Hart C. Anthony, Shears Paul. Color Atlas of Medical Microbiology.pdf
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Urogenital Tract 635 |
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Table 12.3 Urogenital Tract |
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Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Urethrocystitis |
Escherichia coli |
Microscopy and culture; test |
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Pyelonephritis |
Other Enterobacteriaceae |
midstream urine for significant |
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Pseudomonas aeruginosa |
bacteriuria (p. 210) |
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Enterococci |
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Staphylococcus aureus |
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Staphylococcus saprophyticus |
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(in women) |
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Prostatitis |
Escherichia coli |
Microscopy and culture. |
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Other Enterobacteriaceae |
Specimens: prostate secretion |
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Pseudomonas aeruginosa |
and urine. Quantitative urine |
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Enterococci |
bacteriology (p. 210) required |
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Staphylococcus aureus |
for evaluation. To confirm |
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Neisseria gonorrhoeae |
C. trachomatis, antigen |
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Chlamydia trachomatis |
detection by direct IF or EIA or |
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cell culture or PCR. |
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Nonspecific |
Chlamydia trachomatis |
Microscopy (direct IF) or |
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urethritis |
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antigen detection with EIA, |
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or cell culture or PCR |
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Mycoplasma hominis |
Culture (special mediums) |
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Ureaplasma urealyticum |
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Urethral syndrome |
Chlamydia trachomatis (30%) |
See above: nonspecific |
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(women) |
Escherichia coli (30%) |
urethritis |
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Staphylococcus saprophyticus |
Culture from urine. Bacteriuria |
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(5–10%) |
< |
4 |
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often –10 |
/ml |
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Unknown pathogens (20%) |
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Microsporosis of the |
Encephalitozoon spp. |
Microscopy of urine sediment, |
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genitourinary tract |
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DNA detection (PCR) |
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Nephropathia |
Hantaviruses/Puumala virus |
Serology |
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epidemica |
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Tuberculosis of the |
Mycobacterium tuberculosis |
Microscopy and culture |
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urinary tract |
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Three separate morning urine |
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specimens, 30–50 ml each |
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636 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.3 Continued: Urogenital Tract
Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Listeriosis |
Listeria monocytogenes |
Microscopy and culture from |
(pregnancy) |
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cervical and vaginal secretion, |
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lochia. Blood culture if required |
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Schistosomosis of |
Schistosoma haematobium |
Microscopy of urine sediment; |
the urinary tract |
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serology |
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Vulvovaginitis |
Herpes simplex virus |
Isolation or antigen detection |
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in secretion |
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Candida spp. |
Microscopy, culture if required |
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Trichomonas vaginalis |
Microscopy (native). Submit |
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two slides with air-dried secre- |
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tion (for Giemsa staining or |
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immunofluorescence), culture |
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from vaginal secretion |
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Nonspecific vaginitis |
Several bacterial spp. often |
Attempt microscopy and |
(vaginosis) |
contribute to infection: |
culture of vaginal secretion. |
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Gardnerella vaginalis |
Look for “clue cells” in |
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Mycoplasma hominis |
microscopy. Interpretation of |
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Mobiluncus mulieri |
many findings is problematic |
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Mobiluncus curtisii |
because the bacteria are part |
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Gram-negative anaerobes |
of the normal flora |
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Cervicitis |
Neisseria gonorrheae |
Microscopy and culture from |
Endometritis |
Chlamydia trachomatis |
swab material. Use transport |
Oophoritis |
Mixed anaerobic flora |
mediums. For detection of |
Salpingitis |
Less frequently: |
chlamydiae: direct IF micro- |
Pelveoperitonitis |
Enterobacteriaceae |
scopy, EIA antigen detection, |
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Streptococcus spp. |
cell culture or PCR. PCR kit |
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Gardnerella vaginalis |
available to detect gonococci |
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Mycoplasma hominis |
simultaneously. |
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Mycobacterium tuberculosis |
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Genital Tract 637 |
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Table 12.4 Genital Tract (venereal diseases) |
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Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Gonorrhea |
Neisseria gonorrhoeae |
Microscopy (send two slides to |
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the laboratory, for gram staining |
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and IF); culture (swab in special |
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transport medium); rapid anti- |
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gen detection with antibodies in |
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swab material; PCR (kit available |
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to detect C. trachomatis simulta- |
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neously) |
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Syphilis (lues) |
Treponema pallidum |
Microscopy (dark field) of mate- |
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(ssp. pallidum) |
rial from stage I and II lesions. |
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Serology (see p. 321 for basic |
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diagnostics) |
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Lymphogranuloma |
Chlamydia trachomatis |
Microscopy (direct IF) of pus; |
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venereum |
(L serovars) |
cell culture or PCR |
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Ulcus molle |
Haemophilus ducreyi |
Microscopy of pus. |
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(soft chancre) |
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Culture (very difficult) |
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Granuloma inguinale |
Calymmatobacterium |
