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Copy of Your Lower respiratory Tract

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JL lavergne

on 23 September 2015

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Transcript of Copy of Your Lower respiratory Tract

Your Lower Respiratory Tract
And you . . .
Who Lives in Your Mouth
You are an ecosystem
You are the host to billions of guests
The Tree of Life
First Things First
I have no conflicts of interest or funding from outside sources.

I am in charge of antimicrobial stewardship for VCH and I hope to bring you along to roles as antimicrobial stewards
Many of them help you survive
You rely on the organisms in and on you to:

-Help digest your food
-Provide you with vitamins
-Protect you from harmful bacteria
- Many other things we don't understand
Some of them make you sick
Most Can Do Either
This session will introduce basic concepts of bacteriology as it is relevant to pathogenesis, diagnosis and treatment of disease. Students will learn how to classify pneumonia from a microbiological and epidemiological perspective. Examples of specific lower respiratory tract pathogens will be presented in order to further students understanding of the pathogenesis of these infections.


1. Understand the basic classification of bacteria as relevant to the treatment of respiratory tract infections

2. Recognize the natural flora of the respiratory tract and the pathogenesis of common bacterial pneumonias

3. Know the different organisms that cause pneumonia in normal and abnormal/compromised hosts

4. Understand the microbiological tests used to diagnose pneumonia

5. Understand the requirements for isolation and public health notification for respiratory tract infections

6. Understand duration of therapy and when not to give antibiotic therapy
things that live on you
gram positive
Gram Negative
Intracellular organisms

Bacteria that have a thick cell wall with no outer membrane


Cocci (meaning round)
in chains: Streptococcus
in clusters: Staphylococcus

Bacilli (meaning rod-like)
irregular: corynebacteria
regular: arcanobacterium, listeria
with spores: bacillus
Bacteria that have a double membrane with a thin protected cell wall

Bacilli (means rod like):

Enterobacteriaceae: E. coli, K. pneumonia, P. mirabilis . . .

Non-fermentors: Pseudomonas, acinetobacter, Burkholderia

coccobacilli (fastidious):
Haemophilus, pasturella, capnocytophaga

Gram Negative


Branching: actinomyces

Spore forming: clostridium

Irregular: priopionibacterium



Small: Bacteroides

fusiform: Fusobacterium


Organisms that can't live in the presence of Oxygen
Gram Positive
Organisms that can only be seen by "acid-fast" stain
Occasionally will be seen as gram positive rods

Have very waxy cell wall

Require special stains to be seen
Live inside the hosts cells
Includes a number of organism groups
Such as:

Chlamydia Chlamydiophila
Legionella Mycoplasma
Coxiella Rickettsia

Some organisms infect your body and cause damage to your tissues and organs

Almost all organisms
can result in harm to tissues and organs if the host is compromised physically or physiologically
Normal Flora:
Gram positives: Viridans Streptococci, S. pneumoniae
Gram negatives: Neisseria spp., pasturella, Haemophilus, Capnocytophaga, Eikenella
Anaerobes: Actinomycetes, gram negative cocci, peptostreptococci, fusobacterium
Fungi: Candida Spp.

Your Lungs' Ecosystem Runs From Your Mouth to the Smallest Alveoli
The whole system is called your microbiome
While your lungs have relatively few organisms, there is no dividing line between the mouth and the rest of the respiratory system.
Most lung infections get there through the mouth
This is known as "Normal Respiratory Flora" remember this you will see it on lab reports
Other Flora -- Not necessarily Abnormal
Gram positives: Staphylococcus, Beta-hemolytic Streptococci,
Gram negatives: Enterobacteriaceae, non-fermentors
Anaerobes: bacteroides, others.
Normal flora changes with age, disease, medications and dental health. Changes in flora may or may not represent disease, but will definitely alter lung infections.
Abnormal Flora -- if present, always represents disease
Gram negatives: Neisseria Gonorrhea
Viruses: HSV
Healthy ecosystems have a diverse balance of normal flora with respect for physiologic boundaries
Unhealthy ecosystems loose biodiversity and have either unusual flora or flora where there should be none (or less)
The balance of organisms determines health and disease
Are organisms which require a host cell to survive
viruses co-opt their host's cellular machinery to reproduce.

they are composed of a capsule, a nucleic acid and sometimes an envelope
Are Eucaryotic organisms that have several forms
We commonly refer two two types:
Yeast Filamentous Fungi

