Medical Microbiology Flashcards
What is clinical microbiology?
The study of how microorganisms cause disease, how it’s managed, the clinical presentation of a disease and how a disease is diagnosed
Where is normal flora found in the human body?
Mouth
Skin
Intestinal tract
Genital tract
What professions deliver a clinical microbiology service?
Clinical microbiologists
Infection control & link nurses
Doctors
Anti microbial pharmacists
Biomedical scientists
Lab assistants
Lab managers
What are the 2 pathways of transmission?
Horizontal- Transmitted from host to host
Vertical- Transmitted from one generation to the next through congenital infection
What are the 2 types of direct, horizontal transmission?
Direct contact- Through touch or exchange of bodily fluids with another person
Droplet- Through coughing and sneezing
What are the 3 types of indirect, horizontal transmission?
Airborne- Via infectious agent remaining in the air from coughing, sneezing, laughing or breathing
Vehicle- Through an inanimate object that can pass on disease from person to person (via touch)
Vector- Mostly transmitted by insect bites
Define infection
Invasion and multiplication of microorganisms in body tissues, especially that causing local cellular injury due to competitive metabolism, toxins, Intracellular replication or antigen- antibody response
What are the 5 major types of pathogens?
1- bacteria
2- Viruses
3- Fungi
4- Protozoan (water borne)
5- Parasitic worm
List the routes of entry for invading pathogens
Ears
Nose
Mouth
Vagina
Urethra
Anus
Conjunctiva of eye
Broken skin and insect bites
What are the 6 steps of the chain of infection?
- Infectious agent
- Reservoir (pathogen itself often found in reservoir)
- Exit portal
- Transmission
- Entry portal
- Susceptible host
Explain the index, primary, secondary and tertiary cases
Index- first patient identified with disease
Primary- case that brings infection to the population
Secondary- Infected by a primary case
Tertiary- Infected by a secondary case
What characteristics should pathogens have?
Ability to enter the body
Multiply in the tissue
Damage tissue
Result the host defence
Define pathogenicity
Pathogenicity- Ability of microbial species to produce disease
Define virulence
Ability of microbial strains to produce disease
Where does pathology receive their specimens from?
In-patient
Out-patient (follow up etc)
Emergency admissions
General practice
Care homes, Hospice and Convalescents
Environment
List the different types of specimens
Blood
Urine
Swab
Sputum
Faeces
Tissue
Food/ water
Where can fluid samples be collected from?
Urinary tract
Gastrointestinal tract- Bile and washings
Respiratory tract- Sputum and alveolar lavage
CNS- Cerebrospinal fluid and pus
Skin and soft tissue- Vesical fluid and pus
Bone and joints- Pus and aspirate
Other (e.g Septicaemia (blood))
Where can tissue samples be collected from?
Urinary tract- Renal biopsy
Gastrointestinal tract- Liver biopsy, rectal swab
Respiratory tract- Lung biopsy, nasal/ throat swab
CNS- Brain biopsy
Genital tract- Endometrial biopsy, urethral/ cervical swab
Skin and soft tissue- skin/ wound swab
Where are swab specimens collected from?
Skin and soft tissue- skin biopsy and scrapings
Bone and joint- Bone
Other- e.g Endocarditis- Heart valve
Why are specimens taken?
Due to signs of infection
Rule out infection
Routine upon admission (for MRSA)
Check levels
Look for abnormalities
To see treatment needs to begin/ withdrawn
What are the methods of rapid detection?
Light microscopy (Gram stain etc)
Immunofluorescence (tagged antibodes)
Antigen detection (monoclonal antibodies)
Molecular tests (PCR)
Colonial appearance/ selective agar
MALDI- TOF
List the different ways in which bacteria are classified
Gram reaction
Cell shape
Sporulation
Atmospheric preference
Requirements from special media/ intracellular growth
List the different types of media and describe what they are used for
General purpose- Grow a broad spectra of microorganisms (blood agar)
Enriched - Enhance the growth factors of bacterium
Selective- Enhance the growth of desired bacteria and inhibit others
Differential- Show the differences between bacteria
What are the identification enzyme tests that can be carried out on bacteria?
Catalyse
Oxidase
When is the best time to take a patients blood culture sample?
Before antibiotics are given
What are the different isolation procedure requirements?
Liquid or solid media
Apppropriate temp
Appropriate gaseous conditions (aerobic, anaerobic, facultative or microaerophillic- 2-10% O2)
What are the basic requirements that bacteria have to grow?
Nutrients- H2O, CHO’s, proteins and minerals
Neutral pH (slight variation between each bacteria)
Sterile
30-35 degrees temp for bacteria
40 degrees for fungi
What are the 2 general strategies to grow bacteria?
- Enriched media for non-selective growth
- Selective media- for large numbers of bacteria (normal flora)
What is solid media?
Nutrients and chemicals added to encourage growth + identification poured into a Petri dish for lab use
Practically no bacteria can digest it
What is liquid media?
Specialised broths used for the recovery of organisms from sterile sites
Don’t dry out= a good maintence media
What are the 4 types of media?
- Selective- selects what you want to grow, useful for sites with normal flora
- Enrichment- good for sterile sites
- Differential- used to work out the different types of different types of bacteria are present
- Specialised- cultivation of rare and unusual isolates
What is blood agar and what is it used for?
Basal media
5% horse blood (rest is sheep/ human)
Shows alpha, beta and gamma haemolysis (break down of red blood cells)
Not selective
What is Cetrimide agar differential for?
Differential for Pseudomonus
Fluoresces when pseudomonas is present with a distinctive smell
What is Candida Brillinace agar differential for?
Candida species
Present a range of colours from blue-red depending on what yeast is grown/ present
What is MacCockney agar differential for, and what colour change occurs?
