Microbiology Flashcards
Which are the two approaches used to identify microorganisms in clinical specimens?
Direct microbiological diagnosis and indirect microbiological diagnosis.
How are the infective conditions acquired during hospitalization called?
Nosocomial infections (HAI)
What does sterility refer to?
The elimination of all forms of life present onto a certain surface.
What do the Koch’s postulates establish?
The causative relationship between a microbe and a disease?
What is the classification of bacteria based on?
- Anatomical features
- Staining characteristics
- Metabolic properties
- Genetic analysis
- Antigenicity
Which are the different classes of bacteria that can be identified?
- Cocci
- Bacilli
- Coccobacilli
- Vibri
- Fusiform bacilli
- Spirilli
- Spirochetes
What is the gram staining based on?
The different permeability to stains provided by the difference in the thickness of the peptidoglycan layer.
Why are mycobacteria and mycoplasmas stained with the acid-fast techinque?
Because they respectively have an abnormal layer of peptidoglycans and no layer of peptidoglycans.
Which are the main roles of the external structures of bacteria?
They act as:
1. Permeability barrier
2. Adhesins
3. Enzymes
4. Protective structures
5. Antigen disguises
6. Endotoxins
7. Sensing proteins
Why is the cell wall essential for most bacteria?
It prevents osmotic lysis and provides sites for the attachment of drug components and viruses
Which is the most important peptidoglycan making up the cell wall?
Murein
What is a peptidoglycan composed of?
Repeating disaccharides of NAM and NAG associated with 4/5 amino acids:
1/2. vary among bacteria
3. Diamino aminoacids
4. D-alanine
5. Lengthens the cross-links
Which are the enzymes involved in the synthesis of peptidoglycans?
Transglycosilase, transpeptidase and carboxypeptidase.
Which are the drugs that target the enzymes involved in the synthesis of peptidoglycans?
Penicillin and beta-lactam antibiotics.
How can lysozyme disrupt the bacterial cell wall?
By cleaving the polysaccharide chain
What can we find in the cell wall of gram + bacteria?
Virulence proteins, teichoic acid and lipoteichoic acid
What is the composition of the cell wall of gram - bacteria?
Thin layer of peptidoglycans + outer membrane (its outer leaflet is composed of LPS)
Why are LPS important?
Provide permeability and stimulate innate immune responses by binding to PRRs (endotoxins).
What are flagella composed of?
Flagellin
What powers the bacterial flagella?
Proton motive force (chemio-osmotic potential)
What is the axial filament of spirochetes?
An inner flagellum
What is the difference between pili and flagella?
Pili are smaller and not coiled
What are pili composed of?
Pilin protein
What do type I and type II pili-mediated adhesion of bacteria to human cells cause?
Binding of platelets and fibrin to the bacteria, preventing phagocytosis, binding of fibrin to heart valves, and formation of blood clots
Why are F-pili important?
They allow extrachromosomal genetic exchange between bacteria
What are adhesins?
Proteins that bind specific receptors on host cells ensuring a better adhesion.
What are the capsule, S layer, and glycocalyx composed of and what is the difference between them?
Repesting oligosaccharide units of 2/4 monosaccharides that may contain acetic acid or piruvic acid.
Differ based on the quantity of their components and their location:
Capsule –> discrete, outside cell wall
Slime layer –> less discrete, in the matrix
Glycocalyx –> thin layer on the surface of bacteria growing in nature
What are pili composed of?
Pilin protein
What are the functions of the capsule?
- Antiphagocytosis
- Prevention of neutrophil killing
- Prevention of complement-mediated cell lysis
- Inhibition of PMN leukocyte migration
- Adhesion
- Toxicity
- Protection of anaerobes against oxygen
- Determination of colonial type: smooth, rough or mucoid
What happens in the quellung reaction?
Antibodies bind to the bacterial capsule allowing it to be visualized under microscope
Where and in what form can we find the DNA in a bacteria?
In the nucleoid, in form of a single chromosome
What is the importance of the extrachromosomal DNA?
