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Frontiers in Infectious diseases > L16 - How will genome sequencing help us control bacterial infections > Flashcards

L16 - How will genome sequencing help us control bacterial infections Flashcards

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1
Q

What is Whole Genome Sequencing (WGS)?

A

A method of analysing the complete DNA of an organism, used for rapid identification of bacterial pathogens and antibiotic resistance genes.

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2
Q

How does traditional culture-based diagnosis work?

A

It involves growing patient samples on selective media, followed by identification and antibiotic susceptibility testing, taking 48-72 hours or longer.

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3
Q

What are the benefits of WGS over traditional methods?

A

Faster pathogen identification, precise detection of resistance genes, and improved outbreak management through shared databases.

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4
Q

How does WGS help in diagnosing Staphylococcus aureus infections?

A

It allows rapid detection of antibiotic resistance genes, reducing diagnostic time compared to culture-based methods.

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5
Q

How does WGS aid in the detection of Mycobacterium tuberculosis?

A

It accelerates TB diagnosis, identifying genetic markers of resistance and reducing diagnostic time from months to days.

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6
Q

What role did WGS play in the Escherichia coli outbreak in Germany?

A

It traced the outbreak strain’s genetic origins, revealing acquired virulence genes and resistance plasmids, leading to better outbreak management.

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7
Q

Why is Staphylococcus aureus a concern?

A

It is a multi-drug resistant pathogen on the WHO priority list due to its significant health burden.

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8
Q

What impact does WGS have on public health?

A

It improves disease surveillance, outbreak tracking, and personalised treatment strategies for bacterial infections.

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9
Q

What is Antimicrobial Resistance (AMR)?

A

The ability of bacteria to survive antibiotic treatment, making infections harder to treat.

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10
Q

How does WGS assist in managing AMR?

A

It identifies resistance genes, helping clinicians select effective antibiotics for treatment.

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11
Q

What are some limitations of WGS?

A

High costs, technical expertise requirements, and data storage challenges.

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12
Q

How does WGS contribute to precision medicine?

A

By providing detailed genetic information to tailor treatments to specific bacterial strains.

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13
Q

How can WGS improve outbreak responses?

A

By enabling rapid identification and comparison of bacterial strains to determine transmission pathways.

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14
Q

What is phenotypic identification in traditional diagnostics?

A

The process of identifying bacteria based on observable traits like gram staining and biochemical tests.

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15
Q

How does WGS help with virulence factor detection?

A

It identifies genes associated with bacterial pathogenicity, aiding in risk assessment and treatment planning.

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16
Q

How can WGS data be shared internationally?

A

Through global genomic databases, improving surveillance and response to emerging bacterial threats.

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17
Q

What is the future of WGS in bacterial diagnostics?

A

As technology advances and costs decrease, it is likely to replace traditional culture-based methods in many settings.

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18
Q

What are some challenges in implementing WGS?

A

Cost, accessibility, need for specialised training, and ethical considerations regarding data sharing.

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19
Q

How does WGS impact antibiotic stewardship?

A

It helps guide appropriate antibiotic use by identifying resistance patterns, reducing unnecessary prescriptions.

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20
Q

What role does mass spectrometry play in traditional diagnostics?

A

It is used for phenotypic identification of bacteria by analysing their protein composition.

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21
Q

How does WGS affect treatment decision-making?

A

It provides clinicians with detailed resistance profiles, enabling more targeted and effective treatments.

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22
Q

How does WGS compare to PCR in bacterial identification?

A

WGS provides comprehensive genetic information, whereas PCR targets specific genes or regions.

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23
Q

How does WGS improve TB diagnostics?

A

It detects drug resistance mutations rapidly, reducing diagnostic time and improving treatment outcomes.

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24
Q

Why is data interpretation a challenge in WGS?

A

The vast amount of genetic data requires complex bioinformatics analysis to extract clinically relevant insights.

