Microbiology Flashcards
1
Q
What does mycoplasma look like?
A
Spherical filamentous cells with no cell walls
2
Q
What stain is used in gram staining?
A
Crystal violet or methylene blue
Stains the peptidoglycan cell wall = positive = purple
Negative= pink or red
3
Q
Properties of gram positive bacteria?
A
Thick peptidoglycan wall
Outer liposaccharide membrane
4
Q
What are fimbria?
A
Long filamentous polymeric protein structures located at the surface of epithelial cells
Allow binding
5
Q
What is an endospore?
A
Differentiated cell within gram positive bacteria
Very resistant
Genus bacillius
Genus clostridium
6
Q
What are the classifications of haemolysis in culture?
A
Beta- Complete
Alpha- Partial
Gamma- none
7
Q
Agglutination test?
A
H antigen- associated with flagella
O antigen- form liposaccharide membrane
8
Q
Baltimore classification system
A
(Group I); single-stranded DNA viruses
(Group II); double-stranded RNA viruses
(Group III); positive single-stranded RNA viruses
(Group IV); negative single-stranded RNA viruses
(Group V); positive single-stranded RNA viruses with DNA intermediates
(Group VI), commonly known as retroviruses;
the double-stranded DNA retroviruses (Group VII)
9
Q
What are the key stages in virus infection?
A
- Attachment
- Penetration
- Un-coating
- Gene expression
- Replication
- Assembly
- Release
10
Q
What methods can be used to detect viruses?
A
Serologic assay
PCR
Haemagglutination assays
ELISA
11
Q
What are the defence systems of the GI tract?
A
Adaptive
Innate
Bile salts
Defensins
Acidity
Peristalsis
Mucys
Bacterial interference
12
Q
HOw can GI disease be investigated?
A
Homogenisation, dilution and plating faeces
Choose selective media
Indicator media for closely related bacteria
13
Q
What is molecular detection of bacteria?
A
Detecting species by quantitating of their nucleic acid
Can be used to quantitavely count or show presence of bacteria
14
Q
What is the miles Misra method?
A
Technique to determine the number of colony forming units in a bacterial suspension or homogenate
15
Q
How is the gut flora established
A
Sterile until birth
Neonate acquires organisms from the surface parts of the birth canal and env
Compete for the niche in the gut
Complexity inc with time
Stabilises
16
Q
How can flora development due to ageing affect infection risk?
A
Maternal immunity, bottle feeding and pre ruminant GI affect flora
Acquired immunity affects flors
Weaning increases flora so less likely infection
Old age reduces immunity
17
Q
What are the colonisation factors?
A
Surface structures
LPS and membrane integrity
Motility -> niches
General gene regulation
Transporters of nutrients
Invasion to sustain colonisation
18
Q
How might anatomy affect bacteria at different sites
A
Free living or attached to villi or deep in villus crypts
19
Q
What do bacteria compete for?
A
Space
Co factors
Electron acceptors
Carbon sources
20
Q
How can antimicrobials affect the flora?
A
Remove sensitive organisms from niche
Intrinsically resistant bacteria left
Causes overgrowth of unwanted organisms
21
Q
What are the nutritional benefits of the GI flora in pigs?
A
B12 production
Synthesised by clostridium butyricum
22
Q
How does the microflora bacteria affect xenobiotic metabolism?
A
transforms compounds
Activate or inactivate drugs
Affect toxic metabolites
23
Q
What is PCR?
A
Polymerase chain reaction - pathogen DNA
Rapid and simple method for copying and amplifying specific DNA sequences
DNA melting, annealing and synthesis
Need to know DNA sequence for each end of larger sequence to be amplified
24
Q
What is the role of the oligonucleotide formation in PCR?
A
Serves as primaries for in vitro DNA sythesis
25
What do immuno diagnostics detect?
Antibodies
Can detect maternal antibodies too
26
How long does PCR and ELISA take?
24-72 hours
27
What are the most and least sensitive detection tests?
Most = PCR
Least= snap
28
When might ELISA be used?
Determine health status of herd or individual to manage endemic diseases and disease outbreaks
Can test bulk milk samples
29
Define mutation
Changes to the nucleotide sequence of DNA that leads to genetic diversity but can also lead to genetic disease
30
What is the importance of genetic diversity in microbes?
Disease susceptibility and specific traits
Identify types of mutations and their impact
31
Silent mutation
Substitution of nucleotide but doesnt change the amino acid
32
Missense mutation
Substitution leads to change of amino acid
33
How does sickle cell anaemia occur?
