1
Q
What are common methods for identification and classification of bacteria?
A
- microscopy: morphologys and staining properties
- bacterial Ag: Ab to detect H,K,O
- detect bacterial nucleic acids; PCR, sequencing
- culture: metabolic properties, biochemical testing
- Ab response to bacteria: ELISA, western blot, immunostaining
2
Q
What is a cocci?
A
Sphere
3
Q
What is a bacilli?
A
Rod- straight or curved
4
Q
What is a spirochetes?
A
Spiral
5
Q
What are the layers of a gram positive bacterial cell wall?
A
Thick peptidoglycan
plasma membrane
6
Q
What are the layers of a gram negative cell wall?
A
Thick outer membrane
thin peptidoglycan
periplasmic space
plasma membrane
7
Q
What are the steps of a gram stain?
A
- Crystal violet turns everything purple
- Precipitate with gram iodine = still purple
- Decolorizer = crystal violet can’t get out of gram positive bilayer so it stays purple
- safranin red = turn gram negative pink
8
Q
What is the function and importance of peptidoglycan?
A
In both gram +/- organisms
- unique to bacteria for drug targeting
- layer provides protection: osmotic and physical bilayer
9
Q
What is the structure of peptidoglycan?
A
- linear chains of NAG and NAM with Beta 1-4 linkages
- tetrapeptide crosslinks linear polymers
- pentaglycine bridge in some gram +
10
Q
What effects does peptidoglycan have?
A
Proinflammatory
- activate complement
- bind pattern recognition receptors to trigger inflammatory cytokines
11
Q
What are the components of a gram-positive envelope?
A
- Peptidoglycan: many layers with crosslinks
- teichoic and lipoteichoic acid: which attach peptidoglycan to membrane, attach to other bacteria and host cells, and are virulence factors
12
Q
What are the components of a gram-negative envelope?
A
- peptidoglycan: greatly reduced in comparison to gram+, in periplasmic space
- surrounded by outer membrane rich in porins and lipopolysaccharide
13
Q
What are the components of a gram-negative outer membrane?
A
- stiff sack for structure and permeability barrier
- rich in porins = metabolites
- LPS in outer leaflet
14
Q
What are the components of lipopolysaccharide/endotoxin?
A
- Lipid A: endotoxin activity = proinflammatory cytokines
- Core polysaccharide: 9-12 sugars for structure and rigidity
- O Ag: linear polysaccharide allows distinguish between organisms
15
Q
What are the effects of LPS/endotoxin?
A
- bind CD14 and TLR4 on phagocytes
- activate immune system
- cause inflammation through TNF-a, IL-1, IL-6
16
Q
What are acid-fast bacteria?
A
- mycobacteria and nocardia
- mycolic acid: LBCFA thick waxy cell wall
- slow growing and difficult for nutrition to get in
- difficult for Ab to get in
17
Q
What are the components of an acid-fast bacterial wall?
A
- inner plasma membrane overlaid with peptidoglycan
- lipoarabinomannan (LAM): related to LPS
- arabinogalactans: branched polysaccharides that bind to mycolic acid
- mycolic acid: waxy
18
Q
What is the purpose of pili/fimbrae?
A
- protein subunits (pilin) form hollow tube
- common or somatic: sued in attachement
- sex: 1/cell used in gene transfer, plasmid transfer
19
Q
What is the purpose of flagella?
A
- locomotion
- different arrangements = identification
- virulence = able to dessimate more easily if can migrate through tissues
20
Q
What is a capsule/K-Ag?
A
- loose polysaccharide layer surrounding some gram + or - bacteria
- hydrophilic
- aides in protection from immune system
21
Q
What is a biofilm?
A
Organized community of microbial cells that has a capsule/slime layer over the entire population.
22
Q
What is an endospore?
A
- in some gram + in harsh environment
- convert from vegetative to dormant
- give rise to single bacteria when environment favorable
- dehydrated, with single copy of chromosome
- Ca bind to dipicolinic acid to stabilize genome
- inner membrane peptidoglycan layers with outer keratin coat
23
Q
What do endospores mean for human pathology?
