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CAM201 Microbiology > URTI II & III > Flashcards

URTI II & III Flashcards

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1
Q

Pneumonia clinical history

A

Clinical history should define:

  • The symptoms sonsistent with a doagnosis of pneumonia
  • The setting in which the pneumonia takes place
  • Defects in host defences that could predispose to the development of pneumonia.
  • Possible exposures to specific pathogens.
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2
Q

Pneumonia investigations

A
  • Micriobiology
  • Examination of sputum and other respiratory tract samples (with minimal oropharyngeal contamination)
  • Blood cultures; serology; and urine examination (antigen detection)
  • Radiologic examination
  • CORB and SMART-COP determination
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3
Q

Community acquired pneumonia epidemiology

A

Classically defined as pneumonia occurring in patients who have not been hospitalised or living in health-care facility at least 2 weeks prior to the onset of symptoms.

Difficult to diagnose and treat because caused by:

  • Bacteria
  • Viruses
  • Fungi
  • Protozoa
  • Atypical organisms

Susceptibility increases with increasing age (ie. >50 years of age); patients, usually have underlying disease.

Occurs throughout the year; more cases occurring during the winter months.

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4
Q

Microbiology of CAP

A

Bacteria are the most common cause of CAP:

  • Streptococcus pneumoniae
  • haemophilus influenzae
  • Group A Streptococci (S. pyogenes)
  • Staphylococcus aureus
  • Moraxella catarrhalis
  • Gram negative bacilli (Acinetobacter species; Stenotrophomonas maltophilia)
  • Atypical bacteria *(Mycoplasma pneumoniae; Chlamydophila pneumoniae; Chlamydophila psittaci; Legionella *species).

Examples of viruses associated with CAP

  • Influenza
  • RSV
  • Paraindluenza viruses
  • Adenovirus
  • Human metapneumoniavirus (HMPV)
  • Varicella
  • Severe acute respirtaory syndrome (SARS coronavirus)
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5
Q

Presentation of CAP

A
  • Sudden onset of a chill (true rigors)
  • Fever
  • Pleuritic chest pain
  • COugh with mucopurulent/bloody sputum

Nonrespiratory symptoms

  • Fatigue
  • Anorexia
  • Sweats
  • Nausea

Physical examination fails

  • Tachypnoea (24 to 30 breaths per minute)
  • Tachycardia (>100 beats/min)
  • New chest examination reveals infiltrates/consolidation
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6
Q

Influenza virus

A

Influenza viruses are divided into three distinct antigeic sybtypes (A, B and C) determined by the nucleoprotein (NP) or matrix (M) proteins.

Host ranges

  • Influenza A - human, swine, equine, avian, and marine mammals
  • Influenza B - humans only; and
  • Influenza C - humans and swine

Note: influenza A is further divided based on their antigenic properties of the H and N glycoproteins: so far 15 HAs (H1-15_ and 9 NAs (N1-9) have been described.

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7
Q

Influenza virus naming

A

Virus strains are eventually named according to influenza virus type, place where first isolated, isolate number, year of isolation and major type of important proteins

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8
Q

Influenza virus epidemiology

A

Outbreaks with carying severity usually occur during winter.

Recurret epidemics ever 1-3 years.

Pandemics

  • 2009 swine flu (H1N1)
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9
Q

Antigenic drift

A

Antigenic drift occurs in both influenza A and B in which relatively minor gradual changes in amino acid of heamaglutinin (H) and neuroaminidase (N) resulting in a differen strain of virus. The extent of population immunity determines the new viral variant.

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10
Q

Antigen shift

A

Major and suffen changes in antigens.

  • ‘Looks’ like a new virus.
  • No community immunity
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11
Q

Influenza virus uncomplicated clinical manifestations

A

Uncomplicated (upper respiratory tract infection)

  • Abrupt onset (incubation period of 1 to 2 days) with:
    • Fever
    • Chilld
    • Headaches; myalgia; malaise; anorexia
  • Upper respiratory symptoms: dry cough, severe pharngeal pain, nasal obstruction; and discharge
  • Cinvalescence 1-2 weeks
  • Incidence generally higher in children than adults
  • Fever generally higher among children
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12
Q

