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

1
Q

What is attachment?

A

Attachment is the emotional bond that develops between an infant and their primary caregiver, providing security and influencing future relationships.

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2
Q

What are the four attachment styles identified by Ainsworth?

A

Secure, Insecure-Avoidant, Insecure-Resistant, and Disorganised.

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3
Q

Describe the Secure attachment style.

A

Securely attached children feel confident that their caregiver will meet their needs, showing distress when separated and happiness upon reunion.

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4
Q

Describe the Insecure-Avoidant attachment style.

A

Children with this style avoid or ignore the caregiver, showing little emotion when they leave or return.

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5
Q

Describe the Insecure-Resistant attachment style.

A

These children are anxious, clingy, and difficult to soothe, displaying ambivalence towards the caregiver.

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6
Q

What is the Strange Situation experiment?

A

Ainsworth’s controlled observation measuring attachment by assessing separation and reunion behaviours in infants.

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7
Q

Who developed Attachment Theory?

A

John Bowlby.

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8
Q

What is Bowlby’s Monotropic Theory?

A

Suggests infants form a primary attachment crucial for survival, influencing future relationships through an internal working model.

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9
Q

What is the Critical Period in attachment?

A

Bowlby proposed that attachment should form within the first 2.5 years of life for healthy development.

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10
Q

What is the Internal Working Model?

A

A mental representation of relationships based on early attachment experiences, guiding future interactions.

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11
Q

What is Maternal Deprivation?

A

Bowlby’s idea that prolonged separation from a primary caregiver during early years can lead to emotional and intellectual consequences.

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12
Q

What is the difference between Privation and Deprivation?

A

Privation is the lack of any attachment from infancy, whereas deprivation is the loss of an existing attachment.

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13
Q

What is the Continuity Hypothesis?

A

The idea that early attachment styles influence future relationships and emotional development.

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14
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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15
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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16
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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17
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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18
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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19
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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20
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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21
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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22
Q

What is Antimicrobial Resistance (AMR)?

A

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

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23
Q

How does WGS assist in managing AMR?

A

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

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24
Q

What are some limitations of WGS?

A

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

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25
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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26
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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27
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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28
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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29
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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30
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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31
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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32
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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33
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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34
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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35
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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36
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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37
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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38
Q

How does WGS help in tracking bacterial evolution?

A

By comparing genomic sequences over time, researchers can study mutation rates and adaptation mechanisms.

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39
Q

How does WGS contribute to personalised medicine?

A

It allows tailored treatment strategies based on the genetic makeup of bacterial infections.

40
Q

What role do resistance plasmids play in bacterial infections?

A

They carry antibiotic resistance genes, enabling bacteria to survive treatment and spread resistance.

41
Q

How does WGS help in rapid outbreak containment?

A

By identifying bacterial strains quickly, enabling targeted interventions to prevent further spread.

42
Q

What ethical concerns exist with WGS?

A

Issues include patient privacy, data security, and consent for genomic data sharing.

43
Q

Why is TB diagnosis challenging with traditional methods?

A

TB bacteria grow slowly, requiring weeks or months for culture-based diagnosis.

44
Q

How does WGS enhance epidemiological surveillance?

A

It allows real-time monitoring of bacterial strains and resistance trends.

45
Q

What does the future hold for WGS in global health?

A

As costs decrease and technology advances, WGS will become a standard tool for bacterial diagnostics worldwide.

46
Q

Why is RNA fragmented before sequencing?

A

To fit the technological constraints of sequencing platforms like Illumina, which work optimally with cDNA fragments around 300 nucleotides long.

47
Q

How has sequencing speed improved over time?

A

Modern sequencing technologies can now sequence 2000 nucleotides in a matter of hours, whereas early methods like Sanger sequencing took about a week.

48
Q

What insights can be gained by integrating RNA-Seq and proteomics?

A

It allows researchers to compare RNA and protein expression levels, revealing regulatory mechanisms during viral infections.

49
Q

How can computational methods enhance the integration of RNA-Seq and proteomics?

A

They can infer protein lists from transcriptomic data, which can then be validated through mass spectrometry.

50
Q

How is quantitative mass spectrometry useful in virology?

A

It enables researchers to compare the expression of viral proteins in infected versus uninfected cells, shedding light on how viruses manipulate host cellular functions.

51
Q

What discoveries have been made using combined RNA-Seq and proteomics approaches?

A

Previously unknown viral proteins and host responses to infections, such as those in Adenovirus and SARS-CoV-2, have been identified.

52
Q

How does WGS help in diagnosing bacterial infections?

A

WGS allows for precise identification of bacterial pathogens, antibiotic resistance genes, and virulence factors.

53
Q

What are the three key objectives of WGS in bacterial infection control?

A

Diagnosis, outbreak investigation, and antimicrobial resistance (AMR) surveillance.

54
Q

What is the traditional method for diagnosing bacterial infections?

A

Culture-based methods, followed by biochemical testing and antibiotic susceptibility testing.

55
Q

How long do traditional culture-based methods take?

A

Typically 24–72 hours, but for some bacteria like Mycobacterium tuberculosis, it can take weeks.

56
Q

What are the four main steps in traditional bacterial diagnosis?