A
- spores can be aeroslized
- found in variety of environments for extended times
- must sterilize surfaces
- can exist for centuries
24
Q
What is the main difference between bacteria and eukaryotes?
A
The metabolic differences between these two cell types can be utilized for the development of antibacterial therapies
25
What are the different phases of the optimal growth curve for bacteria?
1. Lag: initial period of adaptation. sensitive to antimicrobials. little cell division
2. exponential: multiply rapidly by binary fission. most susceptible to certain antibiotics
3. stationary: nutrients depleted. stopped but not dying. sporulation begins
4. decline: more bacteria killed than division
26
What is obligate aerobic?
exclusively uses respiration to meet its energy need
27
What is obligate anaerobic?
exclusively uses fermentation to meet its energy need
28
What is microaerophilic?
Grow best at low O2 but can grow without O2 as well
29
What are the two enzymes present in aerobic bacteria?
Catalase and superoxide dismutase
30
What is the function of catalase?
H2O2 = water + O2
31
What is the function of superoxide dismutase?
detox superoxide anion
32
What is respiration?
substrate oxidation coupled to electron transport
- aerobic = O2 final acceptor
- anaerobic = other final acceptor
- efficient ATP generation
33
What is fermentation?
Anaerobic process, metabolic intermediate derived from fermentable substrate end products can be measured
34
Is aerobic or anaerobic more efficient?
Anaerobic less sufficient = 2ATP/glucose while TCA = 38ATP/glucose
35
What is unique of nucleic acid biosynthesis of bacteria?
-bacteria synthesize folate while humans gain from diet for synthesis of purines and thymidine
36
What is unique of bacterial DNA replication?
Topoisomerase II or IV are required for DNA recombination and repair and are target of quinolones.
37
What is unique of bacterial transcription and translation?
- 70S ribosomal subunit, humans have 80S
- occur simultaneous b/c no nuclear envelope
- inhibited by rifampin
38
What are the steps of peptidoglycan synthesis?
1. activation of carbohydrate subunits by binding with UDP
2. Pentapeptide added on independent of mRNA and ribosomes (ending with 2x D-ala)
3. activated NAM-UDP transferred to bactophrenol with pyrophosphate link and UMP release
4. NAG from NAG-UDP transferred to bactophrenol-NAM-pentapeptide
5. bactophrenol carrier trasnports NAG-NAM across to outside membrane
6. disacchardie attached to end of growing chain by transglycosylases
7. pyrophosphobactophrenol is converted back to phosphobactophrenol and recycled
8. transpeptidation: link peptide side chains at free amino of diamino and 3rd position so D-ala is released
39
What is transpeptidation?
-cross linking of peptide chains by peptide bond exchanger
-occurs on outer leaflet
=transpeptidase and carboxypeptidase (penicillin binding proteins) remove D-ala to limit cross links
40
What is a bacterial chromosome?
Large, circular DNA that comes in variety of sizes
41
What is a plasmid?
small DNA molecule separate from chromosome
- can be replicated or split
- can be incorporated into host
42
How do bacteria regulate gene expression of self?
- sensory proteins to detect environment
- highly regulated to prevent waste of energy
- regulon: a group of genes that are regulated as a unit and have further effectors on eachother
43
How do bacteria regulate gene expression on the population level?
low level low density autoinducers
| -modify transcription
44
What is transformation in bacteria?
Uptake of free DNA from envrionment
| -can gain new genes and resistance very quickly
45
What is conjugation in bacteria?
- acquisition of new DNA from another viable bacterium
- DNA transfer directly by sex pilus
- requires Fertility factor with tra genes for sex pilus and oriT for where break occurs
46
How does an F+ x F- conjugation occur?
- unidirectional
- f- goes to F+
- oRt transfers to cell then the enitre plasmid transfers over and circularizes
47
How does a Hfr x F- conjugation occur?