Microscopy of scrapings or |
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granulomatis |
biopsy material (look for |
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Donovan bodies); culture |
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(embryonated hen’s egg or |
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special mediums) |
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Gastrointestinal Tract 639 |
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Table 12.5 Continued: Gastrointestinal Tract |
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Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Salmonellosis |
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Enteric form |
Salmonella enterica |
Culture from stool |
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(enteric serovars) |
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Typhoid form |
Salmonella enterica |
Culture from blood and |
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(typhoid serovars) |
stool; serology |
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(or possibly enteric |
(Gruber-Widal results of |
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salmonellae in |
limited significance) |
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predisposed persons) |
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Cholera |
Vibrio cholerae |
Culture from stool, possibly |
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also from vomit |
Whipple’s disease |
Tropheryma whipplei |
Microscopy and DNA |
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detection from small |
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intestine biopsy. |
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Culture not possible |
Protozoa |
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Amebosis |
Entamoeba histolytica |
Microscopy of stool, |
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detection of coproantigen |
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(or DNA); serology |
Giardiosis |
Giardia intestinalis |
Microscopy of stool or |
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duodenal fluid, |
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coproantigen detection |
Cryptosporidiosis |
Cryptosporidium species |
Microscopy of stool, |
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coproantigen detection, |
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DNA detection |
Microsporosis |
Enterocytozoon bieneusi |
Microscopy of stool, DNA |
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detection |
Cyclosporosis |
Cyclospora cayetanensis |
Microscopy of stool |
Sarcocystiosis |
Sarcocystis spp. |
Microscopy of stool |
Isosporiosis |
Isospora belli |
Microscopy of stool |
Blastocystosis |
Blastocystis hominis |
Microscopy of stool |
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640 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.5 Continued: Gastrointestinal Tract
Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Helminths |
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Trematode infections |
Schistosoma spp. |
Microscopical detection |
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of worm eggs in stool; |
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serology |
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Fasciolopsis buski |
Microscopical detection |
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of worm eggs in stool |
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Heterophyes heterophyes |
Microscopical detection |
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and others |
of worm eggs in stool |
Cestode infections |
Taenia spp. |
Microscopical detection |
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Hymenolepis spp. |
of worm eggs and/or |
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Diphyllobothrium spp. |
proglottids in stool |
Nematode infections |
Ascaris lumbricoides |
Microscopical detection |
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Trichuris trichiura |
of worm eggs in stool |
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Ancylostoma and |
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Necator spp. |
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Strongyloides stercoralis |
Microscopy and culturing |
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of larvae in stool (serology) |
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Enterobius vermicularis |
Microscopical detection of |
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worm eggs (anal adhesive |
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tape on slide) or worms in |
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stool |
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Digestive Glands and Peritoneum 641
Table 12.6 Digestive Glands and Peritoneum
Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Mumps |
Mumps virus |
Serology |
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(parotitis epidemica) |
(paramyxovirus) |
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Infectious hepatitis |
Hepatitis A virus |
Serology (IgM) |
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Hepatitis B and D virus |
Antigen and antibody |
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detection in blood, PCR |
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Hepatitis C and G virus |
Serology, PCR |
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Hepatitis E virus |
Serology (IgE, IgM), PCR |
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Yellow fever (liver) |
Yellow fever virus |
Serology; |
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(flavivirus) |
isolation if required |
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(use reference laboratory) |
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Cytomegalovirus |
Cytomegalovirus (CMV) |
Cell culture from saliva, |
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infection (liver) |
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urine and if required from |
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biopsy material. Antigen |
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assay or DNA test (PCR). |
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Serology |
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Leptospirosis (liver) |
Leptospira interrogans |
Serology. Culture from urine |
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(serogroup ictero- |
and blood |
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haemorrhagiae) |
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Cholecystitis/Cholangitis |
E. coli |
Culture from bile |
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Other Enterobacteriaceae |
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Gram-negative anaerobes |
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Fasciola hepatica |
Worm eggs in stool; |
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serology |
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Opisthorchis |
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Clonorchis |
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Dicrocoelium |
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Pancreatitis |
Enterobacteriaceae |
Microscopy and culture |
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Pancreatic abscess |
Staphylococcus aureus |
from pus (punctate or |
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Streptococcus spp. |
biopsy, if specimen |
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Pseudomonas spp. |
sampling feasible) |
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Anaerobes |
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642 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.6 Continued: Digestive Glands and Peritoneum
Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Liver abscess |
Usually mixed bacterial |
Microscopy and culture |
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flora: |
from pus if specimen |
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E. coli |
sampling feasible (punctate, |
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Other Enterobacteriaceae |
biopsy, surgical material) |
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Gram-negative anaerobes |
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Gram-positive anaerobes |