Most occur in the environment and rarely infect humans
Are Eucaryotic organisms that range from single celled protozoans to vertebrates
Most parasites affect less privileged populations and are generally associated with poorer hygiene or nutritional status
How do Lung Infections Happen?
Mouth or stomach Contents are drawn into the lungs due to vomiting or failure to clear secretions Mostly found in the lower lobes or dependent parts of lungs
We all "micro-aspirate" constantly, Evolution has built tools to clear the respiratory tract
More worrisome aspiration occurs when this fails or is overwhelmed
Despite normal flora, most aspirations are *NOT* infections
When infection does occur, it is due to colonizing mouth and stomach organisms
Organisms are carried into to Lung With the Movement of Air
This mechanism requires that the organism be capable of tolerating drying enough to be carried on a droplet nucleus
Many organisms transmitted this way are of public health significance (e.g. MTB), and may require isolation precautions

the upper lobes are most commonly affected
Examples of organisms: Mycobacterium TB., Aspergillus, Cryptococcus, ?viruses
It is your responsibility to know which infections need to be reported to public health, for BC:

Dental hygiene and type of aspiration important for empiric therapy
Infections carried through the blood stream are implanted in the lungs
are often found in the periphery where blood vessels are smaller
Are often associated with systemic disease and have multiple foci
Some infections get to the lungs because of combinations of, or unusual, means
Droplet transmission -- Respiratory droplets make contact with mucous membranes, and are either spread via aspiration, contiguous spread or hematogenously.
Direct innoculation -- either because of fomites or trauma e.g. intubation
Combinations -- some organisms can be trasmitted by multiple routes e.g. influenza, S. aureus
These infections may require isolation
How do I know ?
Diagnosing lung infection requires multiple pieces of information
Clinical: New symptoms attributable to respiratory tract with or without systemic symptoms:
Shortness of Breath, cough, wheeze, change in sputum, hemoptysis, chest pain . . .
Diagnositic: Visible changes on imaging
Diagnosis is clinical and using imaging. Culture does not diagnose lung infections
Microbiology can help determine causative organisms and sensitivities, but cannot determine if an organism is a colonizer or causing infection
The respiratory tract has natural flora
Most of this flora can be either normal or cause disease
The diagnosis of pneumonia is clinical and requires patient and imaging information
The mode of infection can help determine the pattern on imaging and what isolation is necessary
Laboratory testing supports clinical data
You are responsible for reporting some infections to public health
Lab testing
bacterial pneumonia:
"atypical" pneumonia:
mycobacterial pneumonia:
special hosts:
viral pneumonia
Routine culture: will include gram stain and culture
Request specific pathogens, e.g. mycoplasma
Request specific pathogens, ?isolate ?public health
Isolate, request AFB stain and culture, ?other tests
Consider fungal culture, cytology, serologies, ID consult
Know when not to treat:

Understanding Lab Reports
Routine Culture:
4+ polymorphs, 1+ epithelial cells, Good quality
2+ Gram positive cocci, 1+ gram negative rods
Growth of heavy Normal Respiratory flora
Growth of light E. coli
Other Tests
Respiratory virus testing: Sample negative for Influenza A, influenza B and RSV. A negative test does not rule out disease. Correlate clinically.
For all patients: Supportive Care
Admission to hospital vs. follow-up, bronchodilators, chest physiotherapy, suction, oxygen . . .
Most viral infections, Aspiration pneumonitis, COPD exacerbations without bacterial infection, candida, or other culture reports . . .
Know what you are treating
Know when to stop
Mild CAP
Severe CAP
special host
Most common pathogens:
Streptococcus pneumonia, H. influenzae, C. pneumoniae, M. pneumoniae

first line therapy:
doxycycline or
amoxicillin and clarithromycin
Most common pathogens:
Streptococcus pneumoniae, H. influenzae, S. aureus

First Line Therapy:
Ceftriaxone plus doxycycline, azithromycin or clarithromycin
Most common pathogens:
Often chemical
Otherwise mouth flora

First Line Therapy:
supportive or
Amoxicllin-clavulanic acid
Most common pathogens:
Still S. pneumoniae, streptococci, H. influenzae, Staphylococci

Higher risk for more resistant pathogens: MRSA, pseudomonas

First Line thearpy early onset:
Ceftriaxone + ?

First line therapy late onset:
Pipercillin-tazobactam, cover MRSA if at risk
No such thing as "common pathogens":

Bacterial infections still most common

Increasing risk for atypical viral, fungal, parasitic infections

Consult infectious diseases
Treatment duration of 5 days can be sufficient if patient is improving, depending or the organism and the host
I Can't Possibly Cover It All
Pneumonia is the most common cause of hospitalization and death.

As a medical professional it is your job to know how to manage it

Every line of a microbiology report means something, if you aren't sure, ask.
The severity and type of pneumonia determine empiric therapy
microbiology data will help narrow treatment, not diagnose disease in *most* cases (e.g. not TB)
Treatment should be as close to 5 days as clinical improvement allows, 7 for HAP/VAP
special hosts may have unusual infections
The End
Questions/comments: jennifer.grant@vch.ca
Specific viruses and "atypical" pathogens need to asked for by name
Full transcript