Differential for lactose fermenting bacteria
Crystal violet is gar mixture is differential for Gram +ve bacteria and inhibits the growth of Gram -ve bacteria
Lactose +ve bacteria cause the agar to turn from red- bright pink to
Lactose -ve cause a red- organge/ yellow colour change
How is Mannitol salt agar differential and what bacteria is it differential for?
Differential for Staphlycococcus
High concentrations of NaCl only allows halototlerant/ halophillic bacteria to grow
Those bacteria ( staph aureus) that can ferment mannitol, reduces the pH causing the agar to turn the phenol red from light red- yellow
Bacteria that don’t ferment the mannitol can still grow so the agar turns a darker pink (staph epidermis)
What is MEYP agar?
Mannitol egg Yolk Polymyxin agar
How is MEYP differential and what bacteria is it differential for?
Differential for Bacillus that ferment mannitol (particularly for B. Serious)
Contains polymixin which inhibits the growth of Gram -ve bacteria and Gram +ve cocci (staph)
Fermentation dec pH, turns agar pink only b.serious can do this
What are the different atmospheric requirements for growth of bacteria?
Obligate aerobes- obliged to use O2
Microaerohillic- lower amount of O2 than the atmosphere
Capnophiles- high amounts of CO2
Facultative anaerobes- growth in prescence OR abscence of oxygen
Obligate anaerobes- strictly only grow n anaerobic conditions
What are the 5 techniques used to identify a microorganism?
Selective and differential media
Colonial morphology
Gram staining
Confirmatory tests
Antibiotic susceptibility
How should a specimen be handled/collected?
Before antibiotics have started
Labelled appropriately with clinical detail
Transported and stored accordingly
Special transport medium carried out if required
Correct sample type collected
How are specimens processed?
Urgent vs non-urgent samples
Sites with normal flora and sites without
Culture conditions should be correct:
Growth time
Atmospheric conditions
Specific factors in the culture media
Describe chromogenic media
Use in most labs
Acts as an indicator media
Incorporates chromogenic sub rates in the media
Quicker method of identifying and differentiating micro-organisms
Easy to separate mixed cultures
Expensive
What is routine plate selection?
Often selective an enrichment
Indicator in special circumstances
Plates are usually ready the next day
Describe the urease confirmatory test?
Tests for bacteria’s ability to degrade urea
Phenol red is used to test for acidity
Yellow appearance= Acidic
Pink appearance= Alkaline
What are healthcare associated infections?
HCAI are a result of healthcare interventions/ being in contact with a healthcare setting (MRSE or CDI)
Therefore infection prevention and control is a key priority for the NHS
Describe the process and effect of MRSA screening
Initiative to reduce HCAI
Patients screened according to this policy
2/3 swabs of each patient upon admission, during their stay and prior to discharge
Inc lab workload due to need for quick result
What is MRSA?
Discovered in 1981
1 in 3 healthy people are carriers
Widespread in most hospitals
Resistant to most antibiotics
Which bacteria are catalase +ve/-ve?
Staphylococci- +ve
Streptococci- -ve
Gram -ve- +ve
Very few anaerobes are +ve
How does the catalase test work?
Breakdown of hydrogen peroxide
Generation of oxygen “bubbles” (in 20s on a slide)= +ve
Distinguishes between Strep and Micrococcus from Enetrcoccus and Staph
Which bacteria are oxidase +ve/-ve?
Staph and Strep- -ve
Many enviromental organisms- +ve
Many pathogens- +ve
Gram -ve bacteria- -ve
How does the oxidase test work?
Enzyme is only found obligate aerobes that oxidises the TMPD* reagent
Purple/ blue compound is produced in aprox10 seconds
What are the 3 major groups of bacteria and their result for the catalase test?
- Obligate aerobe - Positive
- Facultative anaerobe- Positive
- Obligate anaerobe- Negative
What are the 3 major groups of bacteria and their result for the oxidase test?
- Obligate aerobe- Positive
- Facultative anaerobes- Negative
- Obligate anaerobes- Negative
What is taxonomic analyses?
The process of ordering and classifying bacteria
What are the 5 main categories in phenotypic analysis?
- Morphology- Gram reaction, cell size and shape
- Motility- Nonmotile, gliding motility, swimming (flagella)
- Metabolism- Mechanism of energy conservation, growth factor requirements
- Physiology- Temp, pH, salt ranges for growth, response to oxygen
- Other traits- Pigments, luminescence, antibiotic sensitivity, serotype
What are the 3 different spore positions that help differentiate bacteria?
Terminal
Central
Subterminal
Describe phylogenetic analysis
The representation of the history f a group of organisms in a phylogenetic tree
PCR is used to amplify and sequence DNA so that sequences can be compared and phylogenetic trees can be created
Describe the theoretical aspects of evolutionary analysis
Most widely used molecular clocks are a small subunit rRNA genes
They’re found in small domains of life
16S rRNA in prokaryotes and 18S rRNA in eukaryotes
Functionally constant
Sufficient length
How is genomic hybridisation used as a taxonomic tool?
Genomes of 2 organisms are hybridises to examine proportion of similarities in their gene sequences
Useful for differentiating very similar organisms
List some bacteriological uses when naming bacteria
Bacterial name must be in italics
Name of all taxa must be in italics
Names should only be abbreviated after they save been first used in text
Describe the coagulase test
Tube test- performed enzyme within cell-free coagulase
Considered gold standard for S.aureus identification
Clots rabbit palms in the test tube
What is MALDI TOF MS?
Matrix assisted laser desorption time of flight mass spectrometry
Identification of virtually all clinically relevant bacteria in 20 mins
However only as good as the data base it has
