Midterm Flashcards
1
Q
Some characteristics of Microbes include:
A
microscopic, phylogenetic diverse, metabolic diverse, can be beneficial, and can live in a symbiotic relationship with us
2
Q
Microbiota means
A
collection of microbes colonizing our bodies without normally causing disease
3
Q
Microbiome means
A
total number of microbial genomes in a defined environment
4
Q
Resident Microbiota:
A
part of the normal microbiota throughout life; mostly commensal
5
Q
Transient microbiota:
A
remain in/on the body for short period (in competition from other organisms, and is eliminated by the body’s defense cells)
6
Q
Mutualism/Syntropy
A
all members benefit from the relationship
7
Q
Commensalism
A
one member benefits, the other is unaffected
8
Q
Amensalism
A
one member is harmed, the other is unaffected
9
Q
Parasitism
A
one member benefits, the other is harmed
10
Q
The two classes of microbes are:
A
1) Cellular microbes; 2) Acellular microbes
11
Q
Characteristics of Acellular Microbes
A
Without a cell (Viruses, viroid, prions)
Require other organism to reproduce
Simple structures
Wide variety of shapes
Are ultramicroscopic
12
Q
Characteristics of Cellular Microbes - Prokaryotes
A
Archaea and Bacteria
Common shapes (spheres, rods, spirillum, spirochete, vibrio)
Lack nucleus and membrane-bound organelles
<1.0 um in diameter
13
Q
Key organelles of the Prokaryotic cell (7)
A
- Flagellum
- Ribosome
- Nucleoid
- Plasma membrane
- Cell wall
- Cytoplasm
- Glycocalyx
14
Q
Characteristics of Cellular microbes - Eukaryotes
A
Algae, Protozoa, Fungi
Wide variety of morphology
5-100 um in diameter
Have a nucleus and internal membrane-bound organelles
Often multiple chromosomes
15
Q
Key organelles of the Eukaryotic cell (13)
A
- Nucleolus
- Nuclear envelope with pores
- Ribosome
- Lysosome
- Mitochondrion
- Centriole
- Golgi
- Rough ER
- Smooth ER
- Cytoplasmic membrane
- Cytoskeleton
- Vesicles
- Cilium
16
Q
Primary Pathogens …
A
cause a disease in healthy people; infection get worse by a weak or immature immune system
17
Q
Opportunistic Pathogens …
A
only cause diseases when given opportunity
18
Q
Obligate Pathogens …
A
require a host to fulfil their cycle
19
Q
Facultative Pathogens …
A
host is only one of the niches they can exploit to reproduce
20
Q
What are the two categories for the Host Range of pathogens?
A
Narrow (can only effect one); Broad (can infect many)
21
Q
Pathogenicity:
A
pathogens potential to cause infection or disease
22
Q
Virulence:
A
degree or severity of disease
23
Q
Highly virulent pathogens…
A
always lead to a disease state
24
Q
Pathogens with low virulence …
A
more likely to result in mild disease states
25
Continuum:
from avirulent to highly virulent
26
Fatality rates =
Number of deaths
27
The measures of Virulence are...