It is not vital but it confers selective advantages, such as antibiotic resistance
Why is the lack of the nuclear structure important?
Because it allows transcription and translation to take place simultaneously
Why is bacterial genome different from the eukaryotic one?
It does not have histones and also have fewer non-coding regions and introns
Which subunits make up the bacterial ribosome?
30S + 50S = 70S
What is the bacterial cytoplasmic membrane composed of?
Phospholipids. It lacks sterols which are replaced with terpenoids (also called isoprenoids)
What are granular inclusions?
Storages of ions, metabolites and vitamins.
What does it mean that the bacterial cytoplasm has glass-like properties and how can it be fluidised?
It means that it can change from a liquid-like state to a solid-like state in a component size-dependent fashion. Cell metabolism increases its fluidity.
Where does bacterial chromosome replication starts?
At its origin, attached to the cell wall
What are pili composed of?
Pilin protein
What is the generation time and what defines it?
It is the interval required for a cell or an entire population to divide and it is defined by temperature, pH, nutritional conditions, medium, etc.
What are pili composed of?
Pilin protein
Which are the 4 bacterial growth stage and what chracterizes them?
- Lag phase –> number of cells stable, protein synthesis occurs
- Log phase –> exponential growth
- Stationary phase –> growth rate = death rate
- Death phase –> growth rate < death rate
What are endospores and why are they needed?
They are bacterial structures which enable bacteria to stay alive, without replication, in non favourable conditions and still infect other organisms
What is germination?
It is the proccess thorugh which, under favourable conditions, an endospore can germinate back into a vegetative cell
Why are antibiotics against bacterial DNA selectively toxic?
Because bacterial DNA is packed differently from the eukaryotic one
How can a new genotype be formed?
DNA mutations or genetic exchange
Which are the 2 ways in which genetic exchange can occur?
Recombination or transfer
Which are the 2 types of recombiantion?
Homologous and non-homologous
Which are the 3 transfer mechanisms?
Transformation, transduction and conjugation
What is the competence state of a bacteria?
Is a state of increased cell wall and cell membrane permeability, necessary for transformation to occur. Selected factors and DNA binding proteins are also available in this state.
What is the transformasome?
Is a particular organelle of gram - bacteria that sequesters the uptaken DNA and trasnfers it within the cell.
What occurs during transduction?
DNA is transferred from a cell to another by a bacteriophage
What occurs during transformation?
Bacteria ingest free DNA from the environment and incorporate it in their genome
What is lysogenisation?
Is the process through which a bacteriophage (prophage) injects its genetic material in a bacterium and this is integrated in the bacterial genome.
What is the difference between generalized and specific transduction?
In generalized transduction the phage transduces random sequences of bacterial DNA insted of the viral one.
In specialized transduction the phage transuces specfic sequences of bacterial DNA close to the site of attachment of the prophage.
What are defective phages?
Phages whose essential viral genes have been replaced by host bacterial DNA, therefore cannot mature and replicate, but can still infect other cells.
What occurs during conjugation?
ssDNA from the F plasmid of a donor cell is tranferred into another cell, which lacks the plasmid, through a pilus. DNA Polymerase then synthesizes a complementary strand in both.
What is an episome?
A plasmid able to integrate with the bacterial chromosome after transfer from the host cell.
Which important characteristics are given to the bacteria by the genes found in the plasmid?
- Surface antigens
- Metabolica activities
- Production of antimicrobial agents
- Virulence factors
- Drug resistance traits
Why certain strains of Staphylococcus Aureus are penicillin resistant?
Because of the expression of the genes encoding for the beta lactamase enzyme when penicillin is detected in the environment
What is the R factor?
Plasmids of gram - bacteria that confer antibiotic resistance
Why excessive administration of antibiotics should be avoided in therapy?
Because certain strains are able to change their expression of the antibiotics binding sites when there is a high concentration of antibiotics in the environment
Which are the 3 types of ecological relationships that a bacteria can establish?