A

Sample collection, culture, biochemical identification, and antibiotic susceptibility testing.

57
Q

What is a major drawback of traditional diagnostic methods?

A

They are slow, labor-intensive, and may fail to detect antibiotic resistance mechanisms.

58
Q

How does WGS improve diagnosis speed?

A

It can provide results within 24 hours, reducing the time required for pathogen identification and treatment decisions.

59
Q

Why is WGS more precise than traditional methods?

A

It provides complete genetic information, allowing for accurate species identification and resistance gene detection.

60
Q

How does WGS contribute to outbreak management?

A

It helps identify outbreak sources, track transmission routes, and detect emerging pathogens.

61
Q

How does WGS compare to traditional methods for S. aureus detection?

A

WGS is faster and more accurate, identifying resistance and virulence factors in a single test.

62
Q

What makes Mycobacterium tuberculosis difficult to diagnose?

A

Its slow growth and complex cell wall make traditional culture methods time-consuming.

63
Q

How does WGS accelerate TB diagnosis?

A

It detects Mycobacterium tuberculosis and its resistance genes directly from clinical samples.

64
Q

How does WGS track bacterial transmission?

A

By comparing bacterial genomes, it determines whether infections are linked.

65
Q

Why is WGS useful in hospital settings?

A

It helps detect and control nosocomial infections by identifying transmission patterns.

66
Q

How does WGS assist in public health monitoring?

A

It tracks the spread of resistant bacterial strains globally.

67
Q

How does WGS contribute to AMR surveillance?

A

It detects resistance genes and monitors their global distribution.

68
Q

Why is AMR a major global health concern?

A

It leads to untreatable infections, increased mortality, and higher healthcare costs.

69
Q

How does WGS help combat AMR?

A

By identifying resistance genes early, guiding appropriate antibiotic use.

70
Q

What are two key advantages of WGS over traditional methods?

A

Faster results and higher accuracy in identifying pathogens and resistance genes.

71
Q

Why is WGS becoming the preferred method in bacterial diagnostics?

A

It offers comprehensive, rapid, and precise pathogen characterization.

72
Q

How does WGS impact clinical decision-making?

A

It enables targeted antibiotic therapy, improving patient outcomes.

73
Q

What is a major limitation of WGS in routine diagnostics?

A

High costs and the need for bioinformatics expertise.

74
Q

Why is data interpretation a challenge in WGS?

A

Large datasets require computational analysis to extract meaningful clinical insights.

75
Q

What are some ethical concerns of WGS?

A

Patient privacy, data security, and potential misuse of genetic information.

76
Q

How can WGS become more accessible?

A

By reducing sequencing costs and developing user-friendly analysis tools.

77
Q

How will WGS evolve in the future?

A

Advances in automation and AI will improve speed and accessibility.

78
Q

What impact will WGS have on global health?

A

It will enhance disease surveillance and outbreak response worldwide.

79
Q

How does WGS help with virulence factor detection?

A

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

80
Q

How can WGS improve outbreak responses?

A

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

81
Q

How does WGS impact antibiotic stewardship?

A

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

82
Q

How does WGS compare to PCR in bacterial identification?

A

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

83
Q

How does WGS improve TB diagnostics?

A

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

84
Q

Why is TB diagnosis challenging with traditional methods?

A

TB bacteria grow slowly, requiring weeks or months for culture-based diagnosis.

85
Q

What does the future hold for WGS in global health?

A

As costs decrease and technology advances, WGS will become a standard tool for bacterial diagnostics worldwide.

86
Q

How does WGS help in tracking bacterial evolution?

A

By comparing genomic sequences over time, researchers can study mutation rates and adaptation mechanisms.

87
Q

What role do resistance plasmids play in bacterial infections?

A

They carry antibiotic resistance genes, enabling bacteria to survive treatment and spread resistance.

88
Q

How does WGS help in rapid outbreak containment?

A

By identifying bacterial strains quickly, enabling targeted interventions to prevent further spread.

89
Q

How does WGS enhance epidemiological surveillance?

A

It allows real-time monitoring of bacterial strains and resistance trends.

90
Q

Why is RNA fragmented before sequencing?

A

To fit the technological constraints of sequencing platforms like Illumina, which work optimally with cDNA fragments around 300 nucleotides long.

91
Q

How has sequencing speed improved over time?

A

Modern sequencing technologies can now sequence 2000 nucleotides in a matter of hours, whereas early methods like Sanger sequencing took about a week.

92
Q

What insights can be gained by integrating RNA-Seq and proteomics?

A

It allows researchers to compare RNA and protein expression levels, revealing regulatory mechanisms during viral infections.

93
Q

How can computational methods enhance the integration of RNA-Seq and proteomics?

A

They can infer protein lists from transcriptomic data, which can then be validated through mass spectrometry.

94
Q

How is quantitative mass spectrometry useful in virology?

A

It enables researchers to compare the expression of viral proteins in infected versus uninfected cells, shedding light on how viruses manipulate host cellular functions.

95
Q

What discoveries have been made using combined RNA-Seq and proteomics approaches?

A

Previously unknown viral proteins and host responses to infections, such as those in Adenovirus and SARS-CoV-2, have been identified.