28 June 2011 WHAT PATHOLOGY TESTS TO ORDER WHEN A PATIENT PRESENTS WITH ATYPICAL PNEUMONIA Stephen GRAVES Director Division of Microbiology

28 June, 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]

28 June, bacteria 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) Causes of typical pneumonia

28 June, Viruses Influenza A Rhinoviruses Respiratory Syncytial Virus (RSV) Causes of atypical pneumonia

28 June, Bacteria 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) Causes of atypical pneumonia (cont.)

28 June, 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] Pathology investigations for atypical pneumonia

28 June, 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 Pathology investigations for atypical pneumonia (cont.)

28 June 2011 WHAT PATHOLOGY TESTS TO ORDER WHEN PATIENT PRESENTS WITH JAUNDICE/HEPATITIS Stephen GRAVES Director Division of Microbiology

28 June, viral hepatitis (many possibilities) bacterial septicaemia cholangitis/cholecystitis pyogenic liver abscess peritonitis rare infections malaria (travellers) amoebic liver abscess leptospirosis Q fever brucellosis hydatid cyst INFECTIOUS CAUSES } animal contact

28 June, drug-induced (including alcohol) neoplasia (liver infiltration or biliary obstruction) haemolysis OTHER NON-INFECTIOUS CAUSES OF PATHOLOGY

28 June, 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 INVESTIGATIONS

28 June, Epstein-Barr Virus (EBV) 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) 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 Viral causes of jaundice/hepatitis } (teenagers)

28 June, 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) IgM and IgG in acute illness IgG only if testing for immunity or past infection Investigations

28 June, HBV serology (ethnic risk, IVDU) HBV s Ag – acute infection; chronic infection HBV s Ab – immunity (post-vaccination) HBV c IgG– confirms prior infection HBV c IgM– confirms recent infection HBV e Ag – high risk chronic infection HBV e Ab – past infection HBV DNA- acute infection; chronic infection Investigations (cont.)

28 June, HCV serology IgG – past infection or chronic infection HCV – RNA – acute or chronic infection HCV – RNA (viral load) – response to R x ? HCV – genotype – is virus likely to respond to R x ? »genotype 1 (40% cure) »genotype 2/3 (80% cure) Investigations

28 June, EBV serology monospot/Paul-Bunnell test (heterophile antibody) specific serology »EBV IgM acute infection »EBV IgGpast infection PCR (to detect DNA) acute/chronic/reactivation infection Investigations

28 June, CMV specific serology CMV IgMacute infection CMV IgGpast infection PCR (to detect DNA) acute/chronic/reactivation infection Investigations

28 June, If in doubt what test to order, please phone the Duty Medical Microbiologist on Ext