Hart C. Anthony, Shears Paul. Color Atlas of Medical Microbiology.pdf
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Nervous System 645 |
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Table 12.7 Continued: Nervous System |
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Infection |
Most important pathogens |
Laboratory diagnosis |
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Encephalomyelitis |
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Viruses |
Measles virus |
Serology |
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Epstein-Barr virus |
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HIV-1, HIV-2 |
PCR and isolation in brain |
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Herpes simplex virus |
biopsy or cerebrospinal fluid if |
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Varicella zoster virus |
required |
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Cytomegalovirus |
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Mumps virus |
Additionally: isolation from |
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pharyngeal lavage |
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Enteroviruses |
Additionally: isolation from |
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stool |
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Togaviruses |
In tropical viroses viral serology |
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Bunyaviruses |
in reference laboratories |
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Arenaviruses |
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Rabies virus (lyssa virus) |
Direct Immunofluorescence |
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with brain specimen (autopsy) |
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and/or corneal epithelium |
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Serology |
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Tickborne encephalitis virus |
Serology |
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Bacteria |
Rickettsia spp. |
Serology |
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Brucella spp. |
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Borrelia burgdorferi |
Serology and PCR; culture in |
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biopsy if required |
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Leptospira interrogans |
Serology and culture in biopsy |
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if required |
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Treponema pallidum |
Syphilis serology |
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Listeria monocytogenes |
Try microscopy and culture |
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from cerebrospinal fluid and |
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blood |
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Mycobacterium tuberculosis |
Microscopy and culture from |
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cerebrospinal fluid; DNA test if |
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required |
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Fungi |
Cryptococcus neoformans |
Try microscopy and culture |
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Aspergillus spp. |
from cerebrospinal fluid and |
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Mucorales |
blood; Cryptococcus antigen |
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can be detected in cerebrospi- |
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nal fluid. Serology |
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646 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.7 Continued: Nervous System
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Infection |
Most important pathogens |
Laboratory diagnosis |
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Protozoa |
Naegleria fowleri |
Microscopy (cerebrospinal |
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Acanthamoeba spp. |
fluid), culture, DNA detection |
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Toxoplasma gondii |
Serology, microscopy, culture, |
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DNA detection (cerebrospinal |
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fluid) |
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Trypanosoma brucei |
Microscopy (cerebrospinal |
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gambiense |
fluid); |
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Trypanosoma brucei |
Serology |
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rhodesiense |
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Plasmodium falciparum |
Microscopy (blood); |
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Serology |
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Helminths |
Taenia solium (cysticercosis |
Serology |
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of the CNS) |
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Echinococcus granulosus |
Serology |
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Echinococcus multilocularis |
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Toxocara canis |
Serology |
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Toxocara mystax |
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Cerebral abscess |
Streptococcus milleri |
Microscopy and culture for |
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Epidural abscess |
Gram-negative anaerobes |
bacteria from pus |
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Subdural empyema |
Enterobacteriaceae |
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Staphylococcus aureus |
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Mucorales |
Microscopy and culture for |
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Aspergillus spp. |
fungi from pus; serology |
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Candida spp. |
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Toxoplasma gondii |
Serology. Microscopy; DNA test |
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(in cerebrospinal fluid) |
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Tetanus |
Clostridium tetani |
Toxin (animal test, PCR) in |
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material excised from wound. |
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Try microscopy and culture |
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from excised material |
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Botulism |
Clostridium botulinum |
Toxin detection in blood or |
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food (animal test, PCR) |
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Leprosy |
Mycobacterium leprae |
Microscopy of biopsy specimen |
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(peripheral nerves) |
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or scrapings from nasal mucosa |
