Medical microbiology

Question 1

What is epidemiology the study of

Answer 1

he nature, distribution, causation, transfer, prevention and control of disease (infectious/microbial in this case)

Question 2

How many deaths did infection cause

Answer 2

1.68 billion

Question 3

What vaccinations were made last century

Answer 3

Measels, HIV/AIDS/ hepatitis/ influenza pandemics/ respiratory viruses/ smallpox

Question 4

What vaccinations have been made now and are planned to in the future

Answer 4

HIV/AIDS, influenza, SARS and ebola virus, Covid-19

Question 5

Major global disease examples

Answer 5

respiratory - myobacterium tuberculosis.
Diarrheal - vibrio cholerae

Question 6

What do infections involve

Answer 6

host, microorganisms and environment interactions

Question 7

What are opportunistic pathogens

Answer 7

pathogens capable of causing damage and infection in a compromised host

Question 8

What are obligate pathogens

Answer 8

causes damage and infection as part of its growth and replication

Question 9

What are facultative pathogens

Answer 9

causes disease as one part of its lifecycle or when in a different host

Question 10

What are commensal pathogens

Answer 10

induces either no damage or clinically inapparent damage to the host but may elicit an immune response

Question 11

Obligate pathogen features

Answer 11

gram-positive, aerobe, phylum: actinobacteria. e.g., TB

Question 12

Facultative pathogen features

Answer 12

gram-negative, facultative anaerobe, class: gammaproteobacterial. e.g., vibrio cholerae

Question 13

Opportunistic pathogen features - pseudomonas aeruginosa

Answer 13

gram negative, phylum: proteobacteria, class: gammaproteobacteria.

Question 14

Opportunistic pathogen features - staphylococcus aureus

Answer 14

gram positive, phylum: firmicutes, class: bacilli

Question 15

commensal pathogen features

Answer 15

gram positive, phylum: firmicutes, class: bacilli e.g., epithelial or gut bacteria. Lactobacillus acidophilus

Question 16

Example of how cf lung infections are diagnosed

Answer 16

sputum/cough swab -> microbial growth -> pure culture -> pathogen identification -> antibiotic susceptibility -> treatment and management

Question 17

how can a pathogen be identified

Answer 17

species PCRs, sequencing, strain typing, MALDI-TOF MS

Question 18

Issues to consider in medical microbiology

Answer 18

respiratory sample types, microorganisms present, growth media, multiple pathogens, indentification tests, useful antibiotics?, treatment strategies, pathogenic mechanisms

Question 19

What knowledge do we have about different strains

Answer 19

knowledge of clonality or genetic identity - ribotyping, macro restriction and PFGE, PCR-fingerprinting, DNA sequencing

Question 20

What are species

Answer 20

consist of large numbers or strains which share similar phenotypic and genetic properties (16S rRNA gene (>97% identity), gyrB or recA gene > 70% DNA-DNA hybridisation, average nucleotide identity)

Question 21

What can identify a meroclone and a clone

Answer 21

whole-, core-, and accessory- genome multilocus sequencing type

Question 22

What can identify a strain

Answer 22

ribosomal multilocus sequencing type

Question 23

What can identify a species, lineage or clonal complex

Answer 23

multilocus sequencing type

Question 24

What can identify phylum, class, order, family and genus

Answer 24

16S rRNA sequences

Question 25

What does PCR genotyping and pulsed-field gel electropheresis (PFGE) identify

Answer 25

define strains just below the species level. Cannot work above or below this

Question 26

Multilocus sequence typing (MLST)

Answer 26

Initially PCR based (1988). Sequence several conserved genes. Approx. 500 bp from a PCR fragment. Define genetic linkage between strains. Globally searchable strain database

Question 27

MLST identified Burkholderia, how was this useful?

