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 Antimicrobial Resistance and Modernising Microbiology

Introduction

Antimicrobial resistance (AMR) is recognised to be a major threat to modern medicine. Better and faster diagnostic tests are key to improved treatment of infections. By accurately identifying whether a bacteria or virus (pathogen) is present, we can identify whether antibiotics should be used. Sequencing the DNA from the bacteria or virus allows for quick identification of the pathogen causing the disease and provides information on whether it can be treated or not and if it is similar to other pathogens that have been seen previously.

The BRC is supporting our activities in developing time- and cost-saving methodologies to isolate bacterial or viral DNA directly from a clinical sample, rather than waiting for it to grow. Once DNA is obtained we use whole genome sequencing methods (WGS) to accurately “read” the genetic code of the pathogen. This code is then compared to a database containing changes, or mutations, which are known to cause resistance to certain drugs. Comparing our DNA of interest to the catalogue determines whether any of those mutations are present and therefore whether certain drugs would kill the bacterial or virus and thus successfully treat the infection. Our group is developing and improving computer programs to look at WGS quickly and accurately and also expanding the databases containing mutations that cause resistance to drugs for certain pathogens. This work will lead to new, quicker and innovative ways to diagnose and treat infection within a clinical setting.

We are also establishing the use of computers to look at health records and sequence data. Combining sequence data with electronic health records can revolutionise the treatment and management of infectious diseases in the National Health Service (NHS) and help England’s health system monitor what infectious diseases are present (national surveillance). We have demonstrated this by investigating the epidemiology and impact of COVID-19 in Oxford University Hospitals NHS Foundation Trust.

To see our latest projects Click here

 

Infections in Oxfordshire Research Database (IORD)

The Infections in Oxfordshire Research Database (IORD) is an important part of the Antimicrobial Resistance and Modernising Microbiology Theme. It includes routinely collected electronic data from hospital and GP records, covering about 1% of England.

The overall goal of IORD is to improve the management of infections and potentially infection-related episodes in UK hospitals.

It does this by bringing together increasingly rich types of data to investigate, for example,:

  • Trends in incidence of infections caused by different microbes in Oxfordshire, and infection-associated syndromes (like pneumonia or sepsis), within and outside the hospital: are new microbes starting to cause problems?
  • Predictors of infection with different microbes or infection-associated syndromes: what increases the risk of developing infections?
  • Severity of infection with different microbes or infection-associated syndromes, including adverse outcomes: are some infections becoming more or less serious? Are particular strains of a microbe becoming more dangerous (or “virulent”), and how might this happen?

 To find out more about IORD please Click here

Antimicrobial Resistance and Modernising Microbiology

Introduction

Antimicrobial resistance (AMR) is recognised to be a major threat to modern medicine. Better and faster diagnostic tests are key to improved treatment of infections. By accurately identifying whether a bacteria or virus (pathogen) is present, we can identify whether antibiotics should be used. Sequencing the DNA from the bacteria or virus allows for quick identification of the pathogen causing the disease and provides information on whether it can be treated or not and if it is similar to other pathogens that have been seen previously.

The BRC is supporting our activities in developing time- and cost-saving methodologies to isolate bacterial or viral DNA directly from a clinical sample, rather than waiting for it to grow. Once DNA is obtained we use whole genome sequencing methods (WGS) to accurately “read” the genetic code of the pathogen. This code is then compared to a database containing changes, or mutations, which are known to cause resistance to certain drugs. Comparing our DNA of interest to the catalogue determines whether any of those mutations are present and therefore whether certain drugs would kill the bacterial or virus and thus successfully treat the infection. Our group is developing and improving computer programs to look at WGS quickly and accurately and also expanding the databases containing mutations that cause resistance to drugs for certain pathogens. This work will lead to new, quicker and innovative ways to diagnose and treat infection within a clinical setting.

We are also establishing the use of computers to look at health records and sequence data. Combining sequence data with electronic health records can revolutionise the treatment and management of infectious diseases in the National Health Service (NHS) and help England’s health system monitor what infectious diseases are present (national surveillance). We have demonstrated this by investigating the epidemiology and impact of COVID-19 in Oxford University Hospitals NHS Foundation Trust.

To see our latest projects Click here

 

Infections in Oxfordshire Research Database (IORD)

The Infections in Oxfordshire Research Database (IORD) is an important part of the Antimicrobial Resistance and Modernising Microbiology Theme. It includes routinely collected electronic data from hospital and GP records, covering about 1% of England.

The overall goal of IORD is to improve the management of infections and potentially infection-related episodes in UK hospitals.

It does this by bringing together increasingly rich types of data to investigate, for example,:

  • Trends in incidence of infections caused by different microbes in Oxfordshire, and infection-associated syndromes (like pneumonia or sepsis), within and outside the hospital: are new microbes starting to cause problems?
  • Predictors of infection with different microbes or infection-associated syndromes: what increases the risk of developing infections?
  • Severity of infection with different microbes or infection-associated syndromes, including adverse outcomes: are some infections becoming more or less serious? Are particular strains of a microbe becoming more dangerous (or “virulent”), and how might this happen?

 To find out more about IORD please Click here