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4.1 Medical Microbiology > Lower Respiratory Tract Infections > Flashcards

Lower Respiratory Tract Infections Flashcards

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1
Q

What are the two types of lower respiratory tract infections?

A

Acute
Chronic

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2
Q

What three structures are involved in the lower respiratory tract

A

Trachea/windpipe
Bronchial tubes
Alveoli/lungs

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3
Q

What are the four acute infections of the lower respiratory tract?

A

Bronchitis
Bronchiolitis
Pneumonia
Influenzae and Covid

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4
Q

What are the five chronic infections of the lower respiratory tract?

A

TB
Aspergilosis
Lung abscess
Pleural effusion
Empyema

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5
Q

What infection of the lower respiratory tract can be classed as both acute and chronic????

A

Cystic fibrosis

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6
Q

What are the 4 different types of pneumonia?

A

Community acquired
Nosocmial
Atypical
Viral

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7
Q

What is the most common cause of bronchiolitis

A

RSV

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8
Q

Where is atypical pneumoniae seen?

A

Seen more in community than hospital

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9
Q

What has changed about diagnostics of viral pneumonia in the lab over the years?

A

Viral work up/investigation is becoing more and more common -> used to just send everything to the NVRL

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10
Q

Give a short description of how a healthy host respiratory tract prevents infection
(3)

A

Ciliated respitatory epithelium moves mucous layer upwards towards the mouth

The epiglottis and the cough reflex helps prevent particulate matter from entering the lower airwars

In alveoli, macrophages, humoral facts (iG and complement), and neutrophils work together to prevent or clear infections

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11
Q

Classify host responses in the RT that prevent infection

A

Mechanical defenses

Immune response

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12
Q

Classify host responses in the RT that prevent infection

A

Mechanical defenses

Immune response

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13
Q

What three mechanical defenses does the RT have to prevent infection?

A

Ciliary function
Cough reflex
Pulmonary Secretions

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14
Q

What is the ciliary function of the RT?

A

Mucocilliary transport system removes particles from the RT

Very small particles between 0.2 and 2um i.e. most bacteria and viruses can evade these defenses and reach the alveoli

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15
Q

What role does the cough reflex have in defense?

A

Helps expel foregin particles and pathogens

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16
Q

What role do pulmonary secretions have in defense in the RT

A

Mucous
Lysozyme
Lactoferrin
Components of the alveolar lining such as surfactant, phospholipids, IgA and IgG

All of these play a role in activating alveolar macrophages

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17
Q

What are the immune components of the alveolar lining?

A

surfactant, phospholipids, IgA and IgG

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18
Q

What are the three main immune responses of the RT?

A

Polymorphonuclear Neutrophils and Alveolar Macrophages -> phagocytosis

Cell-Mediated Immunity -> T lymphocytes identify and eliminate infected cells

Humoral immunity -> IgG and IgA antibodies + complement proteins neutralise and remove pathogens

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19
Q

What factors interfer with normal host defense mechanisms?
(7)

A

Impaired Mucociliary Clearance

Compromised Immune System

Physical Barriers and Reflexes

Hospital-Related Factors

Environmental and Lifestyle Factors

Age-Related Factors

Nutrition and General Health

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20
Q

In what two ways can mucociliary clearance be impaired?

A

Ciliary dysfunction
Excessive mucous production

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21
Q

What physical barriers and reflexes can interfere with host defense mechanism?

A

Reduced cough reflex e.g. post surgery or stroke
Anatomical abnormalities e.g. structural lung disorders

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22
Q

What hospital-related factors interfere with normal host defense mechanisms?

A

Mechanical ventilation -> HUGE Interference -> frequently causes pneumonia

Prolonged hospitalisation this greatly increases risk of picking up MDR organisms

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23
Q

How can environment and lifestyle affect host defense mechanisms?

A

Smoking

Air pollution and occupational exposure e.g. working in power/nuclear plants or mines, building sites, etc etc

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24
Q

How can environment and lifestyle affect host defense mechanisms?