- F facor in chromosome
- form bridge
- DNA transfer begins with OriT
- bridge doesnt stay long enough for entire chromosome to transfer but enough for f factor to transfer
- no sex change occurs because no tra genes exchanged because they are at the end
48
What is transduction in bacteria?
- transfer of bacterial DNA via a bacteriophage
- lytic/virulent phage = lytic replication upon entry
- temperate phage = integration into chromosme and can excises and undertake lytic replication later
49
Why are lysogenic phages important?
- toxins are encoded on bacteriophage
- if give antibiotic that kill bacteria, cause increase in bacteriophage because senses state
- start replicating and increase genetic material of the phage
- upregulate the toxin and cause the disease to be much worse
50
What is intrinsic antibiotic resistance?
- not transferable horizontally between bacteria
- not increasing among bacterial populations
- ex: lack of Ab target (no cell wall in some species)
51
What is chromosome-mediated antibiotic resistance?
- through random mutation
- homologous recombination with antibiotic resistance gene
- mutation occurs in chromosome that allows bacteria to now be resistant
52
What is plasmid-mediated antibiotic resistance?
- genes encoding antibiotic resistance are located on a plasmid
- degrade/modify and antibiotic or an efflux pump to get it out of cell
- resistance factor R = what it needs for conjugation
- resistance determinant- drug for resistance
53
What are bacterial transposons?
- mobile DNA elements that can transfer themselves from one mol DNA to another
- in bacterial cells and viruses
- indirect repeat sequences on end
- gene for transposase the enzyme for transposon movement
- can contain a single or multiple antibiotic resistance genes
54
What are integrons?
- diverse group of genetic elements
- encode site specific recombination system
- can capture antibiotic resistance gene
- associated with large mobile genetic elements like plasmids or transposons
- important role in spread of drug resistance
55
What are pathogenicity islands?
- large transpsons
- large pieces of dna that dont normally carry antibiotic resistance
- carry virulence genes surrounded by insertion sequences that cause toxins and pili to hop between bacteria
56
What is selective toxicity?
leverage biochemical differences to kill or inhibit the growth of a microorganism without harming host cells
57
What is bacteriostatic chemotherapy?
stunts growth so immune system can come in and kill
58
What is bactericidal chemotherapy?
when immune system cant be counted on, used to kill bacteria
59
What are broad-spectrum antibiotics?
Cover a large spectrum of bacteria
- pro: more likely to cover unknown cause of infection
- con: possible disruption of normal microbiota
60
What are narrow-spectrum antibiotics?
Cover only a small subset of bacteria
- pro: avoids disruption of the normal microbiota
- con: must identify causitive agent to be confident of coverage
61
What is antibiotic synergism?
Combination of two antibiotics will enhance bactericidial activity
62
What is antibiotic antagonism?
combination of antibiotics in which one interferes with the activity of the other
63
How does antibiotic resistance arise?
- naturally occurring acquisition from other bacteria or mutation
- antibiotic select against sensitive bacteria for resistant
- antibiotic use leads to antibiotic resistance
64
What is minimum inhibitory concentration?
lowest concentration of antibiotic that inhibits growth
| -test with kriby-bauer/disk-diffusion assay
65
What is minimum bactericidal concentration?
lowest concentration of antibiotic that kills 99.9% of cells
66
How is a kirby-bauer/disk-diffusion assay performed?
- spread bacteria evenly on agar plate
- drop paper discs with defined amounts of antibiotics on agar
- allow to grow
- measure zone of inhibition and compare to known values
67
What is a sensitive category resistance?
implies the isolates are inhibited by the usually achieved concentrations of the antibiotic
68
What is an intermediate category resistance?
implies the isolates will be inhibited in body sites where the drug is physiologically concentrated or when a high dosage of drug can be used
69
What is a resistant category resistance?
implies the isolates are not inhibited by the usually achieved concentrations of the antibiotic
70
What are the mechanisms of antibiotic resistance?
