Respiratory Tract Microbiology Flashcards
What is the difference between colonisation and infection?
- Infection - inflammation as a consequence of the pathogen
* Colonisation - presence of pathogen, may not suffer from disease
What are host defences of the upper respiratory tract?
Nasopharynx
- Nasal hairs
- Ciliated epithelia
- IgA
Oropharynx
- Saliva
- Sloughing
- Cough
What is sinusitis?
Inflammation of paranasal sinuses
What is rhinitis?
Inflammation of nose
What is pharyngitis?
Inflammation of pharynx, tonsils, uvula
What is epiglottitis?
Inflammation of epiglottis, superior larynx
What is laryngitis?
Inflammation of the larynx
What are some gram positive upper respiratory tract colonisers?
- α-haemolytic streptococci (Strep pneumoniae)
- ß-haemolytic streptococci (Strep pyogenes)
- Staphylococcus aureus
What are some gram negative upper respiratory tract colonisers?
- Haemophilus influenzae
* Moraxella catarrhalis
What colour will haemophilia influenzae appear on a gram stain?
Pink - it is gram negative
What shape of bacterium is H.Influenzae?
Coccobacilli
What is moraxella catarrhalis?
A gram negative coccus
What are host defences of the conducting airways?
- Mucocilliary escalator
- Cough
- Antimicrobial peptides
- Cellular and humoral immunity
When does infection of the conducting airways occur?
Infections occur when there are changes
- Trauma/intubation of airway
- Abnormalities of defence e.g. cilliary escalator as occurs in COPD/CF
- Virulent pathogen/large inoculum
How can intubation lead to infection of the conducting airways?
Inhibits the final stage of the cilliary escalator - prevents the expulsion of mucous and foreign material from being swallowed or coughed up
What are the clinical presentations of acute bronchitis?
- Infection & inflammation of the bronchi
- Productive cough
- Wheeze
- Fever
- Normal chest examination & CXR
What are the microbiological features of acute bronchitis?
- 90% viral
- Preceded by URT infection
(Acute bronchitis is an infection of the conducting airways)
What I the treatment for acute bronchitis?
Antibiotics not usually indicated
What are the clinical presentations of acute exacerbations of chronic obstructive pulmonary disease?
- Productive cough or acute chest illness
- Breathlessness
- Wheezing
- Increased sputum purulence
- Exacerbations often follow bacterial/viral infection or fall in temp & increase in humidity (i.e. Winter)
What pathogens can cause acute exacerbations of COPD?
- Haemophilus influenzae
- Moraxella catarrhalis
- Streptococcus pneumoniae
What percentage of acute COPD exacerbations are caused by viruses?
- 30% - viral
- 50% - bacterial
- 20% - unknown
What is purulent sputum?
Typically yellow or green - contains pus, composed of white blood cells, cellular debris, dead tissue, serous fluid, and mucus
What is pertussis?
Whooping cough - acute trachea-bronchitis
What are the symptoms of pertussis?
- cold like” symptoms for two weeks
- paroxysmal coughing (2 weeks)
- repeated violent exhalations with severe inspiratory “whoop”
- vomiting common
- residual cough for month or more
What pathogen causes pertussis?
Bordetella pertussis
What are the features of bordetella pertussis?
- Gram negative coccobacillus
- Exclusively human pathogen
- Vaccine preventable
In what time frame is bordetella pertussis contagious?
- From the period where symptoms start
* To over 2 weeks
How long after exposure to bordetella pertussis do symptoms start?
- 7-10 days is typical range
* But can range from 4-24 days
How is bordetella pertussis diagnosed?
Bacterial culture
- Pernasal swab (<21 days)
- Culture (charcoal-blood agar)
PCR
* Pernasal swab (<21 days)
Serology (paired sera)
Clinical signs and symptoms (low numbers of organisms by onset of paroxysmal cough)
What is the treatment for bordetella pertussis?
Treatment with Antibiotics if <21 days cough
after 21 days, post-infective cough - not caused by pathogen
What are the 3 main routes of disease transmission?
- Contact (touch)
- Airborne
- Droplet
What are the airborne precautions to reduce transmission of infectious diseases?
- Wash hands before entering and leaving room
- PPE (filtering face piece 3 - FFP3)
- Keep in door closed
- Dispose of/decontaminate all equipment used before leaving
- Dispose of FFP3 after leaving
Why do airborne diseases have a large spread?
- Small particles (<5 microns) can travel long distances and remain airborne
What diseases are airborne?
- Multi-drug resistant TB
- some viruses
- RTI undergoing aerosol generating procedures
What are droplet precautions?
- Wash hands before entering and leaving room
- PPE
- Keep door closed
- Dispose of/decontaminate all equipment used before leaving
Why do droplets have less spread than airborne diseases?
Larger particles > 5 microns, fall to the floor within 2m
How are droplet diseases spread?
- Direct contact of droplets with mucous membranes
* Droplet > surface > contact spread
What is cystic fibrosis?
Inherited disease leads to abnormally viscous mucous – blockages of many tubular structures including conducting airways & lungs
What are the clinical features of cystic fibrosis?
Repeated chest infections & chronic colonisation
What are the microbiological features of cystic fibrosis?
- Inefficient clearance and build-up of mucus
- Staph aureus
- Haemophilus influenzae
- Strep pneumoniae
- Pseudomonas aeruginosa
- Burkholderia cepacia
Is cystic fibrosis caused by pathogens?
No, it is a host defence problem - cannot clear phlegm
What are host defences of the lower respiratory tract?
- No ciliary escalator
- Alveolar lining fluid - surfactant, Ig, complement protein, free fatty acids, antimicrobial peptides
- Alveolar macrophages
What are the clinical features of community acquired pneumonia?