A

Smoking

Air pollution and occupational exposure e.g. working in power/nuclear plants or mines, building sites, etc etc

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25
Q

How can age affect defense mechanisms

A

Infants and young children -> compromimsed immune systems

Elderly -> might loose ability to cough etc

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26
Q

How can nutrition and general health affect defense mechanisms

A

Malnutrition -> seen in under 5s in developing countries

Chronic alcoholism

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27
Q

What is bronchitis?
(7)

A

Inflammation of the mucous membrane lining the bronchial tubes

Infection does not involve the alveoli

Chest X ray appears normal

Affects all ages but most common in young and elderly

Usually a self limiting infection which occurs during winter months (seen year round since covid)

Last about 10 days (cough can remain for 5 weeks)

Often follows an URTI that extends to bronchial tree

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28
Q

What are some predisposing factors for bronchitis?
(7)

A

Allergy
Asthma
Poor nutrition
Smoking
COPD
Air pollution
Exposure to cold and damp weather

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29
Q

What is the aetiology of bronchitis?
(3)

A

80-90% are caused by viruses

Can be due to bacterial infection which arises as a complication of a viral infection

Often resolves on its own but can progress to pneumonia in some cases

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30
Q

What viruses cause bronchitis?

A

Rhinovirus
Coronavirus
Influenza virus
Adenovirus

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31
Q

What viruses cause bronchitis?

A

Rhinovirus
Coronavirus
Influenza virus
Adenovirus

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32
Q

What bacteria can cause bronchitis?
(4)

A

Strep pneumoniae
Non-typable Haemophilus influenzae

Rare:
- Mycoplasma pneumoniae
- Chlamydophila pneumoniae

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33
Q

What is pneumoniae?
(4)

A

An infection characterised by the inflammation of one or both lungs

Alveolar sacs become filled with exudate, inflammatory cells and fibrin

Often occurs as a secondary infection following a primary viral URTI

Significant cause of mortality and momrbidity

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34
Q

What is pneumoniae?
(4)

A

An infection characterised by the inflammation of one or both lungs

Alveolar sacs become filled with exudate, inflammatory cells and fibrin

Often occurs as a secondary infection following a primary viral URTI

Significant cause of mortality and momrbidity

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35
Q

Write a note on the mortality of pneumonia - in the world

A

Most common cause of infection-related death

9th leading cause of death in the world

Leading cause of death in children

18% of all deaths are in children <5 in developing world

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36
Q

Write a note on the mortality of pneumonia in Ireland, based on a point prevalent study

A

Mortality associated with HAI particularly ICU -> VAP

29.3% of total infections are pneumonia (ICU)

Most common cause of HAI in 2017 -> 28.9%

Treatment represents 50% of all antimicrobial usage

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37
Q

Comment on mobidity of pneumonia

A

Majpr cause of morbifity -> 10% of all hospital admissions

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38
Q

What is the clinical presentation of pneumonia?
(8)

A

Fever
Productive cough
Acute chest pain
Shortness of breath
Purulent sputum
Rigors
Abnormal chest sounds -> cracking sound
characteristic infiltrates on xray

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39
Q

What is CAP?

A

Community acquired pneumoniae

Acquired outside a healthcare setting

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40
Q

What is HAP?

A

Hospital acquired pneumonia

Acquired during hospital stay, 48 hours or more after admission

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41
Q

What is VAP?

A

Ventilator-associated pneumonia

Occurs in patients on mechanical ventilation e.g. in ICU -> often see rapid decline in health

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42
Q

What is VAP?

A

Ventilator-associated pneumonia

Occurs in patients on mechanical ventilation e.g. in ICU -> often see rapid decline in health

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43
Q

What is aspiration pneumoniae?

A

Pneumonia resulting from inhaling food, liquid or vomit into the lungs

Breakdown of mechanicals in the trachea -> drowning patients or drunks vomiting or stroke patients -> really foul smelling cough associated with anaeobes

44
Q

What organisms most commonly cause CAP?
(3)

A

S. pnuemoniae
H. influenzae
Mycoplasma pneumoniae

45
Q

What organisms most commonly cause CAP?
(3)

A

S. pnuemoniae
H. influenzae
Mycoplasma pneumoniae

46
Q

What three organisms most commonly cause HAP?

