Organ System Infections

VI
Organ System
Infections
Kayser, Medical Microbiology 2005 Thieme
All rights reserved. Usage subject to terms and conditions of license.
Medical microbiology explores how infectious diseases originate and de-
velop. The focus of this branch of the life sciences is of course on infective
pathogens, the causes of infections. This explains why the taxonomy of these
microorganisms determines the structure of textbooks of medical microbiol-
ogy, and this one is no exception. This approach does not, however, satisfy all
the requirements of clinical practice. The practicing physician is confronted
with a pathological problem affecting a specific organ or organ system, and
therefore might well find good use for a brief reference tool covering the
pathogenic agents that potentially affect specific organs and systems.
Medical microbiology must address two tasks: 1. describing the origins
and development of an infection and 2. obtaining a laboratory diagnosis
of the resulting disease that is of immediate clinical relevance to patient
treatment. Chapter 12 of this book was written to help bridge the gap be-
tween basic microbiological science and the demands of medical practice.
Concise information on etiology and laboratory diagnosis has been grouped
in tabular form in 12 sections corresponding to the most important organs
and organ systems. Infections that affect more than one organ system are
listed with the system that is affected most severely and/or most frequently
or in which the disease manifests most clearly. The pathogens in question are
also listed with the other organ manifestations. In the tables, the most fre-
quent causative pathogens in eachcase are printed in bold letters. Readers are
referred to textbooks on internal medicine or specialist literature on infective
diseases for exhaustive information on clinical aspects extending beyond
etiology and laboratory diagnosis (see references at the end of the book).
The descriptions of the diagnostic procedures used to clarify the different in-
fections had to be kept concise in accordance with the tabular format. Since
each laboratory offers its own specific set of testing techniques, a physicians
choices are defined and limited by what is feasible and available in a given
case. This applies in particular to the many different antibody assays now
available (= serology). The most important serological tests are listed together
with the relevant pathogens in the respective chapters.
629
12
12 Etiological and Laboratory Diagnostic
Summaries in Tabular Form
FH Kayser, J Eckert, and KA Bienz
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
630 12 Etiological and Laboratory Diagnostic Summaries in Tabular Form
12
Table 12.1 Continued: Upper Respiratory Tract
pathogens*
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 +
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,
Blood culture. Culture from
swab (caution: respiratory
arrest possible in taking
the swab)
* The pathogens that occur most frequently are in bold type.
Upper Respiratory Tract 631
12
Table 12.2 Lower Respiratory Tract
pathogens
Acute bronchitis.
Acute bronchiolitis
(small children)
Type A influenza viruses
Adenoviruses
Serology, combined with
isolation from pharyngeal la-
vage 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
of chronic obstructive
pulmonary disease
(COPD)
Streptococcus pneumoniae
Moraxella catarrhalis
Culture from sputum or
bronchial secretion
Tuberculosis Mycobacterium tuberculosis
other mycobacteria
Microscopy and culture
(time requirement:
368 weeks)
Pneumonia
Viruses (1520%)
(usually community-
acquired)
(children)
(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
12
Table 12.2 Continued: Lower Respiratory Tract
pathogens
Pulmonary hantaviruses
(USA)
Serology
Enteroviruses Isolation from pharyngeal
lavage or bronchial
secretion
Rhinoviruses Laboratory diagnosis not
recommended
Bacteria (8090%)
Community-acquired
pneumonia
(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
Laboratory procedures
see above at community-
acquired 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)
Lower Respiratory Tract 633
12
Table 12.2 Continued: Lower Respiratory Tract
pathogens
Pneumocystis carinii
(Pneumocystis carinii
pneumonia (PCP) frequent
in AIDS patients)
Pathogen detection in
induced sputum or
bronchial lavage by means of
microscopy, immunofluores-
cence 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
Respiratory Syndrome)
SARS Corona Virus Reverse transcriptase PCR
(RT-PCR) in respiratory tract
specimens (swabs, lavage
etc.).
Serology (EIA).
Empyema Streptococcus pneumoniae
Numerous other bacteria are
potential pathogens
Microscopy and culture from
pleural pus specimen
Pulmonary abscess
Necrotizing pneumonia
Usually endogenous
infections with Gram-
negative/Gram-positive
Aerobes also possible
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
12
Table 12.3 Urogenital Tract
pathogens
Urethrocystitis
Pyelonephritis
Escherichia coli
Other Enterobacteriaceae
Enterococci
Staphylococcus saprophyticus
(in women)
Microscopy and culture; test
midstream urine for significant
bacteriuria (p. 210)
Prostatitis Escherichia coli
Enterococci
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
(510%)
Unknown pathogens (20%)
See above: nonspecific
urethritis
Culture from urine. Bacteriuria
often
<
10
4
/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, 3050 ml each
Urogenital Tract 635
12
Table 12.3 Continued: Urogenital Tract
pathogens
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 secre-
tion (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
Mixed anaerobic flora
Less frequently:
Enterobacteriaceae
Streptococcus spp.
