. The organism has never been grown in bacteriologic media or cell culture, but has been grown in mouse foot pads. Incidence An estimated 500,000 new Hansen's disease cases are identified each year, with about 300 of these occurring in the United States. Most cases come from 55 countries where disease continues to be endemic. In 1998, WHO listed those countries reporting the most cases as Bangladesh, Brazil, India, Indonesia, Myanmar, and Nigeria.""Worldwide, 1-2 million persons are permanently disabled as a result of Hansen's disease. However, persons receiving antibiotic treatment or having completed treatment are considered free of active infection."


Other species, non-tuberculous mycobacteria;
Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium bovis.

PHIL ID# 965 Title: Mycobacterium avium-intracellulare infection of lymph node in patient with AIDS. Ziehl-Neelsen stain. Content Provider(s): CDC/Dr. Edwin P. Ewing, Jr. Provider E-Mail: epe1@cdc.gov Creation Date: 1983 Description: Histopathology of lymph node shows tremendous numbers of acid-fast bacilli within plump histiocytes. Source Library: PHIL http://phil.cdc.gov/public/965.htm

M avium-intracellulare in lymph node

WebPath online Mycobacterium tutorial: http://medstat.med.utah.edu/WebPath/TUTORIAL/MTB/MTB.html

Mycobacterium avium-intracellulareAFB stain of lymph node from WebPath:

The Graduate School of Biomedical Sciences, University of Texas Medical Branch, online Textbook of Medical Microbiology, chapter 33, Mycobacteria and Nocardia is an excellent source of information on mycobacteria.http://gsbs.utmb.edu/microbook/ch033.htm

Nocardia have glycolic acids in their cell wall. The side chains of the glycolic acids in nocardia are shorter than mycobacteria, C40 to C56 for the former vs C60 to C90 for the latter, which reduces their retention of carbol fuchsin dye on decolorization as compared to the members of the genus Mycobacterium. They are thus "partially" acid fast. Nocardiasp. are described in the section on gram positive bacilli.

Rickettsia , cause Rocky Mountain spotted fever, Tsutsugamushi fever, etc.

"The rickettsiae are a diverse collection of obligately intracellular Gram-negative bacteria found in ticks, lice, fleas, mites, chiggers, and mammals. They include the genera Rickettsiae, Ehrlichia Orientia, and Coxiella, eg., Coxiella burnetii. These zoonotic pathogens cause infections that disseminate in the blood to many organs.""Pathogenesis Rickettsia and Orientia species are transmitted by the bite of infected ticks or mites or by the feces of infected lice or fleas. From the portal of entry in the skin, rickettsiae spread via the bloodstream to infect the endothelium and sometimes the vascular smooth muscle cells. Rickettsia species enter their target cells, multiply by binary fission in the cytosol, and damage heavily parasitized cells directly.""Rickettsioses are difficult to diagnose both clinically and in the laboratory. Cultivation requires viable eukaryotic host cells, such as antibiotic-free cell cultures, embryonated eggs, and susceptible animals. Confirmation of the diagnosis requires comparison of acute- and convalescent-phase serum antibody titers."http://gsbs.utmb.edu/microbook/ch038.htm

PHIL ID# 922 Title: Rickettsia tsutsugamushi budding from mouse peritoneal mesothelial cell. Content Provider(s): CDC/Dr. Edwin P. Ewing, Jr. Provider E-Mail: epe1@cdc.gov Creation Date: 1976 Description: The rickettsia is covered by the host cell plasma membrane. TEM. Source Library: PHIL http://phil.cdc.gov/public/922.htm


PHIL ID# 926 Title: Rickettsia tsutsugamushi dividing within the cytoplasm of a mouse peritoneal mesothelial cell. Content Provider(s): CDC/Dr. Edwin P. Ewing, Jr. Provider E-Mail: epe1@cdc.gov Creation Date: 1976 Description: The rickettsia is undergoing a pinching type division characteristic of gram-negative bacteria including rickettsias. TEM. Source Library: PHIL http://phil.cdc.gov/public/926.htm

Rickettsia dividing

The Rickettsia prowazekii Genome Sequence Sequence reveals closest relative to mitochondria.

Members of the genus Treponema cause yaws, syphilis, endemic syphilis, pinta, etc.

"Classification of the pathogenic treponemes is based primarily upon the clinical manifestations of the respective diseases they cause. Treponema pallidum subsp pallidum causes venereal syphilis; T pallidum subsp pertenue causes yaws; T pallidum subsp endemicum causes endemic syphilis; and T carateum causes pinta. Venereal syphilis is transmitted by sexual contact; the other diseases are transmitted by close nonvenereal contact."

"Treponemes are highly invasive pathogens which often disseminate relatively soon after inoculation. Evasion of host immune responses appears to be, at least in part, due to the unique structure of the treponemal outer membrane (i.e., its extremely low content of surface-exposed proteins). Although treponemes lack classical lipopolysaccharide (endotoxin), they possess abundant lipoproteins which induce inflammatory processes."

"Diagnosis relies heavily on clinical manifestations. In addition, the finding of treponemes within exudative lesions and positive serology aids the diagnosis."

"Penicillin treatment eradicates all stages, including congenital infection in pregnancy"


Treponema pallidum, the causitive agent of syphilis.

"Despite the availability of effective therapy (penicillin), syphilis remains a commonly sexually transmitted disease worldwide (over 100,000 cases were reported in the United States in 1992)."http://www.wadsworth.org/databank/treponem.htmTechnically a gram negative bacillus with a spiral morphology, it is not grown on solid media in the laboratory, nor is it visualized by microscopy under routine conditions. Instead it is detected by serological tests. In 1999, the CDC reported for both primary and secondary syphilis a total of 5,460 cases

Treponema pallidum

Left: cell infiltration of spirochetes in tissue; Right: spirochetes visualized by silver staining.http://www.wadsworth.org/databank/treponem.htm

Centers for Disease Control
National Center for Infectious Diseases
Division of Bacterial & Mycotic Diseases
Morbidity and Mortality Weekly Report, CDC, epidemiological trends, clear perspective.
Guide to Dennis Kunkel's electron microscopy, bacteria images:http://www.pbrc.hawaii.edu/kunkel/catalog/by_category/bacteria/

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