A

Psuedomonas aeruginosa
Staphylococcus aureus
Enterobacter species

-> HAP is more resistant so think of your resistant bacteria

47
Q

What three organisms most commonly cause VAP?

A

Acinetobacter baumanni
Klebsiella pneumoniae
Stenotrophomonas maltophilia

(again think of resistance)

48
Q

Comment on resistance in VAP

A

Resistance seen in Klebsiella pneumoniae, acinetobacter and stenotrophomonas not of major concern as of right now but they will be a major issue in 5 years time

49
Q

What organisms are most commonly seen in Aspiration pneumonia?

A

Anaerobes
Mixed flora from mouth and throat etc

50
Q

What are the 6 different types of pneumoniae?

A

CAP
HAP
VAP
Aspiration pneumonia
Atypical pneumoniae
HCAP

51
Q

What are the 6 different types of pneumoniae?

A

CAP
HAP
VAP
Aspiration pneumonia
Atypical pneumoniae
HCAP

52
Q

What is atypical pneumonia?

A

Pneumonia caused by atypical pathogens often with milder symptoms

53
Q

Give three examples of organisms that cause atypical pneumonia

A

Mycoplasma pneumonia
Chlamydophila pneumoniae
Legionella pneumophila

54
Q

What is HCAP?

A

Health Care Associated Pneumoniae

Occurs in patients with recent contact with healthcare settings

similar organisms to HAP

55
Q

What are some of the challenges of lab investigation of typical bacterial pneumonia?

A

Wide range of microbial agents involved

Sputum is a non-invasive sample and can be used for both bacterial and fungal investigation but commonly contaminated with normal flora in URT

Poor sensitivity and specificity of sputum culture especially for VAP

Challenging to identify microbial cause in clinically relevant time period-appropriate antimicrobial treatment

56
Q

What are some sample types provided on VAP patients?

A

BALs
Bronchial aspirates
Bronchial washings
Transtracheal aspirates

57
Q

Suggest an alternative to sputum for pneumonia investigation, give pros and cons

A

Invasive sampling such as BALS -> reduced contamination but difficult and dangerous to take

Not tolerated by patients near as well as a sputum sample

58
Q

When should you query a fungal pneumonia?

A

HIV
CF
ICU
Immunocompromised

59
Q

How should sputum samples be collected for pneumonia investigation?
(5)

A

Samples should be fresh

Taken before antimicrobial treatment

Early morning especially if query TB

Deep cough expectorate -> want purulent mucous not salivary -> physio can be brought up if patient has dry cough or if old and frail etc -> an aerosol can also be inhaled to induce expectorate

Cough swab on children -> cough reflex -> not ideal

60
Q

How should sputum be stored?

A

Specimens must be transported and processed within the working day on arrival into the laboratory

Sputum must be refrigerated for up to 2-3h without an appreciable loss of pathogens

If specimens are not processed on the same day as they are collected interpretation of results should be made with care

61
Q

Why cant we process samples beyond 48hour?

A

This allows overgrowth of gram-negative bacilli
Haemophilus and S.pneumoniae may die

62
Q

Why cant we process samples beyond 48hour?

A

This allows overgrowth of gram-negative bacilli
Haemophilus and S.pneumoniae may die

63
Q

What is the first step in sputum processing?

A

Describe the appearance

The quality of specimen is described on the basis of macroscopic appeance

64
Q

How is sputa graded based on appearance?

A

Bloodstained
Purulent, mucopurulent (P1, P2, P3)
Pure mucoid (M1), Mucosalivary (M2), Salivary

65
Q

What sputa samples are generally rejected?

A

M1, M2 or saliva specimens

66
Q

What sputa samples are generally rejected?

A

M1, M2 or saliva specimens

67
Q

Under what conditions are mucosalivary or salivary sputa samples accepted?
(6)

A

Immunocompromised
Intubated patients
Query legionella
Query Mycobacerium
Cancer wards
ICU

68
Q

Give a quick run-through on the processinf of sputa

A

Sputa must be handled in a class I safety cabinet
Describe appearance
Sputasol + homogenise
Inncubate at 37 degrees for 15 mins with gentle agitation -> usually left for longer while and not agitated as no labs have these

69
Q

Why do we sputasol and vortex our sputa samples?