Influenza virus complicated clinical manifestations

A

Lower respirtaory tract infection

  • Uncomplicated URTI followed by
    • Progression of fever
    • Productive cough
    • Dyspnoea
    • Cyanosis
  • Rapid progression to pnumonia (more severe if comorbidities)
  • Examination of a CXR may show signs of infiltration/consolidation
  • Often leads to secondary bacterial infection:
    • Streptoccus pnumoniae
    • *Haemophilus influenzae; *or
    • Staphyloccus aureus
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13
Q

Diagnosis of influenza virus

A
  • Based on clinical symptoms and signs (esp. in outbreaks)
  • Viral isolation via nasopharyngeal swab or aspirate rather than throat swab or sputum
  • Rapid antigen kits
  • RT-PCR
  • Serology (IgM, IgG): usually done retrospectively to establish diagosis of influenza infection
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14
Q

Treatment and management of influenza virus

A

If <48 hours, consider oseltamivir, zanamivir (neuraminidase inhibitors)

  • Will decrease symptom duration by 1 day
  • If >48 hours, supportive therapy only

_Only _us abx if secondary bacterial infection.

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15
Q

Influenza virus prevention

A

Annual vaccine available towards types most liekly in that season - not 100%. Usually administered to:

  • All people >65 years
  • Children >6 months
  • Pregnant women
  • Adults if chronic illness:
    • Chronic cardiac conditions
    • Chronic lung disease (ie. COPD)
    • Diabetes
    • Immunodeficient
    • High risk (health care workers, house hold members)
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16
Q

Streptococcus pneumoniae CAP

A

Epidemiology and microbiology

Usually found colonising the nasopharynx

  • 20-40% of healthy children
  • 5-10% of healthy adults
  • Rates of colonisation can increase throughout the year; often higher in midwinter

Pneumococcal disease relatively common in

  • Newborns and infants up to 2 years of age
  • In adults >65 years of age
  • Indigenous population (unclear to what extent genetic and environmental factors are responsible)
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17
Q

Streptococcus pneumoniae microbiology

A
  • Gram positive diplococci
  • Catalase negative (unabel to break down H2O2)
  • Produces pnumolysin (alpha-haemolysin) which breaks down haemoglobin
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18
Q

S. pneumoniae pathogenesis

A
  • Bacteria proliferate ain the alveolar spaces and spread via the alveolar septa.
  • Exudative fluid build up in the septa and alveoli; combined with presence of bacteria defines signs of pneumonia.
  • Diagnosis made on radiography
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19
Q

S. pneumonia clinical and physical findings

A
  • Cough, fatigue, fever (38.8-39.4), chills and swets
    • Older patients might be afebrile, are more likely to have increased respiratory rates.
  • Tachycardia (90-110 bpm)
  • Tachypnoea (>20 bpm)
  • Production of rusty/mucoid sputum
  • Respiatory excursion (splinting) on the affected side because of severe pleuritis pain.
  • Crackles are heart and dullness on perfussion.
  • Chest radiography reveal infiltration and/or consolidation involving one or more segments within a single lobe.
  • Lung abscess (rare)
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20
Q

Laboratory investigations of S. pneumoniae

A

Cultures form sputum/blood

  • Gram positive diplococcus
  • Alpha-haemolytic
  • Susceptible to optochin
  • Urinary antigen detection kit (NOW antigen test) detects teh C polysaccharide cell wall antigen common to all S. pneumoniae strains)
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21
Q

*S. pneumoniae *treatment

A
  • Benzylpenicillin (penicillin G) until significant improvement; then administer amoxycillin.
  • Ceftriazone/cefotaxime (child) or moxifloxacin (adult) might be administered in cases of penicillin hypersensitivity.
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22
Q

S. pneumoniae prevention

A

13 valent pneumococcal conjugate vaccine. Recommended for:

  • 2, 4 and 6 months of age
  • and at 12-18 months for Aboriginal and Torrest Strait Islander children in high risk areas

23 valent vaccination recommended for:

  • Children with underlying medical condition (4 years of age)
  • Indigenous children (15 years and over)
  • Indigenous and >50 years old
  • All people >65 years of age
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23
Q

Haemopholus influenzae epidemiology

A

*H/ influenzae *is recovered exclusively from humans (upper and lower airways)

Nasopharyngeal colonisation in the first year of life is associated with increased risk of recurrent otitis media.

