Clinically significant fungi
Classification-growth form.
There are over 200 species identified as fungi that are called pathogens, they can
cause human infections.
There is 1.7 infections worldwide causing 1.5 million deaths.
We can classify fungi into 4 different types:
1. Moulds: these are multicellular, they have filamentous (hyphae), and they
reproduce by producing spores.
2. Yeast like fungi: these grow like yeast but have elongated parts. So, they grow as
yeast and partly like elongated cells.
3. True Yeasts: these are unicellular, and they reproduce by budding.
4. Dimorphic fungi: they are able to change depending on the temperature of the
environment, they are moulds in cultures at 25 degrees and they can become yeasts
in the human body thus causing severe infection.
Classification-type of infection
Severe infections due to fungal infections are rare in healthy individuals.
They are typically opportunistic pathogens or nosocomial (this means it is a hospital
spread infection)
Types of infection:
1. Superficial mycoses- this is the outer layer of skin, hair or nails. Example: pityriasis
versicolor and it is caused by Malassezia. Malassezia causes white patches on darker
skin tones, showing signs of infection. People with a lighter skin done will have
darker patches. This condition is treatable and common.
2. Subcutaneous mycoses- subcutaneous suggests that it is in a deeper layer of the
skin. This infection produces boil like projections from the skin. Example: mycetoma.
3. Systemic mycoses- the most dangerous type of infection is a systemic infection.
This is an infection that can spread to the blood, the lungs, internal organs. Example:
candidemia,
Candida auris
First identified in japan in 2009.
This type of infection is linked to climate change.
Normally, this infection would not be spreading in temperatures of around 37
degrees, but as we have a warmer earth it has allowed a selective advantage for this
candida, and it can now survive at 37 degrees which is the human body temperature
thus causing human disease.
Unlike most other candida types, it colonises the skin and it is known to be spread
via the groin.
It is a hardy yeast this is worrying because it spreads a lot through hospital
environments (nosocomial infection), so it can withstand high salt concentrations.
This is worrying because it means that it is resistant to a lot of the disinfectants that
we use to clear it in the hospital setting.
Spreads rapidly in environment.
It is resistant to most anti-fungals that we use to treat the infection.
, There are outbreaks reported in 20 countries: India, Pakistan, Venezuela, south
Korea and the uk.
It is an opportunistic pathogen so healthy individuals will not be infected.
The target groups for this pathogen are elderly, people with diabetes mellitus,
surgery, neutropenia (low levels of neutrophils), immunosuppressed people, people
on broad spectrum antibiotics/ antifungals.
Candida auris- specimen.
To diagnose candida Auris infection in the laboratory:
We take a swab sample, and it is transported in amies transport medium.
Amies transport medium has charcoal in there and this allows the viability of
pathogenic organisms to be a bit longer. This is so we can culture them onto plates.
Typically, a panel of swabs are taken:
In an adult: a nose swab, a throat swab and a perineum swab.
In a child: a nose swab, a throat swab and a groin swab.
It is then transported into the laboratory in a clear bag.
Laboratory diagnosis (4 STAGES)
1. Microscopic detection (this is the simplest form of identification).
you conduct a gram stain and separate it based on the peptidoglycan layer and
anything that is gram positive will stain purple and anything that is gram negative
will stain pink. We view this under light microscopy at X100 focus. Another test that
we can conduct is a germ tube and a calcofluor white test.
2. Isolation, culture and identification.
We have to isolate the culture and identify whether it is candida Auris infection or
not. We have a variety of different media types that are incubated that allow us to
do that.
3. Susceptibility testing
Once we know what pathogen it is we need to know what anti-fungal agents are
going to be susceptible to that pathogen, so we need to some susceptibility testing
against anti-fungal agents.
4. Serology
We do some serology which is the presence of antibodies against fungal organisms.
5. PCR
We extract the genetic material from the fungi and amplify it with PCR and we are
able to detect it and get peaks.
Laboratory diagnosis- microscopy
Microscopy is the first line of defence.
It doesn’t breakdown what you are seeing. For example, it will just show you if
there are large oval yeast cells. You can only deduce from this that you have a
yeast infection.
Gram stain will give you purple budding cells, these are typical cells of candida.
However, this will only tell you that it is candida, it will not differentiate it into
species.
Germ tube- test that we can conduct in the laboratory. You add the patient
sample to animal serum, and you incubate it for 2-4 hours at 37 degrees.
