Corporate Banner
Satellite Banner
Next Gen Sequencing
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

NIH Uses Genome Sequencing to Help Quell Bacterial Outbreak in Clinical Center

Published: Friday, August 24, 2012
Last Updated: Thursday, August 23, 2012
Bookmark and Share
Genomics and microbiology experts collaborate in hospital infection control.

For six months last year, a deadly outbreak of antibiotic-resistant bacteria kept infection-control specialists at the National Institutes of Health’s Clinical Center in a state of high alert.

A New York City patient carrying a multi-drug resistant strain of Klebsiella pneumoniae, a microbe frequently associated with hospital-borne infections, introduced the dangerous bacteria into the 243-bed research hospital while participating in a clinical study in the summer of 2011.

Despite enhanced infection-control practices, including patient isolation, the K. pneumoniae began to spread to other Clinical Center patients at the alarming rate of one a week, ultimately colonizing 17 patients, of whom 11 died - six from infection and five from their underlying disease while infected.

To get the outbreak under control, Clinical Center staff collaborated with investigators at the National Human Genome Research Institute (NHGRI), also part of NIH, to use genome sequencing in the middle of this active hospital epidemic to learn how the microbe spread.

A report in the Aug. 22, 2012, early online edition of Science Translational Medicine describes how that collaboration helped quell the outbreak.

"Infectious outbreaks happen in every hospital in the world, afflicting millions of patients each year in the United States alone," said NHGRI Director Eric D. Green, M.D., Ph.D.

Green continued, "By marshaling the ability to sequence bacterial genomes in real time to accurately trace the bacteria as it spread among our Clinical Center patients, our researchers successfully elucidated what happened, which in turn has taught us some important lessons. This study gives us a glimpse of how genomic technologies will alter our approach to microbial epidemics in the future."

The outbreak began in June 2011 when a New York City hospital transferred a seriously ill 43-year-old woman to NIH. The admitting nurse noted that the patient’s medical history included multiple-drug resistant infections, leading Clinical Center staff to put her in isolation immediately and institute a number of other restrictions.

Despite these measures, immune-suppressed patients elsewhere in the hospital began to develop K. pneumoniae infections, but the Clinical Center staff could not determine whether the same strain of bacteria carried by the New Yorker caused the new infections.

"For decades, we used pulsed-field gel electrophoresis to differentiate bacterial strains," said Tara N. Palmore, M.D., the NIH Clinical Center's deputy hospital epidemiologist who led the outbreak investigation. This test produces a barcode-like pattern of bacterial DNA that shows whether strains are genetically similar. In K. pneumoniae, however, 70 percent of the strains in the United States belong to one strain type with one pattern. “This test is not very helpful for that organism," she said.

As the outbreak began, the Clinical Center staff teamed up with NHGRI researchers led by Julie Segre, Ph.D., an NHGRI senior investigator.

Dr. Segre had been working with the Clinical Center's Clinical Microbiology Department to study the evolution of bacterial antibiotic resistance when she heard about the outbreak.

“We were already trying to develop clinical molecular diagnostics tools,” Dr. Segre said, “We thought we could use genome sequencing to tell whether the K. pneumoniae from the first patient was the same strain as the one that infected the second patient.”

The hospital team sent samples of bacteria isolated from infected patients to the NIH Intramural Sequencing Center (NISC), a component NHGRI. NISC sequenced the DNA samples, and Dr. Segre’s team analyzed the results.

Where the pulse-field gel electrophoresis technique shows relatively crude patterns, genome sequence data shows precise differences, down to single genetic letters in the bacterial genome.

This sequencing proved that the strain of K. pneumoniae sickening all the patients in the Clinical Center originated with the patient from New York; that is, the outbreak had a single source.

“Genomic data can identify unexpected modes of transmission,” Dr. Segre said. “Though the transmission path is difficult to detect, the genomic data is indisputable.”

When combined with the traditional epidemiology tracking data, the genome sequence results showed that Patient 1 transmitted the bacteria to other patients on two separate occasions from infections on different parts of her body, creating two major clusters of infected patients.

Even as the epidemiologic and genomic investigation proceeded, the infection-control team in the NIH Clinical Center employed increasingly intensive strategies to stop the infection from spreading.

For example, they used a vapor of hydrogen peroxide to sanitize rooms and removed sinks and drains where K. pneumoniae had been detected. They also limited the activities of hospital staff and the use of equipment exposed to infected patients so the microbe could not spread to uninfected patients.

In addition, the NIH doctors treated the first patient’s infection with colistin, an older, toxic antibiotic considered a drug of last resort. Fortunately, the treatment worked and the patient recovered.

The infection-control interventions proved successful, and by the end of the year, no new cases arose in the Clinical Center, stemming the outbreak.

“Genome sequencing and analysis is our best hope for anticipating and outpacing the pathogenic evolution of infectious agents,” said Dr. Segre. “Though our practice of genomics did not change the way patients were treated in this outbreak, it did change the way the hospital practiced infection control.”

“This study makes it clear that genome sequencing, as it becomes more affordable and rapid, will become a critical tool for healthcare epidemiology in the future,” said David Henderson, M.D., NIH Clinical Center deputy director for clinical care and associate director for quality assurance and hospital epidemiology. His team is preparing a paper that will outline the use of genome sequencing within the methodology of infection control for similar outbreaks. “Now that we know what genome sequencing can do,” he said, “I anticipate this methodology will be rapidly adopted by the hospital epidemiology community.”

