Respiratory Tract Infections

Associate Professor Raymond Lin

Head, Clinical Microbiology

BLT18/2008

The upper and lower respiratory tract is a continuum, along with organisms may track

Defence mechanisms Anatomical e.g. cilia Surface defences at epithelium:

lysozymes, IgA, phagocytes Colonization resistance

Types of pathogens Infect healthy persons Infect those with poor defence

“opportunistic” Use respiratory route to spread to rest of

body

Normal oropharyngeal flora viridans streptococci, Neisseria spp.,

Moraxella catarrhalis, diphtheroids, anaerobes

S. pneumoniae, Haemophilus influenzae, Haemophilus spp.

“colonization resistance” Flora gets replaced with disease, antibiotics,

devices, hospital stay May track to lower respiratory tract

“aspiration”

Pathogens Common respiratory viruses “URTI”

Rhinovirus, influenza, parainfluenza, adenovirus, respiratory syncytial virus (RSV)

Enterovirus, hu coronaviruses, hu metapneumovirus

Pharyngitis (“sore throat”) Group A

streptococcus (S. pyogenes)

Viruses

Upper respiratory cavity infections

Acute bacterial sinusitis Acute suppurative otitis media Common bacteria

Streptococcus pneumoniae Haemophilus influenzae Moraxella catarrhalis

Eustachian tube in infants – wider & horizontal

Otitis externa External ear infected

Pseudomonas aeruginosa Aspergillus niger

Otitis externa

sinusitis

“CROUP”laryngo-tracheo-bronchitis

hoarse voice, barking cough severe cases - airway obstruction

Laryngitis

Parainfluenza viruses

Bronchitis

Bronchiolitis

Bronchiectasis

Pleural effusionEmpyemaPneumothorax

Pneumonia Pathogen varies with age, underlying disease Hospital vs. community-acquired Hospital

Immunocompromised ICU - ventilator Antibiotics Multi-resistant bacteria

MRSA, Acinetobacter baumannii

Pneumonia - pathogens Streptococcus pneumoniae

(“pneumococcus”) Haemophilus influenzae Mycoplasma pneumoniae Chlamydia pneumoniae Viruses: adenovirus, influenza

Viruses more important in children.

Pneumonia Environment

E.g. legionella E.g. melioidosis

Cooling tower - a possible source of Legionella infection

Pets, animals e.g. Q fever Psittacosis hantavirus pulmonary syndrome “zoonosis”

Pneumonia – immunocompromised patients

Examples: transplant patients, neutropenic, ICU Unusual organisms not affecting normal

adults E.g. Pneumocystis jiroveci (P. carinii),

cytomegalovirus, aspergillus

Hospital pathogens

Laboratory approaches Sputum culture and gram stain Respiratory virus culture/ IF/ PCR Blood culture Serology

E.g. mycoplasma, legionella

Investigations Sputum culture

Easy to collect and do May be contaminated with oropharyngeal

flora – check epithelial cells on Gram stain Some bacteria are non-cultivable

Investigations Blood culture

More definite proof of causative organism Not sensitive Some bacteria don’t grow in usual media e.g.

Mycoplasma pneumoniae Serology

Host response; good if specific enough Delayed result; cross-reactivity; background

positives E.g. legionella, mycoplasma

Investigations Viruses

Antigen detection e.g. IF – rapid Virus isolation – slow – can find new

viruses PCR – many agents to look for Serology – not usually useful – need paired

titre

Sputum specimen composed of saliva and purulent material

Organisms that can be missed in a sputumOrganisms that can be missed in a sputum

BALBAL- - Legionella Legionella

- - Pneumocystis jiroveciPneumocystis jiroveci

Respiratory Tract SpecimensRespiratory Tract Specimens

Mycobacteria

TB bacillusMycobacterium tuberculosis

Non-TB bacillimany speciesM leprae, M avium, M kansasi etc

TB bacillusMycobacterium tuberculosis

Acid fast bacilli (AFB)when stained with ZN technique

Normal habitatinfected humansinfected cattle

Pathogenicityabout 10 million people affected3 million deaths

Spreaddroplets > lungs > lymph / blood > kidney, bone, joints

Mycobacterium tuberculosis Primary infection Latent infection – no symptoms Dormancy – remains in lymph nodes for

many years Reactivation disease – when elderly or

immunocompromised

Tuberculosis - diagnosis Clinical symptoms: cough, night sweats,

loss of weight CXR Lab tests

Tests for tuberculosis Sputum or BAL or gastric aspirate

Acid-fast smear (“AFB” smear) Molecular detection e.g. MTD, PCR Culture e.g. L-J media, broth (MGIT, BacTAlert)

Immunity or exposure Mantoux test Interferon gamma tests

Quantiferon TBSpot (ELISPOT)

Bordetella pertussis (“whooping cough”)

Affects mainly children, milder symptoms in adults

Vaccine preventable (part of childhood DPT immunization)

Clinical features: coughing fits and vomiting, inspiratory “whoop”, pneumonia

Occasional cases in children; epidemics when immunization low

pertussis Laboratory workup

Direct IF Culture : Bordet-Gengou media PCR : most sensitive test now Serology : IgA, IgM – not so reliable – not

used in Singapore

Summary Be able to

List the main pathogens for each site e.g. pneumonia, sinusitis, otitis media, URTI

Outline the diagnostic approaches with examples; limitations of each

TB: know some basic concepts