Respiratory system infections

Microbiology Lecture 1 RS Module

Ashraf KhasawnehFaculty of Medicine

The Hashemite University

THE RESPIRATORY SYSTEM

• A major portal of entry for infectious organisms

• It is divided into three tracts – upper , middle and lower.– The division is based on structures and functions in each part.

• The three parts have different types of infection.

• The upper respiratory tract:– Mouth, nasal cavity, sinuses and pharynx

– Infections are fairly common.

– Usually nothing more than an irritation

• The middle respiratory tract:– Epiglottis, larynx, trachea, bronchi and bronchioles

– 80-90% of infections are viral

• The lower respiratory tract:– Lungs and alveoli

– Infections are more dangerous.

– Can be very difficult to treat

ANATOMY OF THE RESPIRATORY SYSTEM

• The most accessible system in the body:– Breathing brings in clouds of potentially

infectious pathogens.

• The body has a variety of host defense

mechanisms:– Innate immune response

– Adaptive immune response

• Upper respiratory tract is continuously

exposed to potential pathogens.

• Lower respiratory tract is essentially a

sterile environment.

NORMAL FLORA OF THE RESPIRATORY TRACT

• Generally limited to the upper respiratory tract

• Gram-positive bacteria (streptococci and staphylococci)

very common

• Disease-causing bacteria are present as normal flora; can

cause disease if their host becomes immunocompromised

or if they are transferred to other hosts (Streptococcus

pyogenes, Haemophilus influenza, Streptococcus

pneumonia, Neisseria meningitides, Staphylococcus

aureus)

PATHOGENS OF THE RESPIRATORY SYSTEM

• Many bacterial organisms infect the

respiratory system.

• Upper respiratory tract also portal of entry for

viral pathogens.

• Vaccination has eliminated many respiratory

infections.– Some still seen in underdeveloped parts of the

world.

PATHOGENS OF THE RESPIRATORY

SYSTEM

• Respiratory pathogens are easily transmitted from human to human.

– They circulate within a community.

– Infections spread easily.

• Some respiratory pathogens exist as part of the normal flora.

• Others are acquired from animal sources –zoonotic infections.

– Q fever from farm animals

– Psittacosis from parrots and other birds

PATHOGENS OF THE RESPIRATORY SYSTEM

• Water can be a source of respiratory infections.– Legionellosis– Contaminated water can be aerosolized.– Droplets can be inhaled, and infection can result.

• Fungi are also a source of respiratory infection.– Usually in immunocompromised patients– Most dangerous are Aspergillus and Pneumocystis.

• Some pathogens are restricted to certain sites.– Legionella only infects the lung.

• Other pathogens cause infection in multiple sites.– Streptococcus can cause:

• Middle ear infections.• Sinusitis.• Pneumonia.

DEFENSES OF THE RESPIRATORY SYSTEM

• The respiratory system has significant

defenses.

• The upper respiratory tract has:– Mucociliary escalator.

– Coughing.

• The lower respiratory tract has:– Alveolar macrophages.

DEFENSES OF THE RESPIRATORY SYSTEM

BACTERIA INFECTING THE RESPIRATORY

SYSTEM

• Can be divided into groups depending on the

infections they cause– Otitis media, sinusitis, and mastoiditis

– Pharyngitis

– Typical and atypical community-acquired

pneumonia

– Hospital-acquired (nosocomial) pneumonia

Upper Respiratory Tract Diseases Caused by

Microorganisms

• Rhinitis, or the Common Cold

– Symptoms: sneezing, scratchy throat, runny nose

(rhinorrhea)

– Symptoms begin 2-3 days after infection

– Usually not accompanied by fever

– Net result: nasal obstruction, nasal discharge

– Causative agents: Rhinovirus, Adenovirus, Coronavirus,

Parainfluenza virus, Influenza virus, RSV

– Rarely caused by bacteria or Fungi

Pharyngitis

• Inflammation of the throat

• Pain and swelling, reddened mucosa, swollen tonsils,

sometime white packets of inflammatory products

(exudate), petechial hemorrhages

• Mucous membranes may swell, affecting speech and

swallowing

• Often results in foul-smelling breath

• Incubation period: 2-5 days

• DDx of follicular tonsillitis: Strep. Pyogens,

Adenoviral infection, Candida albicans.