A

Makes them easier to handle
Distributes organisms -> if irregularly distributed this can lead to inaccurate results
Liquefaction and thorough mixing of sputum allows unifrom sampling

70
Q

What two methods of culture are used for sputa investigation?

A

Direct: qualitative
Dilution: quantitative

71
Q

What is the principle behind use of a dilution plate?

A

Dilution and quantification help to differentiate true infection from colonisation

Pathogen should be present in greater numbers than commensals therefore pathogen should still grow on dilution but commensal should be diluted out

72
Q

Under what circumstances do we not use dilution plates for sputa and why?

A

Not done for ICU or chemo patients

Anything that grows in these is significant as they are immunocompromised

73
Q

How do you put up a direct and dilution culture?

A

Direct:Using a 10ul sterile loop inoculate blood and choc with homogenised sputum

Dilution: Using 10ul sterile loop inoculate 10ul of homogenised sputum into 5ml sterile H2O (10^-3 dilution), then inoculate a 10ul loopful of diluted specimen onto a choc plate

74
Q

What does 1 colony represent on a dilution plate?

A

1 colony = 10^5 CF/ml

75
Q

Talk about the use of microscopy on sputa

A

Hospital specific -> not many hospitals still do grams for sputa

Allows us to determine quality of sample

Gives us a quick idea of what is in the sample

76
Q

How are blood plates put up for sputa?

A

Blood agar with optochin for strep
incubated in CO2 for haemophilus

77
Q

What additional plates are put up for immunocompromised, HIV, oncology etc patients?

A

Direct chocolate (not dilute)
MacConkey - for ents and pseudo
Malt Extract Agar for fungi

78
Q

What additional plates are put up for immunocompromised, HIV, oncology etc patients?

A

Direct chocolate (not dilute)
MacConkey - for ents and pseudo
Malt Extract Agar for fungi

79
Q

What additional plates are put up for CF patients

A

Burkholderia plates
Pseudocel agar
SAID for S. aureus
etc
etc

80
Q

What plates are put up for query fungal infection?

A

Malt Extract Agar

81
Q

What is a BAL?

A

A bronchoalveolar lavage

Segment of lung washed with sterile fluid after insertion of bronchoscope and fluid is aspirated out for investigation

82
Q

What are the main benefits of BALS?

A

Use on ventilated patients
Improved yield of funi especially Aspergillus species
Particularly useful in diagnosis of P. jirovecii and atypical pneumonia caused by L. pneumophila
Mycobacteria

83
Q

What is a bronchial aspirate?

A

Involves direct aspiration of material from the large airways of the respiratory tract using a flexible bronchoscope

84
Q

What is a bronchial aspirate?

A

Involves direct aspiration of material from the large airways of the respiratory tract using a flexible bronchoscope

85
Q

What is a bronchial brushing

A

Use of a protected brush catheter in the bronchoscope to tease material from the airways

86
Q

What is a transtracheal aspiration?

A

A procedure which carries considerable risk and is therefore reserved for special cases

The technique entails the insertion of a large bore needle containing a catheter int the trachea

The needle is then removed leavng the catheter in place

A syrnge attatched to the catheter is used to aspirate the secretions

87
Q

How should BALS be processed?

A

Specimens should be transported and processed as soon as possible - if processing is delayed, refrigerate

Delays of over 48 hours are undesirable as with sputa

All must be processed in a class I cabinet

BALS should be handed directly to the lab - usually processed in cat 3

88
Q

How are BALS processed?

A

Pre-treatment if mucoid with sputasol

Non-mucoid -> centrifuge for 10mins @1200g

Discard the supernatant, leaving approx 0.5ml

Re-suspend deposit in the remaining fluid

If mucoid - add equal volume fresh sputasol and incubate for 15 mins with gentle agitation

89
Q

How do you carry out dilution culture for BALS?

