Microbiology Flashcards
What are the domains of life?
- eubacteria /prokaryotes
- eukaryotes
- archea
What are the major groups of human pathogens?
Protozoa, fungi, bacteria, viruses
What are Protozoa?
Single called animals (eukaryotes)
What are fungi?
Higher plant like organisms (eukaryotes)
What are bacteria?
Generally small, single celled prokaryotes
What are viruses?
Very small obligate parasites (non-living)
Describe features of eukaryotes
- larger in size than prokaryotes (5-50mm)
- complex (compartmentalise)
- frequently multi-cellular
- linear chromosomes + histones
- introns/exons
- 80s ribosomes
- no/ flexible cell wall
- cell cycle includes meiosis and mitosis
Describe the features of prokaryotes
- relatively smaller than eukaryotes (0.5-10mms)
- simple
- often single celled
- single circular chromosome
- introns are rare
- 70s ribosomes
- co-transcription/ translation
- rigid cell walls (PG)
- rapid cell cycle
Describe nucleotides (in bacteria)
- they have no nuclear membrane
- contains DNA and proteins
- chromosomes are single circular molecules
- primitive DNA segregation machinery
Describe the features of the cytoplasmic membrane
- electrons are released from high energy compounds in cytoplasm
- reach membrane and passed through a series of electron acceptors
- as a consequence protons passed outside the membrane producing a positive charge and proton gradient across the membrane
Describe the features of the cell wall
- Made of Peptidoglycan (NAM and NAG)
- rigid layer and barrier formed from a repeated polysaccharide structure.
- target of penicillin
- can be gram positive (thick multilayer PG) or gram negative (outer membrane, periplasm and thinner PG layer)
Describe the features of lipopolysaccharide (LPS)
- gram negative (outer membrane is asymmetric, surface nearly all LPS)
- glycolipid
- lipid molecule attached to a polysaccharide
It has a structural role and is an antigen and bacterial toxin.
What are flagella and what are the features?
Long whip like structures which help some single celled organisms move.
Can be gram positive or negative
Are made up of flagellin (protein unit) making a multi stranded filament with core.
What are fimbriae?
Gram positive non-flagella protein appendages.
Thinner and shorter than flagellum
What are pilus?
Hair-like appendages found on the surface of many bacteria and archea.
Pilus have no motor and are composed of the pilin repeating unit.
Length, number, arrangement, shape and function can vary
Describe prokaryotic protein synthesis
- Has distinct proteins
- involves co-transcription/translation
- occurs in cytoplasmic membrane
- no polyadenylation of transcript
- target for antibiotics
What basic structures can be found in prokaryotes?
cytoplasm, plasma membrane, cell wall, outer membrane, LPS, chromosome, ribosome, pili, fimbriae, flagella
What is required for prokaryotic growth?
- food and nutrition
- appropriate temperature
- appropriate hydrogen ion conc.
- osmotic protection
- appropriate oxygen conc.
What are the growth phases of bacteria?
Lag, exponential /log, stationary, decline
How do most bacteria live?
In large communities
What are the common shapes of bacteria?
Cocci (spheres), bacilli (rods), spiral shaped, fusiform (elongated slender), vibrio (slightly curved rods)
Describe coccus/cocci
Division in one plane produces two cocci eventually resulting in a chain (eg streptococcus)
Division in three planes results in clumps (staphylococcus)
(Spheres)
Describe bacilli
(Rodshaped)
Makes chains of bacilli
Describe vibrio
Slightly curved rod
Gram negative
Describe spirillum
Spiral shaped
Can be flexible
Moves in a corkscrew motion which is dynamically more efficient
Describe fusiform
Elongated, slender microorganisms
Adhesive
What are spores?
Inert structures, resistant to physical and chemical change so undergo no cell processes
Encased in a shell
What is a gram stain?
A simple method that distinguishes two major classes of bacteria according to cell wall structure.
(Not all organisms stain well with gram stain)
What are the terms relating to aerobic and anaerobic bacteria?
Aerobic = grows in oxygen Obligate aerobes = requires oxygen Obligate anaerobes = killed by oxygen Facultative anaerobes = tolerates oxygen Capnophilic = prefers higher CO2 levels
What is a selective medium?
A medium where the presence of specific substances permits the growth of one organism over another
What is a differential medium?
Incorporation of chemicals produces visible changes in colonies that facilitate identification
How is streptococcus identified?