- altered permeability, decreased influx or increased efflux
- alteration of target
- modification or breakdown of the antibiotic
- lack of target
71
What are cell-wall active antibiotics?
- disrupt peptidoglycan synthesis
| - effective against actively dividing bacteria
72
What are membrane active antibiotics?
- disrupts or interferes with membrane integrity/synthesis
| - effective against resting and actively dividing bacteria
73
What are beta-lactams?
- peptidoglycan synthesis inhibitors
| - bind transpeptidases and prevent crosslinking of strands
74
What are mechanisms of beta-lactam resistance?
- decreased uptake
| - antibiotic degradation with b-lactamase
75
What are B-lactamase inhibitors?
- irreversibly bind and inhibit action of susceptible b-lactamases
- in situations where resistance may be a problem
- given with b-lactam
76
What is vancomycin?
-prevents polymerization of the growing peptidoglycan chain via binding to terminal D-ala D-ala
77
What is vancomycin resistance?
modficiation of peptidoglycan subunits with terminal d-ala and d-lactate to prevent vancomycin binding
78
What are tetracyclines?
- bind 30 s subunit
| - tetracycline, doxycycline
79
What are aminoglycosides?
- bind 30s subunits
| - gentamicin kanamycin
80
What are macrolides?
- bind 50s subunit
| - erythromycin, azithromycin
81
What are quinolones?
-inhibit DNA replication, recombination, and repair via interaction with DNA gyrases
82
What are rifampin and rifabutin?
binds to DNA-dependent RNA polymerase and inhibits initation of RNA syntehsis
83
What are metronidazole?
reduced by bacteria = toxic compounds that damage DNA
84
What are microbiota?
community of microbes that live in or on an individual
85
What is microbiome?
collection of genes from the microbiota
86
How does intestinal microbiota protect from infection?
- occupy available niches to prevent colonization
- primes innate imunity by stimulating mucin, IgA, and antimicrobial peptide production/secretion
- promotes epithelial cell resistance and low level recruitment of inflammatory cells
87
What are strict pathogens?
organsims always associated with disease
88
What are opportunistic pathogens?
- members of nomal microbiota
| - take advantage of certain conditions to cause disease
89
What gets in with contamination of intravenous catheters?
- staph epidermis (skin)
| - staph aureus (skin)
90
What gets in with wounds or surgical site infections?
- staph aureus (skin, nares)
- k pneumoniae (intestine)
- pseudomonas aeruginosa (skin)
91
What gets in with tooth decay?
-strep mutans (teeth)
92
What occurs with aspiration pneumonia?
-inhalation of fluid = mixed infection
93
What causes UTI?
e coli (intestine)
94
What causes pseudomembrane colitis?
c diff (intestine)
95
what causes otitis media?
strep pneumoniae, H influenze, and moraxella catarrhalis (nasopharynx)
96
What is pathogenicity?
ability of a microorgansim to cause disease
97
What is virulence?
measurement of pathogenicity
98
what are virulence factors?
-factors produced by organisms that enable: colonization, immune evasion and immunosuppression, entry into, survival within and exit from host cells, obtain nutrients
99
Where are entry points into the host?
- transplacental
- secretions- aerosols and mucosal
- stool: fecal to oral
- skin: cuts
- blood: sti and drug use
- zoonotic: animal to human vector
- arthropod: reservoir or vector
100
What is adherence?
binding of bacterial adhesin to the host cell surface
- adhesins often associated with bacterial pili
- specific adhesin and receptor combinations
101
What are biofilms?
- sessile
- group encased in exopolymeric substance
- slower metabolism, increased resistance to antibiotics
- increased genetic exchange
- resistant to disinfection
- commonly on moist/wet
102
What is the pathogenic action of bacteria?
- toxin production
- hijack machinery to facilitate uptake
- modulate maturation of the phagosome to promote survival
- move from the original site of infection to cause disease elsewhere in the body
- some send toxins elsewhere
103
What are the effects of bacteria?