Classification-growth form.
There are over 200 species identified as fungi that are called pathogens, they can
cause human infections.
There is 1.7 infections worldwide causing 1.5 million deaths.
We can classify fungi into 4 different types:
1. Moulds: these are multicellular, they have filamentous (hyphae), and they
reproduce by producing spores.
2. Yeast like fungi: these grow like yeast but have elongated parts. So, they grow as
yeast and partly like elongated cells.
3. True Yeasts: these are unicellular, and they reproduce by budding.
4. Dimorphic fungi: they are able to change depending on the temperature of the
environment, they are moulds in cultures at 25 degrees and they can become yeasts
in the human body thus causing severe infection.
Classification-type of infection
Severe infections due to fungal infections are rare in healthy individuals.
They are typically opportunistic pathogens or nosocomial (this means it is a hospital
spread infection)
Types of infection:
1. Superficial mycoses- this is the outer layer of skin, hair or nails. Example: pityriasis
versicolor and it is caused by Malassezia. Malassezia causes white patches on darker
skin tones, showing signs of infection. People with a lighter skin done will have
darker patches. This condition is treatable and common.
2. Subcutaneous mycoses- subcutaneous suggests that it is in a deeper layer of the
skin. This infection produces boil like projections from the skin. Example: mycetoma.
3. Systemic mycoses- the most dangerous type of infection is a systemic infection.
This is an infection that can spread to the blood, the lungs, internal organs. Example:
candidemia,
Candida auris
First identified in japan in 2009.
This type of infection is linked to climate change.
Normally, this infection would not be spreading in temperatures of around 37
degrees, but as we have a warmer earth it has allowed a selective advantage for this
candida, and it can now survive at 37 degrees which is the human body temperature
thus causing human disease.
Unlike most other candida types, it colonises the skin and it is known to be spread
via the groin.
It is a hardy yeast this is worrying because it spreads a lot through hospital
environments (nosocomial infection), so it can withstand high salt concentrations.
This is worrying because it means that it is resistant to a lot of the disinfectants that
we use to clear it in the hospital setting.
Spreads rapidly in environment.
It is resistant to most anti-fungals that we use to treat the infection.
, There are outbreaks reported in 20 countries: India, Pakistan, Venezuela, south
Korea and the uk.
It is an opportunistic pathogen so healthy individuals will not be infected.
The target groups for this pathogen are elderly, people with diabetes mellitus,
surgery, neutropenia (low levels of neutrophils), immunosuppressed people, people
on broad spectrum antibiotics/ antifungals.
Candida auris- specimen.
To diagnose candida Auris infection in the laboratory:
We take a swab sample, and it is transported in amies transport medium.
Amies transport medium has charcoal in there and this allows the viability of
pathogenic organisms to be a bit longer. This is so we can culture them onto plates.
Typically, a panel of swabs are taken:
In an adult: a nose swab, a throat swab and a perineum swab.
In a child: a nose swab, a throat swab and a groin swab.
It is then transported into the laboratory in a clear bag.
Laboratory diagnosis (4 STAGES)
1. Microscopic detection (this is the simplest form of identification).
you conduct a gram stain and separate it based on the peptidoglycan layer and
anything that is gram positive will stain purple and anything that is gram negative
will stain pink. We view this under light microscopy at X100 focus. Another test that
we can conduct is a germ tube and a calcofluor white test.
2. Isolation, culture and identification.
We have to isolate the culture and identify whether it is candida Auris infection or
not. We have a variety of different media types that are incubated that allow us to
do that.
3. Susceptibility testing
Once we know what pathogen it is we need to know what anti-fungal agents are
going to be susceptible to that pathogen, so we need to some susceptibility testing
against anti-fungal agents.
4. Serology
We do some serology which is the presence of antibodies against fungal organisms.
5. PCR
We extract the genetic material from the fungi and amplify it with PCR and we are
able to detect it and get peaks.
Laboratory diagnosis- microscopy
Microscopy is the first line of defence.
It doesn’t breakdown what you are seeing. For example, it will just show you if
there are large oval yeast cells. You can only deduce from this that you have a
yeast infection.
Gram stain will give you purple budding cells, these are typical cells of candida.
However, this will only tell you that it is candida, it will not differentiate it into
species.
Germ tube- test that we can conduct in the laboratory. You add the patient
sample to animal serum, and you incubate it for 2-4 hours at 37 degrees.
