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May 10, 2019

Upper Respiratory Tract : Etiological and Laboratory Diagnostic Summaries in Tabular Form

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Etiological and Laboratory Diagnostic Summaries in Tabular Form

Table 12.1 Upper Respiratory Tract
Infection
Most important pathogens*
Laboratory diagnosis
Rhinitis (common cold)
Rhinoviruses
Coronaviruses
Influenzaviruses
Adenoviruses
Laboratory diagnosis not recommended
Sinusitis
Streptococcus pneumoniae
Haemophilus influenzae
Staphylococcus aureus
Moraxella catarrhalis
(children)
Streptococcus pyogenes rarely: anaerobes
Microscopy and culturing from sinus secretion/pus (punctate) or sinus lavage

Influenzaviruses
Serology

Adenoviruses
Rhinoviruses
Coronaviruses
Laboratory diagnosis not recommended
Pharyngitis/tonsillitis/ gingivitis/stomatitis
Viruses
Adenoviruses
Influenzaviruses
RS virus
Rhinoviruses
Coronaviruses
Isolation, if required, or direct detection in pharyngeal lavage or nasal secretion; serology
Herpangina
Coxsackie viruses, group A
Isolation if required
Gingivitis/stomatitis
Herpes simplex virus
Isolation Serology
Upper Respiratory
Table 12.1 Continued: Upper Respiratory Tract
Infection
Most important pathogens*
Laboratory diagnosis
Infectious mononucleosis
Epstein-Barr virus (EBV)
Serology

Cytomegalovirus (CMV)
Culture from pharyngeal lavage and urine; serology
Bacteria
Streptococcus pyogenes,
rarely: streptococci of groups B, C, or G
Culture from swab; rapid antigen detection test for A-streptocci in swab material if required
Plaut-Vincent angina
Treponema vincentii + mixed anaerobic flora
Microscopy from swab
Acute necrotic ulcerous gingivostomatitis
Treponema vincentii + mixed anaerobic flora
Microscopy from swab
Diphtheria
Corynebacterium diphtheriae Culture from swab
Laryngotracheobronchitis (croup)
Parainfluenza viruses
Influenza viruses
Respiratory syncytial virus
Adenoviruses Enteroviruses
Isolation from pharyngeal lavage or bronchial secretion, combined with serology

Rhinoviruses
Laboratory diagnosis not recommended
Epiglottitis
Haemophilus influenzae (usually serovar “b”) More rarely:
Streptococcus pneumoniae,
Staphylococcus aureus,
Streptococcus pyogenes
Blood culture. Culture from swab (caution: respiratory arrest possible in taking the swab)
* The pathogens that occur most frequently are in bold type.
12.2 Lower Respiratory Tract
Infection
Most important pathogens
Laboratory diagnosis
Acute bronchitis.
Acute bronchiolitis
(small children)
Respiratory syncytial virus
Parainfluenza viruses
Type A influenza viruses
Adenoviruses
Serology, combined with isolation from pharyngeal lavage or bronchial secretion

Rhinoviruses
Not recommended

Mycoplasma pneumoniae
Serology

Chlamydia pneumoniae
Serology if required
Pertussis
Bordetella pertussis
Culture; special material sampling and transport requirements
Direct immunofluorescence in smear
Acute exacerbation Streptococcus pneumoniae Culture from sputum or of “chronic obstructive Haemophilus influenzae bronchial secretion pulmonary disease” Moraxella catarrhalis
(COPD)
Tuberculosis
Mycobacterium tuberculosis other mycobacteria
Microscopy and culture (time requirement: 3–6–8 weeks)
Pneumonia
Viruses (15–20%) (usually communityacquired)
Parainfluenza viruses
(children)
Respiratory syncytial virus
(children)
Influenza viruses
Adenoviruses
Serology, combined with isolation from pharyngeal lavage or bronchial secretion or antigen detection in nasal secretion

Epstein-Barr virus (EBV)
Serology

Cytomegalovirus (CMV)
(in transplant patients)
Measles virus
Serology, combined with isolation from pharyngeal lavage or bronchial secretion; cell culture if CMV pneumonia suspected. Antigen or DNA assay.
Serology
Lower Respiratory
Table 12.2 Continued: Lower Respiratory Tract
Infection
Most important pathogens
Laboratory diagnosis

Pulmonary hantaviruses (USA)
Serology

Enteroviruses
Isolation from pharyngeal lavage or bronchial secretion

Rhinoviruses
Laboratory diagnosis not recommended
Bacteria (80–90%) “Community-acquired pneumonia”
Streptococcus pneumoniae
(30%)
Haemophilus influenzae (5%)
Staphylococcus aureus (5%)
Klebsiella pneumoniae
Legionella pneumophila
Mixed anaerobic flora
(aspiration pneumonia)
Microscopy and culturing from expectorated sputum, or better yet from transtracheal or bronchial aspirate, from bronchoalveolar lavage or biopsy material. If anaerobes are suspected use special transport vessels

