Lower Respiratory Tract Infections Flashcards
1
Q
What are the two types of lower respiratory tract infections?
A
Acute
Chronic
2
Q
What three structures are involved in the lower respiratory tract
A
Trachea/windpipe
Bronchial tubes
Alveoli/lungs
3
Q
What are the four acute infections of the lower respiratory tract?
A
Bronchitis
Bronchiolitis
Pneumonia
Influenzae and Covid
4
Q
What are the five chronic infections of the lower respiratory tract?
A
TB
Aspergilosis
Lung abscess
Pleural effusion
Empyema
5
Q
What infection of the lower respiratory tract can be classed as both acute and chronic????
A
Cystic fibrosis
6
Q
What are the 4 different types of pneumonia?
A
Community acquired
Nosocmial
Atypical
Viral
7
Q
What is the most common cause of bronchiolitis
A
RSV
8
Q
Where is atypical pneumoniae seen?
A
Seen more in community than hospital
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
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
11
Q
Classify host responses in the RT that prevent infection
A
Mechanical defenses
Immune response
12
Q
Classify host responses in the RT that prevent infection
A
Mechanical defenses
Immune response
13
Q
What three mechanical defenses does the RT have to prevent infection?
A
Ciliary function
Cough reflex
Pulmonary Secretions
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
15
Q
What role does the cough reflex have in defense?
A
Helps expel foregin particles and pathogens
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
17
Q
What are the immune components of the alveolar lining?
A
surfactant, phospholipids, IgA and IgG
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
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
20
Q
In what two ways can mucociliary clearance be impaired?
A
Ciliary dysfunction
Excessive mucous production
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
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
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
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
25
How can age affect defense mechanisms
Infants and young children -> compromimsed immune systems
Elderly -> might loose ability to cough etc
26
How can nutrition and general health affect defense mechanisms
Malnutrition -> seen in under 5s in developing countries
Chronic alcoholism
27
What is bronchitis?
(7)
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
28
What are some predisposing factors for bronchitis?
(7)
Allergy
Asthma
Poor nutrition
Smoking
COPD
Air pollution
Exposure to cold and damp weather
29
What is the aetiology of bronchitis?
(3)
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
30
What viruses cause bronchitis?
Rhinovirus
Coronavirus
Influenza virus
Adenovirus
31
What viruses cause bronchitis?
Rhinovirus
Coronavirus
Influenza virus
Adenovirus
32
What bacteria can cause bronchitis?
(4)
Strep pneumoniae
Non-typable Haemophilus influenzae
Rare:
- Mycoplasma pneumoniae
- Chlamydophila pneumoniae
33
What is pneumoniae?
(4)
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
34
What is pneumoniae?
(4)
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
35
Write a note on the mortality of pneumonia - in the world
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
36
Write a note on the mortality of pneumonia in Ireland, based on a point prevalent study
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
37
Comment on mobidity of pneumonia
Majpr cause of morbifity -> 10% of all hospital admissions
38
What is the clinical presentation of pneumonia?
(8)
Fever
Productive cough
Acute chest pain
Shortness of breath
Purulent sputum
Rigors
Abnormal chest sounds -> cracking sound
characteristic infiltrates on xray
39
What is CAP?
Community acquired pneumoniae
Acquired outside a healthcare setting
40
What is HAP?
Hospital acquired pneumonia
Acquired during hospital stay, 48 hours or more after admission
41
What is VAP?
Ventilator-associated pneumonia
Occurs in patients on mechanical ventilation e.g. in ICU -> often see rapid decline in health
42
What is VAP?
Ventilator-associated pneumonia
Occurs in patients on mechanical ventilation e.g. in ICU -> often see rapid decline in health
43
What is aspiration pneumoniae?
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
What organisms most commonly cause CAP?
(3)
S. pnuemoniae
H. influenzae
Mycoplasma pneumoniae
45
What organisms most commonly cause CAP?
(3)
S. pnuemoniae
H. influenzae
Mycoplasma pneumoniae
46
What three organisms most commonly cause HAP?
Psuedomonas aeruginosa
Staphylococcus aureus
Enterobacter species
-> HAP is more resistant so think of your resistant bacteria
47
What three organisms most commonly cause VAP?
Acinetobacter baumanni
Klebsiella pneumoniae
Stenotrophomonas maltophilia
(again think of resistance)
48
Comment on resistance in VAP
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
What organisms are most commonly seen in Aspiration pneumonia?
Anaerobes
Mixed flora from mouth and throat etc
50
What are the 6 different types of pneumoniae?
CAP
HAP
VAP
Aspiration pneumonia
Atypical pneumoniae
HCAP
51
What are the 6 different types of pneumoniae?
CAP
HAP
VAP
Aspiration pneumonia
Atypical pneumoniae
HCAP
52
What is atypical pneumonia?
Pneumonia caused by atypical pathogens often with milder symptoms
53
Give three examples of organisms that cause atypical pneumonia
Mycoplasma pneumonia
Chlamydophila pneumoniae
Legionella pneumophila
54
What is HCAP?
Health Care Associated Pneumoniae
Occurs in patients with recent contact with healthcare settings
similar organisms to HAP
55
What are some of the challenges of lab investigation of typical bacterial pneumonia?