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Cardiovascular system 647 |
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Table 12.8 Cardiovascular system |
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Infection |
Most Important Pathogens |
Laboratory diagnosis |
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Endocarditis |
Streptococcus spp. (60–80%) |
Blood culture, three sets |
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Staphylococcus spp. (20–35%) |
from three different sites, within |
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Gram-negative rods (2–13%) |
1–2 h, before antimicrobials if |
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Numerous other bacterial spp. |
possible. |
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(5%) |
10–20 ml venous blood into |
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Fungi (2–4%) |
one aerobic and one anaerobic |
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Culture negative (5–25%) |
bottle, respectively. |
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Myocarditis/ |
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pericarditis |
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Viruses |
Enteroviruses |
Serology, if necessary |
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Adenoviruses |
combined with isolation and |
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Herpes virus group |
PCR of punctate |
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Influenzaviruses |
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Parainfluenzaviruses |
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Bacteria |
Staphylococcus aureus |
Microscopy and culture from |
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Streptococcus pneumoniae |
punctate |
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Enterobacteriaceae |
DNA test from punctate if re- |
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Mycobacterium tuberculosis |
quired |
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Mycoplasma pneumoniae |
Serology; culture from punctate |
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Neisseria spp. |
Microscopy and culture from |
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Gram-negative anaerobes |
punctate |
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Actinomyces spp. |
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Nocardia spp. |
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Rickettsia spp. |
Serology |
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Chlamydia trachomatis |
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Fungi |
Candida spp. |
Serology; microscopy (direct IF); |
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Aspergillus spp. |
cell culture or PCR if required |
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Cryptococcus neoformans |
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Protozoa |
Toxoplasma gondii |
Serology, if necessary in |
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Trypanosoma cruzi |
combination with culture and |
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microscopy from punctate |
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Helminths |
Trichinella spiralis |
Serology |
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648 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.9 Hematopoietic and Lymphoreticular System
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Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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HIV infection |
HIV-1; HIV-2 |
Serology: EIA and Western blot. |
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(AIDS) |
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Also p24 antigen assay for primary |
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infection. Quantitative genome test |
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with RT-PCR for therapeutic indica- |
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tion and course (viral load). |
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Infectious |
Epstein–Barr virus (EBV) |
Serology |
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mononucleosis |
Cytomegalovirus (rare) |
Isolation from urine and saliva; |
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serology |
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Brucellosis |
Brucella abortus |
Blood culture: three sets from |
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Brucella melitensis |
three different sites, within 1–2 h, |
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Brucella suis |
before antimicrobials if possible. |
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10–20 ml venous blood into one |
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aerobic and one anaerobic bottle, |
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respectively. |
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Incubation for up to 4 weeks is |
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necessary—inform laboratory of |
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suspected Brucella infection. |
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Serology |
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Tularemia |
Francisella tularensis |
Culture from lymph node biopsy, |
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sputum and blood; serology |
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Plague |
Yersinia pestis |
Microscopy and culture from |
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bubo pus, possibly from sputum |
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(pulmonary plague) |
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Melioidosis |
Burkholderia pseudomallei |
Microscopy and culture from |
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sputum, abscess pus or blood |
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Malleus (glanders) |
Burkholderia mallei |
Microscopy and culture from nasal |
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secretion, abscess pus or blood |
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Rat-bite fever |
Streptobacillus moniliformis |
Culture from lesion specimen |
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Sodoku |
Spirillum minus |
Attempt microscopical detection in |
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blood or wound secretion |
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Hematopoietic and Lymphoreticular System 649
Table 12.9 Continued: Hematopoietic and Lymphoreticular System
Infection |
Most important |
Laboratory diagnosis |
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pathogens |
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Oroya fever and |
Bartonella bacilliformis |
Blood culture (see above for |