- Cough
- Increased sputum
- Chest pain
- Dyspnoea
- Fever
- CXR with infiltrates
Explain the pathology of community acquired pneumonia?
- Organism reaches lungs
- Immune activation & infiltration (systemic response)
- fluid & cellular build up in alveoli leads impaired gas exchange
What are the causative organisms of community acquired pneumonia?
- Streptococcus pneumoniae - 70%
- Atypicals/viruses - 20%
- Haemophilus influenzae - 5%
Staphylococcus aureus - 4% - Other bacteria - 1%
What are the risk factors of community acquired pneumonia?
- Increasing age
- Immunocompromised/suppressed patients
- Smoking
How is community acquired pneumonia diagnosed?
- Sputum culture
- Purulence
- Viral PCR
What does a sputum culture show in community acquired pneumonia?
* Gram stain sputum - pus cells, Gram pos/neg cocci/bacilli * Culture on blood agar - alpha haemolysis (partial haemolysis, where the organism grows blood agar becomes green-brown colour)
What is used to treat pneumonia caused by streptococcus pneumoniae?
Sensitive to amoxicillin, doxycycline and co-trimoxazole (if allergic to penicillin, doxycycline used)
What types of infections can be caused by streptococcus pneumoniae in children?
- Ear infection
- Sinus infection
- Upper respiratory tract infection
What types of infections can be caused by streptococcus pneumoniae in the immunosuppressed?
Can spread to blood stream and cause pneumococcal disease
What is pneumococcal disease that spreads to the blood stream referred to as?
Invasive pneumococcal disease
Why is the PCB vaccine so important?
Pneumococcal vaccine reduces cases by 76%
Why is pneumonia such a significant disease?
It is the world’s biggest killer of children
What are the different types of pneumonia?
- Acute and chronic
- Typical (step pneumoniae) and atypical (Mycoplasma pneumoniae , Legionella pneumonia, Chlamydophila pneumonia, Chlamydia psitacci, etc)
- Hospital acquired and community acquired
- Aspiration pneumonia (when food, saliva, liquids, or vomit is breathed into the lungs)
- Pneumonia in the immunosuppressed/special populations
How is severity of pneumonia graded?
CURB65
What is legionella pneumonia?
Atypical pneumonia
How is legionella pneumonia diagnosed?
- Legionella urinary antigen (detects serogroup 1 only)
- Culture - slow on selective media
- Paired serology
- PCR available direct from Sputum
What is the treatment for legionella pneumonia AKA Legionnaires’ disease?
- Clarythromycin
- Erythromycin
- Quinolones (e.g. levofloxacin)
Why are quinolones not used for treatment of Legionnaires’ disease unless very serious?
One of the 4C’s - can cause C.difficile infection
What are characteristics of Legionella pneumophila?
- Common environmental Gram-negative bacteria (unusual cell wall structure)
- Obligate intracellular organism
- Resides with water amoeba – provide nutrients & protection
Describe the pathogenesis of legionella pneumophila?
Invades alveolar macrophages & replicates
What are the clinical features of legionella pneumonia?
- Flu-like illness which may progress to severe pneumonia
- Mental confusion
- Acute renal failure
- GI symptoms
What is the mortality of Legionnaire’s disease?
5-30%
What is the epidemiology of Legionella Pneumophila?
- No person-to-person spread
* Transmitted by inhalation of contaminated water droplets
What are the risk factors for Legionella pneumonia?
- Exposure to contaminated aerosolised water
* Impaired immunity - >55YO, diabetes, smoking, malignancy, altered immunity
What is the treatment of Legionnaires’ disease?
- Antibiotics
- No vaccine available
- Water supply systems should be cooled below 20oC or heated above 60oC
What is walking pneumonia?
Atypical pneumonia - caused by mycoplasma pneumoniae
What is the treatment for mycoplasma pneumonia/walking pneumonia?
Organism has no cell wall so amoxicillin is not the treatment of choice
What are the clinical features of walking pneumonia?
Target lesion (erythema multiformae) - walking pneumonia is most common cause of this rash
What are risk factors for staphylococcus pneumonia?
- Influenza infection
* Haematogeneous spread (normally related to drug use)
Why is staph pneumonia particularly necrotic?
PVL (Panton–Valentine leukocidin) toxin produced by staph aureus
What are the characteristics of a CXR of someone with staphylococcus pneumonia?
Septic emboli caused by staph aureus
What is relative bradycardia?
Increase in heart rate of 10 beats per degree rise in temperature
What diseases in relative bradycardia shown in?
- Mycoplasma pneumoniae
- Legionella pneumonia
- Chlamydia psitacci
What is treatment for mild/mod CAP?
Amoxicillin (5 days)
What is treatment for mild/mod CAP if penicillin allergic?
Doxycycline
What is treatment for severe CAP?
Co-amoxiclav + doxycycline
What is treatment for severe CAP if penicillin allergic?
IV levoflaxin (quinolone)
What is treatment for mild/mod HAP?
Amoxicillin + metronidazole (5 days)
What is treatment for mild/mod HAP if penicillin allergic?
Co-trimoxazole + metronidazole
What is treatment for severe HAP?
Iv amoxicillin + metronidazole + Gentamicin
What is treatment for severe HAP if penicillin allergic?
IV co-trimoxazole + Metronidozole + Gentamicin
What is the microbiology of hospital acquired pneumonia?
- 60% gram negative
What are other causes of pneumonia?
- Parasites (Ascaris, Schisto, Dirofilaria etc)
- Brucella
- Endemic mycoses
- Psittacosis
- tuberculosis