Medium Lethal Dose (LD50); Medium infectious dose (ID50)
28
LD50:
number of pathogens required to kill 50% of an experimental group of animals hosts
29
ID50:
number of pathogens needed to cause disease signs in 50% of an experimental group of hosts
30
Disease:
disruption of the normal structure or function of any body part, organ or system
31
Infectious disease:
disease caused by a pathogen that caused a disruption of the normal structure of function
32
Infection:
condition of a successful multiplication/colonization of a host by a microorganism
33
Sign:
something that can be observed by a person examining a patient
34
Symptom:
something that can be felt only by the patient
35
Syndrome:
collection of signs and symptoms that signify a particular disease
36
Asymptomatic/Subclinical
infections lack symptoms but may still have signs of infection
37
Stages of Pathogenesis
Exposure, Adhesion, Damage or invading of host cells, infection, transmission
38
Invasion:
ability of pathogens to enter (invade) host cells
39
Invasiveness:
ability of a bacterial pathogen to rapidly spread through tissue
40
Koch's postulates (1884):
systemic approach to confirm causative relationships between a disease and a pathogen
41
Molecular Koch's postulates (1988)
inactivation of genetic factors results in diminishing virulence of the pathogen
42
Adapting Koch's postulates (2016)
disease causation must take microbial interactions into account
43
Diseases can be classified in a number of ways (4)
Contraction of Disease
Pattern of infection and body spread
Longevity and severity of the developed disease
Outcome of the disease - mortality and morbidity
44
Communicable diseases:
infection spread between persons by direct or indirect mechanisms
45
Contagious diseases:
communicable diseases that is easily spread
46
Non-communicable diseases:
infection not spread between persons
47
Iatrogenic diseases;
infection contracted via a medical procedure
48
Nosocomial disease
infection acquired during a hospital stay
49
Zoonotic disease
infection is transmitted from animals to humans
50
Pattern of infection - Localized
infection confined to a body area
51
Pattern of infection - systemic
widespread infection in many body systems
52
Pattern of infection - Focal
infection site serves as source of the pathogen for a disease at another body site
53
Pattern of infection - mixed
multiple species contribute to infection
54
Pattern of infection: primary-secondary
Primary: infection in a previously healthy individual
Secondary: successive infection which can occur due to weakened immunity
55
Bacteremia
presence of bacteria in blood, usually transient, no replication
56
Septicemia
presence and replication of bacteria in blood
57
Viremia
presence of viruses in the blood
58
Toxemia
presence of toxins in the blood
59
Acute
pathological changes develop rapidly over hours or days
60
Chronic
pathological changes develop gradually over months or years and are slow to resolve
61
sub-acute
pathological changes take longer to develop than acute but arise more quickly than chronic
62
Latent
pathological changes appear a long time after infection, pathogen dormant
63
Morbidity
existence of a disease state and the rate of incidence of the disease
64
Mortality
measure of how many patients have died from a disease
65
5 stages of infection (in order)
Incubation Period
Prodromal Period
Illness
Decline
Convalescence
66
Viruses are
Obligate pathogens and can infect every organism
67
Narrow host range
most viruses infect only particular host's cells
68
Broad host range
Generalists infect many kinds of cells or many different hosts
69
Non-enveloped viruses enclose by ...
the capsid
70
enveloped viruses are wrapped in
hosts plasma membrane
71
Prokaryotic host infections via . . .
bacteriophages
72
Virulent phages trigger . . .
bacterial lysis (lytic cycle)
73
Temperate phages integrate into . . .
host genome
74
Life cycle of viruses (5 steps)
Attachment
Penetration
Uncoating
Replication
Assembly and release
75
Virion abundance in lytic life cycle (3 steps)
Inoculation
Eclipse
Burst
76
Burst size
number of virions
77
Viral titer
number of virions per volume
78
Latency
animal viruses remain dormant in host cells
79
Hantavirus pulmonary syndrome
rodent-borne disease infecting the lower respiratory system
80
Rapid mutation leads to antigenic drift ... what is antigenic drift?
a population of viruses no longer recognized by host antibodies
81
Epidemiology examines what?
infectious diseases
82
Population-centered analyses focused on ...
morbidity
83
total morbidity is
the number of diseased individuals
84
Incidence is
the number of new cases of a disease in that location over a specific time
85
Prevalence is
the total number of cases of a disease in a given location regardless of when the first case developed
86
Sporadic disease...
few cases within an area
87
endemic disease ...
constant presence in a community
88
epidemic disease...
development of many cases in a community in a short time (outbreak)
89
pandemic disease ...
worldwide spread of disease
90
Reproduction number (R0) defines...
contagiousness
91
when R0 <1, what happens?
disease will disappear
92
when R0 = 1, what happens?
endemic
93
when R0 > 1, what happens?
disease will spread
94
Spread can be modified by measures leading to the _______ __________ ________
Effective reproduction number (R)
95
5 Types of Pandemics discussed in class...
Black death
Smallpox
Spanish Flu
HIV/AIDS
COVID-19
96
Who is the father of Epidemiology?
