MICROBIOLOGICAL APROACH TO
IMMUNO-COMPROMISED PATIENTS
Prof. Dr. Ayşe Kalkancı
Immune deficiency
• Cellular
• Humoral
Immuno-compromised patients
• Neutropenia
• Cancer patients
• Organ transplantation
• AIDS
Neutropenia
Neutropenia
• Number of polymorphonuclear (PMNL) cells
<500/mm3
• Number of PMNL 500-1000 /mm3 but,
decreasing
Keys for diagnosis
• Underlying disease
• Duration of neutropenia
• Diagnostic approach for possible causative agents
• Blood culture
• Other methods (Bacteria, fungi, virus, parasite)
Microbiology of adult and pediatric neutropenia
Microorganisms Frequent Rare
Gram positive [Link]
KNS
Corynebacterium jeikeium
Bacillus spp
bacteria Enterococcus Clostridium spp.
Viridans Streptococcus
Gram negative E. coli
K. pneumoniae
Enterobacter spp
Acinetobacter spp
bacteria [Link] Stenotraphomonas maltophilia
Citrobacter freundii
Legionella spp
Mycobacteria M. fortuitum
M. cheloneae
Fungi C. albicans
Other Candida spp
Mucorales
Trichosporon spp
Aspergillus spp Malessezia spp
Pneumocystis jirovecii
Virus HSV
CMV
VZV
Parasite Toxocara canis
Strongloides stercoralis
Physical examination of neutropenic
patients
Physical examination Comment
Skin rush Bacteriemia-Candidemia
Ectima gangrenosum [Link], [Link] and
Candida spp
Black peel Fungi, Aspergillus and
Mucorales spp
Checking invasive KNS, [Link], Gram
catheters negative bacteria, Candida
spp
Physical examination of neutropenic
patients
Physical examination Comment
Oral examination Viridans streptococci,
anaerobs
Sinusal touchiness Fungal infection
Right lower abdomen Cecum inflamation
touchiness
Peri-rectal inflamation Pseudomonas, rarely
anaerobs
Physical examination of neutropenic
patients
Postero-anterior lung Comment
radiology
Localised infiltration Bacterial and
mycobacterial infection
Nodulary, cavitary Filamentous fungi,
lesion Aspergillus, Nocardia
Diffuse interstitiel Virus and Pneumocystis
infiltration
Physical examination of neutropenic
patients
Other factors Comment
Antibiotic treatment Fungal infection
for 1 week, but
persistance of fever
Fever and abdominal Hepato-splenic
pain, recovery of candidiasis
neutropenia
Bone marrow Different
transplanted patients microorganisms
Organ transplantation
Organ transplantated patients
• Fever
• Chilling
• Pulmonary infiltrates
• Skin rush
• Allograft disfunction
Differential diagnosis
Transplant :
1. Liver,
2. Lung,
3. Heart,
4. Bone marrow,
5. Kidney
Differential diagnosis
Immuno-suppression :
Duration,
Type and drug
CMV serology of donors and recipients
History of the infections;
Travel,
Tuberculosis,
Animals,
Profession
Solid organ transplant recipients
• Liver
• Kidney
• Lung
Other than blood and bone marrow
transplantation
Case 1
• 42-year-old female with diagnosis of acute
lymphoblastic leukemia (ALL), presents fever
in the neutropenia period.
Microbiology of adult and pediatric neutropenia
Microorganisms Frequent Rare
Gram positive [Link]
KNS
Corynebacterium jeikeium
Bacillus spp
bacteria Enterococcus Clostridium spp.
Viridans Streptococcus
Gram negative E. coli
K. pneumoniae
Enterobacter spp
Acinetobacter spp
bacteria [Link] Stenotraphomonas maltophilia
Citrobacter freundii
Legionella spp
Mycobacteria M. fortuitum
M. cheloneae
Fungi C. albicans
Other Candida spp
Mucorales
Trichosporon spp
Aspergillus spp Malessezia spp
Pneumocystis jirovecii
Virus HSV
CMV
VZV
Parasite Toxocara canis
Strongloides stercoralis
Case 1
• Chest X-ray presents infiltration and fungus
ball in cavitary lesions.
Case 1
• Sputum sample revealed hyphae in direct
examination.
• Septated, thiny, dichotomous branching
WHAT IS YOUR DIAGNOSIS ?
Case 1
• Microbiological culture results in a powdery,
cottony mould colony.
Microscobic examination of the colony
shows septated hyphae, conidiaphores,
vesicule, phialides, and conidia chains.