Gardnerella vaginalis
Mycoplasma hominis
Mycobacterium tuberculosis
swab material. Use transport
mediums. For detection of
chlamydiae: direct IF micro-
scopy, EIA antigen detection,
cell culture or PCR. PCR kit
available to detect gonococci
simultaneously.
12
Table 12.4 Genital Tract (venereal diseases)
pathogens
Gonorrhea Neisseria gonorrhoeae Microscopy (send two slides to
the laboratory, for gram staining
and IF); culture (swab in special
transport medium); rapid anti-
gen detection with antibodies in
swab material; PCR (kit available
to detect C. trachomatis simulta-
neously)
Syphilis (lues) Treponema pallidum
(ssp. pallidum)
Microscopy (dark field) of mate-
rial from stage I and II lesions.
Serology (see p. 321 for basic
diagnostics)
Lymphogranuloma
venereum
(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 hens egg or
special mediums)
Genital Tract 637
12
Table 12.5 Gastrointestinal Tract
pathogens
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
Adenoviruses
Rarely: enteroviruses,
coronaviruses, astroviruses,
caliciviruses, Norwalk virus
Direct virus detection
with electron microscopy
(reference laboratories)
or direct detection with
immunological methods
(e.g., EIA)
Bacteria Staphylococcus aureus intoxi-
cation (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 antibiotic-
associated)
Clostridium difficile Toxin detection
(cell culture) in stool.
DNA assay for toxin
possible
Shigellosis (dysentery) Shigella spp. Culture from stool
12
Table 12.5 Continued: Gastrointestinal Tract
pathogens
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
Whipples 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
Gastrointestinal Tract 639
12
Table 12.5 Continued: Gastrointestinal Tract
pathogens
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
Cestode infections Taenia spp.
Hymenolepis spp.
Diphyllobothrium spp.
of worm eggs and/or
proglottids in stool
Nematode infections Ascaris lumbricoides
Trichuris trichiura
Ancylostoma and
Necator spp.
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
12
Table 12.6 Digestive Glands and Peritoneum
pathogens
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 ictero-
haemorrhagiae)
Serology. Culture from urine
and blood
Cholecystitis/Cholangitis E. coli
Culture from bile
Fasciola hepatica
Opisthorchis
Clonorchis
Dicrocoelium
Worm eggs in stool;
serology
Pancreatitis
Pancreatic abscess
Enterobacteriaceae
Streptococcus spp.
Pseudomonas spp.
Anaerobes
from pus (punctate or
biopsy, if specimen
sampling feasible)
Digestive Glands and Peritoneum 641
12
Table 12.6 Continued: Digestive Glands and Peritoneum
pathogens
Liver abscess Usually mixed bacterial
flora:
E. coli
Gram-positive anaerobes
Streptococcus milleri
Entamoeba histolytica
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
from pus if specimen
sampling feasible; blood
culture
Peritonitis
Primary peritonitis
(rare; usually the
result of hematogenous
dissemination)
Gram-negative/-positive
anaerobes;
Enterobacteriaceae;
enterococci; rarely
from pus; (specimen
sampling during
laparotomy, or puncture if
necessary)
Secondary peritonitis
(endogenous infection
caused by enteric
bacteria)
Usually mixed aerobic-
anaerobic flora
Enterobacteriaceae
Gram-negative and
from pus (specimen sam-
pling during laparotomy,
or puncture if necessary)
12
Table 12.6 Continued: Digestive Glands and Peritoneum
pathogens
Peritonitis following
peritoneal dialysis
(CAPD)
Gram-positive bacteria
(6080%):
Staphylococcus spp.
Streptococcus spp.
Corynebacterium spp.
Gram-negative bacteria
(1530%):
Enterobacteriaceae
Pseudomonas spp.
Acinetobacter spp.
Candida spp. (rare)
from cloudy dialysis fluid.
Concentration of fluid
necessary (e.g., filtration
or centrifugation)
Intraperitoneal abscesses Usually mixed aerobic-
anaerobic flora:
Enterobacteriaceae
Gram-negative/
-positive anaerobes
from pus (specimen
sampling during laparot-
omy, or puncture if
necessary)
Protozoan infections (liver)
Visceral leishmaniasis Leishmania donovani
Leishmania infantum
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
Digestive Glands and Peritoneum 643
12
Table 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 cere-
brospinal fluid if necessary
Bacteria Neisseria meningitidis
(20%)
(30%)
Haemophilus influenzae b
(Less frequent now due to
vaccination in children)
Rare:
Enterobacteriaceae (senium)
Leptospira interrogans
Listeria monocytogenes
cerebrospinal fluid;
antigen detection if required
(rapid test)
Neonates:
E. coli
Group B streptococci
Fungi Cryptococcus neoformans
Candida spp.