Microbial interactions, host-parasite interactions and environmental interactions
How can we divide ecological interactions?
Symbiosis, Mutualism, Commensalism and Parasitism
What occurs during transformation?
Bacteria ingest free DNA from the environment and incorporate it in their genome
What are the microbiota, the resident flora and the transient flora?
- Complex of all microorganisms present in a certain location
- Microorganisms typically occupying a specific niche in our body
- Microorganisms that occupy a specific niche of our body only transiently
Which are the contaminated sites and which are the sterile sites in our body?
- Skin, upper respiratory tract, GI tract, genito-urinary tract, conjunctivae and the outer ear
- CNS, blood, internal organs, inner and middle ear, lower respiratory tract, muscles, bone, bone marrow and sinuses
What does microbial growth depend on?
Nutrient availability, environmental parameters, competition and host immune system
Which are the 4 steps of an infectious process?
- Entrance
- Colonisation
- Invasion
- Multiplication
What is a vector?
It is a carrier of a microorganism which facilitates its entry into the human body (usually animals, in particular arthropodes)
What is a carrier individual?
Is a symptomless individual which harbours the microorganism and is able to transmit it to an healty individual
What is the difference between an epidemic, and endemic and a pandemic?
- Occurs suddenly with numers clearly over the expectancy
- Disease prevalent in a population or geographic area
- Widespread epidemic occurring throughout a region, country, continent or globally
What occurs during transformation?
Bacteria ingest free DNA from the environment and incorporate it in their genome
What are emerging infectious diseases?
New diseases and deseases with increasing incidence, such as HCV
What is pathogenicity?
It is the ability to produce pathologic changes in a host
What is virulence and what describes it?
It is a measure of pathogenicity defined by the quantity of microorganisms of microbial products necessary to induce disease in an experimental animal. It is defined by:
1. Dosage –> number of pathogenic microorganisms entering the host and causing disease
2. LD50 –> number of microorgansims required to cause lethality in 50% of the test hosts
3. True pathogen –> infectious agent capable of causing disease in a host
4. Opportunistic pathogen –> harmless microorganism that becomes pathogenic only under favourable conditions
What is an infection?
Colonisation and/or invasion and multiplication of pathogenic microorganissms in the host with or without the manifestation of disease
What is a disease?
Is an abnormal condition of body functions or structures that is considered to be harmful to the affected individual
How can diseases be divided?
- Benign –> abnormal condition which is not life-threatening
- Malignant –> serious disease which tends to get progressively worsen and potentially lethal.
What is morbidity
Is the condition of suffering from a disease.
What is the difference between direct and indirect tissue damage?
Direct tissue damage is mediated by toxins and enzymes while indirect tissue damage is due to the host immune responses (hypersensitivity reactions)
Which are the factors influencing bacterial pathogenicity?
- Colonisation factors
- Invasins
- Degradative enzymes
- Toxigenicity
Which type of bacteria produce endotoxins and which are their effects?
Endotoxins are components of the outer membrane of gram - bacteria and their effects include: fever, leukopenia or leukocytosis, metabolic effects, release of lymphocyte factors, septic shock, disseminated intravascular coagulation and organ necrosis
How do gram - and gram + bacteria promote septic shock?
- LPS - LPS binding protein complex bind to CD14 and TLR4 on macrophages causing release of proinflammatory cytokines
- Glycopeptide/techoic acid complex binds TLR2 on macrophages causing release of proinflammatory cytokines
Which type of bacteria produces exotoxins and which are the 3 different types?
Exotoxins are produced by both gram + and gram - bacteria and can be divided into superantigens, cytotoxins and AB toxins.
3 types of superantigens
- Toxic shock syndrome toxins
- Staphylococcal enterotoxins
- Erythrogenic toxin A or C
What to cytotoxins target and which are 3 types of cytotoxins?
They target cell membrane components and include:
1. Phospholipases
2. Thyol-activated cytolisins
3. Detergent-like activity on cell membrane
What to AB cytotoxins target, what is their structure, and which are the major ones?