Nontypeable strains frequently colonise the lower airways of people with COPD or CF

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24
Q

Haemophilus influenzae

A

Gram negative, facultative anaerobic bacilli.

Two major types:

  • Encapsulated strains: 6 serotypes (a, c, d, e and f; includes H. influenzae type b)
  • Non-encapsulated strains: which are ‘non-typeable’ can be identified upon sequencing.
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25
Q

Who is most often affected with the different types of *H. influenzae *

A
  • H. Influenzae *type b:
  • typically the patient is between 4 months and 4 years of age

Nontypeable H. influenzae

  • Important cause of pneumonia in adults (ie the elderly) and those with”
    • COPD
    • HIV/AIDS
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26
Q

Clinical features of the pneumonia caused by H. influenzae

A

Insidious onset (over several days) with:

  • Fever
  • Rigors
  • Cough
  • Dyspnoea
  • Purulent sputum; and
  • CXR revealing infiltrates that may show patchy or lobar distribution
27
Q

*H. influenzae *laboratory investigations

A

Gram stain of sputum (small gram-negative bacilli)

Culture: generally requires special nutritional factors be added to chocolate agin:

  • X = hemin (contains iron)
  • V = NAD (nicotinamide-adenine-dinucleotide)

Cultured organisms can be identified further by a positive catalase and oxidase test.

28
Q

Treatment of H. influenzae

A

Treatment regimes might include:

  • Amoxycillin; benzylpenicillin

Second line therapy:

  • Amoxycillin + clavulanate
  • Cefotaxime
  • Ceftriaxone
  • Cefuroxime
  • Doxycycline
29
Q

Health-care Associated Pneumonia definition

A

Pneumonia that occurs after (>48 hours) admission to a hospital; or in a healthcare setting (places like nursing homes; and other long term care facilities).

30
Q

Epidemiology and risk factors for HAP

A
  • Age (usually >70 years of age)
  • Severe underlying disease (COPD, alcoholism, CNS dysfunction)
  • Patients being ventilated; intubated (ie. endotracheal tube)
  • Sedated patients (ie. predisposition to aspiration)
  • Patients on prolonged courses of abx (multidrug resistant organisms)
  • Surgery
31
Q

Diagnosis of HAP

A

Differential diagnosis of pneumonia should be considered when one or more of the following criteria are present:

  • Temperature >38 degrees, or hypothermia
  • Leukocytosis, leukopenia
  • Purulent sputum (or tracheal) secretions, and new or persistent radiographic infiltrate of CXR
  • Oxygen requirement
32
Q

HAP microbiology

A

Can be caused by a wide variety of pathogens; and can be polymicrobial (especially higher rates in acute respirtaory distress syndrome [ARDS] patients)

Gram negative bacilli

  • *Escherichia coli *
  • Klebsiella pneumoniae
  • Seratia marcesens
  • Enterobacter spp
  • Acinetobacter spp
  • Pedumonas aeruginosa

​Gram positive cocci

  • *Staphylococcus aureus *(and MRSA)
  • S. pneumoniae

​Other

  • *Legionella spp *(outbreaks)
33
Q

Klebsiella pneumoniae

A

Can be associated with aspiration pneumonia.

Abrupt onset with:

  • fever
  • rigors
  • Blood stained ‘black currant’ and mucoid sputum
  • Prudces necrosis and cavities in lobes (revealed on CXR)
34
Q

Klebsiella pneumoniae treatment

A

Might include regimes with cefotaxime; ceftriaxone; gentamicin; or piperacillin + tazobactam

Second line therapy: ciprofloxacin or meropenem

35
Q

Pseudomonas aeruginosa

A

Rarely causes CAP and generally affects people with:

  • Immunodeficiencies
  • COPD
  • CF
  • Bronchiecstasis

In the healthcare setting, usually associated with ventilator associated pneumonia (organism has the capacity to form biofilms)

  • Typically produces bilateral pneumonia with:
    • (micro) abscess formation
    • Tissue necrosis
36
Q

*P. aeruginosa *laboratory diagnosis

A
  • Grows well from sputum/lung aspirates/blood cultures
  • Grape like odour (aminoacetophenone)
  • Diffusible pigements (pyocyanin [blue-green])
  • Pyoverdine [yellow-green fluorescent]; pyorubin [red-brown])
  • C390 (phenylacridine hydrochloride) resistant
37
Q