Missense mutation in beta haemmoglobin
CTC-> CAC means Val->Glu
34
How does SPAID occur?
Shar pei autoinflammatory disease
gene G-> A in the MTBP
35
Nonsense mutation
Normal codon for stop codon
Means that there is premature termination of translation
Less effect if closer to the 3' end
36
Effect of addition or substitution in promotor region
Affects expression of protein - higher, lower or no expression
37
Effect of addition or substitution in coding region
Affects whole reading frame
Protein might not be produced
= frame shift
38
What are pathovars based on?
Clinical propertied
39
What are serovars based on?
Serotyping
40
What are the 2 types of serotyping?
MLST- requires sequencing
Spoligotyping- PCR based for TB strains
41
Phylum that has the most gram positive bacteria?
Firmicutes GP
- listeria
- Staphylococcus
- Enterococcus
- Lactobacillus
- Streptococcus
Commensal and pathogenic
Mycoplasmas lack cell wall
42
Which firmicutes are gram positive and endospore forming?
Clostridium
Bacilus
43
Which gram type bacteria belong to phylym bacterioidetes?
Gram negative
Wide distribution
Commensal
Generas - bacteroides (faeces) , porphymonas (oral cavity)
44
What is the gram status for proteobacteria?
Gram negative
Commensal and pathogenic
Defined by rRNA sequence for meta genomes
Facultative or obligate aerobes
45
What are the 5 divisions of proteobacteria?
- Alphaproteobacteria= Rickettsia
- Beta Proteobacteria= Neisseriaceae + Burkholderia
- Gammaproteobacteria= pseudomonadaceae+ Enterobacteriaceae
- Deltaproteobacteria= Myxobacteria
- Epsilonproteobacteria= helicobacter and campylobacter
46
Which genera of proteobacteria are clinically relevant to the GI tract?
Gammaproteobacteria- enterobacteriaceae fam
- Escherichia
- Salmonella
Elipsonproteobacteria + Vibrio family - microaerophilic
- Helicobacter
- Campylobacter
47
What phyla does the acid fast mycobacteria belong to?
Actinomycetota
Gram positive
Main = Bifidobacterium and cornybacterium
Commensal or pathogenic
48
Properties of cornybacterium
Branched Gram P
Anearobic
Found in GIT
Commensal
Ferments carbs and oligosaccharides
49
What are the major facultative anaerobes found in the GIT
Gram P rods =
Enterobacteriaceae
Escherichia coli
Enterobacter sp
Proteus
Gram N rod= lactobacillus
Gram N cocci= streptococcus, staphylococcus and enterococcus
50
Bacteriodes genus
Commensal - complex molecule processing
Gram N
Bacillus
anaerobes
simple sugar diet
51
Streptococci genus
Gram P
Coccoid
Facultative anaerobes
Phylum= firmicutes
Grow in chains or pairs
Commensals or opportunistic pathogens
52
Enterococcus species
Gram P
Facultative anaerobe
Commensal or opportunistic
GI tract
53
Clostridia
Gram P
Endospore forming
Rods
Obligate anaerobes
54
How can overgrowth and food poisoning of clostridia form in rabbits?
Overgrowth of C. spiroform in GIT of rabbits treated with penecillin
55
Which bacteria causes gas gangrene
Clostridia perfringens
56
How might an animal ingest viruses that are shed in faeces?
Aerosols
Food stuffs
Poor disinfection of env
57
What are the common features of enteric virus infections?
Small infectious dose
Short incubation period
Large amounts shed in faeces
Low pH survivors
Secondary bacteria infection = common
58
What is the main pathogenesis of enteric virus infections?
Severe infection = denudation of microvilli
SHortening
Flattening and atrophy of villi
Cause malabsorption
59
What are the main viruses which cause major clinical signs associated with the GIT?
- rotavirus
- Parvovirus
- Coronavirus
- Paramyxovirus
- Pestivirus (BVDV)
60
What is the structure or rotaviruses?
Icosahedral, non enveloped virus
Outer middle and inner capsid
Core contains a dsRNA segmented genome
Stable to wide pH, temp and detergents
61
How do rotaviruses replicate?
Cytoplasmic replication with own polymerase
62
What processes does rotavirus effect?
Reduced lactase production and impaired Na transport as villi shorter and
Reduced lactase= undigested milk in lower GIT = bacterial overgrowth = osmotic diarrhoea = watery scour
63
What is the basis of virus entry into cells?
virus binds to sialic acids
Then integrins
The other proteins on cell surface
64
Which species do rotavirus infect?
