Computational methods reveal how hospital-acquired bacteria spread

January 16, 2013

Scientists at the Academy of Finland's Centre of Excellence in Computational Inference Research have developed novel computational methods that have yielded essential knowledge of how hospital-acquired bacteria spread and develop. These new methods, based on randomised algorithms, make it possible to analyse extensive genomic data significantly faster and more efficiently than previously. By applying these results, it is possible to better follow hospital-acquired infections in the future, or even fight them in real time.

The new methods are used to develop models of the evolution of bacteria and viruses. "Essential for the evolution of the bacteria that cause hospital-acquired infections is the . It means that several different transfer genes between the lineages of the same and different species so that the bacterium becomes resistant to antibiotics and the virulence factor rapidly spreads in the population," explains group leader, Professor Jukka Corander. Corander's group is part of the Centre of Excellence in Computational Inference Research.

This so-called recombination of bacteria makes it much more complicated to carry out evolution analyses. To facilitate such analyses, Corander's group in cooperation with researchers from Harvard University and the Wellcome Trust Sanger Institute has developed a number of methods based on smart randomised algorithms. These methods facilitate efficient and reliable analyses of extensive . With the current, most commonly used this work would take several months or even several years.

Two of the group's methods have recently been applied by an international study. This study demonstrated that more than half of the of the MRSA bacteria (i.e. methicillin-resistant strains of ) is caused by horizontal genomic transfer. This shows that the of the strains of bacteria are necessary when investigating the spread of bacteria in a host population. This horizontal variation significantly distorts the results received from normal evolutionary analyses.

"On the basis of the results from these analyses, i.e. the evolutionary variation, we're able to estimate when a certain strain of the MRSA bacterium has entered a country and started to spread to hospitals. This is the first time we have been able to prove that the interplay between the horizontal genomic variation and the mutational genomic variation may vary significantly across geographical locations and even between individual hospitals," Corander says. According to Corander, these insights open up new opportunities for in-depth studies on the spread and variation of MRSA and related causalities.

In another recently published study, Corander's group investigated the origin and evolution of the Enterococcus faecium bacterium that has adapted to survive in hospital environments. By using its analysis methods, the group found out that the forms of the bacteria originate from several independent sources, which is contrary to previous knowledge. In the nuclear genome of hospital strains of E. faecium, fewer signs of horizontal transfer were found than expected. This discovery led to a hypothesis that strains of bacteria that have adapted to survive in hospital environments may become either genetically or ecologically more isolated after horizontal transfer.

MRSA is a globally spread bacterium that is especially troublesome in hospitals. It is resistant to most antibiotics and annually causes the death of tens of thousands of people in the US, for instance. According to cautious estimates, the annual costs incurred by MRSA infections amount to several billion US dollars. In recent years, the E. faecium has become one of the major causes of hospital-acquired infections and its antibiotic- have caused severe hospital epidemics worldwide.

Explore further: How one strain of MRSA becomes resistant to last-line antibiotic

More information: Santiago Castillo-Ramirez, Jukka Corander, Pekka Marttinen, Mona Aldeljawi, William P Hanage, Henrik Westh, Kit Boye, Zeynep Gulay, Stephen D Bentley, Julian Parkhill, Matthew T Holden and Edward J Feil (2012) Phylogeographic variation in recombination rates within a global clone of Methicillin-Resistant Staphylococcus aureus (MRSA) Genome Biology, 13:R126 doi:10.1186/gb-2012-13-12-r126.
genomebiology.com/2012/13/12/R126/abstract

Rob J. L. Willems, Janetta Top, Willem van Schaik, Helen Leavis, Marc Bonten, Jukka Sirén, William P Hanage and Jukka Corander (2012) Restricted gene flow among hospital subpopulations of Enterococcus faecium. mBio, 3, e00151-12.
mbio.asm.org/content/3/4/e00151-12.full.html#

Related Stories

How one strain of MRSA becomes resistant to last-line antibiotic

May 22, 2012
Researchers have uncovered what makes one particular strain of methicillin-resistant Staphylococcus aureus (MRSA) so proficient at picking up resistance genes, such as the one that makes it resistant to vancomycin, the last ...

Scientist warns of new MRSA threat

February 2, 2012
(Medical Xpress) -- An MRSA expert from the University’s Department of Biology & Biochemistry has warned that a new, more toxic strain of the disease poses a serious threat to people in Britain as it migrates from the ...

Scientists link quickly spreading gene to Asian MRSA epidemic

April 22, 2012
National Institutes of Health (NIH) scientists and their colleagues in China have described a rapidly emerging Staphylococcus aureus gene, called sasX, which plays a pivotal role in establishing methicillin-resistant S. aureus ...

MRSA superbug spreads from big city hospitals to regional health centers, study suggests

May 14, 2012
Hospitals in large cities act as breeding grounds for the superbug MRSA prior to it spreading to smaller hospitals, a study suggests.

Recommended for you

Google searches can be used to track dengue in underdeveloped countries

July 20, 2017
An analytical tool that combines Google search data with government-provided clinical data can quickly and accurately track dengue fever in less-developed countries, according to new research published in PLOS Computational ...

MRSA emerged years before methicillin was even discovered

July 19, 2017
Methicillin resistant Staphylococcus aureus (MRSA) emerged long before the introduction of the antibiotic methicillin into clinical practice, according to a study published in the open access journal Genome Biology. It was ...

New test distinguishes Zika from similar viral infections

July 18, 2017
A new test is the best-to-date in differentiating Zika virus infections from infections caused by similar viruses. The antibody-based assay, developed by researchers at UC Berkeley and Humabs BioMed, a private biotechnology ...

'Superbugs' study reveals complex picture of E. coli bloodstream infections

July 18, 2017
The first large-scale genetic study of Escherichia coli (E. coli) cultured from patients with bloodstream infections in England showed that drug resistant 'superbugs' are not always out-competing other strains. Research by ...

Ebola virus can persist in monkeys that survived disease, even after symptoms disappear

July 17, 2017
Ebola virus infection can be detected in rhesus monkeys that survive the disease and no longer show symptoms, according to research published by Army scientists in today's online edition of the journal Nature Microbiology. ...

Mountain gorillas have herpes virus similar to that found in humans

July 13, 2017
Scientists from the University of California, Davis, have detected a herpes virus in wild mountain gorillas that is very similar to the Epstein-Barr virus in humans, according to a study published today in the journal Scientific ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.