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4.2 Medical Microbiology > Bacterial Genetics > Flashcards

Bacterial Genetics Flashcards

1
Q

Why is bacterial genetics relevant to medical microbiology

A

Emergence of antibiotic resistant pathogens and pathogens with enhanced virulence are driven by genetic variation processes

Some antibiotics target genetic processes e.g. DNA gyrase targets

Genetic methods have been developed that facilitate early detection of pathogens allowing more timely treatment

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2
Q

What is meant by the bacterial genome

A

The total collection of genes carried by a bacterium both on its chromosome and on plasmids or in the form of bacteriophages

It contains genetic information required for all cellular processes

It contains approximatelt 4000 genes, 5 million DNA base pairs

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3
Q

What is the plasmid?

A

A circular molecule of double stranded DNA (helix)

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4
Q

What are the two ways alterations in genotypes can occur?

A

Mutations through vertical gene transfer

Transfer of DNA by horizontal gene transfer (HGT)

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5
Q

What is vertical gene transfer?

A

Whereby an organism receives genetic material from a parent cell
Down from a parent cell to a daughter cell

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6
Q

What is horizontal gene transfer?

A

Whereby an organism incorporates genetic material from another organism without being the offspring of that organism

It can be from one species to another

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7
Q

How does vertical gene tranfer occur

A

Changes in the genetic material that occurs as DNA is passed from a parent bacterial cell to its daughter cell during reproduction

It occurs through processes like binary fission, the primary method of bacterial reproduction

DNA replication is an efficient process with each daughter cell acquiring an exact copy of the parental genome

Mutations during VGT can result in genetic variation which is critical for adaption and evolution

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8
Q

How frequent are mutations in binary fission?

A

Frequency of error is about 1 in 10^5 -> 1 in 10^10 per cell division

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9
Q

What are the four types of mutations?

A

Point mutations
Frame shift mutations
Large scale mutations
Spontaneous mutations

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10
Q

What are point mutations?

A

A single nucleotide change (substiutions, insertions or deletions)
They may result in silent, missense or nonsense mutations depending on the impact of the encoded proteins

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11
Q

What are frame shift mutations?

A

Addition or loss of DNA bases
Can cause frameshift mutations if they disrupt the reading frame of a gene

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12
Q

What are large-scale mutations?

A

These involve rearrangements, duplications or deletions of large DNA segments

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13
Q

What are spontaneous mutations?

A

These occur due to errors in DNA replication or repair mechanisms
They typically happen at a low but signficant rate

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14
Q

When do point mutations occur?

A

They occur after DNA replication when a single nucleotide is replaced by a different nucleotide leading to a base pair substitution

A single nucleotide replacing what was in the parent cell

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15
Q

What are the three types of point mutations?

A

Samesense/silent mutations
Missense mutations
Nonsense mutations

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16
Q

What is a samesense/silent mutation?

A

This is where the new codon encodes the same amino acid as the original codon resulting in no change to the protein

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17
Q

What is a missense mutation

A

This is where the new codon specified a different amino acid, potentially alterin the proteins structure and function

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18
Q

What is a nonsense mutation?

A

This is where a new codon becomes a stop signal causing premature termination of translation and likely producing a truncated, nonfunctional protein

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19
Q

How do point mutations affect bacterial proteins

A

The effects of base subsitutions in protein-coding regions depend on the type of mutation and its specific location within the gene, these mutations can range from having no impact to causing significant changes in the protein function

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20
Q

How do frameshift mutations occur

A

Thes occur due to the insertion or deletion of a nucleotide
This disrupts the grouping of nucleotides into a codon causing a shift in the reading frame which leads to improper grouping of all downstream nucleotides

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21
Q

How do frameshift mutations affect proteins

A

The resulting protein typically undergoes significant changes in its amino acid sequence and is often truncated due to the generation of a premature stop codon
Depending on the affected region, the altered protein may retain some biological activity or in rare cases function normally

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22
Q

Define horizontal gene transfer

A

The process by which genetic material is transferred between organisms that are not parent and offspring

HGT allows bacteria and other organisms to acquire and exchange genes across species -> physical exchange of genetic material

Contributs to genetic diversity, adaptation and evolution

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23
Q

How does horizontal gene transfer contribute to genetic diversity adaptation and evolution?