Over one million healthcare-associated infections (HAIs) occur across the spectrum of healthcare each year; in hospitals alone, the Centers for Disease Control and Prevention estimates that 1 in 20 hospitalized patients has an HAI.

These infections can be life threatening and also add to our growing health care costs, accounting for billions of dollars in excess health expenditures each year.

Multi-drug resistant K. pneumoniae is among the more dreaded infections because few effective treatments exist and it has a mortality rate of 40 percent.


Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,500+ scientific posters on ePosters
  • More than 3,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Genetic Link For Rare Intestinal Cancer
Researchers recommend screening for people with family history.
Thursday, April 16, 2015
Tumor DNA in Blood Reveals Lymphoma Progression
Using an advanced genetic test, researchers were able to detect diffuse large B-cell lymphoma (DLBCL) in blood serum before it could be seen on CT scans.
Tuesday, April 14, 2015
Comprehensive Genomic Study of Sub-Saharan Africans Conducted
New data resource will enhance disease research and genomic diversity studies.
Thursday, December 04, 2014
NIH Exceptional Responders to Cancer Therapy Study Launched
Study to investigate the molecular factors of tumors associated with exceptional treatment responses of cancer patients to drug therapies.
Friday, September 26, 2014
NIH Awards $14.5M for DNA Sequencing Techniques
For the past several years, nanopore research has been an important focus of the program’s grants.
Tuesday, August 05, 2014
NIH Funds $24M into Alzheimer’s Disease Genome Research
Scientists will analyze genome sequence data to identify gene risk, protective factors.
Tuesday, July 08, 2014
Genetic Disorder Causing Strokes, Vascular Inflammation in Children Discovered
NIH researchers have identified gene variants that cause a rare syndrome of sporadic fevers, skin rashes and recurring strokes, beginning early in childhood.
Thursday, February 20, 2014
Speeding Validation of Disease Targets
NIH, industry and non-profits join forces to develop new treatments earlier, beginning with Alzheimer’s, type 2 diabetes, and autoimmune disorders.
Tuesday, February 04, 2014
NCI Launches Trial to Assess the Utility of Genetic Sequencing to Improve Patient Outcomes
Trial could identify patient sub-groups that are likely to benefit from certain treatments.
Saturday, February 01, 2014
NIH Deposits First Batch of Genomic Data for Alzheimer’s Disease
Researchers can now freely access the first batch of genome sequence data from the Alzheimer’s Disease Sequencing Project (ADSP).
Monday, December 02, 2013
NIH Awards Focus on Nanopore Technology For DNA Sequencing
The use of nanopore technology aimed at more accurate and efficient DNA sequencing is the main focus of grants awarded by the NIH.
Monday, September 09, 2013
New Genes for Childhood Epilepsies Discovered
New strategy may find more genes and provide a better understanding of these and other complex neurological disorders.
Monday, August 12, 2013
NIH, Lacks Family Reach Understanding to Share Genomic Data of HeLa Cells
New NIH policy requires researchers to apply for access to the full genome sequence data from HeLa cells.
Thursday, August 08, 2013
NIH Funds New Grants Exploring Use of Genome Sequencing in Patient Care
NIH has awarded four grants for up to four years to multidisciplinary research teams to explore the use of genome sequencing in medical care.
Wednesday, July 24, 2013
NIH Researchers Conduct First Genomic Survey of Human Skin Fungal Diversity
Location on the body surface determines fungal composition with the greatest diversity on feet.
Thursday, May 23, 2013
Scientific News
The Changing Tides of the In Vitro Diagnostics Market
With the increasing focus in personalized medicine, diagnostics plays a crucial role in patient monitoring.
Genetic Overlapping in Multiple Autoimmune Diseases May Suggest Common Therapies
CHOP genomics expert leads analysis of genetic architecture, with eye on repurposing existing drugs.
Surprising Mechanism Behind Antibiotic-Resistant Bacteria Uncovered
Now, scientists at TSRI have discovered that the important human pathogen Staphylococcus aureus, develops resistance to this drug by “switching on” a previously uncharacterized set of genes.
Data Mining DNA For Polycystic Ovary Syndrome Genes
A new Northwestern Medicine genome-wide association study of PCOS – the first of its kind to focus on women of European ancestry – has provided important new insights into the underlying biology of the disorder.
Viral Comparisons
ORNL team applies genomics expertise to analyze, map virus sequence database.
The Tree of Life — More Like A Bush
New species evolve whenever a lineage splits off into several. Because of this, the kinship between species is often described in terms of a ‘tree of life’, where every branch constitutes a species.
Ancient Origins of Deadly Lassa Virus Uncovered
Working as part of an international team in North America and West Africa, a researcher at The Scripps Research Institute (TSRI) has published new findings showing the ancient roots of the deadly Lassa virus, a relative of Ebola virus, and how Lassa virus has changed over time.
Furthering Data Analysis of Next-gen Sequencing to Facilitate Research
Researchers at Cincinnati Children's Hospital Medical Center have developed a user-friendly, integrated platform for analyzing the transcriptomic and epigenomic "big data.
Statistical Technique Helps Researchers Understand Tumor Makeup, Personalize Cancer Treatments
A new statistical method for analyzing next-generation sequencing (NGS) data that helps researchers study the genome of various organisms such as human tumors and could help bring about personalized cancer treatments has been unveiled.
‘Fishing Expedition’ Nets Nearly Tenfold Increase in Number of Sequenced Virus Genomes
Newly developed computational tool finds 12,500 genomes of viruses that infect microbes.
SELECTBIO

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,500+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FREE!