Genome Sequencing and Bacterial Infections

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30 Questions

What is the primary route of transmission for Escherichia coli?

Faecal oral route of transmission

What was the outcome of the S. aureus whole genome sequencing study in the 2012 outbreak?

The healthcare worker was decolonized and the ward was reopened

What percentage of the human population is colonized with Staphylococcus aureus?


What is the primary benefit of using genome sequencing for diagnostics in bacterial infections?

Rapid identification of outbreaks and sources of infection

What was the duration of the prospective surveillance study mentioned in the text?

12 months

What is the percentage of pulmonary TB cases among active TB cases?


What was published in 2001 regarding Staphylococcus aureus?

The first genome sequence

What is the primary reason for the female vs male split in patients, according to the study?

Dietary differences between men and women

What is the name of the staining technique used to identify MTB?

Ziehl-Neelsen stain

What is the type of betalactamase carried by the NICU strains in the Melbourne study?


What is the purpose of using acidic solution in MTB staining?

To retain certain stains on MTB

What is the mortality rate of untreated TB?

More than half

What is the primary advantage of whole-genome sequencing in identifying and typing M.tuberculosis complex?

It offers higher molecular resolution for outbreak investigations

What was the patient's Rockwood score?

Very fit

What percentage of cases were found to be part of transmission clusters?

Over 40%

What is the typical timeframe for identifying Mycobacterium tuberculosis complex using traditional methods?

1 to 2 months

What was the result of the comparison of sequence data between cultured and direct samples in the 2017 study?

Good concordance

What was the diagnosis of the patient who had a 43-day stay in the ICU?


What was the patient's condition on April 14th?


How many clusters were found to involve both hospital and community contacts?

28 clusters

What was the significance of the study by Young et al. (2012) on the evolutionary dynamics of Staphylococcus aureus?

It revealed the dynamics of Staphylococcus aureus during progression from carriage to disease

What was the method used to sequence the colonies from each nasal swab in the study by Coll et al. (2017)?

Whole-genome sequencing (WGS)

What was the conclusion of the study by Coll et al. (2017) regarding MRSA transmission?

There is equal transmission of MRSA in hospitals and the community

What was the significance of the German 2011 EHEC outbreak study by Man et al. (2011)?

It showcased the use of rapid next-generation sequencing technology in outbreak investigation

What is the primary cause of mortality in patients with cystic fibrosis?

Pulmonary insufficiency

What is the estimated number of deaths caused by multidrug-resistant Pseudomonas aeruginosa in the United States in 2017?


Where are Pseudomonas bacteria commonly found in the environment?

In soil and water

What is the name of the type of Pseudomonas that often causes infections in humans?

Pseudomonas aeruginosa

What is the consequence of antibiotic resistance in Pseudomonas aeruginosa?

Reduced effectiveness of antibiotics

What is the estimated number of infections caused by multidrug-resistant Pseudomonas aeruginosa in hospitalized patients in the United States in 2017?


Study Notes

Bacterial Pathogens and Genome Sequencing

  • Escherichia coli (E. coli) is one of the most common bacterial causes of gastroenteritis, with a faecal oral route of transmission (contaminated food or water).
  • Staphylococcus aureus is an opportunistic bacteria present in the nasal passages of 30% of the human population, but can cause serious infections when the innate immune system is breached.

Genome Sequencing for Diagnostics

  • The first S. aureus whole genome sequence was published in 2001, requiring 5 years of work and a large team of people.
  • Genome sequencing can be used to diagnose and investigate outbreaks, as demonstrated by a 2012 study on a neonatal MRSA outbreak.
  • Genome-wide single nucleotide polymorphism (SNP) analysis can identify the source of an outbreak and differentiate between strains.

Mycobacterium tuberculosis (TB)

  • Active TB cases are predominantly pulmonary TB, with symptoms including chest pain, coughing-up blood, and a productive, prolonged cough.
  • X-ray imaging and histological staining techniques can identify MTB in expectorate samples from sputum.
  • Whole-genome sequencing can be used for rapid susceptibility testing of M. tuberculosis, replacing current methods that take 1-2 months.

Rapid Whole-Genome Sequencing for Outbreak Investigations

  • A 2013 study demonstrated the use of rapid whole-genome sequencing for investigating a neonatal MRSA outbreak.
  • The study showed that sequencing data could be used to identify the source of the outbreak, decolonize the healthcare worker, and reopen the ward.

Staphylococcus aureus and Genome Sequencing

  • A 2017 study sequenced at least one MRSA isolate from 1465 individuals and recorded epidemiological data.
  • The study revealed transmission patterns in hospitals and the community, highlighting the need to review existing infection control policy and practice.

Pseudomonas aeruginosa

  • Pseudomonas aeruginosa is a type of bacteria commonly found in the environment, which can cause infections in humans, particularly in people with weakened immune systems.
  • Antibiotic resistance is a significant problem, with multidrug-resistant P. aeruginosa causing an estimated 32,600 infections among hospitalized patients and 2,700 deaths in the United States in 2017.

Learn how genome sequencing can help control bacterial infections, focusing on three major pathogens: Escherichia coli, Staphylococcus aureus, and Mycobacterium tuberculosis. Understand the transmission routes and pathogenic mechanisms of these bacteria.

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