- tissue destruction by byproducts of bacterial growth
- destruction by bacterial secretion of degradative enzymes and toxins
- endotoxin-lipid A products that directly harm tissue or lead to destructive biological activities
104
What are superantigens?
bind both t cell receptor and MHC 2 without a requiring antigen
0activate large numbers of t cells and increase inflammatory cytokines
105
How do bacteria escape host defenses?
- encapsulation: poor Ag, mask Ag epitopes on bacterial surface, prevent Ab bind
- antigenic mimicry: bacteria produce compounds the host sees as self
- antigenic variation/shift: some bacteria quickly change Ag make up of proteins on cell surface
- inactivation of Ab: secretion of proteases that degrade Ab isotypes
- ressitance to complement mediated killing; limiting access to membrane and degradation of components of complement
106
What are the two important differences about fungal cells in comparison to humans?
- have a cell wall without peptidoglycan
| - membrane is composed of ergosterol
107
What are yeast?
- unicellular spherical
- reproduce by budding
- can create pseudohyphae
- candida = germ tube
108
What is mold?
- ribbons and fuzzy cotton
- hyphae = single strand; mycelium = group of strands
- septated or aseptated
- asexual reproduction: offspring are conida
- sexual reproduction: offspring are spores
109
What are superficial mycoses?
infection of outermost layers of skin and hair
110
What are cutaneous mycoses?
infection which extends deep into the epidermis as well as invasion of hair and nail infections
111
What are subcutaneous mycoses?
infections involving the dermis, subcutaneous tissues, muscle, and fasica
112
What are systemic mycoses?
infections that originate primarily in the lung but may spread to any organ in the body
113
What are opportunistic mycoses?
infection associated primarily with suppressed individuals
114
What do polyenes target?
bind to ergosterol in fungal cell membrane
| -ex: amphotericin B
115
what do azoles target?
inhibit ergosterol biosynthesis
116
What do allymines/thiocarbamates/morpholines target?
Inhibit enzymes involved in ergosterol synthesis
117
what do echinocandins target?
-inhibit beta-glucan syntehsis
| 0hgihly selective in treating candida and aspergillus
118
How are fungal infections diagnosed?
visualization
- koh prep if needed
- specialized stains
- all stain gram positive
119
What does india ink stain for?
Cryptococcus neoformans
120
What does germ tube test for?
candida albicans
121
What is a virus?
acellular infectious agent
- obligate parasite
- replicate by assembly of pre-formed components
122
What is in a basic virion?
- nucleic acid genome
| - capsid
123
What can also be on a virion?
- lipid layer envelope
- viral attachment proteins
- matrix between envelope and capsid to jumpstart replication cycle
124
How does +ssRNA in virus work?
RNA in orientation that can produce proteins
125
How does -ssRNA in virus work?
complementary as mRNA and are inert if without viral enzymes
126
What is the single stranded DNA family?
parvoviridae
127
What is the dsDNA families (5)?
```
Herpesviridae
Hepadnaviridae
Adenoviridae
Poxviridae
Papovaviridae
```
128
What are dsRNA family?
Reoviridae
129
What are -ssRNA families (6)??
```
Orthomyxoviridae
Paramyxoviridae
rhabodoviridae
Bunyaviridae
Arenaviridae
Filoviridae
```
130
What are +ssRNA families (7)?
```
Togaviridae
Flaviviridae
Cornoaviridae
Retroviridae
Picornaviridae
Caliciviridae
Hepeviridae
```
131
What are properties of RNA virus genomes?
- rna is more labile and transient and replicates more quickly and hangs out in cytoplasm
- cells cannot replicated RNA so virus must encode rna-dependent rna polymerase
- rna polymerase prone to mutation
132
What is the viral naked/non-enveloped capsid structure?
- environemntally stable
- released from cell by lysis
- spreads easily, dry out and retain infectivity
- survive gut
133
What is the structure of viral envelope?
