Solving a mystery: How the TB bacterium develops rapid resistance to antibiotics

Date:
November 19, 2020
Source:
San Diego State University
Summary:
These slow growing bacteria have long puzzled TB researchers with
their fairly rapid resistance to antibiotics. Researchers may have
been barking up the wrong tree in exploring genetics, because the
answer seems to lie in the epigenetic domain.



FULL STORY ==========================================================================
For a slow-growing microbe that multiplies infrequently, Mycobacterium tuberculosis, the pathogen that causes tuberculosis (TB) has long puzzled researchers as to how it develops resistance to antibiotics so quickly,
in a matter of weeks to months.


==========================================================================
Now, TB researchers at San Diego State University have uncovered a
crucial clue to the mystery: the answer may lie in the epigenetic domain
rather than the genetic domain where most scientists have concentrated
their efforts.

Their discovery could help advance new diagnostics, therapeutics and
vaccine targets.

Epigenetics is the study of inheritable changes in gene expression that
do not involve a corresponding change to the underlying DNA sequence --
meaning changes to the phenotype but no change in the genotype. This
affects only the physical structure of the DNA, through a process called
DNA methylation where a chemical 'cap' is added to the DNA molecule,
preventing or facilitating the expression of certain genes.

The SDSU researchers describe the rapid response phenomenon they
discovered as 'intercellular mosaic methylation,' a process by which Mycobacterium tuberculosis diversifies, creating multiple subpopulations
each with its own phenotype. While antibiotics could kill many of
these mutant subpopulations, at least a few do survive and develop
drug resistance.

"We believe this also explains why diagnostic testing in some patients
does not predict treatment failure, and why some patients come back
months later with the disease reemerging in a far more resistant state,"
said Faramarz Valafar, a TB expert with SDSU's School of Public Health
who studies the genetics and epigenetics of pulmonary diseases. "This is
also why CT scans of the lungs of many "cured" patients show lesions with possible bacterial activity." Worldwide, TB is among the top 10 causes of death. It killed 1.4 million people in 2019, and about 10 million people
fall ill with it each year, according to the World Health Organization.



========================================================================== Valafar's team collected hundreds of samples of drug resistant varieties
of the bacteria from patients in India, China, Philippines and South
Africa, as well as Europe, through collaborations with TB researchers worldwide.

Their study was published in eLife in late October. Valafar and project scientist Samuel Modlin began exploring epigenetics for the TB bacterium
in 2016, and doctoral student Derek Conkle-Gutierrez joined them in
2018, in the Laboratory for Pathogenesis of Clinical Drug Resistance
and Persistence.

Modlin, an SDSU alumnus, and Conkle-Gutierrez utilized skills and
knowledge they acquired at SDSU to carry out this research -- data and statistical analysis, coding skills, and bioinformatics knowledge.

"We've known for decades that bacterial epigenetics can influence the expression of certain genes, which can lead to a variety of phenotypes
even when they have identical genotypes," Conkle-Gutierrez said. "We
discovered evidence of that phenomenon in the TB bacterium." Antibiotic resistance is typically caused by genomic mutations, but this bacterium
is one of several that leverages alternative mechanisms in the epigenetic domain to enable rapid adaptation.

"We found that some of them had mutations that led to variable DNA
methylation and those strains had much more diversity in their epigenome,
and thus more potential to be drug resistant," Modlin said.



==========================================================================
The researchers found there were no set patterns and methylation was
fairly random. They used advanced comparative genomic and epigenetic
techniques to identify variations across cells within a colony from a
single isolate, from a single patient -- including tiny variations that nevertheless impacted gene expression. They were able to do this because, rather than assuming the reference genome has a common structure, they reconstructed each genome from scratch and analyzed its epigenetic
signatures.

They will now focus on testing and confirming the key genes they
identified with methylation signatures. There is more work to be done
before their discovery can eventually be used for diagnostics.

"There is a lot of resistance in TB that escapes current molecular
diagnostics and we don't really know why. That's problematic," Valafar
said. "This study offers a new domain, new tools, and a new approach
to looking for alternative mechanisms. We move away from the classical
view of molecular diagnostics and use a novel, comprehensive approach
to analyzing bacteria." Current standard of care treatments use two
types of antibiotics - - bacteriostatics that prevent bacteria from
multiplying but don't kill them, and bactericides that do kill them.

"We found a new mode of variation and if we can inhibit that
diversification mechanism, we can inhibit short-term epigenetic resistance
and kill the bacteria before mutations in the genome develop and cause long-term, genetic resistance," Modlin said.

This may be how some bacterial populations survive treatment and
make the patient ill again with far greater antibiotic resistance or hypervirulence.


========================================================================== Story Source: Materials provided by San_Diego_State_University. Original written by Padma Nagappan. Note: Content may be edited for style and
length.


========================================================================== Journal Reference:
1. Samuel J Modlin, Derek Conkle-Gutierrez, Calvin Kim, Scott
N Mitchell,
Christopher Morrissey, Brian C Weinrick, William R Jacobs, Sarah M
Ramirez-Busby, Sven E Hoffner, Faramarz Valafar. Drivers and sites
of diversity in the DNA adenine methylomes of 93 Mycobacterium
tuberculosis complex clinical isolates. eLife, 2020; 9 DOI:
10.7554/eLife.58542 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/11/201119083925.htm

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