A

It typically involves functional genes that are likely to be expressed phenotypically such as those responsible for antibiotic resistance or virulence

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24
Q

What are the two forms of HGT

A

Integration into the host genome

Retention on a plasmid

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25
Q

Talk about Integration into the Host Genome as a method of HGT

A

The transferred DNA may recombine with the recipients cells chromosome

Foreign DNA to become a stable part of the recipients genome where it can be expressed and passed on to future generations during vertical gene transfer

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26
Q

Talk about retention on a plasmid as a form of HGT

A

If the transferred DNA is part of a plasmid it can exist as an independent, self-replicating genetic element within the recipient cell
Plasmids do not require recombination with the host genome for replication and can be maintained autonomously
Plasmids often carry genes that provide selective advantages such as antibiotic resistance, metabolic pathways or virulence factors which may be expressed phenotypically

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27
Q

What are the three methods of HGT?

A

Transformation
Transduction - transfer of DNA by bacteriophage
Conjunction - transfer of DNA via a conjugative pilus

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28
Q

What is transformation?

A

The uptake of free DNA fragments from the environment by a bacterial cell
The DNA can integrate into the recipient’s genome through recombination

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29
Q

Give an example of transformation?

A

Competent bacteria like streptococcus pneumoniae can take up DNA from lysed cells

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30
Q

Where is transformation important, why is this?

A

Transformation is frequently used in molecular biology but it is the least clinically relevant mechanism of gene transfer due to its dependence on specific conditions and natural competency which is rare in bacteria

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31
Q

What are the five steps of transformation?

A

Transformation involves the uptake by a recipient of naked DNA released from a donor (dead degraded bacterium):
1. donor cell lysisi
2. release of donor DNA and cleavage into smaller fragments
3. dsDNAbinds to receptors on recipients cell surface
4. one strand of donor DNA is nicked and degraded by bacterial enzymes
5. remaining strand of donor DNA is incorporated into the bacterial chromosome by specialised transport proteins

Results in recombinant DNA

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32
Q

What is transduction?

A

The transfer of DNA from one bacterium to another via a bacteriophage
DNA from the host cell is mistakenly packaged into the phage particle and delivered to a new bacterial cell
Phages act as post-men to transfer from one cell to another

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33
Q

What are the different types of transduction

A

Generalised transduction
Specialised transduction

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34
Q

What is generalised transduction

A

Whereby random fragments of host DNA are transferred between cells

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35
Q

What is specialised transduction?

A

Specific regions of the host genome near the prophage are transferred

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36
Q

What is the impact of transduction

A

Contributes to genetic diversity and can transfer traits such as antibiotic resistance or virulence factors

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37
Q

What is the impact of transduction

A

Contributes to genetic diversity and can transfer traits such as antibiotic resistance or virulence factors

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38
Q

What are the steps in generalised transduction?

A
  1. Attachment of bacteriophage to donor cell
  2. Penetration of genetic material into the chromosome DNA of donor cell
  3. Degradation of chromosomal DNA
  4. Assembly of bacteriophage which occasionally carries bacterial DNA and cause cell lysis
  5. Attachment and penetration of bacteriophage that carries donor cell DNA into the recipient cell -> injection of DNA into new cell
  6. Recombinant DNA which carries phage DNA and the recipient chromosomal DNA
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39
Q

What are the steps in specialised transduction?

A
  1. attachment and penetration of bacteriophage to donor cell
  2. integration of phage genetic material into the chromosomal DNA of donor cell
  3. deintegration of phage DNA picks up the piece of chromosomal DNA
  4. assembly of bacteriophage carries the prophage DNA
  5. attachment and penetration of bacteriohage that carries prophage DNA into the recipient cell
  6. recombinant DNA which carries donor cell DNA and the recipient chromosomal DNA
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40
Q

Explain in your own words how specialised transduction works

A

Bacteriophage attaches
Bacteriophage integrates into recipient DNA
Bacteriophages multiply
Bacteriophage carrying integrated DNA infects another cell

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41
Q

What is conjugation?

A

A form of bacterial ‘mating’ where DNA is transferred from one bacterium to another through direct cell-to-cell contact via a conjugate pilus

Plasmid moves through tunel connecting two cells

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42
Q

What can be transferred through conjugation?