Answer 27

Burkholderia bacteria may spread between CF patients. MLST scheme established. Allowed global strain tracking. Infection control reduced spread

Question 28

What are virulence factors

Answer 28

molecules that assist the bacterium colonize the host

Question 29

virulence factor examples

Answer 29

acid host colonization, host destrcution, nutrient scavenging, poisoning, intracellular entry, sndotoxin, exotoxin and adhesions

Question 30

What may pathogen genomes also encode

Answer 30

virulence factors on mobile genetic elements

Question 31

what virulence factor could clostridium botulinum encode for

Answer 31

neurotoxin

Question 32

multiple virulence factor plasmids - E.coli

Answer 32

enterotoxins, haemolysins, pili, urease

Question 33

genomic islands

Answer 33

classical pathogenicity islands e.g., uropathogenic E.coli - haemolysis, serum resistance and adhesions

Question 34

Intergrative conjugative element (ICE)

Answer 34

e.g., Tn917 system in Enterococcus faecalis. Large conjugative transposons, mobilised by a type IV secretion system

Question 35

Transposable elements (TE)

Answer 35

e.g., V.cholerae - cholera toxin, CTX compound transposons

Question 36

Linking Burkholderia epidemiology to virulence: an epidemic strain marker

Answer 36

The B. cepacia epidemic strain marker (BCESM). Identified in transmissible CF strains by RAPD fingerprinting. Risk marker for potential patient – to –patient spread

Question 37

what is a microbiome

Answer 37

“the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eukaryotes, and viruses), their genomes (I.e., genes), and the surrounding environmental conditions”

Question 38

What are microbiota

Answer 38

“the assemblage of microorganism present in a defined environment”

Question 39

what is an ecological niche

Answer 39

the functional role on organism plays within an ecosystem

Question 40

What is a commensal relationship

Answer 40

a relationship where one organism benefits and the other is unaffected 

Question 41

What is a mutualistic relationship

Answer 41

a mutually beneficial relationship between 2 organisms

Question 42

Essential roles of the human bacteriome

Answer 42

1. Extracting energy from food 2. Producing essential vitamins 3. Regulating our immune system 4. Regulating our glucose levels and metabolism 5. Protecting us against disease-causing microbes

Question 43

Role of the bacteriome in the nose

Answer 43

mucus production, antimicrobial compound production

Question 44

Role of the bacteriome in the mouth

Answer 44

aid digestion, inhibit pathogens - “colonization resistance”

Question 45

Role of the bacteriome in the lungs

Answer 45

lubricate pulmonary tissue

Question 46

Role of the bacteriome in the stomach

Answer 46

prevents gastric complications

Question 47

Role of the bacteriome in the colon

Answer 47

digestion of complex carbohydrates

Question 48

Role of the bacteriome in sexual organs

Answer 48

maintain pH, produce H2O2 to kill pathogens

Question 49

Role of the bacteriome in the skin

Answer 49

fortify immune system, scent

Question 50

What are the metabolome and what do they do

Answer 50

the global collection of all low molecular weight metabolites that are produced by cells during metabolism, and provides a direct functional readout of cellular activity and physiological status

Question 51

Why is the microbiome important when considering pathogenicity

Answer 51

1. Reservoir of opportunistic pathogens 2. Reservoir of genes 3. Source of antimicrobials and stimulatory components 4. Interacts with the host

Question 52

What is dybiosis

Answer 52

any change to the composition of resident commensal microbial communities relative to the community found in healthy individuals

Question 53

Which diseases are linked to gut dybiosis

Answer 53

obesity, type 2 diabetes, inflammatory bowel disease, irritable bowel syndrome, allergy. Asthma, cardiovascular disease, anxiety/mood disorders

Question 54

What is pathobiont

Answer 54

any potential pathological or5ganisms which, under normal circumstances, lives as a non-harming symbiont

Question 55

how many species of bacteria are in the gut alone

Answer 55

>1000

Question 56

Where are samples for the microbial population usually taken from

Answer 56

1. faeces 2. urine/genital swabs 3. Sputum - lung