Scientists Decode Genomes of Diverse TB Isolates

An international collaboration led by researchers in the US and South
Africa today announced the first genome sequence of an extensively drug
resistant (XDR) strain of the bacterium Mycobacterium tuberculosis,
one linked to more than 50 deaths in a recent tuberculosis (TB)
outbreak in KwaZulu-Natal, South Africa.

As part of this work, genomes
of multi-drug resistant (MDR) and drug sensitive isolates were also
decoded. Initial comparisons of the genome sequences reveal that the
drug-resistant and drug-sensitive microbes differ at only a few dozen
locations along the four-million-letter DNA code, revealing some known
drug resistance genes as well as some additional genes that may also be
important to the spread of TB.

The researchers have taken an unusual
step of immediately sharing both the genome sequence and their initial
analysis far in advance of submitting a scientific paper, in order to
accelerate work on drug-resistant TB by researchers around the world.

“Tuberculosis
is a major threat to global public health that demands new approaches
to disease diagnosis and treatment,” said Megan Murray, one of the
project’s principal investigators, an associate member of the Broad
Institute of MIT and Harvard and an associate professor at the Harvard
School of Public Health. “By looking at the genomes of different
strains, we can learn how the tuberculosis microbe outwits current
drugs and how new drugs might be designed.”

“Genome information
is a powerful tool for understanding the biology of infectious disease,
such as tuberculosis,” said Eric Lander, founding director of the Broad
Institute of Harvard and MIT. “It is important that genomic data be
made immediately available, particularly to researchers in areas most
heavily burdened by disease.”

“The sequenced strain is
responsible for the vast majority of the more than 300 XDR cases
identified thus far in the KwaZulu-Natal province of South Africa,”
said Willem Sturm, one of the project’s principal investigators and a
leading researcher of the XDR epidemic in KwaZulu-Natal, dean of the
Nelson Mandela School of Medicine, and director of the MRC Genital
Ulcer Disease Research Unit at the University of KwaZulu-Natal.
“Genetic characterization of this strain is essential for developing
tools to get this epidemic under control.”

Globally,
tuberculosis (TB) is a major cause of infectious disease deaths. Nearly
2 billion people, comprising roughly one third of the world’s
population, are thought to carry M. tuberculosis,
the culprit bacterium.

Major obstacles to controlling the disease stem
from the microbe’s ability to evade current treatments, which typically
require prolonged use by patients and are often not curative. MDR
strains, for example, are resistant to two of the most effective
first-line TB drugs, and XDR strains can circumvent first-line as well
as some second-line drugs. Adding to the problem, inefficient
diagnostic methods for TB make it difficult for doctors to determine
whether an individual harbors a drug-resistant strain, often delaying
proper therapy.

To shed light on the genetic changes that
mediate drug resistance, an international team of scientists undertook
a large-scale effort to sequence the genomes of drug-sensitive, MDR,
and XDR TB isolates of a strain responsible for the current XDR-TB
epidemic in KwaZulu-Natal, South Africa.

This strain corresponds to one
found in patients in Tugela Ferry, a rural town in KwaZulu-Natal that
has recently experienced a severe outbreak of XDR TB among patients
infected with the human immunodeficiency virus (HIV). There, 52 of 53
people infected with this strain died.

The research reflects a
collaboration among researchers in the Microbial Sequencing Center at
the Broad Institute of Harvard and MIT, Megan Murray of the Harvard
School of Public Health, and Willem Sturm and his colleagues at the
Nelson Mandela School of Medicine in South Africa.

The draft genome sequences of the various TB strains each cover roughly 95% of the M. tuberculosis
genome. Comparing the DNA sequences in these regions allows the
researchers to pinpoint the key differences among them, shedding light
on the genetic factors that contribute to TB drug resistance.

Strikingly, comparisons of the draft sequences reveal surprisingly few
genetic differences among the drug-sensitive, MDR and XDR strains:
there are only a few dozen small DNA changes. Some of these differences
are located in genes known to be involved in TB drug resistance, while
others are found in novel genes, whose roles have not been previously
investigated. Some of these genes may represent new drug-resistance
genes, while others may simply contain random mutations.

“That
a limited set of genetic differences separates one TB strain from
another is important,” said James Galagan, the associate director of
microbial genome analysis at the Broad Institute. “With the analysis of
additional XDR strains, it should be feasible to systematically unravel
the biological significance of each genetic variation.”

“These
results also lay the groundwork for the development of a rapid
diagnostic test for TB,” said Murray. “Such a test would enable more
rapid and accurate diagnoses, and help to prevent the spread of TB —
especially the most virulent strains.”

A significant fraction
of the new TB research was accomplished through the use of a powerful
new technology for decoding DNA. That approach, based on the principle
of single-molecule sequencing, makes it possible to read hundreds of
millions of DNA letters simultaneously.

“New technologies for
sequencing DNA can accelerate the pace of genomic research,
particularly for infectious disease,” said Bruce Birren, director of
the Microbial Sequencing Center at the Broad Institute. “It is
important that these technologies also be made available to researchers
in the field, where they are needed most.”

Importantly, all of
these data have been released far in advance of publication and can be
accessed by TB researchers worldwide, helping to spark work on an
infectious disease that constitutes a leading threat to global public
health. In the next phase of their work, the scientists plan to refine
the draft genome sequences and their comparative analysis, and expand
the scope of their research to include additional TB strains.

Data access

These
data can be accessed through the Broad Institute website, at
www.broad.mit.edu/XDR_TB, or through the TB database, www.tbdb.org.