03 November 2017

Hunting for antibiotic-resistant microbes

Scientists from Russia are closer to revealing the secret of the birth of "superbugs"

RIA News

Russian bioinformatics scientists have created a computer algorithm that allows you to quickly find the genes of "superbugs" in the DNA of the human intestinal microflora and reveal the ways of evolution and distribution of these parts of the genome, according to an article published in the journal Bioinformatics.

"As a rule, the appearance of such genes among microbes of the microflora does not pose a risk to a person, but if he becomes infected with pathogenic microbes, these genes can be transmitted to them from harmless intestinal bacteria. Our algorithm allows us to obtain information about these genes and select the most rational options for the use of antibiotics, which will help to contain the spread of "superbugs", – write Vladimir Ulyantsev and his colleagues from ITMO University in St. Petersburg.

In recent years, the problem of the appearance of so-called "super–bacteria" - microbes resistant to the action of one or more antibiotics - has become more and more acute for doctors. Among them there are both rare pathogens of infections, and very common and dangerous pathogens, such as Staphylococcus aureus or Pneumococcus (Klebsiella pneumoniae). There is a real danger that all antibiotics will lose their effectiveness and medicine will return to the "dark ages".

The main "incubators" of such microbes, according to scientists today, are hospitals and livestock farms, where antibiotics are used to accelerate the growth of meat breeds of livestock.  Both on farms and in hospitals, large numbers of potential carriers of infection, bacteria themselves, and antibiotics are concentrated, forcing them to evolve and preventing "ordinary" bacteria from displacing less prolific super-microbes.

Recently, Russian scientists have shown that another important "incubator" of these superbugs can be the human intestine and the beneficial or harmless microbes of microflora living there, often in contact with antibiotics when treating their hosts for diseases.

The search for these genes, as noted by Ulyantsev and his colleagues, is an extremely difficult task – tens of millions of microbes live in our intestines and in other parts of the body, and decoding the DNA of each of them individually will take a very long time and will require an astronomical amount of money. Therefore, scientists usually study the so–called metagenome - the whole set of genes of all microbes and viruses living in a particular environment.

"Conventional" methods of metagenome analysis, as the researchers say, can find the genes of "superbugs", but do not allow us to understand how and where they could appear, and how many microbes possess them, and how they could be transmitted from one type of bacteria to another. There are often situations that several types of bacteria can be carriers of "supergens" at once, or a very small number of representatives of one strain of harmless microbes can possess them, from which they can get into the genomes of pathogens.

Russian scientists were able to solve this problem using the MetaFast method of rapid analysis and comparison of bacterial microflora genomes, which they developed and presented to the world last year.

Using this algorithm, scientists have created a new program, MetaCherchant, which can analyze individual genes of "superbugs" and search for their analogues and progenitors in the metagenomic "soup".

Testing the work of this program, Ulyantsev and his colleagues discovered the "progenitors" of several invulnerable strains of the Helicobacter pylori microbe that causes stomach infections and cancer by analyzing metagenomes collected in Kazan hospitals before and after attempts to get rid of colonies of these bacteria with antibiotics.

Such an approach, according to bioinformatics, will allow their colleagues to study the evolution of such microbes in the human intestine and develop methods to combat them, which would maximally restrain their further development.

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