John Snow (1813-1858)
97
Common source spread is a
single-source for all of the individuals infected
98
Incubation period is
time from exposure to the causative agent until the first symptoms develop characteristic for each disease agent
99
Propagated Spread
direct or indirect person-to-person contact with the disease source
100
3 types of agencies that track global diseases
Global Health Security Agenda (GHSA)
Health Canada
WHO
101
Chain of Infection (6 links)
Pathogen
Reservoir
Portal of Exit
Mode of Transmission
Portal of Entry
Susceptible Host
102
Three types of Reservoirs
Human Carriers
Animal Reservoirs
Environmental Reservoirs
103
Passive Carriers
individuum is not infected; instead transfers pathogen mechanically to another host
104
Active Carriers
individuum with or without signs or symptoms (asymptomatic or immune to the disease)
105
Zoonoses
diseases that normally afflict animals or insects but can be transferred to humans
106
Environment Reservoirs
presence of microorganisms in soil, water, air and food
107
Three groups of Transmission
Contact transmission
Vehicle transmission
Vector transmission
108
Direct contact transmission
person-to-person, involved body contact between hosts
109
Vertical transmission
example, from mother to child during pregnancy and birth
110
Horizontal transmission
kisses between hosts
111
Droplet transmission
spread of pathogens in droplets of mucus by exhaling, coughing, and sneezing
112
Indirect contact transmission
pathogens are spread from host to host by inanimate object called fomites
113
Vehicle transmission of pathogens is through things such as...
water, food and air
114
Waterborne transmission
spread of pathogens via water; important for many gastrointestinal diseases
115
Airborne transmission
spread of pathogens via aerosols
116
Foodborne transmission
spread of pathogens in and on foods
117
Bodily fluid transmission
bodily fluids such as blood, urine and saliva can carry pathogens
118
Vectors
living organisms that can transmit infectious diseases
119
Mechanical vectors
an animal that carries a pathogen from one host to another without being infected itself
120
Biological vectors
transmit pathogens and serve as host for some stage of the pathogen's life cycle
121
Disease vectors mainly belong to two classes of arthropods:
Arachnida and Insecta
122
Prominent vector-borne diseases
Malaria, Dengue, Chagas disease, leishmaniasis and schistosomiasis
123
Ways to break the chain of infection are
controlling or eliminating agent at the source of transmission; protect portals of entry; increase host's defenses
124
Physical methods of Control - heat (examples)
boiling, dry-heat oven, incineration, autoclave, pasteurization
125
Physical methods of control - cold (examples)
Refrigeration, freezing
126
Physical methods of control - pressure (examples)
High-pressure processing, hyperbaric oxygen therapy
127
Physical methods of control - desiccation (examples)
Simple desiccation, reduce water activity, lyophilization
128
Physical methods of control - Radiation (exmaples)
ionizing radiation, nonionizing radiation
129
Physical methods of control - Sonication (example)
sonication
130
Physical methods of control - filtration (examples)
HEPA filtration, membrane filtration
131
High-level germicides . . .
kill vegetative cells, fungi, viruses and endospores, and can lead to sterilization
132
intermediate-level germicides . . .
cannot kill all viruses and are less effective against endospores
133
Low-level germicides . . .
kill vegetative cells and some enveloped viruses, but are ineffective against endospores
134
methods leading to microbial death (ends with what suffix)
-cide or -cidal
135
Methods leading to microbial growth inhibition (ends with what suffix)
-stat or -static
136
Degree of control is described by a
death curve
137
In-use test determines the . . .
effectiveness of a chemical disinfectant for a microbe
138
Disk-diffusion methods tests ...
the effectiveness of a chemical disinfectant against a particular microbe
139
The white (or clear) area surrounding the microbial disk is called
the zone of inhibition
140
BSL-I has what severity
little to no pathogenic potential
141
BSL-II has what severity
greater pathogenic potential but vaccines and treatments are readily available
142
BSL-III has what severity
serious or lethal human disease for which vaccines and treatments may be available
143
BSL-IV has what severity
extremely dangerous pathogens for which no treatments or vaccines are available
144
Bacteria reproduce fast and efficient asexually; three main methods of this are?
Binary fission
Snapping division
Budding
145
Generation time means
doubling time
146
Gram-positive cell wall has _________ layers of peptidoglycan
multiple
147
What two acids are covalently linked to peptidoglycan
Teichoic and lipoteichoic acids
148
Gram-positive cell wall has an outer membrane.
