microbiology pneumonia

8/12/2019 Microbiology Pneumonia

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Pneumonia

Dr Andrew Dodgson

Consultant Microbiologist


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Terminology

Histological/Radiological Lobar vs bronchopneumonia Lobar vs. interstitial

Microbiological Bacterial, viral, fungal

Clinical/ Microbiological Atypical vs. typical

Clinical/epidemiological Community acquired vs. nosocomial

All have clinical relevance though none is absolute


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Terminology

Histological/Radiological Lobar vs bronchopneumonia Lobar vs. interstitial

Microbiological Bacterial, viral, fungal

Clinical/ Microbiological Atypical vs. typical

Clinical/epidemiological Community acquired vs. nosocomial

All have clinical relevance though none is absolute


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Importance

the most widespread and fatal of all acute diseases, pneumoniais now Captain of the Men of Death Osler, 1901 (Principles andPractice of Medicine, 4thEd.)

Pneumonia is 6thleading cause of death in US Leading infectious cause of death

5 million deaths/year worldwide

High mortality rate

Outpatient: 5% Inpatient: 12%

ITU: 40%


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Clinical Presentation

Cough (productive vs. non-productive)

Fever

Dyspnoea

Fatigue

Headache

Nausea, vomiting, diarrhoea

Myalgia


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Predisposing factors

Age

COPD

Diabetes

Heart failure

Immunocompromised states

Alcoholism

Smoking

Travel/occupational/recreational exposure


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Physical signs

Tachycardia

Tachypnoea

Hypotension Creps

Bronchial breathing

Fever


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Physical signs

Physical exam has a sensitivity of 47-60% andspecificity of 50-75%

However in pts with creps, fever, cough and

tachycardia the possibility of pneumoniaincreases from 18 to 42%

Also, pts with none of RR>20, HR>100 and

temp>37.8C have a


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Investigation

Chest X-ray

FBC

CRP

U&Es ABGs

Sputum culture

Blood culture (+ve in 1-16% of pts requiringadmission)

Serology/PCR/antigen


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Severity assessment

CURB-65

Confusion

Urea >7mmol/L

Respiratory rate >30

Blood pressure diastolic


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Aetiology

Community Acquired

S. pneumoniae

H. influenzae

Atypicals S. aureus

Kleb. pneumoniae

Hospital Acquired

Gram negatives

E.g. E.coli, Klebsiella,

Pseudomonas

S. aureus

Atypicals infrequent

S. pneumoniaerare


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Pathogens

S. pneumoniae

Gram +ve diplococci

Almost all S to

penicillins,cephalosporins (R morecommon is southernEurope and S. Africa)

Most S to erythromycin

H. influenzae

Gve cocco-bacilli

S to amoxycillin

25% produce B-lactamase, thus AmoxyR.

S to Co-Amoxyclav,

cephs, Ciprofloxacin R Eryth


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Pathogens

S. pneumoniae

Gram +ve diplococci

Almost all S to

penicillins,cephalosporins (R morecommon is southernEurope and S. Africa)

Most S to erythromycin

H. influenzae

Gve cocco-bacilli

S to amoxycillin

25% produce B-lactamase, thus AmoxyR.

S to Co-Amoxyclav,

cephs, Ciprofloxacin R Eryth


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Pathogens

S. aureus

Seen classically after flu

Severe necrotising pneumonia in young adultsseen in PVL (toxin) producing strains-emergingpathogen

Rx flucloxacillin, eryth.Vancomycin, linezolid for MRSA


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Atypical pneumonia

Caused by organisms that will not grow underroutine culture conditions

Non-productive cough

Negative culture

Clinical signs often do not match severity of

clinical (and radiological) presentation Legionella, Mycoplasma, C. psittacci, C. pneumoniae, C.

burnetii,viruses (esp. influenza)


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Aspiration pneumonia

Occurs in patients with abnormal gag reflex (alteredconsciousness, CVA)

Combination of chemical (acid) injury, bronchial

obstruction and bacterial infection. Bacteria involved will reflect oropharyngeal flora-

anaerobes and Streps & haemophilus (community) orgram negs (nosocomial)

Rx often broad spectrum B-lactam e.s. co-amoxyclav orpipperacillin/tazobactam +/- metronidazole


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Sputum culture

Interpretation

Macroscopic appearance

Mucoid or purulent?

Presence of leukocytes

Organism isolated

Pure culture or mixed?

Amount? Likely pathogen given the situation?

Whats happening to the patient?


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Diagnosing Atypical Pneumonia

Clinically Laboratory:

Culture-not likely to be useful Serology-detects antibody response

Usually take time Requires demonstration of a single high level or 4-fold rise (after 10-14 days) Immunocompromised patients?

Antigen detection Good strategy but only available for Legionella

PCR

Detects DNA/RNA of organism Potentially excellent strategy Only available in reference centres currently Will likely be method of choice in future


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Diagnosis of LegionellaAm J Med, 2001; 110:41-48

Sputum cultureSelective mediaResults in 2 -7 days10% sensitivity vs serology61% sensitivity vs DFABetter if endotracheal/BAL

Urine antigenResults in 1 -6 hoursCan take ~ 5 days to turn posCan remain pos for up to 6 wkInexpensiveSerogroup 1 specific

70-80% sensitivity100% specificity (serogrp 1)Direct Fluorescent Antibody

Stain (DFA) of sputumNeed large numbers of orgs.Sensitivity approx 50%60 - 70% specificity for particular

serotypes

Serology - ELISAAcute & convalescent samplesneeded

4-12 weeks for AB responseSingle titre of 1:256 = disease20% have no AB responsePCR

Fast sensitivity of ~ 70%Can be used for sputumCurrently research use only


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Treatment

Need to consider:

Setting

Community or hospital

Severity

CURB-65 score


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Treatment-Community acquired

CURB65 0-1Amoxycillin 500-1g TDS

CURB65 2Amoxycillin AND Clarithromycin 500mg BD

CURB65 3 Co-amoxyclav 1.2g TDS AND Clarithromycin

500mg BD-Both given IV


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Treatment-Nosocomial

Occurring 48 hrs post admission

Usually

Co-amoxyclav

However if severe or recently on ITU or recentAbx

Piperacillin/tazobactam


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Treatment-Specific organisms

S. pneumoniae Benzylpenicillin or amoxycillin

S. aureus Flucloxacillin

Legionella Clarithromycin (or a quinolone e.g. Cipro)

Psitacosis or Q fever Doxycycline

Mycoplasma Clarithromycin

C. pneumoniae Clarithromycin


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Other aetiologies

TB

Viral

Fungal Pneumocystis


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