Which of the following fungal agent is the most
probable causative pathogen ?
A) Candida
B) Rhizopus
C) Aspergillus
D) Trichosporon
E) Cryptococcus
Which of the following fungal agent is the most
probable causative pathogen ?
Agent Neutropenia Infiltration Septated Conidiaphores,
and fungus Hyphae vesicule,
ball phialides, and
conidia chains
Candida
Mucorales
Aspergillus
Cryptococcus
Trichosporon
Which of the following fungal agent is the most
probable causative pathogen ?
Agent Neutropenia Infiltration Septated Conidiaphores,
and fungus Hyphae vesicule,
ball phialides, and
conidia chains
Candida Yes Rare No No
(Pseudohyphae)
Mucorales Yes Yes No No
(Non-septated)
Aspergillus Yes Yes Yes Yes
Cryptococcus Yes Rare No No
Trichosporon Yes Rare No No
(Pseudohyphae)
Which of the following fungal agent is the most
probable causative pathogen ?
Agent Neutropenia Infiltration Septated Conidiaphores,
and fungus Hyphae vesicule,
ball phialides, and
conidia chains
Candida Yes Rare No No
(Pseudohyphae)
Mucorales Yes Yes No No
(Non-septated)
Aspergillus Yes Yes Yes Yes
Cryptococcus Yes Rare No No
Trichosporon Yes Rare No No
(Pseudohyphae)
WHAT IS YOUR DIAGNOSIS ?
• Acute Invasive pulmonary aspergillosis
Case 2
• 54-year-old woman presented to a large
teaching hospital with a 2-week history of
fevers, difficulty in breathing and a non-
productive cough.
Case 2
• This was preceded by a 3-week history of
malaise, nausea, and sharp chest and back
pains.
• There was no history of palpitations or
radiation of chest pain.
• She described a 9-month history of
unintentional weight loss of 3–4 kg, with an
accompanying loss in appetite and
odynophagia.
Case 2
• Two weeks prior to presentation, she had seen
her general practitioner who had empirically
diagnosed a lower urinary tract infection and
prescribed a week-long course of trimethoprim,
followed by another week’s course of
amoxicillin/clavulanic acid.
• She did not improve following these
treatments, and called ambulance services
when she developed clinical anorexia, vomiting,
fevers and difficulty in breathing.
Case 2
• No significant prior medical history
• She was an ex-smoker with a 7 pack-year
history.
• She described a recent alcohol intake history
of an estimated 60 units per week for at least
a few months.
• She did not take any illicit substances, injected
or otherwise
• Her last HIV test was 5 years prior and was
negative.
Case 2
• On day 1 of the admission period, the patient
became markedly hypoxic.
• On day 2, the patient’s HIV test was reported
as positive using two separate fourth-
generation test kits.
Case 2
• The clinical picture of hypoxia, cough and
consolidative changes in the lung in the
context of a new HIV diagnosis with a history
of weight loss signifying chronicity of disease
suggested a ……………………….
Case 2
• The clinical picture of hypoxia, cough and
consolidative changes in the lung in the
context of a new HIV diagnosis with a history
of weight loss signifying chronicity of disease
suggested a unifying diagnosis of P. jirovecii
pneumonia.
Microbiological diagnosis of P. jirovecii pneumonia
Diagnostic steps
• Direct examination of
sputum
• Culture ?
Microbiological diagnosis of P. jirovecii pneumonia
Diagnostic steps
• Direct examination of
sputum
Microbiological diagnosis of P. jirovecii pneumonia
Diagnostic steps
• Direct examination of
sputum
– Giemsa
– Immunflorescence
• Other methods ?
Diagnostic steps
• Direct examination of
sputum
– Giemsa
– Immunflorescence
• PCR
– Pneumocystis DNA
– Oral wash sample
• Serology
– Beta-D-glucan in serum
Diagnostic steps Diagnostic steps
• Direct examination of • No sputum
sputum • ???
– Giemsa
– Immunflorescence
• PCR
– Pneumocystis DNA
– Oral wash sample
• Serology
– Beta-D-glucan in serum
Diagnostic steps Diagnostic steps
• Direct examination of • No sputum
sputum
– Giemsa
• PCR
– Immunflorescence
– Pneumocystis DNA in Oral
wash sample
• PCR • Serology
– Pneumocystis DNA – Beta-D-glucan in serum
– Oral wash sample
• Serology
– Beta-D-glucan in serum
Microbiological approach to pneumonia in
immunocompromised patient
Sputum BAL Biopsy
Order special
stains !!
Direct Culture PCR
examination Serology
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