The role of the laboratory and the choice of an appropriate test in the diagnosis of infective diseases

Dr F Noordeen Department of Microbiology Faculty of Medicine University of Peradeniya May 2013

Learning outcomes
Be able to List the common investigations that aid the diagnosis of infective diseases Discuss the concepts of sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) + apply it to common tests

Role of microbiology in clinical medicine

Direct Benefit to patient reason for admission Indirect Use of accumulated data of infection iatrogenic Aetiology Choice of antibiotics Immunization Sanitation Pest control

Planning of policy

Direct benefit to patient

Confirm diagnosis
Complete clinical diagnosis Incomplete clinical diagnosis Clinical diagnosis not possible

Assist management
Determines aetiology Choice of antibiotics Prevention strategies Allows choice of antibiotic Enables prognosis Determine source(s)

Clinical diagnosis
Based on observations History Examination SHOULD BE ACCURATE AND COMPLETE

Complete clinical diagnosis possible

(including aetiology)
Very specific history Very specific signs UNCOMMON Eg: Chicken pox Meningococcal septicaemia

Role of laboratory
Minimal Scientific vigour Unusual presentation Chicken pox in the immunocompromised Clinical trial of intervention Antiviral therapy New antibiotics

Partial clinical diagnosis possible

(aetiology requires laboratory confirmation)
Acute meningitis Pneumonia Peritonitis Cellulitis (Erysipelas) UTI Sinusitis Otitis media

Partial diagnosis
Role of laboratory is to complete the diagnosis Laboratory test is the criterion for diagnosis
UTI >105 organisms/ml

Laboratory test confirms the diagnosis

Malaria

Laboratory test adds essential information for management

Penicillinase production by Neiseria gonorrhoea MRSA isolated from blood culture

Diagnosis not possible without laboratory investigations

Eg: Fever No clues
Healthy 30 year old man presenting with fever

With clues
Diabetic farmer with fever 23 year old girl with a past history of rheumatic fever

Expectation from a laboratory investigation

What is the purpose of doing test Is this test for diagnosis or further management

Purpose
Confirm an already made diagnosis Refute an already made diagnosis Decide on differential diagnosis Move one step in the differential diagnosis

Pneumonia
Clinical diagnosis Chest X Ray
CONFIRM Evidence of consolidation REFUTE No evidence of consolidation

Equivocal evidence of consolidation THINK

URINARY TRACT INFECTION

SUSPECT Urine culture > 105/ml
CONFIRM YES REFUTE NO

103-4/ml
REPEAT

The actual test

Responsibility of Laboratory

Accuracy Reproducibility Predictive value of a laboratory test How useful is the test
Diagnosis of a acute infection Diagnosis of a chronic / latent infection Epidemiological study (prevalence of disease)

What is a test?
An investigation done on a patient to assist in the management of the patients illness
Laboratory
Haematology Biochemistry Histopathological Microbiological
Bacteriological Virological Mycology Parasitology Immunology

Detect presence of organism Microscopy Isolation Antigen detection Nucleic acid detection Detect presence of reaction to organism Immune response (AB/skin tests) Pathological Haematological/biochemical changes

Imaging
X-ray Ultrasound CT scan MRI scan Radio-isotope scans

Test results
No of positive results No with disease No without disease Total No of negative results Total

True False positive (TP) negative (FN) False True positive (FP) negative (TN) TP + FP TN + FN

TP + FN

TN + FP

TP + FP + TN + FN

Sensitivity
% Positive in disease Sensitivity = True positives Total No with disease x 100

TP x 100 TP + FN

Specificity
Negativity in non-disease (health) Specificity = True negatives x 100 Total No without disease

TN TN+ FP

x 100

Positive predictive value

% of patients with positive tests who have the disease PPV = True positive Total No of positive tests x 100

TP x 100 TP+ FP

Negative predictive value

% of patients with negative tests who do not have the disease NPV = True negative Total No of negative tests x 100

TN TN+ FN

x 100

Importance of denominator

If the denominator is not accurate these indices can be seriously misleading

Increased sensitivity is often at an expense of specificity Test should have a high predictive value if it is to be useful in an individual patient Choice of test High sensitivity High specificity High efficiency

Treatable serious disease

Tuberculosis

Non treatable disease HIV infection disease with social consequences STD

False positive and false negative equally serious

Plague, small pox

CHOICE OF TEST
DIAGNOSIS High positive and negative predictive value Reliability and accuracy of results Early detection of disease SURVEILLANCE High specificity Detectable in healthy persons Past infection Subclinical infection Latent infection Immunization Maternal antibodies

Application in typhoid
Recommended test for diagnosis Blood culture Not universally available Previous antibiotic use Sensitivity and negative predictive value poor Specificity and positive predictive value high Test commonly used in diagnosis SAT Test methods Tube dilution methods - Validated Slide tests - often not validated

Application in typhoid
(using O antibody titre of 1/120) Positive SAT Negative SAT Total

Patients with typhoid Patients without typhoid Total

79

85

17

85

102

96

91

187
CMJ 1992 37 48-51

Application in typhoid
(using O antibody titre of 1/120 Sensitivity Specificity Positive predictive value Negative predictive value Efficiency 79 85 x 100 93% 83% 82% 93% 88%
(CMJ 1992 37 48-51)

85 x 100 102 79 96 85 91 164 187 x 100 x 100 x 100

Diagnostics in current use in Sri Lanka

Dengue fever (DF) What is the test Dengue specific IgM/IgG PCR for viraemia What do you expect - Diagnosis of dengue fever Prediction of complications (DHF ; DSS) When should you do the test which time during illness How much does the test cost / who is paying? Is it cost-effective Of what benefit is the test - to the patient - to society

Diagnostics in current use in Sri Lanka

Infective endocarditis
Blood culture How many? When do you take blood cultures? Why may they be negative in IE? (False negatives) Could there be false positives? How do they affect treatment?

Diagnostics in current use in Sri Lanka

Leptospirosis
What is the best specimen? Why? When do you take samples? Where do you send it? Can you interpret the results? How does the test influence management? Does the test have any other use?

Diagnostics in current use in Sri Lanka

Community acquired pneumonia
What is the diagnostic test for pneumonia? How is the microbiology laboratory connected to diagnosis? What tests are available? Pneumococcal pneumonia Mycoplasma pneumonia Chlamydia pneumoniae pneumonia Tuberculosis Legionellosis Others (pneumonia in the immunocompromised)

Diagnostics in current use in Sri Lanka

Meningitis
What is/are specimens to be taken? What is/are tests to be requested? What is the positive predictive value/negative predictive? (Value/s for tests which have been requested)
CSF
WBC Protein Sugar Gram stain Culture Antigen detection PCR

Blood culture

2.1 Briefly outline the uses of a microbiology laboratory in clinical practice 2.2 In a study on the usefulness of the SAT in the diagnosis of typhoid, the following values were obtained. Calculate the sensitivity, specificity, positive predictive value and negative predictive value of using an O antibody titre of 1/120 as a diagnostic titre in typhoid.
O antibody titre 1/120 79 17 O antibody titre 1/60 06 85

Patients with typhoid Patients without typhoid