*P. aeruginosa *treatment

A

Gentamicin plus either ceftazidime or meropenem; or

Second line therapy with gentamicin plus with piperacillin + tazobactam or ciprofloxacin

38
Q

*Staphylococcus aureus *pneumonia

A

Ventilator associated (ie often after neurosurgery or head trauma)

39
Q

Clinical manifestations and complications S. aureus

A
  • Fever
  • Rapid onset of productive cough (purulent to blood stained sputum)
  • Neutropenia
  • CXR reveals patchy infiltrates with consolidation of abscesses (necrotising pneumonia)
  • Pleural effusions
  • Empyema
  • **Infections **with MRSA strains are difficult to treat
40
Q

S. aureus laboratory investigations

A
  • Cultures from sputum/blood grow easily in/on most culture media
  • Catalase and coagulase positive
  • Gram stain reveals cocci in clusters
41
Q

*S. aureus *treatment

A

Severe cases: treat for non MRSA and MRSA pneumonia (expert advise may be necessary)

42
Q

Atypical pneumonia

A

Pneumonia caused by ‘atypical bacteria’ which is often classified by the relevant causative agent:

  • Mycoplasmia pneumoniae
  • CHlamydophila pneumoniae
  • Chlamydphila psittaci
  • *Legionella *spp.

It is very difficult to determine disease caused by these agents without lab testing.

Note: patient Hx, age, gender, and underying disease, all predispose to infection with these agents.

43
Q

*Mycoplasma *general characteristics

A
  • Smallest known prokaryotes (genome of about 800,000 base pairs)
  • Most are facultative anaerobes
  • No cell wall
  • Bounded by cell membrane which contains sterols
  • Lack pathways for purine/pyrimidine synthesis
  • Parasite of humans, animal, plants and insects; many species are commensals
  • Adhere to respiratory, urinary, and genital mucosa.
44
Q

*M. pneumoniae *epidemiology/transmission

A

High incidence of M. pneumoniae infection worldwide

Attack rates higher in 5 to 20 year olds (bronchitis and pneumonia); especialy high in 15-19 year olds.

Epidemics occur among confined populations:

  • Schools
  • Families
  • Military bases

Transmission by respirtaory droplets (coughin); spread of disease is slow because bacteria divide slowly (6 hours) and need close contact with ill people.

45
Q

*M. pneumoniae *clinical manifestations

A
  • Pneumonia
  • Extrapulmonary involvement
46
Q

Clinical signs and symptoms of Pneumonia caused by M. pneumoniae

A

Generally mild. After 1-3 weeks incubation, disease has an insidious onset with:

  • Fever
  • Sore throat
  • Malaise, heafache
  • Characteristic ‘hacking’ cough
    • Usually nonproductive, but later on can yield clear or blood-flecked sputum
  • CXR usually shows unilateral lower lobe bronchopneumonia
  • Gastrointestinal symptoms unusual
  • Usually self-limiting illness (symptoms and signs generally resolve over a 1-4 week period)
47
Q

Clinical signs and symptoms of extrapulmonary involvement of M. pneumoniae

A

Skin

  • Erythema multiforme
  • Urticaria

Cardiac

Neurologic (encephalitis)

Joints

  • Polyarthralgia
  • Arthritis
48
Q

*M. pneumoniae *laboratory investigations

A

PCT: gene makers can include (16S rRNA, P1 adhesin)

Serology (may not be early enough to guide therapy)

  • Specific IgM; indicate recent infection; A titre> 1:32 is suggestive of infection. May be absent in early infection (7-10 days)
49
Q

Treatment of M. pneumoniae

A
  • Doxycycline
  • Macrolides (clarithromycin or roxithromycin) are usually preferred for young children.
  • Usual duration of therapy is 7-14 days
50
Q

Chlamydiaceae general characteristics

A
  • Unique class of bacteria; althought classified as gram negative, they lack peptidoglycan.
  • Extremely small genome; 2nd smallest (1-1.2 million base paires)
  • Obligate intracellular bacteria; dependent on host cell for energy (ie. ATP) and are often referred to as ‘energy parasites’
  • Tropism for epithelial cells
51
Q