Mycoplasma pneumoniae
(10%)
Coxiella burnetii
Chlamydia psittaci
Serology
Serology
Serology: CFT can detect only antibodies to genus. Microimmunofluorescence
(MIF) species-specific

Chlamydia pneumoniae
Serology: MIF
“Hospital-acquired pneumonia”
Enterobacteriaceae
Pseudomonas aeruginosa
Staphylococcus aureus
Laboratory procedures see above at “communityacquired pneumonia”
Fungi
Aspergillus spp.
Candida spp.
Cryptococcus neoformans
Histoplasma capsulatum Coccidioides immitis Blastomyces spp. Mucorales
Microscopy and culture, preferably from transtracheal or bronchial aspirate, bronchoalveolar lavage or lung biopsy. Serology often
possible
(see Chapter 5)
12.2 Continued: Lower Respiratory Tract
Infection
Most important pathogens
Laboratory diagnosis

Pneumocystis carinii
(Pneumocystis carinii pneumonia (PCP) frequent in AIDS patients)
Pathogen detection in “induced” sputum or bronchial lavage by means of microscopy, immunofluorescence or DNA analysis
Protozoa
Microspora
As for P. carinii, DNA detection (PCR)

Toxoplasma gondii
Serology
Helminths
Echinococcus spp.
Serology

Schistosoma spp.
Serology; worm eggs in stool

Toxocara canis (larvae)
Serology

Ascaris lumbricoides (larvae)
Serology (specific IgE) (worm eggs in stool)

Paragonimus spp.
Worm eggs in stool and sputum; serology
SARS (Severe Acute SARS Corona Virus
Respiratory Syndrome)
Reverse transcriptase PCR (RT-PCR) in respiratory tract specimens (swabs, lavage etc.).
Serology (EIA).
Empyema Streptococcus pneumoniae
Staphylococcus aureus
Streptococcus pyogenes Numerous other bacteria are potential pathogens
Microscopy and culture from pleural pus specimen
Pulmonary abscess Usually endogenous
Necrotizing pneumonia infections with Gramnegative/Gram-positive mixed anaerobic flora Aerobes also possible
Microscopy and culture from transtracheal or bronchial aspirate, bronchoalveolar lavage or lung biopsy. Transport in medium for anaerobes
Candida spp.
Aspergillus spp. Mucorales
Microscopy and culture, serology as well if required
Urogenital
Table 12.3 Urogenital Tract
Infection
Most important pathogens
Laboratory diagnosis
Urethrocystitis Pyelonephritis
Escherichia coli
Other Enterobacteriaceae Pseudomonas aeruginosa
Enterococci
Staphylococcus aureus
Staphylococcus saprophyticus
(in women)
Microscopy and culture; test midstream urine for significant bacteriuria (p. 210)
Prostatitis
Escherichia coli
Other Enterobacteriaceae Pseudomonas aeruginosa
Enterococci
Staphylococcus aureus
Neisseria gonorrhoeae
Chlamydia trachomatis
Microscopy and culture. Specimens: prostate secretion and urine. Quantitative urine bacteriology (p. 210) required for evaluation. To confirm C. trachomatis, antigen detection by direct IF or EIA or cell culture or PCR.
Nonspecific urethritis
Chlamydia trachomatis
Microscopy (direct IF) or antigen detection with EIA, or cell culture or PCR

Mycoplasma hominis
Ureaplasma urealyticum
Culture (special mediums)
Urethral syndrome (women)
Chlamydia trachomatis (30%)
Escherichia coli (30%)
Staphylococcus saprophyticus
(5–10%)
Unknown pathogens (20%)
See above: nonspecific
urethritis
Culture from urine. Bacteriuria often –<104/ml
Microsporosis of the genitourinary tract
Encephalitozoon spp.
Microscopy of urine sediment, DNA detection (PCR)
Nephropathia epidemica
Hantaviruses/Puumala virus
Serology
Tuberculosis of the urinary tract
Mycobacterium tuberculosis
Microscopy and culture Three separate morning urine specimens, 30–50 ml each
12.3 Continued: Urogenital Tract
Infection
Most important pathogens
Laboratory diagnosis
Listeriosis (pregnancy)
Listeria monocytogenes
Microscopy and culture from cervical and vaginal secretion, lochia. Blood culture if required
Schistosomosis of the urinary tract
Schistosoma haematobium
Microscopy of urine sediment; serology
Vulvovaginitis
Herpes simplex virus
Isolation or antigen detection in secretion