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
What are some sample types provided on VAP patients?
BALs
Bronchial aspirates
Bronchial washings
Transtracheal aspirates
57
Suggest an alternative to sputum for pneumonia investigation, give pros and cons
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
When should you query a fungal pneumonia?
HIV
CF
ICU
Immunocompromised
59
How should sputum samples be collected for pneumonia investigation?
(5)
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
How should sputum be stored?
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
Why cant we process samples beyond 48hour?
This allows overgrowth of gram-negative bacilli
Haemophilus and S.pneumoniae may die
62
Why cant we process samples beyond 48hour?
This allows overgrowth of gram-negative bacilli
Haemophilus and S.pneumoniae may die
63
What is the first step in sputum processing?
Describe the appearance
The quality of specimen is described on the basis of macroscopic appeance
64
How is sputa graded based on appearance?
Bloodstained
Purulent, mucopurulent (P1, P2, P3)
Pure mucoid (M1), Mucosalivary (M2), Salivary
65
What sputa samples are generally rejected?
M1, M2 or saliva specimens
66
What sputa samples are generally rejected?
M1, M2 or saliva specimens
67
Under what conditions are mucosalivary or salivary sputa samples accepted?
(6)
Immunocompromised
Intubated patients
Query legionella
Query Mycobacerium
Cancer wards
ICU
68
Give a quick run-through on the processinf of sputa
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
Why do we sputasol and vortex our sputa samples?
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
What two methods of culture are used for sputa investigation?
Direct: qualitative
Dilution: quantitative
71
What is the principle behind use of a dilution plate?
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
Under what circumstances do we not use dilution plates for sputa and why?
Not done for ICU or chemo patients
Anything that grows in these is significant as they are immunocompromised
73
How do you put up a direct and dilution culture?
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
What does 1 colony represent on a dilution plate?
1 colony = 10^5 CF/ml
75
Talk about the use of microscopy on sputa
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
How are blood plates put up for sputa?
Blood agar with optochin for strep
incubated in CO2 for haemophilus
77
What additional plates are put up for immunocompromised, HIV, oncology etc patients?
Direct chocolate (not dilute)
MacConkey - for ents and pseudo
Malt Extract Agar for fungi
78
What additional plates are put up for immunocompromised, HIV, oncology etc patients?
Direct chocolate (not dilute)
MacConkey - for ents and pseudo
Malt Extract Agar for fungi
79
What additional plates are put up for CF patients
Burkholderia plates
Pseudocel agar
SAID for S. aureus
etc
etc
80
What plates are put up for query fungal infection?
Malt Extract Agar
81
What is a BAL?
A bronchoalveolar lavage
Segment of lung washed with sterile fluid after insertion of bronchoscope and fluid is aspirated out for investigation
82
What are the main benefits of BALS?
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
What is a bronchial aspirate?
Involves direct aspiration of material from the large airways of the respiratory tract using a flexible bronchoscope
84
What is a bronchial aspirate?
Involves direct aspiration of material from the large airways of the respiratory tract using a flexible bronchoscope
85
What is a bronchial brushing
Use of a protected brush catheter in the bronchoscope to tease material from the airways
86
What is a transtracheal aspiration?
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
How should BALS be processed?
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
How are BALS processed?
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
How do you carry out dilution culture for BALS?
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
What media is put up for BALS?
Chocolate agar (direct and dil)
Blood with optochin (direct)
MacConkey
Malt agar
91
What media is put up for BALS?
Chocolate agar (direct and dil)
Blood with optochin (direct)
MacConkey
Malt agar
92
How would you confirm ID of S. pneumo in the lab?
Gram positive diplococci
Alpha haemolysis
draughtsman colonies
mucoid colonies
Bile soluble
Optochin susceptible
MALDI ID
Vitek sens
Urinary streptococcal antigen test
93
Talk about the use of urinary streptococcal antigen kits in S. pneumo diagnosis
86% positive in patients with pneumococcal pneumonia
Not useful in children though as they have a high carriage rate of approx 40%
94
How is S pneumo pneumonia treated
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
How would you go about confirming ID of a Haem influenzae in the lab
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
Comment on NTHI resistant pneumonia treatment
Resistance to ampicillin emerged after 1970s
Ampicillin resistance most likely due to B-lactamase production -> detected using a chromogenic cefinase disc
97
Comment on NTHI resistant pneumonia treatment
Resistance to ampicillin emerged after 1970s
Ampicillin resistance most likely due to B-lactamase production -> detected using a chromogenic cefinase disc
98
How would you go about confirming ID of M. catarrhalis
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
Comment on resistance in M Catarrhalis
Up to 90% are ampicillin resistant, B lactamase positive
100
How would you go about confirming ID of an Enterobacteria in the lab?
GNB
Growth on BA, Choc, often mucoid
Biochemical API ID
VITEK
MALDI
101
Comment on Enterobacteria resistance
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
What are the main challenges for culture-dependent methods in pneumonia investigation
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
What are some challenges faces by molecular detection of bacteria in sputum
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
What PCR based methods are now used in labs for pneumonia ID?
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
What are some pros and cons of using Unyvero PCR to detect bacterial agents in sputa?
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