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25
How does WGS help in tracking bacterial evolution?
By comparing genomic sequences over time, researchers can study mutation rates and adaptation mechanisms.
26
How does WGS contribute to personalised medicine?
It allows tailored treatment strategies based on the genetic makeup of bacterial infections.
27
What role do resistance plasmids play in bacterial infections?
They carry antibiotic resistance genes, enabling bacteria to survive treatment and spread resistance.
28
How does WGS help in rapid outbreak containment?
By identifying bacterial strains quickly, enabling targeted interventions to prevent further spread.
29
What ethical concerns exist with WGS?
Issues include patient privacy, data security, and consent for genomic data sharing.
30
Why is TB diagnosis challenging with traditional methods?
TB bacteria grow slowly, requiring weeks or months for culture-based diagnosis.
31
How does WGS enhance epidemiological surveillance?
It allows real-time monitoring of bacterial strains and resistance trends.
32
What does the future hold for WGS in global health?
As costs decrease and technology advances, WGS will become a standard tool for bacterial diagnostics worldwide.
33
Why is RNA fragmented before sequencing?
To fit the technological constraints of sequencing platforms like Illumina, which work optimally with cDNA fragments around 300 nucleotides long.
34
How has sequencing speed improved over time?
Modern sequencing technologies can now sequence 2000 nucleotides in a matter of hours, whereas early methods like Sanger sequencing took about a week.
35
What insights can be gained by integrating RNA-Seq and proteomics?
It allows researchers to compare RNA and protein expression levels, revealing regulatory mechanisms during viral infections.
36
How can computational methods enhance the integration of RNA-Seq and proteomics?
They can infer protein lists from transcriptomic data, which can then be validated through mass spectrometry.
37
How is quantitative mass spectrometry useful in virology?
It enables researchers to compare the expression of viral proteins in infected versus uninfected cells, shedding light on how viruses manipulate host cellular functions.
38
What discoveries have been made using combined RNA-Seq and proteomics approaches?
Previously unknown viral proteins and host responses to infections, such as those in Adenovirus and SARS-CoV-2, have been identified.
39
How does WGS help in diagnosing bacterial infections?
WGS allows for precise identification of bacterial pathogens, antibiotic resistance genes, and virulence factors.
40
What are the three key objectives of WGS in bacterial infection control?
Diagnosis, outbreak investigation, and antimicrobial resistance (AMR) surveillance.
41
What is the traditional method for diagnosing bacterial infections?
Culture-based methods, followed by biochemical testing and antibiotic susceptibility testing.
42
How long do traditional culture-based methods take?
Typically 24–72 hours, but for some bacteria like Mycobacterium tuberculosis, it can take weeks.
43
What are the four main steps in traditional bacterial diagnosis?
Sample collection, culture, biochemical identification, and antibiotic susceptibility testing.
44
What is a major drawback of traditional diagnostic methods?
They are slow, labor-intensive, and may fail to detect antibiotic resistance mechanisms.
45
How does WGS improve diagnosis speed?
It can provide results within 24 hours, reducing the time required for pathogen identification and treatment decisions.
46
Why is WGS more precise than traditional methods?
It provides complete genetic information, allowing for accurate species identification and resistance gene detection.
47
How does WGS contribute to outbreak management?
It helps identify outbreak sources, track transmission routes, and detect emerging pathogens.
48
How does WGS compare to traditional methods for S. aureus detection?
WGS is faster and more accurate, identifying resistance and virulence factors in a single test.
49
What makes Mycobacterium tuberculosis difficult to diagnose?
Its slow growth and complex cell wall make traditional culture methods time-consuming.
50
How does WGS accelerate TB diagnosis?
It detects Mycobacterium tuberculosis and its resistance genes directly from clinical samples.
51
How does WGS track bacterial transmission?
By comparing bacterial genomes, it determines whether infections are linked.
52
Why is WGS useful in hospital settings?
It helps detect and control nosocomial infections by identifying transmission patterns.
53
How does WGS assist in public health monitoring?
It tracks the spread of resistant bacterial strains globally.
54
How does WGS contribute to AMR surveillance?