Piglets, calves and foals
Can have secondary infection of E coli or other viruses
65
How is rotavirus diagnosed?
- Sample faeces/gut contents
- Detection of viral antigen
- ELISA or latex agglutination test
- Detection of viral RNA
- RT-PCR
Virus is often present in faeces of healthy calves
66
Control of rotavirus?
Good colostrum
all in all out management
Good hygeine
Vaccines for horses and cows
67
What are the structural properties of corona viruses?
Corona= crown
Positive sense ssRNA
Enveloped
Virus order- Nidovirales
Reasonably tolerant to low pH but destroyed by deterdents
68
Which coronavirus affects the main species?
- pig TGE, EDV, PDCoV, SADs-CoV, All enteric
- Dog, CCoV- enteric
- Cattle, BCV - enteric and respiratory
- Cat, FCoV - enteric
69
Properties of coronavirus transmissable gastroenteritis virus
Highly contagious
Piglets and young pigs mainly
Diarrhoea
Rapid dehydration
100% mortality in piglets
70
Properties of porcine coronavirus PED?
Porcine endemic diarrhoea virus
- Similar to TGEV
- Historically was less severe now high mortality
- As a consequence is now notifiable in UK (APHA)
- Control measures are industry led (AHDB Pork)
71
What are the new emerging porcine coronaviruses?
PDCoV
SADS- CoV
72
How do coronaviruses affect calves?
- scour 4d – 3wk age
- dehydration, acidosis, depression, fever
- recovery in 4-5d
- approx 20% of calf scours due to coronavirus
- cf. rotavirus 33%, cryptosporidia 35%
- Also cause winter dysentry in housed **adult** cattle
73
Properties of canine coronavirus
- Canine enteric CoV CECoV (CCoV)
- Normally mild self limiting diarrhoea
- severe systemic disease (vomiting/diarrhoea but also pyrexia, seizures)
- ultimately fatal
74
What are the major properties of feline coronaviruses?
Enteric virus with very mild signs
But can cause systemic signs in some cats
Two biologically distinct phenotypes (biotypes)
feline enteric coronavirus (FeCoV)
feline infectious peritonitis
75
What is FIP
Feline infectious peritonitis
Wet- effusion in body cavity = ascites in abdo= pleural effusion
Dry FIP more challenging to diagnose - pyogranulomatous lesions
76
Causes of FIP
- probably mutation of virus
- Recombination or spontaneous
- Stress
- Viral load
- Not very well understood
77
How can mycobacteria be differentiated from other bacteria?
Acid fast stain
Acid fast bacteria = high content of mycolic acids in cell wall = stain red not blue/green
78
How to carry out acid fast stain?
Bacterial smear, dry, heat fix
Carbol fuchsin stain
Heat until vapour
Wash
Cover with 3% acid alc for 5 mins
wash
malachite green stain = 2 mins
wash and air dry
Microscope using oil immersion
79
What are the main mycobacterium species?
- M. Tuberculosis= humans and captive primates = Tuberculosis
- M. Bovis= Bovine tuberculosis, Mainly affects cattle
- M. Avium- MAC lung disease - tuberculosis affecting mainly birds
80
Which species of mycobacteria causes johnes?
Mycobacterium avium spp paratuberculosis
81
What is johnes disease
An infections wasting condition of cattle and other ruminants caused by mycobacterium avium spp paratuberculosis
The disease is progressive and therefore protein losing enteropathy can lead to submandibular or ventral oedema
82
Route of the pathogen in Johnes?
Ingestion -> peyers patches -> ileum
-> macrophased -> lymph nodes = granulomatous inflammatory response
83
Metagenomics
Study of structure and function of entire nucleotide sequence in a bulk sample
84
What is functional redundancy in the gut ecosystem?
Gut is composed of widely divergent microbial lineages
The genomes of these can contain functionally similar sets of genera
These would give rise to a cooridinated single metabolic outcome
Consequently this means microbiota species are interchangeable
85
What is copper toxicosis?
hereditary
failure of liver to expel copper
Copper = illness and death
recessive trait
86
Summary
Microbiota and its microbiomes vary between individuals and microenvironments
Gut microbiota/microbiome are specific to region and function of GI tract
High level of bacteria diversity and redundancy
Gut microbiota influences the brain development, neural processes and behaviour
Disease diagnostic has revolutionized due to molecular methods such as PCR and DNA sequencing
87
What are the main viral diseases?