Coccidioides immitis
cerebrospinal fluid; antigen de-
tection; serology
12
Table 12.7 Continued: Nervous System
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
blood
Mycobacterium tuberculosis Microscopy and culture from
cerebrospinal fluid; DNA test if
required
Fungi Cryptococcus neoformans
Aspergillus spp.
Mucorales
Try microscopy and culture
blood; Cryptococcus antigen
can be detected in cerebrospi-
nal fluid. Serology
Nervous System 645
12
Table 12.7 Continued: Nervous System
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
Enterobacteriaceae
Microscopy and culture for
bacteria from pus
Mucorales
Aspergillus spp.
Candida spp.
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
12
Table 12.8 Cardiovascular system
Infection Most Important Pathogens Laboratory diagnosis
Endocarditis Streptococcus spp. (6080%)
Staphylococcus spp. (2035%)
Gram-negative rods (213%)
Numerous other bacterial spp.
(5%)
Fungi (24%)
Culture negative (525%)
Blood culture, three sets
from three different sites, within
12 h, before antimicrobials if
possible.
1020 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
Enterobacteriaceae
punctate
DNA test from punctate if re-
quired
Mycoplasma pneumoniae Serology; culture from punctate
Neisseria spp.
Actinomyces spp.
Nocardia spp.
punctate
Rickettsia spp.
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
Cardiovascular system 647
12
Table 12.9 Hematopoietic and Lymphoreticular System
pathogens
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 indica-
tion and course (viral load).
Infectious
mononucleosis
EpsteinBarr 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 12 h,
before antimicrobials if possible.
1020 ml venous blood into one
aerobic and one anaerobic bottle,
respectively.
Incubation for up to 4 weeks is
necessaryinform 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
12
Table 12.9 Continued: Hematopoietic and Lymphoreticular System
pathogens
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
microfilaria in nocturnal blood;
serology
Ehrlichiosis Ehrlichia spp. Isolation in cell culture. PCR.
Serology (immunofluorescence)
Hematopoietic and Lymphoreticular System 649
12
Table 12.10 Skin and Subcutaneous Connective Tissue (local or systemic
infections with mainly cutaneous manifestation)
a) Viruses
Smallpox Variola virus
Parapox viruses (orf virus,
milkers 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; labora-
tory diagnosis only possible in
reference laboratories
Molluscum
contagiosum
Molluscum contagiosum virus Microscopy of skin lesions; mol-
luscum 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
12
Table 12.10 Continued: Skin and Subcutaneous Connective Tissue
b) Bacteria and fungi
Furuncles
Carbuncles
Pemphigus
Folliculitis
Impetigo
Erysipelas
swab
Gangrenous
cellulitis
Often mixed flora:
Clostridium spp.
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 (embryo-
nated hens 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)
Skin and Subcutaneous Connective Tissue 651
12
Madura foot
mycosis/mycetoma
Bacteria
Fungi
Nocardia brasiliensis
Actinomadura madurae
Streptomyces somaliensis
Madurella spp.
Pseudoallescheria spp.
Aspergillus spp., and others
lesion material
Microscopy and culture from le-
sion material
Dermatomycoses Dermatophytes
Candida spp.
cutaneous scales
Sporotrichosis Sporothrix schenckii Microscopy and culture from le-
sion pus
Chromomycosis Black molds (various types) Microscopy and culture from le-
sion pus
c) Protozoa, helminths, and arthropods
Cutaneous
leishmaniosis
(oriental sore)
American
cutaneous and
mucocutaneous
leishmaniosis
Leishmania tropica
Leishmania major
Leishmania braziliensis
Leishmania mexicana
Microscopy and culture from le-
sion biopsy; DNA detection
(PCR)
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)
microfilariae in skin snips;
serology
12
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
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)
2. Clostridial cellulitis
(without myonecrosis)
Clostridium perfringens
Other clostridial spp.
wound secretion. Transport
materials in anaerobic system
Bone, Joints, and Muscles 653
12
Table 12.11 Bone, Joints, and Muscles
Necrotizing fasciitis
Type 1
(syn. polymicrobial
gangrene)
Often aerobic/anaerobic
mixed flora: Clostridium spp.,
Gram-positive and Gram-
negative anaerobes,
Staphylococcus aureus,
Streptococcus bovis,
Enterobacteriaceae
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 Gram-
negative anaerobes (rare)
bacteria, preferably based on
biopsy or surgical material.