Candida spp.
Microscopy, culture if required

Trichomonas vaginalis
Microscopy (native). Submit two slides with air-dried secretion (for Giemsa staining or immunofluorescence), culture from vaginal secretion
Nonspecific vaginitis (vaginosis)
Several bacterial spp. often contribute to infection: Gardnerella vaginalis
Mycoplasma hominis
Mobiluncus mulieri
Mobiluncus curtisii
Gram-negative anaerobes
Attempt microscopy and culture of vaginal secretion. Look for “clue cells” in microscopy. Interpretation of many findings is problematic because the bacteria are part of the normal flora
Cervicitis
Endometritis
Oophoritis
Salpingitis
Pelveoperitonitis
Neisseria gonorrheae
Chlamydia trachomatis Mixed anaerobic flora Less frequently:
Enterobacteriaceae Streptococcus spp.
Gardnerella vaginalis
Mycoplasma hominis
Mycobacterium tuberculosis
Microscopy and culture from swab material. Use transport mediums. For detection of chlamydiae: direct IF microscopy, EIA antigen detection, cell culture or PCR. PCR kit available to detect gonococci simultaneously.
Genital
Table 12.4 Genital Tract (venereal diseases)
Infection
Most important pathogens
Laboratory diagnosis
Gonorrhea
Neisseria gonorrhoeae
Microscopy (send two slides to the laboratory, for gram staining and IF); culture (swab in special transport medium); rapid antigen detection with antibodies in swab material; PCR (kit available to detect C. trachomatis simultaneously)
Syphilis (lues)
Treponema pallidum (ssp. pallidum)
Microscopy (dark field) of material from stage I and II lesions. Serology (see p. 321 for basic diagnostics)
Lymphogranuloma venereum
Chlamydia trachomatis (L serovars)
Microscopy (direct IF) of pus; cell culture or PCR
Ulcus molle (soft chancre)
Haemophilus ducreyi
Microscopy of pus.
Culture (very difficult)
Granuloma inguinale
Calymmatobacterium granulomatis
Microscopy of scrapings or biopsy material (look for Donovan bodies); culture (embryonated hen’s egg or special mediums)
12.5 Gastrointestinal Tract
Gastritis type B
Gastric ulceration
Duodenal ulceration
Gastric adenocarcinoma
Gastric lymphoma (MALT)
Helicobacter pylori
Direct fecal antigen detection
Biopsy and histopathology
Urea breath test
Culture from biopsy
Serology for screening
Gastroenteritis/enterocolitis
Viruses
Rotaviruses Direct virus detection
Adenoviruses with electron microscopy
Rarely: enteroviruses, (reference laboratories) coronaviruses, astroviruses, or direct detection with caliciviruses, Norwalk virus immunological methods
(e.g., EIA)
Bacteria
Staphylococcus aureus intoxication (enterotoxins A-E)
Toxin detection (with
antibodies) in food and stool

Clostridium perfringens (foods)
Culture (quantitative) from food and stool

Vibrio parahaemolyticus (food, marine animals)
Culture from stool

E. coli (EPEC, ETEC, EIEC, EHEC, EAggEC)
No simple tests available; if necessary: culture from stool and identification of pathovars by means of DNA assay; serovar may provide
evidence

Campylobacter jejuni
Culture from stool

Yersinia enterocolitica
Culture from stool

Bacillus cereus
Culture from stool
Pseudomembranous
colitis (often antibioticassociated)
Clostridium difficile
Toxin detection
(cell culture) in stool. DNA assay for toxin possible
Shigellosis (dysentery)
Shigella spp.
Culture from stool
Gastrointestinal
Table 12.5 Continued: Gastrointestinal Tract
Infection
Most important pathogens
Laboratory diagnosis
Salmonellosis Enteric form
Salmonella enterica (enteric serovars)
Culture from stool
Typhoid form
Salmonella enterica
(typhoid serovars) (or possibly enteric salmonellae in predisposed persons)
Culture from blood and stool; serology
(Gruber-Widal results of limited significance)
Cholera
Vibrio cholerae
Culture from stool, possibly also from vomit
Whipple’s disease
Tropheryma whipplei
Microscopy and DNA detection from small intestine biopsy. Culture not possible
Protozoa Amebosis
Entamoeba histolytica
Microscopy of stool, detection of coproantigen
(or DNA); serology
Giardiosis
Giardia intestinalis
Microscopy of stool or duodenal fluid, coproantigen detection
Cryptosporidiosis
Cryptosporidium species
Microscopy of stool, coproantigen detection, DNA detection
Microsporosis
Enterocytozoon bieneusi
Microscopy of stool, DNA 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
12.5 Continued: Gastrointestinal Tract
Infection
Most important pathogens
Laboratory diagnosis
Helminths
Trematode infections
Schistosoma spp.
Microscopical detection
of worm eggs in stool;
serology

Fasciolopsis buski
Microscopical detection of worm eggs in stool

Heterophyes heterophyes and others
Microscopical detection of worm eggs in stool
Cestode infections
Taenia spp.
Hymenolepis spp.
Diphyllobothrium spp.
Microscopical detection of worm eggs and/or
proglottids in stool
Nematode infections
Ascaris lumbricoides
Trichuris trichiura Ancylostoma and Necator spp.
Microscopical detection of worm eggs in stool

Strongyloides stercoralis
Microscopy and culturing of larvae in stool (serology)

Enterobius vermicularis
Microscopical detection of worm eggs (anal adhesive
tape on slide) or worms in
stool


