WHAT PATHOLOGY TESTS TO ORDER WHEN A
PATIENT PRESENTS WITH
ATYPICAL PNEUMONIA
Stephen GRAVES
Director
Division of Microbiology
28 June 2011
How does “atypical pneumonia” differ from “typical
pneumonia”
• slower onset of symptoms (days rather than
hours) – longer prodrome.
• less prominent respiratory symptoms
• less/no sputum
• less chest pain
• less dyspnoea
• normal FBC (WCC not raised)
• “normal” CXR (non-lobar changes)
[ treat with doxycycline/clarithromycin/azithromycin
rather than benzypenicillin/amoxycillin]
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Causes of typical pneumonia
• bacteria
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Streptococcus pneumoniae
Haemophilus influenzae
Staphylococcus aureus
Klebsiella pneumoniae (and other Gram-negatives,
especially in hospitalised and intubated patients)
• rarely viral
• Ix sputum (m/c/s)
• blood cultures (x2)
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Causes of atypical pneumonia
• Viruses
• Influenza A
• Rhinoviruses
• Respiratory Syncytial Virus (RSV)
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Causes of atypical pneumonia (cont.)
Bacteria
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Mycoplasma pneumoniae
Legionella sp. (cooling tower waters/potting mix)
Chlamydia pneumoniae
Chlamydia psittaci (bird contact)
Coxiella burnetii (Q fever) (animal contact)
Mycobacterium tuberculosis (immigrant)
Fungi
• Pneumocystis jiroveci (immunosuppressed/HIV)
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Pathology investigations for atypical pneumonia
Depends on what you think is the cause:
1. Baseline serology
(may be negative, but can be used with a later serum to
demonstrate seroconversion) e.g. Mycoplasma pneumoniae
IgM and IgG.
2. Direct immunofluorescence (IF) on respiratory
tract specimens (for respiratory viruses & Pneumocystis)
3. PCR on respiratory tract specimen
(for respiratory viruses & Pneumocystis)
[this is now replacing viral culture]
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Pathology investigations for atypical pneumonia (cont.)
4. Legionella Urinary antigen (for L.pneumophila
serogroup 1 only)
5. Q Fever PCR/serology
6. Culture of respiratory tract specimens for bacteria
7. Consider tests for TB in risk groups
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WHAT PATHOLOGY TESTS TO ORDER
WHEN PATIENT PRESENTS WITH
JAUNDICE/HEPATITIS
Stephen GRAVES
Director
Division of Microbiology
28 June 2011
INFECTIOUS CAUSES
• viral hepatitis (many possibilities)
• bacterial
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septicaemia
cholangitis/cholecystitis
pyogenic liver abscess
peritonitis
• rare infections
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malaria (travellers)
amoebic liver abscess
leptospirosis
Q fever
animal contact
brucellosis
hydatid cyst
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OTHER NON-INFECTIOUS
CAUSES OF PATHOLOGY
• drug-induced (including alcohol)
• neoplasia (liver infiltration or biliary obstruction)
• haemolysis
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INVESTIGATIONS
• Full blood examination (↑ eosinophils suggest parasite or
drug-induced hepatitis)
• Liver function tests
• Blood cultures (x2)
• Urinalysis
• Viral serology (must specify which viruses)
• Special tests
– e.g. serology for specific infections
– e.g. ascites fluid (m/c/s)
base-line (acute) serum (will also be stored for later use)
– if haemolysis, consider serology for
– Mycoplasma pneumoniae & EBV
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Viral causes of jaundice/hepatitis
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Epstein-Barr Virus (EBV)
(teenagers)
Cytomegalovirus (CMV)
Hepatitis A (HAV) (travellers)
Hepatitis B (HBV) (ethnic risk, IVDU)
Hepatitis C (HCV) (IVDU)
Hepatitis D (HDV) (only if Hep B positive)
Hepatitis E (HEV) (travellers)
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The laboratory cannot test for all of these simultaneously!
You must indicate which you think is most likely or indicate a
descending order of probability
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Investigations
Baseline serology in acute illness
(may be negative but can be used in conjunction
with a later serum to demonstrate seroconversion
or rise in antibody concentration/titre)
1. HAV serology (travellers, non-immunised)
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IgM and IgG in acute illness
IgG only if testing for immunity or past infection
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Investigations (cont.)
2. HBV serology (ethnic risk, IVDU)
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HBVsAg – acute infection; chronic infection
HBVsAb – immunity (post-vaccination)
HBVcIgG – confirms prior infection
HBVcIgM– confirms recent infection
HBVeAg – high risk chronic infection
HBVeAb – past infection
HBV DNA - acute infection; chronic infection
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Investigations
3. HCV serology
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IgG – past infection or chronic infection
HCV – RNA – acute or chronic infection
HCV – RNA (viral load) – response to Rx?
HCV – genotype – is virus likely to respond to Rx?
» genotype 1 (40% cure)
» genotype 2/3 (80% cure)
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Investigations
4.
EBV serology
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monospot/Paul-Bunnell test (heterophile antibody)
specific serology
» EBV IgM
» EBV IgG
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acute infection
past infection
PCR (to detect DNA) acute/chronic/reactivation
infection
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Investigations
5.
CMV specific serology
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CMV IgM
acute infection
CMV IgG
past infection
PCR (to detect DNA) acute/chronic/reactivation
infection
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If in doubt what test to order, please
phone the Duty Medical Microbiologist on
Ext. 14000
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