Haemolysis = the rupturing of red blood cells releasing their contents. Alpha haemolysis = partial haemolysis, beta haemolysis = full haemolysis, gamma haemolysis = no haemolysis
How can you characterise a biochemical substance?
Metabolic profiling -using carbon sources and amino acids
Exo-enzyme production such as catalase, coagulase, urease and those that hydrolyse lipids
What are serological tests?
Testing using antibody to antigen interaction
Allows the rapid detection on viruses and can identify specific serotypes of bacteria
What is agglutination ?
The clumping of particles which occurs when an antigen is mixed with its antigen
What is 16sRNA?
RNA component of haloenzyme
The RNA sequences are used to identify bacteria by comparison to understand taxonomic relationships
What is multi locus sequence typing (MLST) ?
When a number of genes are sequenced
What is MALDI-TOF?
(Matrix assisted laser desorption ionisation time of flight)
Generates a series of ions and separates the according to mass and charge. It detects the spectrum of proteins released from a sample and results in a characteristic signature.
(Powerful, rapid, precise, cost effective)
What are the linnaean classifications?
Kingdom, phylum, class, order, family, genus, species
What is the structure of viruses ?
Nucleic acid inside a protein coat which has protein spikes sticking out of it and is in an envelope
Describe the action of viruses
The ligand on the viruses interact with specific receptors in the target cell. The virus then either fuses with the cell membrane or is endocytosed if it is non-enveloped. The viral nucleic acid coat is then released due to viral ion pumps. Nucleic acid is used to produce new viral proteins and these are then packaged, arranged and released.
What are the different ways a virus can be released?
- a process opposite to entry by phagocytosis
- release by budding (released with an envelope derived from the host cell membrane)
- released by lysis (virus lyles the cell)
Describe antibiotics.
- work on bacteria not viruses
- object is selective toxicity
- targets structures such as bacterial ribosomes, growing bacterial cell walls and other bacterial structures (viruses may have a few of these targets)
What are antiviral drugs?
Drugs treating viruses with possible targets of viral nucleic acid polymerase, viral enzymes involved in uncoating, attatchment and release
Describe antiviral resistance.
- can be analysed phenotypically and in vitro
- but is more often analysed genotypically
- most often seen in settings where long periods of treatment are given, especially in immunocompromised patients.
What are the mechanisms by which virus’ cause disease ? (Pathogenesis)
- cell death due to lysis or hijacking
- cell death due to immune system (especially cytotoxic T cells)
- cell proliferation (increase in the number of cells, can cause cancer)
Why might no symptoms be present when a person has a virus?
Convalescent (recovery)
Late stages of incubation
Asymptomatic
Reactivation
How can a virus be stopped by the body?
Cytotoxic T lymphocytes recognise it as foreign and initiate apoptosis in the cell.
Antibodies can neutralise the virus preventing binding to cell receptors
How can recent infection be differentiated from past infection?
Detection of virus specific IgM antibodies, detecting of rising titre of IgG antibodies, detection of very high tiger of IgG antibodies
Paired blood samples
How are viruses detected?
PCR mainly
Antigen detection
Mass spectroscopy
Next generation sequencing
What are endogenous microorganisms?
Microorganisms that normally reside in a closed system
What are exogenous microorganisms?
Bacteria introduced to a closed system from the external world
What is virulence?
The capacity of a microbe to cause damage to the host
What is a pathogen?
A harmful organism that is foreign to the body
What are commensal microorganisms ?
Organisms that is part of the natural flora of the body and is often in a mutualistic relationship
What is an opportunistic pathogen ?
An organism that causes infection when opportunity/ change in natural immunity arises.
What is a contaminant?
An organism that grows in a culture by accident
What are the types of infectious agents?
Bacteria, viruses, fungi, protozoa, parasites and prions
What is an example of a fungal pathogen?
Candidaemia - linked with thrush , can be caused by antibiotics
What are examples of protozoa diseases?
Malaria, taxoplama, GI infections
What are examples of gram negative cocci shaped prokaryotic pathogens?
Neisseria meningitidis - commonest cause of bacterial meningitis.
Neisseria gonorrhoeae -causes gonorrhoea
Describe the gram negative bacteria associated with the GI tract.
Coliform (bacilli that look E.coli like)
Grows best aerobically but can grow anaerobically
Many are already part of the bowel flora
Can cause serious infections (UTI, peritonitis, biliary tract infection)
What is the antibiotic used to treat coliform infections ?