Bovine viral diarrhoea - cattle
Border disease virus - sheep = neuro symptoms and abortion
Classical swine fever = pigs neuro signs and abortion
88
What are the major features of perstiviruses?
- positive sense single stranded RNA genome
- Enveloped
- Icosahedral capsid
Cytoplasmic replication
89
What are the issues related to bovine viral diarrhoea?
Bovine viral diarrhoea virus because causes over a £70 million loss per year
Reduces milk yield
Causes congenital defects
Stunted calves
Decreased fertility
Immunosuppression
90
What are the genotypes of BVDV
BVDV 1 = classical form
BVDV 2= haemorrhagic syndrome severe acute BVD
91
What are the 2 bio types of BVDV?
This describes the biological behaviour in the cell culture
non cytopthic
Cytopathic
NCP and CP isolates of both genotype 1 and genotype 2 exist
NCP is the major cause of BVD
92
What are the outcomes of a cow being infected with BVDV during pregnanacy?
1. Non immune pregnant cow or heifer becomes infected during pregnancy
2. Persistently infected calf may look normal at birth but will suffer early embryonic death or abortion
2.1 Or can be born normally or with congenital defects such as stunted or abortion
1.2 Depends if develops foetal immunocompetance
93
What is the structure of parvoviruses?
Icosahedral capsid
Small linear single stranded DNA genome
Infect and kills actively replicating cells
Persist for long periods in the environment
94
Veterinary important parvoviruses
1. Feline panleukopaenia virus (FPV).
2. 2.Canine parvovirus (CPV).
3. 3.Porcine parvovirus (PPV).
4. 4.Mink enteritis virus (MEV).
5. 5.Aleutian disease (mink).
6. 6.Goose parvovirus.
95
What is parvovirus tropism?
Villi tip cells turnover normally bit are not replaced as villus kills stem cells
Stunted villi, malabasorption and maldigestion
96
What is FIE?
Feline infections enteritis caused by feline parvovirus also known as feline panleukopenia
Faceooral transmission
Infects lymph of nasal and oropharnyx
intestinal cells and bone marrow affected
Affinity for rapidly dividing cells
97
What is the parvovirus pathogenesis for panleukopenia?
decreased white blood cell count, killing of lymphoid and myeloid stem cells *
98
What is the pathogenesis for enteritis caused by parvovirus?
Killing of stem cells in crypts
99
What is the parvovirus pathogenesis for cerebellar hypoplasia?
Perinatal infection of the cerebellum causes wobbly kittens due to the role of the cerebellum being affected
100
How can diagnosis of FPV be confirmed>
Faeces
ELISA or PCR
101
What are the 2 canine parvoviruses?
CPV 1- mild diarrhoea
CPV 2- serious, antigen determines tropism
102
How can CPV 2 affect different systems?
1.Generalised neonatal disease (fading pups)
2.Myocarditis in neonatal puppies (uncommon)
3.Bone marrow → Leukopenia
4.Intestinal villi → Enteritis → Vomiting & Diarrhoea
5.Intestinal and mesenteric lymphoid tissues → immunosupression
103
How can canine parvovirus cause heart failure?
Myocardial necrosis occurs
Inclusion of viral bodies in myocardial cells
Increases the amount of inflammatory cells
Leading to fibrosis
Therefore massive enlargement of heart
Heart failure and pulmonary oedema occur
104
What are the main viruses in the paramyxoviridae family?
*Morbillivirus*
*Rubulavirus*
*Respirovirus*
*Pneumovirus*
*Metapnemovirus*
105
Structure of paramyxoviridae family
Enveloped
negative sense ssRNA
Sensitive to heat and detergent
Cytoplasmic replication and budding
106
What are the notifiable paramyxoviridae viruses?
Rinderpest= cattle plague
Peste des petits ruminats = goat plague
107
What are the properties of canine distemper?
Morbillivirus (Paramyxovirus)
Young dogs especially susceptible
Transmitted by **direct contact**
Virus replicates in URT
Spread to tonsils/lymph nodes
Viraemia and systemic spread to epithelia +/- CNS
108
Clinical signs of canine distemper
Pyrexia, depression
Ocular and nasal discharge
Cough
Vomiting, diarrhoea
Hyperkeratosis of nose/pads (“hardpad”)
Neurosigns if poor immune response
109
Newcastle disease
NOTIFIABLE
Paramoxyviridae
Subfamily= avulavirus
Avian paramyxovirus-1: affects chickens, ducks, pheasants, geese, turkeys
Transmission = aerosols and mechanical transfer
110
What are the different types of newcastle disease?