They target intracellular components and are formed by an A (active) subunit and a B (binding) subunit. Include:
1. Diphteria toxins
2. Shiga/Shiga-like toxins
3. Toxins targeting cAMP –> Cholera toxin, Enterotoxigenic Escherichia Coli and Bordetella Pertussis toxin
4. Clostridium tetani and Clostridium botulinum toxins
What is the definition of microbiota?
It is the community of microbes that live in and on an individual
What is the definition of microbiome?
It is the full complement of microbes, their genes and genomes in a particular
environment
Which are the methods used to study the microbiome?
Bacterial cultures in lab and molecular studies on DNA, RNA, proteins and metabolites
What is the major result of the human microbiome project?
The understanding that each individual has its own microbial communities, which vary depending on:
1. birth conditions
2. breast feeding / food
3. geography
4. hygiene
5. stress
6. age
7. drugs (hormones and antibiotics mainly)
Which factor is responsible for the different concentration of microorganisms in the gut?
Decrease in acidity going from the stomach to the rectum
Why is the metabolization of carbohydrates into short chain fatty acids performed by bacteria important?
Because SCFA are condsidered to be protective for gut physiology (i.e., against cancer)
Which are the major components of the eubiotic gut microbiota?
Bacteroidetes and firmicutes
What is the gut dysbiosis and to what is it associated?
It is an unbalance in the microorganisms of the gut and is related to metabolic diseases such as diabetes, IBD, and colon cancer
Which cells are part of the only layer that divides our organisms from our gut microbiota?
- Enterocytes
- Paneth cells
- M cells
- Goblet cells
- Stem cells
What is the difference between the microorganisms found in the mucous membrane and the ones found in the lumen?
In the mucous membrane there are blood vessels which make oxygen available for aerobial microorganisms, while in the lumen there is a low content of oxygen and an high concentration of hydrogen sulfide, a product of bacteria metabolism
Which are the components of the immune system in the gut?
- GALTs –> in particular Peyer’s patches found underneath the single epithelial layer
- Secretory IgAs found in the mucous layer
- Intraepithelial lymphocytes
- Macrophages, NKs and eosinophils
What is the peculiarity of clostridium difficile infections?
There are 2 patterns of infection:
1. Endogenous –> due to assumption of antibiotics for a long time
2. Exogenous –> cause by spores generated by anaerobial bacteria of the clostridium difficile family which are able to survive in the environment. It accounts for the majority of HAI
Which is the difference between endogenous and exogenous infections?
Endogenous –> we become infected with our own bacteria, our own microflora. This might happen if a barrier between sterile and non-sterile tissues is broken, such as with a bowel perforation.
Exogenous –> we become infected with our own bacteria, our own microflora. This might happen if a barrier between sterile and non-sterile tissues is broken, such as with a bowel perforation.
Which is a major difference between staphylococci and streptococci?
Staphylococci are catalase posoitive while streptococci are catalase negative
Which are the 2 classification methods of streptococci?
Lancefield grouping and the grouping based on haemolytic patterns
How can we test for streptococcus pyogenes infections?
ASO test, antistreptolysin O Ab
Which are the 2 types of streptolysins produced by streptococcus pyogenes?
Streptolysin S and O
Which are the clinical manifestations of streptococcus pyogenes?
- Streptococcal sore throat
- Fever (can be scarlet fever)
- Skin infections –> Impetigo, erysipelas and necrotising fascitiis
If primary infection is not properly treated can lead to:
- Rheumatic fever
- Post streptococcal glomerulonephritis
Which are the symptoms associated with Streptococcus Agalactiae infections?
Neonatal meningitis and sepsis, septic abortion and purpureal gynaecological sepsis in the mother
How can we test for Streptococcus Agalactiae infections?
CAMP test and Hippurate test
Which are the symptoms of Streptococcus pneumoniae infection in children and elderly?
Meningitis and otitis in children younger than 3 years and severe pneumoniae in adults older than 65
Which are 2 types of vaccines against streptococcus pneumoniae?