Digestive Glands and Peritoneum
Table 12.6 Digestive Glands and Peritoneum
Infection
Most important pathogens
Laboratory diagnosis
Mumps
(parotitis epidemica)
Mumps virus
(paramyxovirus)
Serology
Infectious hepatitis
Hepatitis A virus
Serology (IgM)

Hepatitis B and D virus
Antigen and antibody detection in blood, PCR

Hepatitis C and G virus
Serology, PCR

Hepatitis E virus
Serology (IgE, IgM), PCR
Yellow fever (liver)
Yellow fever virus
(flavivirus)
Serology;
isolation if required (use reference laboratory)
Cytomegalovirus infection (liver)
Cytomegalovirus (CMV)
Cell culture from saliva, urine and if required from biopsy material. Antigen assay or DNA test (PCR). Serology
Leptospirosis (liver)
Leptospira interrogans (serogroup icterohaemorrhagiae)
Serology. Culture from urine and blood
Cholecystitis/Cholangitis
E. coli
Other Enterobacteriaceae
Gram-negative anaerobes
Culture from bile

Fasciola hepatica
Opisthorchis
Clonorchis
Dicrocoelium
Worm eggs in stool; serology
Pancreatitis
Pancreatic abscess
Enterobacteriaceae
Staphylococcus aureus Streptococcus spp.
Pseudomonas spp. Anaerobes
Microscopy and culture from pus (punctate or biopsy, if specimen sampling feasible)
12.6 Continued: Digestive Glands and Peritoneum
Infection
Most important pathogens
Laboratory diagnosis
Liver abscess
Usually mixed bacterial flora: E. coli
Other Enterobacteriaceae
Gram-negative anaerobes
Gram-positive anaerobes
Staphylococcus aureus
Streptococcus pyogenes
Streptococcus milleri
Entamoeba histolytica
Microscopy and culture from pus if specimen sampling feasible (punctate, biopsy, surgical material)
Serology
Splenic abscess
Staphylococcus spp. (in endocarditis) Streptococcus spp.
(in endocarditis)
Enterobacteriaceae
Gram-negative and
Gram-positive anaerobes
Microscopy and culture from pus if specimen sampling feasible; blood culture
Peritonitis
Primary peritonitis Streptococcus pneumoniae (rare; usually the Streptococcus pyogenes
result of hematogenous Gram-negative/-positive dissemination) anaerobes;
Enterobacteriaceae; enterococci; rarely Staphylococcus aureus
Microscopy and culture from pus; (specimen sampling during laparotomy, or puncture if necessary)
Secondary peritonitis Usually mixed aerobic(endogenous infection anaerobic flora
caused by enteric Enterobacteriaceae
bacteria) Gram-negative and
Gram-positive anaerobes
Microscopy and culture from pus (specimen sampling during laparotomy, or puncture if necessary)
Digestive Glands and Peritoneum
Table 12.6 Continued: Digestive Glands and Peritoneum
Infection
Most important pathogens
Laboratory diagnosis
Peritonitis following
peritoneal dialysis
(CAPD)
Gram-positive bacteria (60–80%):
Staphylococcus spp.
Streptococcus spp.
Corynebacterium spp. Gram-negative bacteria (15–30%):
Enterobacteriaceae
Pseudomonas spp.
Acinetobacter spp.
Candida spp. (rare)
Microscopy and culture from cloudy dialysis fluid. Concentration of fluid necessary (e.g., filtration or centrifugation)
Intraperitoneal abscesses
Usually mixed aerobicanaerobic flora:
Enterobacteriaceae
Staphylococcus aureus
Gram-negative/
-positive anaerobes
Streptococcus milleri
Microscopy and culture from pus (specimen sampling during laparotomy, or puncture if necessary)
Protozoan infections (liver) Visceral leishmaniasis
Leishmania donovani
Leishmania infantum
Microscopy and culture from lymph node or bone
marrow punctate; DNA detection; serology
Trematode infections
(liver, bile ducts)
Schistosomosis
Schistosoma mansoni
Microscopical detection of worm eggs in stool; serology
Fasciolosis
Fasciola hepatica
Microscopical detection of worm eggs in stool; serology
Opisthorchiosis
Clonorchiosis
Dicrocoeliosis
Opisthorchis spp.
Clonorchis sinensis
Dicrocoelium dendriticum
Microscopical detection of worm eggs in stool
Cestode infections
Echinococcosis
(liver, peritoneal cavity)
Echinococcosus granulosus Echinococcosus multilocularis
Serology
12.7 Nervous System
Infection
Most important pathogens
Laboratory diagnosis
Meningitis
Viruses
Enteroviruses
Herpes simplex virus
Mumps virus
Isolation from cerebrospinal fluid, stool, pharyngeal lavage; serology if herpes or mumps suspected
PCR from cerebrospinal fluid

Togaviruses
Bunyaviruses
Arenaviruses
In tropical viroses virus isolation from cerebrospinal fluid and blood and serology in reference laboratory