It detects resistance genes and monitors their global distribution.
55
Why is AMR a major global health concern?
It leads to untreatable infections, increased mortality, and higher healthcare costs.
56
How does WGS help combat AMR?
By identifying resistance genes early, guiding appropriate antibiotic use.
57
What are two key advantages of WGS over traditional methods?
Faster results and higher accuracy in identifying pathogens and resistance genes.
58
Why is WGS becoming the preferred method in bacterial diagnostics?
It offers comprehensive, rapid, and precise pathogen characterization.
59
How does WGS impact clinical decision-making?
It enables targeted antibiotic therapy, improving patient outcomes.
60
What is a major limitation of WGS in routine diagnostics?
High costs and the need for bioinformatics expertise.
61
Why is data interpretation a challenge in WGS?
Large datasets require computational analysis to extract meaningful clinical insights.
62
What are some ethical concerns of WGS?
Patient privacy, data security, and potential misuse of genetic information.
63
How can WGS become more accessible?
By reducing sequencing costs and developing user-friendly analysis tools.
64
How will WGS evolve in the future?
Advances in automation and AI will improve speed and accessibility.
65
What impact will WGS have on global health?
It will enhance disease surveillance and outbreak response worldwide.
66
How does WGS help with virulence factor detection?
It identifies genes associated with bacterial pathogenicity, aiding in risk assessment and treatment planning.
67
How can WGS improve outbreak responses?
By enabling rapid identification and comparison of bacterial strains to determine transmission pathways.
68
How does WGS impact antibiotic stewardship?
It helps guide appropriate antibiotic use by identifying resistance patterns, reducing unnecessary prescriptions.
69
How does WGS compare to PCR in bacterial identification?
WGS provides comprehensive genetic information, whereas PCR targets specific genes or regions.
70
How does WGS improve TB diagnostics?
It detects drug resistance mutations rapidly, reducing diagnostic time and improving treatment outcomes.
71
Why is TB diagnosis challenging with traditional methods?
TB bacteria grow slowly, requiring weeks or months for culture-based diagnosis.
72
What does the future hold for WGS in global health?
As costs decrease and technology advances, WGS will become a standard tool for bacterial diagnostics worldwide.
73
How does WGS help in tracking bacterial evolution?
By comparing genomic sequences over time, researchers can study mutation rates and adaptation mechanisms.
74
What role do resistance plasmids play in bacterial infections?
They carry antibiotic resistance genes, enabling bacteria to survive treatment and spread resistance.
75
How does WGS help in rapid outbreak containment?
By identifying bacterial strains quickly, enabling targeted interventions to prevent further spread.
76
How does WGS enhance epidemiological surveillance?
It allows real-time monitoring of bacterial strains and resistance trends.
77
Why is RNA fragmented before sequencing?
To fit the technological constraints of sequencing platforms like Illumina, which work optimally with cDNA fragments around 300 nucleotides long.
78
How has sequencing speed improved over time?
Modern sequencing technologies can now sequence 2000 nucleotides in a matter of hours, whereas early methods like Sanger sequencing took about a week.
79
What insights can be gained by integrating RNA-Seq and proteomics?
It allows researchers to compare RNA and protein expression levels, revealing regulatory mechanisms during viral infections.
80
How can computational methods enhance the integration of RNA-Seq and proteomics?
They can infer protein lists from transcriptomic data, which can then be validated through mass spectrometry.
81
How is quantitative mass spectrometry useful in virology?
It enables researchers to compare the expression of viral proteins in infected versus uninfected cells, shedding light on how viruses manipulate host cellular functions.
82
What discoveries have been made using combined RNA-Seq and proteomics approaches?
Previously unknown viral proteins and host responses to infections, such as those in Adenovirus and SARS-CoV-2, have been identified.
83
How does whole genome sequencing improve bacterial diagnosis?
It enables rapid and accurate identification of bacterial species and resistance genes, often within 1–12 hours.
84
What are the three major applications of whole genome sequencing in bacterial infections?
Diagnosis, outbreak surveillance, and understanding bacterial adaptation to the host environment.
85
What makes Mycobacterium tuberculosis diagnosis challenging using traditional methods?