- Ientogenic
**mild inapparent infection**
- Mesogenic
**mild respiratory disease, some deaths in young birds**
- Neurotropic velogenic
**acute, severe, fatal with respiratory and nervous signs**
- Viscerotropic velogenic
severe, fatal with haemorrhagic intestinal lesions, respiratory disease
111
In newcastle disease, what determines virulence and tropism?
F glycoprotein
Synthesised as an inactive precursor which is then cleaved by the host cell proteases to form the active form
If it is not cleaved then the virus cannot enter
112
Lentogenic vs velogenic newcastle disease?
Lentogenic= GI and Resp tracts with trypsin like proteases
Velogenic= ubiquitous proteoases due to altered cleavage site so many different tissues affected
113
Where may newcastle disease cause haemorrhage
Proventriculus
Trachea
114
What processes lead to introduction of new DNA into a bacteria?
Transformation
Conjugation
Transdution
115
Which processes lead to movement of DNA already in bacteria?
Transposition
Recombination
116
Define homologous recombination
Where two DNA sequences are the same they can intercalate their strands. During replication these can get spliced
117
Define non homologous recombination
Less efficient NA does not match but can be in a random positions
118
Define directed recombination
Insertion elements have release which lead to homologous/ directed insertions in specific sites or enzymes that direct integration at set sites ie. These have hot spots for insertions ad are more effective
119
How do bacteria restrict DNA transfer?
Restriction endonucleases
Restriction endonucleases degrade DNA not made in their own cell
These restriction nucleases do no degrade self- DNA as they act on specific sites
A bacteria methylates its own DNA where its own restriction nucleases cut so blocking the enzyme
This works on any DNA including non self plasmids
120
What is the clinical relevance of gene acquisition?
Gain reisitance
Gain metabolic genes
Virulence genes- attachment, invasion and production of a toxin
121
How does reticulitis spread?
contagious spread from adjactent systems
122
What phyla are accurately described by the line “gram negative rods which are oxidase negative, faculative anearobes and grow on MacConkey” ?
Enterobacteriaceae
123
Escheriachia coli
- most members of this genus are low virulence
- They may cause opportunistic infections
- Pathogenic strains possess virulence factors which allow them to cause disease
- The basic genomes of E. coli are the same but they will have gained some very specific properties
124
What is the LEE?
Locus of enterocyte effacement
Encodes a type 3 secretion system
Transloacted intimin receptor in host cell
125
Species of salmonella
S bongori
S enterica
126
Which serotypes of salmonella cause enterocolitis and septicaecmia
S. Enteritidis
S. Typhimurium
S. Dublin
S. Cholerasuis
127
What is the pathology of salmonella infection?
1. Attachment and invasion. Invasion promoted TTSS-1
2. Penetration of mucosal barrier inflammation . Stimulated by TTSS-1 and the sip’s and sop’s
1. Neutrophils attracted
3. Infection of macrophages
4. Transfer to systemic sites requires TTSS-2 for intracellular survival
128
What are the different TTSS-1 effectors?
Trigger invasion by actin and tubulin remodelling
Trigger cytokine response
Trigger enteropathogenic response
129
Structure of campylobacter jejuni
- gram negative, vibrio
- Flagellated and motile
- Microaerophilic they require 10% CO2 and 5-6% O2
- Optimum Growth temperature is 42 degrees celcius
- Can be seen as commensals
130
What is MLST?
Multi locus sequence typing looks at single base pair changes
This is done by sequencing seven essential genes and clustering the strains based on differences
These clusters are called clades
131
Structure of spirochetes
- spiral motile bacteria
- Endoflagella
- Gram negative
- Many are zoonotic
132
Which member of spirochetes cause GI disease in pigs and poultry?
Brachyspira
Strict anaerobes
doesnt form discrete colonies
133
- Describe the structure of lawsonia
curved gram negative rod
- Obligate intracellular pathogen
- Microaerophilic
- Can NOT be grown on inert media required growth in enterocytes
- Implicated in proliferation enteropathy of pigs and foals
134
Common adhesins
Fimbriae
135
What are the different pathogen mechanisms?
Hypersecretion
Villus atrophy
Infiltrative and proliferative distortion of mucosa
Mucosal necrosis
136
Which pathogenic mechanism does johnes disease use?
infiltrative and proliferative distortion of mucosa
137
How does brachyspira cause mucosal necrosis?
Targets mucosa of the colon
found in erosive lesions of the mucosa
Associated hypersecretion of mucus