Lymphocytic
choriomeningitis virus Tickborne encephalitis virus
(flavivirus)
Serology in blood, in cerebrospinal fluid if necessary
Bacteria
Neisseria meningitidis
(!20%)
Streptococcus pneumoniae
(!30%)
Haemophilus influenzae b (Less frequent now due to vaccination in children) Rare:
Enterobacteriaceae (senium)
Mycobacterium tuberculosis
Leptospira interrogans
Listeria monocytogenes
Neonates:
E. coli
Group B streptococci
Microscopy and culture from cerebrospinal fluid;
antigen detection if required
(rapid test)
Fungi
Cryptococcus neoformans Candida spp.
Coccidioides immitis
Microscopy and culture from cerebrospinal fluid; antigen detection; serology
Nervous System
Table 12.7 Continued: Nervous System
Infection
Most important pathogens
Laboratory diagnosis
Encephalomyelitis Viruses
Measles virus
Epstein-Barr virus
Serology

HIV-1, HIV-2
Herpes simplex virus
Varicella zoster virus
Cytomegalovirus
PCR and isolation in brain biopsy or cerebrospinal fluid if required

Mumps virus
Additionally: isolation from pharyngeal lavage

Enteroviruses
Togaviruses
Bunyaviruses
Arenaviruses
Additionally: isolation from
stool
In tropical viroses viral serology in reference laboratories

Rabies virus (lyssa virus)
Direct Immunofluorescence with brain specimen (autopsy) and/or corneal epithelium Serology

Tickborne encephalitis virus
Serology
Bacteria
Rickettsia spp. Brucella spp.
Serology

Borrelia burgdorferi
Serology and PCR; culture in biopsy if required

Leptospira interrogans
Serology and culture in biopsy if required

Treponema pallidum
Syphilis serology

Listeria monocytogenes
Try microscopy and culture from cerebrospinal fluid and blood

Mycobacterium tuberculosis
Microscopy and culture from cerebrospinal fluid; DNA test if required
Fungi
Cryptococcus neoformans Aspergillus spp. Mucorales
Try microscopy and culture from cerebrospinal fluid and blood; Cryptococcus antigen can be detected in cerebrospinal fluid. Serology
12.7 Continued: Nervous System
Infection
Most important pathogens
Laboratory diagnosis
Protozoa
Naegleria fowleri
Acanthamoeba spp.
Microscopy (cerebrospinal fluid), culture, DNA detection

Toxoplasma gondii
Serology, microscopy, culture, DNA detection (cerebrospinal fluid)

Trypanosoma brucei gambiense
Trypanosoma brucei rhodesiense
Microscopy (cerebrospinal
fluid);
Serology

Plasmodium falciparum
Microscopy (blood); Serology
Helminths
Taenia solium (cysticercosis of the CNS)
Serology

Echinococcus granulosus Echinococcus multilocularis
Serology

Toxocara canis Toxocara mystax
Serology
Cerebral abscess
Epidural abscess
Subdural empyema
Streptococcus milleri
Gram-negative anaerobes
Enterobacteriaceae
Staphylococcus aureus
Microscopy and culture for bacteria from pus

Mucorales Aspergillus spp.
Candida spp.
Microscopy and culture for fungi from pus; serology

Toxoplasma gondii
Serology. Microscopy; DNA test (in cerebrospinal fluid)
Tetanus
Clostridium tetani
Toxin (animal test, PCR) in material excised from wound. Try microscopy and culture from excised material
Botulism
Clostridium botulinum
Toxin detection in blood or food (animal test, PCR)
Leprosy
(peripheral nerves)
Mycobacterium leprae
Microscopy of biopsy specimen or scrapings from nasal mucosa
Cardiovascular system
Table 12.8 Cardiovascular system
Infection
Most Important Pathogens
Laboratory diagnosis
Endocarditis
Streptococcus spp. (60–80%)
Staphylococcus spp. (20–35%) Gram-negative rods (2–13%) Numerous other bacterial spp.
(5%)
Fungi (2–4%)
Culture negative (5–25%)
Blood culture, three sets from three different sites, within 1–2 h, before antimicrobials if possible.
10–20 ml venous blood into one aerobic and one anaerobic bottle, respectively.
Myocarditis/ pericarditis
Viruses
Enteroviruses
Adenoviruses
Herpes virus group
Influenzaviruses
Parainfluenzaviruses
Serology, if necessary combined with isolation and
PCR of punctate
Bacteria
Staphylococcus aureus
Streptococcus pneumoniae
Enterobacteriaceae
Mycobacterium tuberculosis
Microscopy and culture from punctate
DNA test from punctate if required

Mycoplasma pneumoniae
Serology; culture from punctate

Neisseria spp.
Gram-negative anaerobes Actinomyces spp.
Nocardia spp.
Microscopy and culture from punctate