- Streptococcal conjugate vaccine
- Streptococcal polysaccharide vaccine
How can staphylococci be identified?
- Oxidative reaction
- Catalase reaction
- Glucose fermentation
- Coagulase reaction
Which pathogeinic molecules does the cell wall of staphylococci contain?
Techoic acids and protein A
Where is staphylococcus aureus normally present and how can it be transmitted?
It is normally found in anterior nares, axilla, vagina and pharynx and it can be transmitted thorugh direct contact with an infected individual, contaminated objects or through traumatic introduction
Which are predisposing conditions for S. Aureus infection?
Ongoing chronic inflammations, immunosuppression, skin lesions
Which are the main toxins released by S.Aureus and what do they cause?
- Exfoliative toxins A ad B are resonsible for Ritter’s disease and bullous impetigo
- TSST-1 is responsible for T cell activation and subsequent release of cytokines which cause multi systemic failure and ultimately leads to toxic shock syndrome.
- Enterotoxin A, a heat resistant toxin responsible for food poisoning
- Cytolytic toxins, responsible for neutrophil lysis and subsequent release of lysosomal enzymes which damage nearby cells.
Which are 2 important enzymes released by S.Aureus and which are their functions?
- Hyaluronidase –> favours the spread of bacteria by dissociating hyaluronic acids
- Penicillinase –> inactivates penicillin by breaking the beta lactamine rings
What is the peptidoglycan mediated cytotoxicity?
Lysis of S.Aureus causes release in the environment of techoic acids and glycopeptides which bind to TCR on macrophages and DCs causing activation of signaling pathways and subsequent gene transcription of proinflammatory cytokines Il-1, Il-6, Il-8, TNF alpha and PAF
What is the pathogenic factor of S.Epidermidis?
Its polysaccharidic biofilm which physically blocks antibodies and antibiotics, and may also contain fungal cells such as Candida Albicans
Why can S.Epidermidis adhere so well to epithelial cells?
Because of fibrinogen and collagen bindig proteins
Which diseases are caused by S.saprophyticus and which individuals are mainly infected?
UTI infections are more common in sexually active women because of the increased adherence to epithelial cells
Which are the main types of lab diagnosis we can perform to identify and differentiate Staphylococci?
- Microscopy
- Nucleic acid based test
- Culture
- Enzymatic tests
- Antibody detection
Which are the 3 main characteristic that are checked by microscopy?
- Gram staining (+ for staphylococci)
- Cell arrangement (pairs or clusters)
- Presence/absence of PMNs (many PMNs in case of S.Aureus because it gives rise to pyogenic diseases)
How is the catalase reaction performed?
Drop of H2O2 on a colony smeared on a slide. If bubbles form the test is positive, if bubbles don’t form its negative
How is the coagulase reaction performed?
Drop of rabbit blood on a colony spread on a slide. If agglutination occurs the test is positive, otherwise it is negative
How can gram + bacilli be divided?
- Spore forming
- Non sporing
- Bacilli with branching filaments
Which are the 2 main virulence factors of bacillus anthracis?
The capsule and the toxins it produces
Which are the plasmid genes responsible for the synthesis of the capsule and of the toxins and why are they so important?
Respectively they are the pxO2 and pxO1 and bacteria lacking one or more of these plasmids have low virulence. In particular, bacteria lacking the pxO2 (capsule -/toxin +) are used in attenuated vaccines.
Which are the 3 main toxns produced by bacillus anthracis?
- Edema factor
- Protein antigen
- Lethal factor
1+2 = edema toxin
2+3 = lethal toxin
Why can bacillus anthracis infection differ and which are the 3 different presentations?
The infections differ based on the site of entry and can be either cutaneous, pulmonary or gastrointestinal
Which are the 2 major toxins produced by bacillus cereus?
- Heat and acid stable toxin
- Heat lable toxin
Why do clostridia differentiate from gram + bacilli?
Because they are anaerobic bacteria instead of aerobic
Which are the 4 groups of clostridia?