Swab from fistular duct not
useful for diagnosis
Septic arthritis Staphylococcus aureus
Enterobacteriaceae
Pseudomonas spp.
synovial fluid with parallel
blood culture
12
Table 12.12 Eyes and ears
Trachoma Chlamydia trachomatis,
serovars A, B, Ba, C
inclusions in conjunctival cells
(Giemsa stain); direct immuno-
fluorescence; cell culture;
antigen detection using EIA;
PCR. Serology: recombinant
immunoassay for antibodies
to genus-specific antigen
(LPS or MOMP). Microimmuno-
fluorescence for antibodies to
species- and var-specific anti-
bodies.
Conjunctivitis/scleritis
Viruses Adenoviruses
Enteroviruses
Influenzaviruses
Measles virus
Isolation from swab
Bacteria Neisseria spp.
Streptococcus spp.
Haemophilus spp.
Enterobacteriaceae
Pseudomonas spp.
Mycobacterium spp.
Moraxella lacunata
bacteria in conjunctival secre-
tion or in scrapings
(inclusion conjunctivitis)
See at trachoma (this table)
Treponema pallidum Serology (basic diagnostics)
Fungi Candida spp.
Sporothrix schenckii
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
Eyes and ears 655
12
Table 12.12 Continued: Eyes and ears
Keratitis
Viruses Herpes simplex virus
Adenoviruses
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.
bacteria swab or corneal
scrapings
Chlamydia trachomatis Diagnostic procedures with
corneal swab or scrapings
see at trachoma (this table)
Fungi Candida spp.
Aspergillus spp.
Fusarium solani
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
Measles virus
Rubella virus
(german measles)
Cell culture and PCR in
aqueous and vitreous
aspiration; serology with
aqueous humor as required
12
Bacteria Staphylococcus spp.
Streptococcus spp.
Enterobacteriaceae
Pseudomonas spp.
Bacillus spp.
Mycobacterium spp.
Moraxella lacunata
Actinomyces spp.
Nocardia spp.
Microscopy (gram) and culture
for aerobic and anaerobic bac-
teria and mycobacteria in
aspiration.
Chlamydia trachomatis Cell culture or PCR in aqueous
and vitreous aspiration;
serology with aqueous humor
as required; antibodies in blood
Fungi Candida spp.
Aspergillus spp.
Blastomyces dermatitidis
Histoplasma capsulatum
Mucorales
Sporothrix schenckii
Fusarium spp.
Trichosporon spp.
Microscopy (Gram, Giemsa)
and culture for fungi in
aspiration.
Protozoa Acanthamoeba spp. Microscopy and culturing (con-
junctival 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
Eyes and ears 657
12
Otitis externa Pseudomonas aeruginosa
bacteria of swab material
Aspergillus spp.
Candida spp.
fungi of swab material
Otitis media Streptococcus pneumoniae
Moraxella catarrhalis (children)
Respiratory viruses (25%)
bacteria of middle ear
punctate as required
12
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Medical Microbiology and the Internet
An ever-growing number of websites specific to problems in microbiology,
infection, and communicable disease are today available on the Internet.
Below is a compilation of the most important addresses.
Institution Internet address Description
World Health Organization http://www.who.ch/ Home page for the WHO
http://www.who.int/emc/ WHO subsite providing
weekly infectious disease
news, prevention, and travel
information worldwide
Centers for Disease Control
and Prevention (CDC)
http://www.cdc.gov/ Home page for the CDC
http://www.cdc.gov/travel/
index.htm
CDC subsite providing infor-
mation for travelers
http://www.cdc.gov/
ncidod/id_links.htm
CDC subsite with links related
to infectious diseases
http://www.cdc.gov/nip CDC subsite recommending
childhood and adolescent
immunization schedulesUSA
American Society of
Microbiology (ASM)
http://www.asm.org/search Homepage of the ASM.
Links to medical microbology
and infectious diseases
Infectious Disease Society
of America (IDSA)
http://www.idsociety.org/
index.html
Homepage of IDSA providing
links to infectious diseases
International Society for
Infectious Diseases (ISID)
http://idis.org Homepage of ISID providing
links to infectious diseases
Public Health Laboratory
Service (PHLS), equivalent
to CDC for Great Britain
http://www.co.uk Homepage of the PHLS. Links
to clinical microbiology and
infectious diseases, GB
661
Institution Internet address Description
Robert Koch Institut
(RKI), equivalent to CDC
for Germany
http://www.rki.de Homepage of the RKI. Links
to clinical microbiology and
infectious diseases. Health
laws and regulations valid for
Germany
Society for Systematic and
Veterinary Bacteriology (F)
htpp://bacterio.cict.fr List of bacterial names with
standing in nomenclature
(LBSN)
662 Medical Microbiology and the Internet

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