Rickettsia spp.
Chlamydia trachomatis
Serology
Fungi
Candida spp.
Aspergillus spp.
Cryptococcus neoformans
Serology; microscopy (direct IF); cell culture or PCR if required
Protozoa
Toxoplasma gondii
Trypanosoma cruzi
Serology, if necessary in combination with culture and microscopy from punctate
Helminths
Trichinella spiralis
Serology
12.9 Hematopoietic and Lymphoreticular System
Infection
Most important pathogens
Laboratory diagnosis
HIV infection (AIDS)
HIV-1; HIV-2
Serology: EIA and Western blot. Also p24 antigen assay for primary infection. Quantitative genome test with RT-PCR for therapeutic indication and course (viral load).
Infectious mononucleosis
Epstein–Barr virus (EBV) Cytomegalovirus (rare)
Serology
Isolation from urine and saliva; serology
Brucellosis
Brucella abortus
Brucella melitensis
Brucella suis
Blood culture: three sets from three different sites, within 1–2 h, before antimicrobials if possible. 10–20 ml venous blood into one aerobic and one anaerobic bottle, respectively.
Incubation for up to 4 weeks is necessary—inform laboratory of suspected Brucella infection. Serology
Tularemia
Francisella tularensis
Culture from lymph node biopsy, sputum and blood; serology
Plague
Yersinia pestis
Microscopy and culture from bubo pus, possibly from sputum (pulmonary plague)
Melioidosis
Burkholderia pseudomallei
Microscopy and culture from sputum, abscess pus or blood
Malleus (glanders)
Burkholderia mallei
Microscopy and culture from nasal secretion, abscess pus or blood
Rat-bite fever
Streptobacillus moniliformis
Culture from lesion specimen
Sodoku
Spirillum minus
Attempt microscopical detection in blood or wound secretion
Hematopoietic and Lymphoreticular System
Table 12.9 Continued: Hematopoietic and Lymphoreticular System
Infection
Most important pathogens
Laboratory diagnosis
Oroya fever and verruga peruana
Bartonella bacilliformis
Blood culture (see above for
brucellosis)
Relapsing fever
Borrelia recurrentis
Borrelia duttonii
Other borreliae
Microscopy (Giemsa staining) of blood while fever is rising
Bacillary angiomatosis (AIDS)
Bartonella henselae
Serology; microscopy and culture from lymph node biopsy as required
Cat scratch disease
Bartonella henselae;
Bartonella claridgeia
Afipia felis (rare)
Microscopy of puncture pus:
Warthin-Starry silver stain. Culture on special medium (difficult)
Malaria
Plasmodium spp.
Microscopy (blood smear, thick film); antigen detection with ParaSight test. Serology (not in acute malaria)
Babesiosis
Babesia spp.
Microscopy of blood swabs
Toxoplasmosis
Toxoplasma gondii
Serology
Visceral leishmaniosis
Leishmania donovani
Leishmania infantum
Serology; microscopy and culture of lymph node or bone marrow punctate, DNA detection
Filariosis
(lymphatic)
Wuchereria bancrofti Brugia malayi
Microscopical detection of microfilaria in nocturnal blood; serology
Ehrlichiosis
Ehrlichia spp.
Isolation in cell culture. PCR.
Serology (immunofluorescence)
12.10 Skin and Subcutaneous Connective Tissue (local or systemic infections with mainly cutaneous manifestation)
Infection
Most important pathogens
Laboratory diagnosis
a) Viruses
Smallpox
Variola virus
Parapox viruses (orf virus, milker’s nodules virus)
Electron microscopy of vesicle/ pustule content; isolation; serology; (use reference laboratory)
Herpes
Herpes simplex virus
Electron microscopy of vesicle content; cell culture
Varicella
(chicken pox)
Varicella zoster virus
Serology (IgG, IgM); electron microscopy of vesicle content; direct IF, cell culture
Measles
(morbilli, rubeola)
Measles virus (Morbillivirus)
Isolation from pharyngeal lavage and urine if required; serology
German measles
(rubella)
Rubella virus (Rubivirus)
Serology
Hemorrhagic fever
Bunyaviruses (e.g., hantavirus)
Arenaviruses
Flaviviruses (e.g., Dengue
viruses)
Marburg virus
Ebola virus
Serology; cell culture and PCR from blood or liver as required; animal test as required; laboratory diagnosis only possible in reference laboratories
Molluscum contagiosum
Molluscum contagiosum virus
Microscopy of skin lesions; molluscum bodies
Warts
Papillomas
Papillomavirus
Genomic test with DNA probe or electron microscopy
Erythema infectiosum
Parvovirus B19
Serology
Exanthema subitum
Human herpes virus 6 (HHV 6)
Serology
Skin and Subcutaneous Connective Tissue
Table 12.10 Continued: Skin and Subcutaneous Connective Tissue
Infection Most important pathogens
Laboratory diagnosis
b) Bacteria and fungi
Furuncles
Carbuncles
Pemphigus
Folliculitis
Impetigo
Erysipelas
Staphylococcus aureus Streptococcus pyogenes
Microscopy and culture from swab
Gangrenous
cellulitis
Often mixed flora:
Clostridium spp.
Gram-negative anaerobes Pseudomonas spp.
Enterobacteriaceae
Microscopy from swab or pus, use transport medium for anaerobes
Erysipeloid
Erysipelothrix rhusiopathiae
Microscopy and culture from skin lesion swab
Erythema migrans
Borrelia burgdorferi
Serology
Cutaneous anthrax
Bacillus anthracis
Microscopy and culture from skin lesion swab
Leprosy
Mycobacterium leprae