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Staphylococcus aureus |
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Streptococcus pyogenes |
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Streptococcus milleri |
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Entamoeba histolytica |
Serology |
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Splenic abscess |
Staphylococcus spp. |
Microscopy and culture |
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(in endocarditis) |
from pus if specimen |
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Streptococcus spp. |
sampling feasible; blood |
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(in endocarditis) |
culture |
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Enterobacteriaceae |
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Gram-negative and |
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Gram-positive anaerobes |
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Peritonitis |
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Primary peritonitis |
Streptococcus pneumoniae |
Microscopy and culture |
(rare; usually the |
Streptococcus pyogenes |
from pus; (specimen |
result of hematogenous |
Gram-negative/-positive |
sampling during |
dissemination) |
anaerobes; |
laparotomy, or puncture if |
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Enterobacteriaceae; |
necessary) |
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enterococci; rarely |
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Staphylococcus aureus |
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Secondary peritonitis |
Usually mixed aerobic- |
Microscopy and culture |
(endogenous infection |
anaerobic flora |
from pus (specimen sam- |
caused by enteric |
Enterobacteriaceae |
pling during laparotomy, |
bacteria) |
Gram-negative and |
or puncture if necessary) |
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Gram-positive anaerobes |
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Digestive Glands and Peritoneum 643
Table 12.6 Continued: Digestive Glands and Peritoneum
Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Peritonitis following |
Gram-positive bacteria |
Microscopy and culture |
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peritoneal dialysis |
(60–80%): |
from cloudy dialysis fluid. |
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(CAPD) |
Staphylococcus spp. |
Concentration of fluid |
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Streptococcus spp. |
necessary (e.g., filtration |
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Corynebacterium spp. |
or centrifugation) |
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Gram-negative bacteria |
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(15–30%): |
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Enterobacteriaceae |
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Pseudomonas spp. |
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Acinetobacter spp. |
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Candida spp. (rare) |
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Intraperitoneal abscesses |
Usually mixed aerobic- |
Microscopy and culture |
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anaerobic flora: |
from pus (specimen |
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Enterobacteriaceae |
sampling during laparot- |
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Staphylococcus aureus |
omy, or puncture if |
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Gram-negative/ |
necessary) |
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-positive anaerobes |
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Streptococcus milleri |
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Protozoan infections (liver) |
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Visceral leishmaniasis |
Leishmania donovani |
Microscopy and culture |
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Leishmania infantum |
from lymph node or bone |
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marrow punctate; DNA |
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detection; serology |
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Trematode infections |
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(liver, bile ducts) |
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Schistosomosis |
Schistosoma mansoni |
Microscopical detection of |
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worm eggs in stool; serology |
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Fasciolosis |
Fasciola hepatica |
Microscopical detection of |
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worm eggs in stool; serology |
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Opisthorchiosis |
Opisthorchis spp. |
Microscopical detection of |
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Clonorchiosis |
Clonorchis sinensis |
worm eggs in stool |
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Dicrocoeliosis |
Dicrocoelium dendriticum |
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Cestode infections |
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Echinococcosis |
Echinococcosus granulosus |
Serology |
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(liver, peritoneal cavity) |
Echinococcosus multilocularis |
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644 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.7 Nervous System
Infection |
Most important pathogens |
Laboratory diagnosis |
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Meningitis |
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Viruses |
Enteroviruses |
Isolation from cerebrospinal |
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Herpes simplex virus |
fluid, stool, pharyngeal lavage; |
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Mumps virus |
serology if herpes or mumps |
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suspected |
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PCR from cerebrospinal fluid |
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Togaviruses |
In tropical viroses virus isolation |
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Bunyaviruses |
from cerebrospinal fluid and |
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Arenaviruses |
blood and serology in reference |
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laboratory |
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Lymphocytic |
Serology in blood, in cere- |
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choriomeningitis virus |
brospinal fluid if necessary |
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Tickborne encephalitis virus |
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(flavivirus) |
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Bacteria |
Neisseria meningitidis |
Microscopy and culture from |
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(!20%) |
cerebrospinal fluid; |
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Streptococcus pneumoniae |
antigen detection if required |
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(!30%) |
(rapid test) |
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Haemophilus influenzae b |
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(Less frequent now due to |
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vaccination in children) |
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Rare: |
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Enterobacteriaceae (senium) |
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Mycobacterium tuberculosis |
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Leptospira interrogans |
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Listeria monocytogenes |
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Neonates: |
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E. coli |
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Group B streptococci |
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Fungi |
Cryptococcus neoformans |
Microscopy and culture from |
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Candida spp. |
cerebrospinal fluid; antigen de- |
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Coccidioides immitis |
tection; serology |
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