A

Plasmids, transposons or occassionally chromosomal DNA from the donor cell to the recipient cell

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43
Q

What are the steps in bacterial conjugation?

A

Donor ‘F’ cell produces sex pilus that extends towards the recipient ‘F’ cell

Sex pilus connects ‘F’ donor and ‘F’ recipient cells

Replication and transfer of F plasmid through the sex pilus

Complementary strand synthesis and froming a new donor ‘F’ cell

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44
Q

What are the steps in bacterial conjugation?

A

Donor ‘F’ cell produces sex pilus that extends towards the recipient ‘F’ cell

Sex pilus connects ‘F’ donor and ‘F’ recipient cells

Replication and transfer of F plasmid through the sex pilus

Complementary strand synthesis and froming a new donor ‘F’ cell

45
Q

What are the three steps in conjugation called?

A

Initiation

Transfer

Completion

46
Q

What happens in the initiation step of conjunction?

A

A donor cell (F+ cell) containing a conjugative plasmid, such as the F (fertility) plasmid forms a pilus to attach to a recipient cell (F- cell)

47
Q

What happens in the transfer step of conjugation?

A

A single strand of the plasmid DNA is transferred to the recipient through the pilus

The donor synthesises a complementary strand to restore its plasmid, while the recipient synthesizes a complementary strand to complete the plasmid

48
Q

What happens in the completion step of conjugation?

A

Both cells now posses a copy of the plasmid, and the recipient may become a new donor (F+)

49
Q

What are plasmids

A

Circular, double-stranded DNA molecules found in bacteria independent of the chromosomal DNA

They are responsible for the spread of genetic traits

Conjugation facilitats the spread of these traits, contributing t bacterial adaptation and evolution

50
Q

What are plasmids

A

Circular, double-stranded DNA molecules found in bacteria independent of the chromosomal DNA

They are responsible for the spread of genetic traits

Conjugation facilitats the spread of these traits, contributing t bacterial adaptation and evolution

51
Q

What are the three different kinds of plamids and what are they responsible for

A

R plasmids -> antibiotic resistance
Virulence plasmids -> virulence factors
Degradative plasmids -> metabolic capabilities

52
Q

What are conjugative/fertility plasmids

A

Plasmids which facilitate conjugation by enabling DNA transfer between bacteria cells

They contain genes for pilus formation and DNA transfer, essential for bacterial mating

53
Q

What are resistance plasmids

A

plasmids that carry genes that confer antimicrobial resistance

They provide resistance to antibiotics or other haemful agents, contributing to multidrug resistance

54
Q

What are virulence plasmids

A

Plasmids that encode genes that enhance baterial virulence and pathogenicity

They aid in inection by producing toxins, adhesion factors or other virulence related molecules

55
Q

What are degradative plasmids?

A

These enable bacteria to metbaolise unusual or complex substances like toluene or salicylic acid

They provide a metabolic advantage in specialised or contaminated environments

56
Q

Talk about Hfr conjugation, how does it occur?

A

The F plasmid, when it exists as a free plasmid, can only transfer itself during conjugation

In a specialised form of bacterial conjugation, the F (fertility) plasmid integrates into the bacterial chromosome

This integration transforms the donor cell into an Hfr cell

57
Q

What is a Hfr cell?

A

A high frequency recombination cell

58
Q

Why is Hfr conjugation important

A

Hfr cells can transfer both plasmid and chromosomal DNA to a recipient cell during conjugation
This process allows for the trasfer of large sections of chromosomal DNA facilitating genetic diversity
The transfer of advantageous genes such as antibiotic resistance or metabolic capcabilities support bacterial survival under selective pressures

59
Q

What is the only way the F plasmid can be inherited?

A

It can only be transferred between cells during conjugation

60
Q

What are the five steps in Hfr conjugation?

A

F plasmid integrates into chromosome by recombination

Cells join via a conjugation pilus

Portion of F plasmid partially moves into recipient cell trailing a strand of donors DNA

Conjugation ends with pieces of F plasmid and donor DNA in recipient cell: cells synthesise complementary DNA strands

Donor DNA and recipient DNA recombine making a recombinat F- cell

61
Q

Which form of gene transfer has the highest clinical relevance?

A

Conjugation

62
Q

Why does conjugation have the highest clinical relevance?

A

Due to its role in spreading antibiotic resistance and virulence factors

63
Q

Which form of genetic transfer is considerred moderately relevant and why?