Microscopy (Ziehl-Neelsen stain) of material from skin lesions (biopsy) or scrapings from nasal mucosa
Rickettsioses (spotted fever and others)
Rickettsia spp.
Serology, culturing (embryonated hen’s egg) or animal test if necessary
Nonvenereal treponema
infections
(endemic syphilis, pinta, yaws)
Treponema pallidum
(subsp. endemicum)
Treponema pallidum
(subsp. pertenue)
Treponema carateum
Try microscopy of material from skin lesions; serology
(syphilis tests)
12.10 Continued: Skin and Subcutaneous Connective Tissue
Infection Most important pathogens
Laboratory diagnosis
Madura foot mycosis/mycetoma
Bacteria
Fungi
Nocardia brasiliensis
Actinomadura madurae Streptomyces somaliensis
Madurella spp.
Pseudoallescheria spp.
Aspergillus spp., and others
Microscopy and culture from lesion material
Microscopy and culture from lesion material
Dermatomycoses
Dermatophytes Candida spp.
Microscopy and culture from cutaneous scales
Sporotrichosis
Sporothrix schenckii
Microscopy and culture from lesion pus
Chromomycosis
Black molds (various types)
Microscopy and culture from lesion pus
c) Protozoa, helmi
Cutaneous leishmaniosis (oriental sore)
American cutaneous and mucocutaneous leishmaniosis
nths, and arthropods
Leishmania tropica Leishmania major
Leishmania braziliensis
Leishmania mexicana
Microscopy and culture from lesion biopsy; DNA detection (PCR)
Microscopy and culture from skin and mucosal lesion biopsy;
DNA detection (PCR)
Cercarial dermatitis
Cutaneous larva migrans (“creeping eruption”)
Cercariae from Schistosoma spp.
Larvae of Ancylostoma spp. and Strongyloides species
Serology
Clinical diagnosis
Onchocercosis
Onchocerca volvulus (microfilariae)
Microscopical detection of microfilariae in “skin snips”; serology
Bone, Joints, and Muscles
Infection
Most important pathogens
Laboratory diagnosis
Pleurodynia, epidemic myalgia (Bornholm disease)
Coxsackie viruses group B (possibly echoviruses)
Isolation from stool and pharyngeal lavage; serology
Clostridial infections
  1. Gas gangrene
(with myonecrosis)
  1. Clostridial cellulitis
(without myonecrosis)
Clostridium perfringens Other clostridial spp.
Microscopy and culture from wound secretion. Transport materials in anaerobic system
Table 12.10 Continued: Skin and Subcutaneous Connective Tissue
Infection
Most important pathogens
Laboratory diagnosis
Loaosis
Loa loa (migrating filariae)
Microscopy of diurnal blood for microfilariae; serology
Cysticercosis
Taenia solium
Serology (radiology)
Dracunculosis
Dracunculus spp.
Clinical diagnosis
Tickbite
Ixodes ricinus and other tick species
Inspection of skin
Scabies
Sarcoptes scabiei
Microscopy
Louse infestation
Pediculus spp., Phthirus pubis
Inspection of hair, skin, and clothing (body lice) for lice and nits
Myiasis
Fly larvae (maggots)
Inspection
Flea infestation
Various flea species, in most cases from animals
Detection of fleas and flea fecal material on animals and in their surroundings
Sand flea bites
Tunga penetrans
Clinical diagnosis, histology if needed
Table 12.11 Bone, Joints, and Muscles
12.11 Bone, Joints, and Muscles
Infection
Most important pathogens
Laboratory diagnosis
Necrotizing fasciitis
Type 1
(syn. polymicrobial gangrene)
Often aerobic/anaerobic mixed flora: Clostridium spp., Gram-positive and Gramnegative anaerobes, Staphylococcus aureus,
Streptococcus bovis,
Enterobacteriaceae
Microscopy and culture from wound secretion. Transport materials in anaerobic system
Type 2
(syn. Streptococcal necrotizing myositis)
Streptococcus pyogenes
Microscopy and culture from wound secretion
Trichinellosis (Muscle)
Trichinella spiralis
Microscopical detection in muscle biopsy; serology
Cysticercosis (Muscle)
Taenia solium
Serology (radiology)
Osteomyelitis/ostitis
Staphylococcus aureus Coagulase-negative staphylococci Streptococcus spp. Enterobacteriaceae
Pseudomonas spp. Gram-positive and Gramnegative anaerobes (rare)
Microscopy and culture for bacteria, preferably based on biopsy or surgical material. Swab from fistular duct not useful for diagnosis
Septic arthritis
Staphylococcus aureus Streptococcus pyogenes
Streptococcus pneumoniae
Haemophilus influenzae
Neisseria gonorrhoeae Enterobacteriaceae
Pseudomonas spp.
Microscopy and culture from synovial fluid with parallel blood culture
Eyes and ears
Table 12.12 Eyes and ears
Infection
Most important pathogens
Laboratory diagnosis
Trachoma
Chlamydia trachomatis, serovars A, B, Ba, C
Microscopical detection of inclusions in conjunctival cells (Giemsa stain); direct immunofluorescence; cell culture; antigen detection using EIA; PCR. Serology: recombinant immunoassay for antibodies to genus-specific antigen
(LPS or MOMP). Microimmunofluorescence for antibodies to species- and var-specific antibodies.
Conjunctivitis/scleritis
Viruses
Adenoviruses
Enteroviruses
Influenzaviruses
Measles virus
Isolation from swab
Bacteria
Neisseria spp.
Streptococcus spp. Staphylococcus aureus Haemophilus spp.
Enterobacteriaceae Pseudomonas spp.
Mycobacterium spp.
Moraxella lacunata
Microscopy and culture for bacteria in conjunctival secretion or in scrapings