- enviromentally labile and easily disrupted
- modifies membrane in replication
- must stay in moist environment
- spread in large droplets or secretions
- does not need to kill the cell to spread
134
what are the 6 stages of a virus life cycle?
1. attachement
2. entry
3. mRNA production
4. protein and genome synthesis
5. assembly
6. egress
135
How does attachment and entry through direct fusion occur for a virus?
- if enveloped
- fusion b/w protein and envelope to enter membrane
- uncoat and enter cytoplasm
136
How does entry through receptor-mediated endocytosis occur for a virus?
- through vesicle system within walls
- viral attachment on capsid
- invagination
- pinch off to form vesicle
- lysed by naked capsid virion
- if enveloped fusion b/w membrane of vessicle and envelop to be released into interior of cell
137
How does gene transcription occur in viruses?
- if DNA can use host enzyme RNA polymerase to produce mRNA
- ssDNA use host RNA after making it double stranded
- +ssRNA virus no enzyme needed it is the mRNA itself (exception is retrovirus)
- -ssRNA need viral enzyme to produce mRNA, use viral RNA dependent RNA polymerase
- dsRNA also use viral enzyme to get mRNA
138
What is the biggest issue with viral DNA genome replication?
Cellular DNA replication is not always available
- make cellular DNA replication machinery available
- encode viral proteins to syntehsis genome
139
What is biggest issue with viral RNA genome replication?
No cellular RNA dependent RNA polymerase
140
What is the pathway for viral assembly and egress?
1. individual viral proteins form into capsid subunits
2. subunits combine to form complete capsid
3. viral genome and other essential virion components are selectively packaged into capsds
4. envelope acquired
5. virus exits cell
6. virions mature
141
How does budding occur?
release and assembly at same time as budding
- plasma membrane with viral protein patch
- recruit genome and proteins
- bulges out and pinches off
- release viral particle out and membrane is intact
142
How does lysis occur?
Poke holes in cell
| -how virions with naked capsids are released
143
How does viral recombination occur?
1. 2 viruses with double stranded DNA
2. Recognizes by recombination machinery = cross over event
3. get two progeny genomes that are different from either parent
4. can have very different genomic makeup - only works for dsDNA viruses
5. reassortment when have mixtuer of genomic segements
144
what is an acute only infection?
see large bursts of virus replication, immune kicks and kills
-ex: rhinovirus and common cold
145
What is a chronic infection of virus?
burst of virus replication, immune kicks in and starts to fight
-some reason virus is robust or immune is weak and cant rid body of infection and virus continues to replicate for long periods of time
146
What is a latent viral infection?
- acute infection with large burst and immune kicks in and stops infection but does not rid body of infection
- does not produce new genome
- waits in state where it can come out of cell and cause new series of viral disease
- ex: herpes
147
What causes cell injury in virus?
- virus gets in and kills cell
| - cytopathic effect
148
What are viral diagnostic targets?
- Ab = ELISA and western blot
- genomes: PCR and RT-PCR
- Ag =ELISA
- virons = plaque assay
149
What is a plaque assay?
- detects infectious virus
- pro: shows active viral infection
- con: restricted to viruses that replicate in tissue culture and produce cytopathic effect
150
What is electron microscopy?
- detects virion particles
- pro: helpful in ID of emerging viruses
- con: relatively expensive and technically challenging
151
What is antigen detection aka Elisa?
detect: viral proteins and glycoproteins
- pro: sensitive and quick
- con: require specific Ab
152
What is PCR?
detect DNA genomes
- pro: highly sensitive
- con: DNA sequence info must be available
153
What is RT-PCR?
detect RNA genomes
- pro: highly sensitive
- con: RNA sequence info must be available
154
What is serology aka Western Blot?
detect anti-viral Ab
- pro: sensitive and quick
- con: time must be allowed for initiation of the immune response. care must be taken to differentiate present from past infections