verruga peruana |
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brucellosis) |
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Relapsing fever |
Borrelia recurrentis |
Microscopy (Giemsa staining) of |
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Borrelia duttonii |
blood while fever is rising |
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Other borreliae |
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Bacillary |
Bartonella henselae |
Serology; microscopy and |
angiomatosis |
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culture from lymph node biopsy |
(AIDS) |
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as required |
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Cat scratch disease |
Bartonella henselae; |
Microscopy of puncture pus: |
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Bartonella claridgeia |
Warthin-Starry silver stain. Culture |
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Afipia felis (rare) |
on special medium (difficult) |
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Malaria |
Plasmodium spp. |
Microscopy (blood smear, thick |
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film); antigen detection with |
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ParaSight test. Serology (not in |
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acute malaria) |
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Babesiosis |
Babesia spp. |
Microscopy of blood swabs |
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Toxoplasmosis |
Toxoplasma gondii |
Serology |
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Visceral |
Leishmania donovani |
Serology; microscopy and culture |
leishmaniosis |
Leishmania infantum |
of lymph node or bone marrow |
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punctate, DNA detection |
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Filariosis |
Wuchereria bancrofti |
Microscopical detection of |
(lymphatic) |
Brugia malayi |
microfilaria in nocturnal blood; |
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serology |
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Ehrlichiosis |
Ehrlichia spp. |
Isolation in cell culture. PCR. |
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Serology (immunofluorescence) |
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650 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.10 Skin and Subcutaneous Connective Tissue (local or systemic infections with mainly cutaneous manifestation)
Infection |
Most important pathogens |
Laboratory diagnosis |
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a) Viruses |
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Smallpox |
Variola virus |
Electron microscopy of vesicle/ |
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Parapox viruses (orf virus, |
pustule content; isolation; |
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milker’s nodules virus) |
serology; (use reference |
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laboratory) |
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Herpes |
Herpes simplex virus |
Electron microscopy of vesicle |
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content; cell culture |
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Varicella |
Varicella zoster virus |
Serology (IgG, IgM); electron |
(chicken pox) |
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microscopy of vesicle content; |
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direct IF, cell culture |
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Measles |
Measles virus (Morbillivirus) |
Isolation from pharyngeal lavage |
(morbilli, rubeola) |
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and urine if required; serology |
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German measles |
Rubella virus (Rubivirus) |
Serology |
(rubella) |
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Hemorrhagic |
Bunyaviruses (e.g., hantavirus) |
Serology; cell culture and PCR |
fever |
Arenaviruses |
from blood or liver as required; |
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Flaviviruses (e.g., Dengue |
animal test as required; labora- |
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viruses) |
tory diagnosis only possible in |
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Marburg virus |
reference laboratories |
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Ebola virus |
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Molluscum |
Molluscum contagiosum virus |
Microscopy of skin lesions; mol- |
contagiosum |
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luscum bodies |
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Warts |
Papillomavirus |
Genomic test with DNA probe or |
Papillomas |
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electron microscopy |
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Erythema |
Parvovirus B19 |
Serology |
infectiosum |
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Exanthema |
Human herpes virus 6 (HHV 6) |
Serology |
subitum |
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Skin and Subcutaneous Connective Tissue 651
Table 12.10 Continued: Skin and Subcutaneous Connective Tissue
Infection |
Most important pathogens |
Laboratory diagnosis |
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b) Bacteria and fungi |
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Furuncles |
Staphylococcus aureus |
Microscopy and culture from |
Carbuncles |
Streptococcus pyogenes |
swab |
Pemphigus |
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Folliculitis |
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Impetigo |
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Erysipelas |
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Gangrenous |
Often mixed flora: |
Microscopy from swab or |
cellulitis |
Clostridium spp. |
pus, use transport medium for |
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Gram-negative anaerobes |
anaerobes |
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Pseudomonas spp. |
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Enterobacteriaceae |
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Erysipeloid |
Erysipelothrix rhusiopathiae |
Microscopy and culture from |
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skin lesion swab |
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Erythema |
Borrelia burgdorferi |
Serology |
migrans |
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Cutaneous |
Bacillus anthracis |
Microscopy and culture from |
anthrax |
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skin lesion swab |
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Leprosy |
Mycobacterium leprae |
Microscopy (Ziehl-Neelsen stain) |
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of material from skin lesions |
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(biopsy) or scrapings from nasal |