Chlamydia trachomatis (inclusion conjunctivitis)
See at “trachoma” (this table)

Treponema pallidum
Serology (basic diagnostics)
Fungi
Candida spp.
Sporothrix schenckii
Microscopy and culture for fungi in conjunctival secretion or in corneal scrapings
Helminths
Onchocerca volvulus
Microscopy for microfilariae in skin snips (or conjunctival) biopsy; serology

Loa loa
Microscopy for microfilariae in diurnal blood; serology
12.12 Continued: Eyes and ears
Infection
Most important pathogens
Laboratory diagnosis
Keratitis
Viruses
Herpes simplex virus
Adenoviruses
Varicella zoster virus
Cell culture and PCR from swab or corneal scrapings
Bacteria
Staphylococcus spp. Streptococcus spp.
Neisseria gonorrheae Enterobacteriaceae Pseudomonas spp.
Bacillus spp.
Mycobacterium spp. Moraxella lacunata Actinomyces spp.
Nocardia spp.
Microscopy and culture for bacteria swab or corneal scrapings

Chlamydia trachomatis
Diagnostic procedures with corneal swab or scrapings see at “trachoma” (this table)

Treponema pallidum
Serology (basic diagnostics)
Fungi
Candida spp.
Aspergillus spp. Fusarium solani
Microscopy and culture for fungi in swab or corneal
scrapings
Protozoa
Acanthamoeba spp.
Culture and microscopy from conjunctival lavage and contact lens washing fluid, DNA detection
Endophthalmitis
Viruses
Herpes simplex viruses
Varicella zoster virus
Measles virus
Rubella virus
(german measles)
Cell culture and PCR in aqueous and vitreous
aspiration; serology with aqueous humor as required
Eyes and ears
Table 12.12 Continued: Eyes and ears
Infection
Most important pathogens
Laboratory diagnosis
Bacteria
Staphylococcus spp.
Streptococcus spp.
Neisseria gonorrhoeae Enterobacteriaceae Pseudomonas spp.
Bacillus spp.
Mycobacterium spp. Moraxella lacunata Actinomyces spp.
Nocardia spp.
Microscopy (gram) and culture for aerobic and anaerobic bacteria and mycobacteria in aqueous and vitreous aspiration.

Chlamydia trachomatis
Cell culture or PCR in aqueous and vitreous aspiration; serology with aqueous humor as required; antibodies in blood

Treponema pallidum
Serology (basic diagnostics)
Fungi
Candida spp.
Aspergillus spp.
Blastomyces dermatitidis
Histoplasma capsulatum
Mucorales
Sporothrix schenckii Fusarium spp.
Trichosporon spp.
Microscopy (Gram, Giemsa) and culture for fungi in aqueous and vitreous aspiration.
Protozoa
Acanthamoeba spp.
Microscopy and culturing (conjunctival fluid and contact lens washing fluid), DNA detection

Toxoplasma gondii
Serology
Helminths
Onchocerca volvulus
Direct detection of microfilariae in aqueous humor with slit lamp; serology

Toxocara canis
Serology

Taenia solium
(ocular cysticercosis)
Serology
12.12 Continued: Eyes and ears
Infection
Most important pathogens
Laboratory diagnosis
Otitis externa
Pseudomonas aeruginosa Staphylococcus aureus
Streptococcus pyogenes
Microscopy and culture for bacteria of swab material

Aspergillus spp. Candida spp.
Microscopy and culture for fungi of swab material
Otitis media
Streptococcus pneumoniae
Haemophilus influenzae Streptococcus pyogenes
Staphylococcus aureus
Moraxella catarrhalis (children)
Respiratory viruses (25%)
Microscopy and culture for bacteria of middle ear punctate as required



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