http://www.google.jo/url?sa=i&rct=j&q=tonsillitis&source=images&cd=&cad=rja&docid=FrC_altsr6hcHM&tbnid=Nan5tw1oG2fbEM:&ved=0CAUQjRw&url=http://www.tabletsmanual.com/wiki/read/angina&ei=PrIPUbOmAuao0AW0sIGYCg&bvm=bv.41867550,d.ZG4&psig=AFQjCNEIgDp8I_c37Xufbj74FFTbHXOmew&ust=1360068858114437

Sinusitis• Commonly called a sinus infection

• Most commonly caused by

• Local: URTI produce edema of antral tissues, nasal septum deviation, enlarged adenoids, tumor or foreign body in the nasal cavity

• Systemic: Allergy, cystic fibrosis and immunodeficiency.

• Symptoms: nasal congestion, pressure above the nose or in the forehead, feeling of headache or toothache

• Facial swelling and tenderness common, +/- fever

• Discharge appears opaque with a green or yellow color in case of bacterial infection

• Discharge caused by allergy is clear and may be accompanied by itchy, watery eyes

• Causative microorganisms: Strep. Pneumonia, H. Influenza. Less common Strep. Pyogens, Staph. Aureus and M. catarrhalis

Dx: Gram stain and culture of direct sinus aspirate

Rx:

•Acute: Empirical Antibiotic

•Chronic or complicated: obtain cultures and determine

antibiotic sensitivity

Otitis Externa

• Predisposing factors: local trauma, furunculosis, foreign body and

excessive moisture (swimmer’s ear).

• Symptoms: Pain and redness (cellulitis)

• Malignant otitis externa: P aeruginosa

• Most commonly caused by P aeruginosa

• Dx: Clinical examination.

• Rx: Topical agents containing antibiotics.

Acute Otitis Media (Ear Infection)

• Also a common sequel of rhinitis

• Viral infections of the upper respiratory tract lead to inflammation of the

Eustachian tubes and buildup of fluid in the middle ear- can lead to

bacterial multiplication in the fluids

• Bacteria can migrate along the eustachian tube from the upper respiratory

tract, multiply rapidly, leads to pus production and continued fluid secretion

(effusion)

• Chronic otitis media: when fluid remains in the middle ear for indefinite

periods of time (may be caused by biofilm bacteria)

• Symptoms: Fever, sensation of fullness or pain in the ear

• Untreated or severe infections can lead to eardrum rupture or mastoiditis

and CNS involvement.

• Causative microorganisms:

– < 3 months: S pneumonia, group B strep., S aureus, P aeruginosa

– > 3 Months: S pneumonia, H influenza. Less common Strep. Pyogens, Staph.

Aureus and M. catarrhalis

Diphtheria

• Symptoms initially experienced in the upper

respiratory tract

• Sore throat, lack of appetite, low-grade fever

• Pseudomembrane forms on the tonsils or pharynx

• DDx of pseudomembrane:

– Diphtheria

– Vincent’s angina: Oral lesion caused by fusospirochetal

infection (anaerobes)

– EBV: Infectious mononucleosis

Middle respiratory tract infections

• The middle respiratory tract infections include:

• Acute Epiglotitis

• Laryngitis and croup

• Tracheitis

• Bronchitis and Bronchiolitis

Acute Epiglottitis• Abrupt onset of throat and neck pain, fever and inspiratory

stridor, muffled phonation or aphonia and difficult swallowing,

drooling.

• Caused mostly by bacteria (90%). H influenza type b (85%)

and S pneumonia. Less common C diphtheriae and N

meningitidis.

• Medical emergency: Do not use tongue depressor or attempt

throat swab.

• Dx: Blood culture

X-ray: thumb sign

• Rx: adequate airway, humidified air and oxygen.

Specific antimicrobial therapy.

Laryngitis and croup

• Sudden onset or slow onset.

• Fever and inspiratory stridor, hoarse phonation and harsh

barking cough. Croup associated with chest pain and sputum

production.

• Caused mostly by viruses (90%). Parainfluenza, influenza,

adenovirus. Less common RSV, rhinovirus and coronavirus.

• Acute bacterial tracheitis (purulent process).

• Dx: Bacterial cause; Gram stain and culture of secretions

obtained by direct laryngoscopy. Blood culture.

• Rx: adequate airway, humidified air and oxygen.

Specific antimicrobic therapy (bacterial only).

bronchitis and bronchiolitis• Spread from URTI.