Chalmydophila pneumoniae epidemiology

A
  • Spread via respiratory secretions
  • Incubation period is 21 days
  • Clinical syndromes
    • Asymptomatic infection
    • Severe sore throat with hoarseness
    • Pneumonia (frequently among the elderly)
      • Resembles that associated with M. pneumoniae
  • ​Infection also is often associated with:
    • Acute bronchitis
    • Otitis media
    • Sinusitis
    • Pharyngitis
52
Q

*C. pneumoniae *laboratory investigations

A
  • Nasopharyngeal or oropharyngeal specimen
  • Bronchoalveolar lavage or sputum specimen
  • PCR for *ompA, *16S rRNA genes
  • Serology.
    • Diagnostic criteria:
      • IgM titre >1:15
      • IgG titre of 1:512 or higher; or four-fold rise following acute infection (so need acute and convalescent sera)
53
Q

*C. pneumoniae *treatment

A
  • Doxycycline
  • Macrolides - crithromycin, erythromycin, roxithromycin
  • Duration of treatment: 7-14 days
54
Q

Chlamydophila psittaci epidemiology

A

Common in birds and domestic animals.

Occupations at risk

  • Pet shop employees
  • Poultry farmers
  • Abattoir workers
  • Veterinarians
55
Q

C. psittaci clinical manifestations

A

Range from mild to severe

  • Abrupt or slowly evolving
  • Fever (>38)
  • Headache
  • Arthralgia
  • Painful myalgia (esp. head and neck)
  • Severe cough (dry and hacking; sometimes mucoid sputum)
56
Q

*C. psittaci *laboratory diagnosis

A

Serology.

  • Diagnostic criteria
    • IgM titre >1:16
    • IgG titre> 1:64; or four-fold rise following acute infection (so need acute and convalescent sera)

PCR (ie for inclusion membrane protein, IncA)

57
Q

*C. psittaci *treatment

A

Similar regime as for C. pneumoniae

58
Q

*Legionella spp *general characteristics

A

Gram negative, obligate aerobe bacilli

Fastidious nutritional requirements

  • *L. pneumophila *(16 serogroups): 85% of infections
  • L. longbeachae
  • L. micdadei
  • L. bozemanii
59
Q

*Legionella spp *epidemiology

A

Environmental organisms

Found in varierty of habitats

  • Lakes, streams, oceans
  • Cooling towers
  • Humidifiers
  • Showers, hot tubs
  • Occassionally drinking water

Incubation period for most outbreaks 2-10 days

Absence of evidence for person-to-person transmission.

60
Q

*Legionella spp *host risk factors

A
  • Gener (males often more susceptible)
  • Elderly (>50 years old)
  • Immunocompromised
  • Underlying co-morbodities (cardiac, respiratory, renal diseases)
  • Smokers
61
Q

*Legionella spp *clinical presentation

A

Legionaire’s disease

  • Fever
  • Confusion
  • Myalgia
  • Headache
  • Diarrhoea
  • Cough (sometimes with purulent sputum(
  • Chest examination reveals focal crackles and alveolar infiltrates (patchy areas of consolidation)

Pontiac fever

  • Self-limited short-duration
  • Fever, myalgia, headache, and asthenia (loss of strength) without clinical evidence of pneumonia.
62
Q

*Legionella spp *laboratory investigations

A
  • Clinical suspicion on basis of severe penumonia + other clinical features
  • Appropriate respirtaory speciments
    • Expectorated sputum
    • Endotracheal aspirate
    • Bronchoscopy and bronchoalveolar lavage
  • Lung biopsy
  • Gram staining is usually very poor (use basic fuschin stain)
  • Culture; need specific media (CYE plates)
    • Must inform lab (special request)
  • Urine antigen testing
    • Highly specific
    • *L. pneumophila *serogroup 1 (common to most parts of Australia)
  • Serology
    • Paired acute and convalescent sera (four-fold rise in antibody titre)
    • PCR
63
Q

Legionella spp treatment

A

Mld-moderate infection

  • Doxycycline or azithromycin

Severe infection

  • Azithromycin, plus either ciprofloxacin or rifampicin

CAM201 Microbiology (7 decks)

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