It is slow-growing and requires weeks for culture and antibiotic susceptibility testing.
86
How does whole genome sequencing contribute to outbreak investigations?
By comparing genomic data to identify transmission patterns and sources of infection.
87
What was discovered during the E. coli O104:H4 outbreak in Germany through whole genome sequencing?
The outbreak strain was a hybrid combining EAEC virulence genes and Shiga toxin genes, forming a novel pathotype.
88
How did whole genome sequencing reveal within-host evolution in a fatal Staphylococcus aureus infection?
It showed only 8 mutations separating nasal colonisation strains from the bloodstream strain, including truncations in virulence regulators.
89
Why can't current WGS tools detect all resistance mechanisms?
They depend on known gene databases and cannot identify unknown or novel resistance mutations.
90
What is metagenomic next-generation sequencing (mNGS)?
A hypothesis-free method to identify all pathogens in complex samples without culturing.
91
How does WGS outperform traditional phenotypic AST for some pathogens?
It provides higher specificity and sensitivity for known resistance genes and reduces time to diagnosis.
92
What were the benefits of WGS in the neonatal MRSA outbreak study?
WGS confirmed transmission links and excluded unrelated strains, highlighting its use in real-time surveillance.
93
What is the main endocrine therapy for ER+ breast cancer?
Anti-oestrogens, which block the oestrogen receptor.
94
What proportion of breast cancers are ER+?
70-80%.
95
What is the structure and function of the ER?
A nuclear hormone receptor; it binds oestrogen (estradiol), dimerises, binds to DNA (EREs), and activates transcription of target genes involved in proliferation and survival.
96
How does ER signalling affect breast cancer cells?
Promotes proliferation, survival, and expression of growth factors and receptors.
97
What are the types of anti-oestrogens?
SERMs (e.g. tamoxifen), SERDs (e.g. fulvestrant), and aromatase inhibitors (e.g. anastrozole).
98
What does SERM stand for?
Selective Estrogen Receptor Modulator.
99
How does tamoxifen work?
It competes with oestrogen for ER binding, forming a complex that binds DNA but recruits corepressors instead of coactivators in breast tissue.
100
What is the tissue-specific effect of tamoxifen?
It is an ER antagonist in breast but an agonist in endometrium and bone.
101
What are the clinical uses of tamoxifen?
Treatment of ER+ breast cancer in premenopausal women and prevention in high-risk women.
102
What are the side effects of tamoxifen?
Risk of endometrial cancer, thromboembolism, menopausal symptoms.
103
What does SERD stand for?
Selective Estrogen Receptor Degrader.
104
How does fulvestrant work?
Binds ER and causes degradation via the proteasome; acts as a pure antagonist with no agonist effects.
105
What are the advantages of SERDs over SERMs?
No agonist activity and can work in tamoxifen-resistant cancers.
106
What is the role of aromatase?
Converts androgens to oestrogens (testosterone → estradiol, androstenedione → estrone).
107
Where is aromatase activity significant post-menopause?
In peripheral tissues such as fat, where oestrogen is still produced.
108
How do aromatase inhibitors work?
Inhibit aromatase to reduce oestrogen synthesis, particularly effective in postmenopausal women.
109
Name two types of aromatase inhibitors.
Anastrozole and letrozole (non-steroidal), exemestane (steroidal, irreversible).
110
Why are aromatase inhibitors ineffective in premenopausal women?
Because ovarian oestrogen production is still active and not suppressed.
111
What is a major side effect of aromatase inhibitors?
Osteoporosis and fractures due to reduced oestrogen in bone.
112
What mechanisms of resistance exist against endocrine therapy?
ER mutations (e.g. constitutively active ESR1), ER loss, upregulation of growth factor signalling (e.g. HER2, PI3K/Akt), epigenetic silencing.
113
How is resistance to endocrine therapy addressed?
Combination therapy with CDK4/6 inhibitors, PI3K inhibitors, mTOR inhibitors.
114
What are CDK4/6 inhibitors, and why are they used?
Drugs like palbociclib that inhibit cell cycle progression; used with endocrine therapy to overcome resistance.
115
What is the significance of ESR1 mutations in resistance?
Lead to constitutively active ER that no longer requires ligand, causing resistance to tamoxifen/aromatase inhibitors.
116
What is the role of coactivators and corepressors in ER signalling?
They determine whether ER acts as an activator or repressor of gene expression depending on ligand and tissue context.
117
What is the benefit of targeting ER in breast cancer?
Tumour regression, delayed recurrence, and improved survival in ER+ patients.

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