• Fever, cough and sputum production clear at the beginning then turns

purulent.

• Predisposing factors to Chronic bronchitis: smoking, environmental

pollutants, chronic infection (TB), defective clearance of secretions and

bacteria (cystic fibrosis).

• Acute bronchitis: persistent dry cough, rapid or noisy breathing (wheezing)

brief pauses in breathing, feeding less and having fewer wet nappies

vomiting after feeding, being irritable

• caused mostly by viruses (80%). Parainfluenza, influenza, adenovirus and

RSV. Bacteria: B pertussis, H influenza, Mycoplasma and Chlamydia

pneumonia.

• Chronic bronchitis caused by S pneumonia and nontypable H influenza.

• Dx: Nasopharyngeal specimens are used in direct fluorescent antibody and

PCR assays. Gram stain and culture and sensitivity when purulent sputum

produced. Serodiagnosis in the case of Mycoplasma and Chlamydia

pneumonia.

• Rx: humidified air and oxygen. Specific antimicrobic therapy (bacterial

only).

Diseases Caused by Microorganisms Affecting the

Upper and Lower Respiratory Tract

• A number of infectious agents affect both the upper

and lower respiratory tract regions

• Most well-known: whopping cough, respiratory

syncytial virus (RSV), and influenza

Pneumonia

• Anatomical diagnosis

• Inflammatory condition of the lung in which fluid fills the alveoli

• Can be caused by a wide variety of different microorganisms

• Viral pneumonias are usually milder than bacterial

• Community-acquired vs. nosocomial pneumonias

• Begin with upper respiratory tract symptoms, including runny nose and congestion

• Headache common

• Fever is often present

• Onset of lung symptoms follows: chest pain, fever, cough, discolored sputum

Pneumonia

• 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

Clinical Presentation

• Cough (productive vs. non-productive)

• Fever

• Dyspnoea

• Fatigue

• Headache

• Nausea, vomiting, diarrhoea

• Myalgia

Predisposing factors

• Age

• COPD

• Diabetes

• Heart failure

• Immunocompromised status

• Alcoholism

• Smoking

• Travel/occupational/recreational exposure

Physical signs

• Tachycardia

• Tachypnoea

• Hypotension

• Crepitation

• Bronchial breathing

• Fever

Investigation

• Chest X-ray

• CBC

• CRP

• U&E’s

• ABG’s

• Sputum culture

• Blood culture (+ve in 1-16% of pt’s requiring admission)

• Serology/PCR/antigen

S pneumoniae

C pneumoniae*

Viral

M pneumoniae

Legionella spp

H influenzae

G- Enterobacteria

C psittaci

Coxiella burnetii

S aureus

M catarrhalis

Other

PNEUMONIA AETIOLOGY

0 5 10 15 20 25 30Percentage of Cases

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. pneumoniae rare

Pathogens

• S. pneumoniae

• Gram +ve diplococci

• Almost all S to penicillins, cephalosporins (R more common is southern Europe and S. Africa)

• Most S to erythromycin

• H. influenzae

• G –ve cocco-bacilli

• S to amoxycillin

• 25% produce B-lactamase, thus Amoxy R.

• S to Co-Amoxyclav, ceph’s, Ciprofloxacin

• R Eryth

Pathogens

• S. aureus

• Seen classically after flu

• Severe necrotising pneumonia in young adults

seen in PVL (toxin) producing strains-

emerging pathogen

• Rx flucloxacillin, eryth.

• Vancomycin, linezolid for MRSA

Atypical pneumonia

• Caused by organisms that will not grow under routine 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)

Aspiration pneumonia

• Occurs in patients with abnormal gag reflex (altered

consciousness, CVA…)

• Combination of chemical (acid) injury, bronchial

obstruction and bacterial infection.

• Bacteria involved will reflect oropharyngeal flora-

anaerobes and Streps & haemophilus (community) or

gram neg’s (nosocomial)

• Rx often broad spectrum B-lactam e.s. co-amoxyclav

or pipperacillin/tazobactam +/- metronidazole

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

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

Resources

• https://www.youtube.com/watch?v=GoRhRJXp0j8&t=6s

• https://www.youtube.com/watch?v=IAQp2Zuqevc

• https://www.youtube.com/watch?v=dzJNabJAPaE&t=13s

• https://www.youtube.com/watch?v=eup3_i_5uaw