Gentamicin
Why do patients with coliform sepsis become so unwell?
An endotoxin is released from the gram negative cell wall when the bacteria die. This stimulates the release of inflammatory cytokines leading to fever.
Small blood vessels loose fluid which means that the heart has to work harder to maintain oxygen to the tissues and oxygen supply to less essential organs is shut down. Blood clotting increases using up all the clotting factors and leading to increased risk of haemorrhage
What is the mechanism of fever?
Antigens interact with macrophages and release cytokines into the blood stream which then travel to the hypothalamus. Prostoglandin E is released which increases the body’s thermal set point causing the body to perceive it as cold and shiver. This leads to fever. (>38°C)
What are the most common types of gram positive pathogens?
Streptococcus and staphylococcus
What can group A streptococcus cause?
Scarelt fever , necrotising fasciitis, bacterial sore throat, puerperal sepsis, pneumonia
What can non-haemolytic streptococci cause?
Most important group is enterococci which isnt particularly pathogenic but can cause problems if it gets into a normally sterile site. Common cause of UTI -sensitive to amoxicillin
Describe staphylococci
Gram positive and has two types; s. Aureus (causes MRSA and is coagulase positive hemolytic. The most common cause of skin, soft tissue and wound infection) and s. Epidermidis (associated with foreign devices and is coagulase negative hemolytic)
What is clostridium spp. ?
Gram positive anaerobic bacilli
Produces spores that can survive outside the body for many months as well as endotoxins which cause severe tissue damage.
Clostridium difficile = causes antibiotic associated diarrhoea
What is a bacteriostatic antibiotic?
An antibiotic which inhibits the growth of bacteria
What is a bacteriocidal antibiotic?
An antibiotic that kills bacteria
What is the ideal antibiotic?
- selectively toxic, minimal toxicity to the host
- cidal
- long half life
- appropriate tissue distribution
- no adverse drug interactions/ side effects
- can be given in an appropriate way
What are the differences between antibiotics take orally and intravenously ?
Orally is cheaper but slower (peak after approx. An hour) acting and around 30% is excreted in faeces without being absorbed.
Intravenously acts within 15 minutes and more of it is absorbed but it is more expensive .
What are the targets of antibiotics?
Cell walls, ribosomes, nucleic acid (during DNA replication, DNA gyrases, metabolic pathways)
What are the commonly prescribed cell wall antimicrobials (antibiotics) ?
- penicillins (amoxicillin, fluxoacillin, co-amoxiclav etc) *B-lactam
- cephalosporins (ceftriaxone, wider spectrum ones) *B-lactam
- glycopeptides (vancomycin, teicoplanin) *not B-lactam
What are B-lactam antibiotics?
A class of broad spectrum antibiotics consisting of all antibiotic agents that contain a beta lactam ring in their molecular structures. (Penicillins, cephalosporins and carbapenems).
How do B lactams work?
B-lactam ring is recognised by cell wall synthesising enzyme (PBPs)
B-lactam ring is cleaved by cell wall synthase and remains at the active site preventing the enzyme from processing the substrate
The B-lactam is a suicide substrate and halts synthesis and the cell wall is comprised
What are the features of penicillins ?
- safe, very few side effects
- lots of variety
- range from narrow spectrum to broad spectrum
- excreted rapidly
- safe in pregnancy
- patients can be allergic
- some microbes are resistant
-three basic compounds ; benzylpencillin, Phenoxymethylpenicillin, benzathine penicillin
What are the gram positive penicillins?
Flucoxacillin
What are the gram positive and negative penicillins?
Amoxicillin and co-amoxiclav
What are the gram negative penicillins
Temocillin (active against ESBL producing organisms)
What is co-amoxiclav?
(Penicillin)
Amoxicillin and clavulanic acid
What is flucloxacillin useful for?
Staphylococci and streptococci only (narrow spectrum)
MRSA is resistant
What’s the difference between gram positive and gram negative bacteria?
Gram positive have cell walls comprising of a rich mesh of peptidoglycan layers and can retain stains.
Gram negative have a very thin cell wall and hence cannot trap stains/dye.
What are cephalosporins?
Inhibit cell was synthesis and are bactericidal
Longer half life in plasma , excreted via kidneys and urine, few side effects, less allergies
More resistant to B-lactamases
Not widely used in hospitals anymore as they are broad spectrum enough to significantly affect normal bowel flora
Describe glycopeptides.