A

Transduction particularly for the evolution of pathogenic bacteria

64
Q

What form of genetic transfer is least relevant clinically and why?

A

Transformation as it relies on specific conditions and is limited to naturally competent bacteria

65
Q

Talk about the role of conjugation in resistance

A

The conjugative transfer of resistance plasmids has played a significant role in the widespread dissemination of antibiotic resistance genes across and within various bacerial species

In most cases, resistance arises from resistance genes carried on conjugative plasmids

Bacteria can develop MDR either by acquiring multiple separate plasmids or by obtaining a single plasmid that encodes multipl resistance determinants

66
Q

How are bacterial pathogenic capabilites often acquired?

A

Horizontal gene transfer

67
Q

Talk about the spread of virulence genes through HGT

A

Virulence genes are typically found on bateriophages, plasmids or pathogenicity islands

The transfer of virulence genes is primarily facilitated by conjugation (involving plasmids and chromosomal fragments) anad transduction

68
Q

What are pathogenicity islands?

A

Distinct genetic elements found in the genomes of pathogenic bacteria that encode virulence factors, enabling them to infect hosts and cause disease

69
Q

How are pathogenicity islands spread?

A

They are acquired through HGT from other organisms and are a hallmark of bacterial evolution towards pathogenicity

70
Q

What is transposition?

A

The process by which specific DNA sequences known as transposable elements move from one location to another within a genome

71
Q

What are transposable elements also called?

A

Jumping genes

72
Q

What are the three different ways transposition can occur?

A

Within the same DNA molecule
Between different molecules e.g. plasmid to chromosome
Occassionally between cells

73
Q

What is the contribution of transposition?

A

The mechanism contributes to genetic diversity, adaptation and the spread of antibiotic resistance in bacteria

74
Q

List the different transposable elements

A

Insertion sequences (IS elements)

Composite transposons

Non-composite transposons

Retrotransposons(but these are rare in bacteria)

75
Q

What is an insertion sequence?

A

Small, simple transposable elements that only carry genes necessary for transposition e.g. tranposase

Theyre only 1,300-1,500 base pairs long that function as simple transposable elements

Theyre scattered across the bacterial chromosome and sometimes found on plasmids

They facilitate genetic rearrangements and contribute to the spread of traits like antibiotic resistance when part of mobile genetic elements

76
Q

What are composite transponsons?

A

These contain additional genes such as those for antibiotic resistance, flanked by two IS elements

77
Q

What are non-composite transposons?

A

These lack IS elements but still carry functional genes and transposition machinery

78
Q

What are retrotransposons?

A

Thes move via RNA intermediates and reverse transcrpription (more common in eukaryotes)

79
Q

What are the two types of insertion sequence transposition

A

Intracellular: move from one site in DNA to another within the same bacterium, independent of homologous recombination

Intercellular: if integrated into a conjugative plasmid, IS elements can transfer between bacterial cells via conjugation

80
Q

How do transposons compare to ISs

A

Transposons are larger than IS and carry other genes other than those for transposition

Some of these genes confer important properties for the bacterial cell such as antimicrobial resistance

81
Q

Give an example of a transposon

A

Tn3

82
Q

Talk about Tn3

A

A simple transposon containing 38 bp terminal IRs
It also carries ampicillin resistance gene, transposase gene, a repressor/resolvase gene

83
Q

What are the two kinds of transposition?

A

Conserved vs replicative

84
Q

What is conserved transposition?

A

Non replicative transposition
‘cut and paste’ mechanism -> jumps -> exact same
Tn moves to a new site, original site is repaired

85
Q

Give two examples of Conservative/non-replicative Tns?

A

Tn5 and Tn19

86
Q

What is replicative transposition?