A

Inoculate 10ul loop full of homogenised BAL into 5ml sterile water

Using 100ul pipette inoculate 100ul of diluted sample onto choc agar and mac Conkey, spread inoculum using a sterile loop

1 colony on dilute represents 10^4 CFU/ml

In BAL one single colony of a recognised pathogen is significant

A thin smear is also made for gram staining using centrifuge specimen

90
Q

What media is put up for BALS?

A

Chocolate agar (direct and dil)
Blood with optochin (direct)
MacConkey
Malt agar

91
Q

What media is put up for BALS?

A

Chocolate agar (direct and dil)
Blood with optochin (direct)
MacConkey
Malt agar

92
Q

How would you confirm ID of S. pneumo in the lab?

A

Gram positive diplococci
Alpha haemolysis
draughtsman colonies
mucoid colonies
Bile soluble
Optochin susceptible
MALDI ID
Vitek sens
Urinary streptococcal antigen test

93
Q

Talk about the use of urinary streptococcal antigen kits in S. pneumo diagnosis

A

86% positive in patients with pneumococcal pneumonia

Not useful in children though as they have a high carriage rate of approx 40%

94
Q

How is S pneumo pneumonia treated

A

Usually treated with penicillin

Prior to 1990 resistance was very rare

Now we have penicillin non-susceptible S. pneumoniae -> rates of these vary greately from country to coutry - a lot more common in USA

Resistance to other agents e.g. cephalosporins and macrolides are also increasing

95
Q

How would you go about confirming ID of a Haem influenzae in the lab

A

NTHI strains
Gram negative small pleomorphic coccobacilli
Grow on chocolate but not blood
X and V factor discs on DST agar -> needs both
MALDI
VITEK sens
Smells like a snotty nose kid

96
Q

Comment on NTHI resistant pneumonia treatment

A

Resistance to ampicillin emerged after 1970s

Ampicillin resistance most likely due to B-lactamase production -> detected using a chromogenic cefinase disc

97
Q

Comment on NTHI resistant pneumonia treatment

A

Resistance to ampicillin emerged after 1970s

Ampicillin resistance most likely due to B-lactamase production -> detected using a chromogenic cefinase disc

98
Q

How would you go about confirming ID of M. catarrhalis

A

Gram negative diplococci that resist decolorisation
Growth on BA and Choc
Hockeypuck
Taxo discs- fail to ferment glucose, maltose, sucrose and lactose
DNase +, hydrolyses hipurate and tributyrin
Catarrhalis disc test - produce butyrate esterase enzyme

99
Q

Comment on resistance in M Catarrhalis

A

Up to 90% are ampicillin resistant, B lactamase positive

100
Q

How would you go about confirming ID of an Enterobacteria in the lab?

A

GNB
Growth on BA, Choc, often mucoid
Biochemical API ID
VITEK
MALDI

101
Q

Comment on Enterobacteria resistance

A

If HAI 3rd generation cephalosporins + Gentamicin

In last 20 years acquired variety of broad spectrum B-lactamases

AmpC B-lactamase depressed mutant
ESBL and CRE predominates in K. pneumoniae but also prevalent in E. cloacae etc

102
Q

What are the main challenges for culture-dependent methods in pneumonia investigation

A

Array of associated bacterial and viral agents
High % pts on long term antimicrobial treatment results in no growth
Culture is slow, labour intensive
Currently only ID pathogen in about 30-40% of patients -> usually just start treatment

103
Q

What are some challenges faces by molecular detection of bacteria in sputum

A

Sputum too viscous and a very difficult to automate the process

Bacterial pneumonia difficult to interpret -> can ID organisms but hard to know what is colonisation vs what is aactually infection

104
Q

What PCR based methods are now used in labs for pneumonia ID?

A

Biofirm Filmarray respiratory panel is now available for 17 respiratory viruses and 3 atypical bacteria

There has been a receent move to molecular methods for tpical bacterial agents e.g. Unyvero multiplex PCR Array-based detection

105
Q

What are some pros and cons of using Unyvero PCR to detect bacterial agents in sputa?

A

One study showed we were getting a lot of MecA detection but this wasnt actually MRSA but coag neg staphs

expensive but very helpful -> currently works better for gram neg bacteria

hard to know what commensal and what infectious

4.1 Medical Microbiology (30 decks)

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