Microbiology of Respiratory Infection II Dr Michael Lockhart

Respiratory Infections n Infections of throat and pharynx n Infections of middle ear and sinuses n Infections of trachea and bronchi n Infections of the lungs

Infections of throat and pharynx n Sore throat n Diphtheria n Candida/thrush n Vincent’s angina

Infections of throat and pharynx n Diagnosis: – Well taken throat swab

SORE THROAT

Sore throat n VAST MAJORITY (OVER TWO THIRDS) - VIRAL – DO NOT NEED ANTIBIOTICS

Bacterial sore throat n The most common BACTERIAL cause is Streptococcus pyogenes (also known as Group A streptococci) n Clinical: Acute follicular tonsillitis n Treatment:Penicillin

Streptococcus pyogenes

Streptococcal sore throat n Acute complications: – Peritonsillar abscess (quinsy) – Sinusitis/ otitis media – Scarlet fever

QUINSY (PERITONSILLAR ABSCESS)

Streptococcal sore throat n Late complications – Rheumatic fever n 3 weeks post sore throat n fever, arthritis and pancarditis – Glomerulonephritis n 1-3 weeks post sore throat n haematuria, albuminuria and oedema

Diphtheria n Corynebacterium diphtheriae n Clinical: Severe sore throat with a grey white membrane across the pharynx. The organism produces a potent exotoxin which is cardiotoxic and neurotoxic.

DIPHTHERIA

Diphtheria n Epidemiology : Rare, but increased in certain parts of the world eg Russia n Treatment: Antitoxin and Supportive and Penicillin/erythromycin

Candida/Thrush n Candida albicans n Clinical: White patches on red, raw mucous membranes in throat/ mouth n Cause: endogenous n Treatment: Nystatin

ORAL THRUSH

Vincent’s angina n Mixture of organisms (Borrelia vincenti and Fusobacterium sp.) n Clinical:Foul smelling mouth and throat ulcers n Treatment: penicillin

VINCENT’S ANGINA

Respiratory Infections n Infections of throat and pharynx n Infections of middle ear and sinuses n Infections of trachea and bronchi n Infections of the lungs

EAR

OTITIS MEDIA

Infections of middle ear and sinuses n Often viral with bacterial secondary infection n Most common bacteria: Haemophilus influenzae, Streptococcus pneumoniae and Streptococcus pyogenes. n Treat: Amoxycillin

Respiratory Infections n Infections of throat and pharynx n Infections of middle ear and sinuses n Infections of trachea and bronchi n Infections of the lungs

Infections of trachea and bronchi n Acute epiglottitis n Acute exacerbations of COPD n Cystic fibrosis n Pertussis (whooping cough)

Acute epiglottitis n Haemophilus influenzae n Clinical: severe croup in children aged 2-7 years, may progress to respiratory obstruction and death.

EPIGLOTTITIS

Acute epiglottitis n Microbiology of Haemophilus influenzae – Habitat - upper respiratory tract – Microscopy- small gram negative bacillus – Culture - Chocolate agar -small translucent colonies – Identify - “X and V test”; H influenzae requires both factors X and V to grow.

Haemophilus influenzae

Acute epiglottitis n Diagnosis: blood culture (?throat swab) n Treatment: ITU and ceftriaxone

COPD n Acute exacerbations of COPD. – Exacerbations of this chronic condition are often associated with bacterial infection.

Acute exacerbations of COPD n Often follow viral infection, or fall in atmospheric temperature with increase in humidity (often in winter) n Clinical: Patients present with increased breathlessness. The volume and purulence of sputum is increased.

Acute exacerbations of COPD n The most common organisms associated are: – Haemophilus influenzae – Streptococcus pneumoniae – Moraxella catarrhalis n NB All three organisms are present in normal upper respiratory tract flora.

Acute exacerbations of COPD n Treatment: n Give antibiotics if ↑sputum purulence. If no ↑sputum purulence then antibiotics not needed unless consolidation on CXR or signs of pneumonia. n 1ST LINE Amoxicillin 500mg tds 2ND LINE Doxycycline 200mg on day 1 then 100mg daily (5 days) n With time becomes increasingly difficult to treat, due to acquisition of more resistant organisms.

Cystic fibrosis n Inherited defect – leads to abnormally viscid mucus which blocks tubular structures in many different organs including the lungs.

Cystic fibrosis n Chronic respiratory infection is a major problem. n Causal bacteria: – Staphylococcus aureus and Haemophilus influenzae – Pseudomonas aeruginosa – Burkholderia cepacia

Pertussis (whooping cough) n Bordetella pertussis n Clinical: Acute tracheobronchitis – cold like symptoms for two weeks – paroxysmal coughing (2 weeks) n repeated violent exhalations with severe inspiratory whoop, vomiting common – residual cough for month or more

Pertussis (whooping cough) n Diagnosis: – pernasal swab (charcoal blood agar/ Bordet-Gengou medium) – serology – clinical ( by the stage of paroxysmal coughing organism numbers much reduced) n Treatment: most effective in the first 10 days of illness, also reduces spread to susceptible contacts n Vaccination

Pernasal swab

Respiratory Infections n Infections of throat and pharynx n Infections of middle ear and sinuses n Infections of trachea and bronchi n Infections of the lungs