A

Copy and paste
Tn is duplicated and the copy is transposed
One copy of Tn remains at original site and another copy at the new site

87
Q

In what ways does transposition have a cinical relevance

A

Spread of antibiotic resistance
Emergence of virulent pathogens
Increased Genetic Diversity
ESBLs
VREs
CREs

88
Q

Talk about the role of transposons in the spread of antibiotic resistance

A

Transposons frequently carry anibiotic resistance genes such as beta-lactamase or carbapenemase genes
These genes can move between plasmids and chromosomal DNA, facilitating the development of MDR strains

89
Q

Give an example of a transposon that spreads antibiotic resistance

A

Tn3 transposon carrying resistance to beta-lactam antibiotics

90
Q

Talk about the role of transposons in the emergence of virulent pathogens

A

transposable elements can carry virulence genes, such as those coding for toxins or adhesion factors

91
Q

Give an example of a transposon responsibe for the emergence of virulent pathogens

A

In C. difficile, Tn916 contributes to the spread of genes encoding toxin a and b

92
Q

Talk about the role of transposons in increasing gentic diversity

A

Transposition introduces mutatioins or rearrangements, creating genetic varianility in bacterial populations

This variability can enable pathogens to adapt to new environmets, hosts or thereapies

93
Q

Talk about transposons in ESBLs

A

Genes for ESBL priduction are often carried by transposons lik Tn3, spreading resistance in E.coli and K.pneumoniae

94
Q

Talk about transposons in VRE

A

Tn1546 is a key player in the transfer of vancomycin resistance genes

95
Q

Talk about transposons in CRE

A

Transposons like Tn4401 carry carbapenemase genes, contributing to the global rise of CRE

96
Q

Define Transposition

A

Movement of DNA segments (transposable elements) within the same genome or between DNA molecules

97
Q

How does transposition differ from HGT in terms of scope?

A

Transposition is a within-cell mechanism, moving genes internally

HGT transfers genes beteween cells or organisms

98
Q

How does transposition differ from HGT in terms of mechanism?

A

Transposition depends on transposable elements and their encoded enzymes e.g. transposase

HGT occurs through processes like transformation, transduction or conjugation, often involving mobile genetic elements like plasmids or bacteriophages

99
Q

How does transposition differ from HGT in terms of evolutionary impact?

A

Transposition causes local genetic rearrangements

HGT facilitates the acquisition of entirely new genes, accelerating bacterial evolution

100
Q

Talk about HGT and transposition working together

A

Transposable elements e.g transposons can move resistance genes onto plasmids, which are then transferred between bacteria via HGT

Together these mechanisms amplify the spread of antibiotic resistance and virulence factors

101
Q

What role do integrons have?

A

Integrons act like molecular storage systems, collecting advantageous genes from their environment and enabling bacteria to adapt quickly to challenges like antibiotics

Integrons are major drivers of antibiotic resistance in the clinical setting
Integrons express multiple resistance genes

Integrons are not mobile themselves but are often located on mobile genetic elements such as plasmids or transposons, facilitating their spread between bacteria

102
Q

In what ways are integrons clinically significant?

A

Spread of antibiotic resistance
emergence of superbugs
Adaptability and evolution
E. coli and K. pneumoniae
A. baumannii
Salmonella species

103
Q

Talk about Integrons in the spread of antibiotic resistance

A

Integrons can house and express multiple resistance genes, leading to MDR strains

Detected in 22-59% of gram-negative clinical isolates

E.g. class 1 integrons in Enterobacteriaceae frequently carry genes for resistance to beta-lactams, aminoglycosides and sulfonamides

104
Q

talk about the role of integrons in the emergence of superbugs

A

The combination of integrons with mobile genetic elements facilitates the rapid dissemination of resistance genes across species, contributing to the rise of superbugs like carbapenem resistant K. pneumoniae and P. aeruginosa

105
Q

Talk about the role of integrons in adaptability and evolution

A

Integrons allow bacteria to quickly adapt to environmenta pressures such as the presence of antibiotics, by incorporating and expressing resistance genes

106
Q

Talk about integrons in E. coli and K. pneumo

A

Class 1 integrons carry resistanc genes for aminoglycosides and extended-spectrum beta-lactams

107
Q

Talk about integrons in A. baumannii

A

Integrons contriubute to extreme drug resistance, making infections difficult to treat

108
Q

Talk about integrons in salmonella spp

A

Resistance genes for fluoroquinolones and sulfonamides are integrated into class 1 integrons

109
Q

Summarise the relevance of integrons

A

Genetic elements that capture, integrate and express gene cassettes, often carrying resistance genes

Found on plasmids or transposons, aiding in the horizontal tranfer of multidrug resistanc traits

Key player in the emergence of superbugs by enabling bacteria to adapt to antibiotics rapidly

4.2 Medical Microbiology (20 decks)

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