True or False?
False, it often has a protein layer called the Surface (S)-layer and glycosyl-chains
149
Surface (S)-layer is
a self-assembly of identical subunits into crystalline lattices with distinguished by their symmetry
150
Gram-negative cell wall is made up of a
thinner layer of peptidoglycan with a bilayer membrane (containing lipopolysaccharides)
151
Murein lipoproteins stabilize __________ ________ and _____ it to the peptidoglycan
outer membrane; anchor
152
Lipopolysaccharide has three core parts, these are?
Lipid A, Core, O-antigen
153
LPS is known as an
endotoxin
154
Toxin
substances that contribute to pathogenicity
155
Exotoxin
are secreted out of the cell during cell life
156
Endotoxin
are released upon cell lysis
157
A-active subunits cause
changes in host/toxic
158
B-binding binds to
host cell receptors and delivers A subunits to the host range
159
Sporulation
asymmetric cell division; engulfment by the mother cell, synthesis and formation of cortex and coat, maturation and lysis of mother cell
160
Glycocalyx is comprised of
capsule and slime layer
161
Capsule is
well-defined firmly cell-bound polysaccharide layer
162
Slime layer is
loosely associated with cell
163
The function of glycocalyx is
protection against immune system (anti-phagocytotic factors)
164
4 types of anthrax
Cutaneous
Inhalation
Gastrointestinal
Injection
165
Plasma membrane disruption
toxins form pores in host cell membranes that cause cell leakage
166
Cytoskeleton alterations
toxins modulate hosts actin polymerization and thereby cell shape
167
Protein synthesis disruption
Toxins prevent eukaryotic protein biosynthesis
168
Cell cycle disruption
toxins stop or stimulate host cell division
169
Signal transduction disruption
toxins subvert second messenger pathways
170
cell-cell adhesion disruption
toxins cleave proteins that bind host cells together
171
Vesicle trafficking
toxins modulate vesicle traffic and fusion inside host cells
172
Exocytosis
toxins paralyze movement of cytoplasmic vesicles
173
Superantigens
stimulates excessive activation of immune system cells
174
Virulence factors (definition)
factors which cause a severe disease state in a susceptible host
175
Types of virulence factors
Toxins, degradative enzymes, and invasins
176
Bacterial invasion has two types, these are
zipper and trigger
177
Zipper bacterial invasion is defined as
surface proteins bind host receptors that signal phagocytic uptake
178
Trigger bacterial invasion is defined as
injection of bacterial effectors to induce pinocytosis
179
Injectosome
needle for injections of cytotoxins (termed effector proteins)
180
Filamentous adhesins are
appendages extending from bacterial surfaces presenting an adhesion at its distal end
181
examples of filamentous adhesins include:
fimbriae, pili, flagella
182
Pattern of movement in flagella results from
alternating swimming and tumbling - biased random walk
183
Actin-based motility inside host cells spread through
cytoplasm, cellular exit and enter neighboring cells
184
Niche factors are
factors of a pathogen can be a colonization factor of commensal
185
Niche factors include:
adhesion factors
antiphagocytic factors
186
Three main forces have been found to shape genome evolution:
gene gain; gene loss; gene change
187
Prokaryotic pathogens reproduce . . .
asexually
188
Mechanisms of Horizontal gene transfer are
Transformation, Transduction, Conjugation
189
Transformation is:
uptake, uptake, integration and functional expression of naked fragments of extracellular DNA
190
Transduction is:
bacteriophages transfer bacterial DNA from a previously infected donor cell to the recipient cell
191
Pseudolysogeny:
Phage genome fails to replicate (as in lytic production) or become established as a prophage
192
Phage assembly is perfect.
True or false?
False; phage assembly is not perfect.
193
Lysogenic conversion means
process with mutually benefit for phage and host
194
Conjugation:
direct DNA transfer between donor and recipient cell
195
Once a new piece of DNA has entered a cell, what happens to it?