- Tetanus group
- Gas gangrene group
- Acute colitis group
- Food poisoning group
Which are the 5 most lethal toxins produced by clostridium perfringens?
- alpha
- beta
- epsilon
- iota
- C. Perfringens enterotoxin
Which is the reaction used to identify the alpha toxin of clostridium perfringens?
The Nagler reaction
How many different types of C. Perfringens are there?
5, A to E
Which are the symptoms of C. Perfringens type A infection?
Soft tissue infection (cellulitis, fasciitis and gas gangrene), food poisoning and primary septicaemia
Which are the symptoms of C. Perfringens type C infection?
Necrotising enteritis
How is gas gangrene treated?
Surgical debridement and high dose penicillin
How is food poisoning by C. Perfringens treated?
Oral rehydration and intravenous administration of fluids and electrolytes
Why is culture of bacteria not commonly used in lab diagnosis in case of C. Perfringens type A food poisoning?
Because it is a clinical diagnosis
How can C. tetani survive in oxygenated environments?
By production of round spores starting at the terminal end
Which are the 2 toxins produced by C.tetani?
- Oxygen-lable haemolysin (tetanolysin)
- Heat-lable neurotoxin (tetanospasmin)
Which are the neurotransmitters whose production is inhibited by the tetanospasmin toxin?
The inhibitory neurotransmitters glycin and GABA, resulting in unregulated excitatory synaptic activity and consequent spastic paralysis
What does the incubation period depend on?
It is directly proportional to de distance of the primary wound infection from the CNS
Which are the 3 types of tetanus diseases?
- Generalized
- Localized
- Neonatal
What causes the risus sardonicus?
The sustained contraction of the facial muscles, in particular the masseter, in the generalized tetanus
Why can’t tetanospasmin be detected in patients?
Because it is rapidly internalized in motor neurons
What is the treatment for C.tetani?
Surgical debridement of primary wounds, penicillin or metronidazole to kill bacteria and limit toxin production, and passive immunization through human tetanus Ig to neutralize unbound toxins.
How many botulinum toxins are there and which are the ones associated with human diseases?
- A,B,E and F.
The regulation of which neurotransmitter is inhibited by botulinum toxins?
Acethylcholine, resulting in blockage of neurotransmission at peripheral synapsis, which results in flaccid paralysis
Which are the different types of botulism?
- Classical or foodborne
- Infant
- Wound
- Inhalation
What is the treatment required for patients affected by botulism?
- Ventilatory support
- Gastric lavage
- Penicillin/metronidazole
- Trivalent botulinum antitoxin against type A,B and E toxins
Which are the 2 toxins produced by clostridium difficile?
Enterotoxin (toxin A) and cytotoxin (toxin B)
How can C.difficile infections develop?
After alteration of the microbial flora, for example after antibiotic therapy
What is the treatment for C. Difficile infections?
- Discontinuation of previous antibiotic treatment in case of mild disease
- Therapy with vancomycin/metrodinazole in case of severe diarrhea or colitis
How are the non spore-forming gram + bacteria divided?
- Corynebacterium
- Listeria
- Erysipelothrix
How are Corynebacteria structurally arranged?
Into structures that resemble either chinese letters or palisades
Where can we normally find corynebacteria?
Nasopharynx and skin
Which are the 2 main media used to culture Corynebacteria?
- Loeffler’s medium, which identifies Babes-Ernst granules
- Tellurite media, used to differentiate between gram + bacteria
What are the Babe-Ernst granules and which stain is used to identify them?
They are metachromatic granules of polymerised polyphosphoric acid visualized by methylene blue staining
What is peculiar of C.Diptheriae, C.Ulcerans, and C.Pseudotubercolosis colonies grown in tinsdale media?
The formation of ferric sulphide causes the formation of brown halos around the colonies.
How can we classify Corynebacteria based on growth characteristic of the colonies?
- C. Mitis –> black colonies with grey periphery
- C. Gravis –> large grey colonies
- C. Intermedius –> small, dull grey colonies