Infections of the lungs n Community acquired pneumonia n Nosocomial pneumonia n Legionnaires disease n Pneumocysitis carinii pneumonia (PCP) n Fungal chest infection n Tuberculosis

Community acquired pneumonia n Clinical: cough, sputum production, dyspnoea, fever. n Chest x-ray with infiltrates. n Acquired in the community

Community acquired pneumonia n Causative organisms: – Streptococcus pneumoniae 70% – Atypicals/viruses 20% – Staphylococcus aureus 4% – Other bacteria 1% – Haemophilus influenzae 5%

Community acquired pneumonia n Streptococcus pneumoniae – Microbiology: n Microscopy - gram positive cocci n Culture - Alpha haemolytic colonies, typically “draughtsmen” ie with sunken centre. n Identify - “Optochin” sensitive – Treatment - generally penicillin sensitive

Streptococcus pneumoniae

Lobar pneumonia

Community acquired pneumonia n “Atypicals” - old term for pneumonias not attributable to any of the common bacterial causes of pneumonia. n Refer to Dr McIntyre’s talk

Community acquired pneumonia n Treatment, follow the Tayside Critical Care Pathway for the Management of Community-Acquired Pneumonia

CURB65 SCORE 3 OR MORE (SEVERE) ANTIBIOTICS: SEVERE  ALL SHOULD INITIALLY RECEIVE: IV CO-AMOXICLAV 1.2g x3/day PLUS IV CLARITHROMYCIN 500mg x2/day or PO DOXYCYCLINE 100mg x2/day ( PENICILLIN ALLERGY : IV Levofloxacin 500mg2/day)  Step down to oral doxycycline 100mg x 2/day in all patients  ALL SHOULD HAVE: Paired serology, throat swab/gargle for virology PCR, urinary legionella antigen tests  Treat for at least 10 days (IV/oral)

Nosocomial pneumonia n = hospital acquired pneumonia n Predisposing factors: – Intubation – Intensive care unit – Antibiotics – Surgery – Immunosuppression

Nosocomial pneumonia n Organisms -60% gram negative organisms : – includes Pseudomonas aeruginosa, and Coliforms (such as E.coli, Klebsiella sp) – If aspiration pneumonia anaerobes may be involved n Treatment – Severe IV Amoxicillin + Metronidazole + Gentamicin n Step down to Coamoxiclav PO 7-10 days total – Non severe Amoxicillin + Metronidazole for 7 days

Legionnaires disease n Legionella pneumophila n Clinical: – flu like illness which may progress to a severe pneumonia, with mental confusion, acute renal failure and GI symptoms. n Epidemiology – often associated with travel, usually associated with water.

Legionnaires disease n Diagnosis: Legionella urinary antigen/ Serology n Treatment: – Erythromycin/clarythromycin – Fluoroquinolones

Pneumocysitis carinii pneumonia (PCP) n A cause of pneumonia in patients with AIDS n Diagnosis: Bronchioalvelar lavage (BAL) or induced sputum and identification of cysts. n Treatment: Cotrimoxazole, pentamidine.

Fungal chest infection n Aspergillus fumigatus n Clinical: Causes severe pneumonia/systemic infection in the severely immunocompromised. – Or aspergilloma n Diagnosis : Culture n Treatment : iv Amphotereicin B

ASPERGILLOMA

TUBERCULOSIS n Mycobacterium tuberculosis n Acid Alcohol Fast Bacilli n Bread crumb like growth on special medium, after prolonged (up to 3 months) incubation

Acid and Alcohol Fast Bacilli (AAFB)

Growing Tuberculosis

Tuberculosis n For more detailed information see Dr Winters Lecture

Infections in lungs General diagnostic points

Infections of the lungs - Diagnosis n Isolation of causal pathogen – Sputum NB Quality of sputum sample important – Blood culture (organism in blood of one third of patients with pneumonia)

Infections of the lungs - Diagnosis n Detection of bacterial antigen – eg Legionella urinary antigen – Direct immunofluorescence for PCP n Serology – eg Legionella serology

Immunisation n UK guidance is summarised in a document called “The Green Book” available online at: – lthAndSocialCareTopics/GreenBook/fs/en

Pneumococcal immunisation n Pneumococcal polysaccharide vaccine covers 23 different capsule types – Efficacy – 50-70% reduction of bacteremia risk n Pneumococcal conjugate vaccine covers 7 different capsular types – common childhood strains – Efficacy – 97% protection

Pneumococcal immunisation n Indications – All those aged 65 years and over – Childhood immunisation schedule – Risk groups n No spleen n Various chronic diseases including COPD n Immunosuppressed n Patients with CSF shunts

Hib n Invasive Haemophilus infection caused most commonly by Type b capsular strains (Hib). n Conjugate vaccine offered to all children less than 1, and all asplenic individuals n Highly effective

Pertussis immunisation n Acellular vaccine – 5 purified pertussis components n Given as part of the childhood immunisation schedule

Immunisation for Tuberculosis n Live attenuated strain of Mycobacterium bovis n UK efficacy of 70% in protecting against TB n Risk based approach to identify those who receive the vaccine

Community acquired pneumonia n Causative organisms: – Streptococcus pneumoniae 70% – Atypicals/viruses 20% – Staphylococcus aureus 4% – Other bacteria 1% – Haemophilus influenzae 5%