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mucosa |
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Rickettsioses |
Rickettsia spp. |
Serology, culturing (embryo- |
(spotted fever |
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nated hen’s egg) or animal test |
and others) |
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if necessary |
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Nonvenereal |
Treponema pallidum |
Try microscopy of material |
treponema |
(subsp. endemicum) |
from skin lesions; serology |
infections |
Treponema pallidum |
(syphilis tests) |
(endemic syphilis, |
(subsp. pertenue) |
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pinta, yaws) |
Treponema carateum |
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652 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.10 Continued: Skin and Subcutaneous Connective Tissue
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Infection |
Most important pathogens |
Laboratory diagnosis |
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Madura foot |
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mycosis/mycetoma |
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Bacteria |
Nocardia brasiliensis |
Microscopy and culture from |
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Actinomadura madurae |
lesion material |
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Streptomyces somaliensis |
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Fungi |
Madurella spp. |
Microscopy and culture from le- |
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Pseudoallescheria spp. |
sion material |
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Aspergillus spp., and others |
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Dermatomycoses |
Dermatophytes |
Microscopy and culture from |
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Candida spp. |
cutaneous scales |
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Sporotrichosis |
Sporothrix schenckii |
Microscopy and culture from le- |
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sion pus |
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Chromomycosis |
Black molds (various types) |
Microscopy and culture from le- |
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sion pus |
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c) Protozoa, helminths, and arthropods |
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Cutaneous |
Leishmania tropica |
Microscopy and culture from le- |
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leishmaniosis |
Leishmania major |
sion biopsy; DNA detection |
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(oriental sore) |
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(PCR) |
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American |
Leishmania braziliensis |
Microscopy and culture from |
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cutaneous and |
Leishmania mexicana |
skin and mucosal lesion biopsy; |
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mucocutaneous |
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DNA detection (PCR) |
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leishmaniosis |
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Cercarial |
Cercariae from Schistosoma |
Serology |
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dermatitis |
spp. |
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Cutaneous |
Larvae of Ancylostoma spp. |
Clinical diagnosis |
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larva migrans |
and Strongyloides species |
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(“creeping |
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eruption”) |
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Onchocercosis |
Onchocerca volvulus |
Microscopical detection of |
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(microfilariae) |
microfilariae in “skin snips”; |
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serology |
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654 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form 
Table 12.11 Bone, Joints, and Muscles
Infection |
Most important pathogens |
Laboratory diagnosis |
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Necrotizing fasciitis |
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Type 1 |
Often aerobic/anaerobic |
Microscopy and culture from |
(syn. polymicrobial |
mixed flora: Clostridium spp., |
wound secretion. Transport |
gangrene) |
Gram-positive and Gram- |
materials in anaerobic system |
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negative anaerobes, |
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Staphylococcus aureus, |
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Streptococcus bovis, |
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Enterobacteriaceae |
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Type 2 |
Streptococcus pyogenes |
Microscopy and culture from |
(syn. Streptococcal |
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wound secretion |
necrotizing myositis) |
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Trichinellosis (Muscle) |
Trichinella spiralis |
Microscopical detection in |
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muscle biopsy; serology |
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Cysticercosis (Muscle) |
Taenia solium |
Serology (radiology) |
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Osteomyelitis/ostitis |
Staphylococcus aureus |
Microscopy and culture for |
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Coagulase-negative |
bacteria, preferably based on |
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staphylococci |
biopsy or surgical material. |
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Streptococcus spp. |
Swab from fistular duct not |
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Enterobacteriaceae |
useful for diagnosis |
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Pseudomonas spp. |
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Gram-positive and Gram- |
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negative anaerobes (rare) |
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Septic arthritis |
Staphylococcus aureus |
Microscopy and culture from |
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Streptococcus pyogenes |
synovial fluid with parallel |
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Streptococcus pneumoniae |
blood culture |
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Haemophilus influenzae |
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Neisseria gonorrhoeae |
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Enterobacteriaceae |
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Pseudomonas spp. |
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