1. New DNA capable of autonomous replication (plasmid)
2. New DNA not capable of own replication
Then recombination
196
Recombination is when
two DNA molecule exchange portions by breaking and reforming their sugar phosphate backbones
197
Homologous recombination
two recombining molecules have long stretches of sequence homology
198
Site Specific recombination
short sequence motives recognized by a site-specific recombinases
199
Bacterial genomes comprise of:
stable regions: core genome
variable regions: flexible gene pool
200
Pathogens and commensals share habitats with:
bacteriophages, amoeba, insects, annelids, fungi, plants and mammals
201
When diagnosing a patient; what are important things to gather?
medical history, family and social history, physical examination and the signs and symptoms
202
What should be labelled on a sample collection?
patient name, medical record number, patient location, collection date and time, specimen type/source, test required, name of ordering physician
203
identification of microbes often starts with ...
isolation or visualization
204
What is a limitation of identification by colony morphology?
Morphology is media-dependent
205
Complex media supports ...
growth of most aerobic and facultative aerobic organisms
206
Enriched media contains ...
specific growth factors enhancing the growth of certain bacteria
207
Selective media allows ...
some organisms to grow while inhibiting others
208
Differential media allows . . .
for identification of organism based on their growth and appearance on the media
209
Samples from sterile body sites should be done (grown) on. . .
complex media or enriched media
210
Samples of collection site with normal microbiota should be grown on ...
selective media
211
Most pathogenic microbes can be detected in vitro in an overnight culture under aerobic conditions. What are some exceptions . . .
anaerobic bacteria
slow-growing bacteria
fastidious bacteria
obligate intracellular bacteria
212
Acidic dyes stain ...
alkaline structures
213
Basic dyes stain ...
acidic structures
214
Simple stains are composed of
single basic dye
215
Differential stains are used to
distinguish between different cells, chemicals or structures
216
Special stains are used to
identify specific microbial structures
217
Neisseria meningitides characteristic
Diplococcus, gram-negative
218
Streptococcus pneumonia characteristcs
diplococcus, gram-positive
219
Haemophilus influenza characteristics
rod, gram-negative
220
Escherichia coli characteristics
rod, gram-negative
221
Chocolate agar
extreme nutrient-rich media with lysed blood cells
222
Blood agar
rich medium
223
Hektoen agar
selective/differential media to recover gram-negative all-rounders
224
Analytical profile index (API) is
biochemical panel for identification of clinical relevant bacteria
225
API is interpreted as a ...
dichotomous key
226
Most widely used molecular method in the clinical laboratory:
Nucleic acid Amplification tests (NAAT) (like PCR)
227
Goal of PCR
produce copies of a particular DNA fragment for sequencing and visualization of mutagenesis
228
Key ingredients of PCR
DNA polymerase, primers, nucleotides, buffer and template
229
PCR have three cycles (steps), these are:
Denaturation, Annealing, Extension
230
When direct detection of a pathogen is not possible, what may help with diagnosis of acute infections?
Detection of specific antibodies or microbial antigens
231
Immunological tests are ...
culture-independent
232
Agglutination:
process that occurs if an antigen is mixed with its corresponding antibody present in body fluids
233
Direct agglutination:
antibodies react with antigens on cells or acellular particle such as viruses and form agglutinates
234
Indirect agglutination:
antibodies or antigens are bound to latex beads forming larger agglutinates in presence of respective antigen or antibody
235
Hemagglutination assay:
patient's serum can be directly used to detect a specific pathogen
236
Enzyme-linked immunosorbent assays (ELISAs) use . . .
antibodies to detect the presence of antigens or vice versa
237
Direct ELISA:
antigens are immobilized in the well of a microtiter plate
238
Indirect ELISA:
quantifies antigen-specific antibody rather than antigen
239
Point-of-Care devices
obtain diagnostic results in a short time
240
Characteristics of POC devices
Speed, portability, convenience
241
Examples of POC devices
pregnancy, blood sugar, cholesterol, drugs, infectious diseases
242
Good POC have what two attributes
High sensitivity, high specificity
243
5 methods of laboratory diagnosis (for identification of microbes);
Conventional techniques;
Biochemical methods based on semiautomatic and automatic systems;
Molecular-biological techniques;
Immunological techniques;
Mass spectrometry (MS)-based semiautomatic methods.
244
Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry:
generate organism specific mass spectral fingerprints; allows species identification; can be done in less than an hour