Bactericidal
Cell wall active antibiotics
Need to be injected
Work on gram positive bacteria but not gram negative organisms
Describe antibiotics that target protein synthesis.
Antibiotics that inhibit protein synthesis do so by attaching to bacterial ribosomes (different to mammalian).
Usually protein synthesis can resume after the antibiotic is removed so these are normally bacteriostatic. (Exception aminoglycosides)
Describe gentamicin.
It is an aminoglycoside
Must be given intravenously (rarely intramuscularly)
Binds to ribosomes (30s) causing misreading of the anticodon and the wrong amino acid is inserted. This is bacteriocidal (as it’s irreversible)
Active against gram negative organisms
Can be toxic and cause damage to kidneys and cranial nerve
Describe tetracyclines.
Actively transported into cell and binds to 30s subunit Bacteriostatic Broad spectrum Increasing resistance Destructs normal intestinal flora Secreted via biliary system
What are the macrolides?
Erythromycin, clarythromycin, azithromycin
Used when a patient has a penicillin allergy
Excreted via liver
Pass through cell membranes easily
What antibiotics affect nucleic acids?
Metronidazole
Trimethoprim
Fluroquinolones (Bacteriocidal)
What are the quinolones?
Nalidixic acid and ciprofloxacin
Indirectly inhibit DNA synthesis
What antibiotics target folic acid synthesis?
Sulphonamides and trimethroprim (common for UTIs)
What are side affects of antibiotics?
Nausea, vomiting, diarrhoea
Gentamicin =renal and VIII nerve damage
Ciprofloxacin = tendonitis
Metronidazole = interacts with alcohol
What are the antibiotics which we try to avoid using?
Cephalosporins Co-amoxiclav Ciprofloxacin Clindamycin (Increased risk of c. Diff)
Why does natural resistance to antibiotics occur?
- target isn’t present (eg no cell wall)
- target not accessible (gram positive/negative prevents entry)
- developmental structure/state (eg C.diff spore)
- metabolism
What are biofilms?
Communities of microorganisms which is a three dimensional and contains interfaces.
Uneven distribution of population (spatial heterogeneity)
Permeated by water channels
They are organisms resistant to antimicrobial agents and host defences.
What are persistor cells?
Cells which are not resistant, are metabolically inert and exist in sub populations of cells
What are the three types of HGT?
Natural competence = release of DNA
Bacteriophage = release of phage
Sex pilli = release of sex pill
What are the types of resistance?
Cross resistance = single mechanism, usually affects closely related antibiotics
Multiple resistance = multiple mechanisms, can affect unrelated antibiotics
What are the mechanisms of drug resistance ?
- altered permeability (influx or efflux)
- inactivation of B-lactamase or chloramphenicol acetyl transferase
- altered target site
- replacement of a sensitive pathway
Describe colistin.
(Polymyxin antibiotic)
Polycationic molecule that reacts with outer membrane of gram negative bacteria
Last line of treatment for NDM-1 bacteria
What is NDM-1?
A B-lactamase that is resistant to many different antibiotics
Gram negative (E.coli and k.pneumoniae)
Colostin is the last treatment
What can be said about antibiotics given orally?
They are absorbed by the small intestine and spread to all parts of the body.
However significant amounts are excreted unchanged in the faeces
How do bacteria acquire resistance?
1 -genetic mutation
2- DNA transfer that codes for antibiotic resistance (by transformation, conjunction or transduction)
describe the chain of infection
mode of transmission >portal of entry > susceptible host> infectious microbe > reservoir> portal of exit
what are the 5 modes of transmission?
- Inhalation
- Ingestion
- Inoculation – direct & indirect
- Mother to Infant – Vertical transmission
- Intercourse – STI or STD
what are standard infection procedures?
protocols used to protect against all patients
what are transmission based procedures?
= additional steps for known/suspected infections
a) Contact precautions b) Droplet precautions c) Airborne precaution
what are the 5 moments of hand hygiene?
1 - before patient contact 2 - before aseptic task 3 - after body fluid exposure risk 4 - after patient contact 5 - after contact with patient surroundings
what is each bin used for?
orange bag = clinical waste
black bag = domestic waste
sharps = yellow sharps bind
how can we sterilise equipment?
using an autoclave
