TUBERCULOSIS: Phylogeny of Mycobacterium tuberculosis Beijing Strains Constructed from Polymorphisms in Genes Involved in DNA Replication, Recombination and Repair

PLoS ONE • on January 22, 2011
The Beijing family is a successful group of M. tuberculosis strains, often associated with drug resistance and widely distributed throughout the world. Polymorphic genetic markers have been used to type particular M. tuberculosis strains. We recently identified a group of polymorphic DNA repair replication and recombination (3R) genes. It was shown that evolution of M. tuberculosis complex strains can be studied using 3R SNPs and a high-resolution tool for strain discrimination was developed. Here we investigated the genetic diversity and propose a phylogeny for Beijing strains by analyzing polymorphisms in 3R genes.

Methodology/Principal Findings
A group of 3R genes was sequenced in a collection of Beijing strains from different geographic origins. Sequence analysis and comparison with the ones of non-Beijing strains identified several SNPs. These SNPs were used to type a larger collection of Beijing strains and allowed identification of 26 different sequence types for which a phylogeny was constructed. Phylogenetic relationships established by sequence types were in agreement with evolutionary pathways suggested by other genetic markers, such as Large Sequence Polymorphisms (LSPs). A recent Beijing genotype (Bmyc10), which included 60% of strains from distinct parts of the world, appeared to be predominant.

Conclusions/Significance
We found SNPs in 3R genes associated with the Beijing family, which enabled discrimination of different groups and the proposal of a phylogeny. The Beijing family can be divided into different groups characterized by particular genetic polymorphisms that may reflect pathogenic features. These SNPs are new, potential genetic markers that may contribute to better understand the success of the Beijing family.
http://elitestv.com/pub/2011/01/phylogeny-of-mycobacterium-tuberculosis-beijing-strains-constructed-from-polymorphisms-in-genes-involved-in-dna-replication-recombination-and-repair

TUBERCULOSIS: Detection of multiple strains of Mycobacterium tuberculosis using MIRU-VNTR in patients with pulmonary tuberculosis in Kampala, Uganda

Author: Katherine Dickman et al.
BMC Infectious Diseases 2010, 10:349


Many studies using DNA fingerprinting to differentiate Mycobacterium tuberculosis (MTB) strains reveal single strains in cultures, suggesting that most disease is caused by infection with a single strain. However, recent studies using molecular epidemiological tools that amplify multiple targets have demonstrated simultaneous infection with multiple strains of MTB.
We aimed to determine the prevalence of MTB multiple strain infections in Kampala, and the impact of these infections on clinical presentation of tuberculosis (TB) and response to treatment.

Methods:
A total of 113 consecutive smear and culture positive patients who previously enrolled in a house-hold contact study were included in this study. To determine whether infection with multiple MTB strains has a clinical impact on the initial presentation of patients, retrospective patient data (baseline clinical, radiological and drug susceptibility profiles) was obtained.
To determine presence of infections with multiple MTB strains, MIRU-VNTR (Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeats) -PCR was performed on genomic DNA extracted from MTB cultures of smear positive sputum samples at baseline, second and fifth months.

Results:
Of 113 patients, eight (7.1%) had infection with multiple MTB strains, coupled with a high rate of HIV infection (37.5% versus 12.6%, p = 0.049). The remaining patients (105) were infected with single MTB strains.
The proportions of patients with MTB smear positive cultures after two and five months of treatment were similar. There was no difference between the two groups for other variables.

Conclusion:
Infection with multiple MTB strains occurs among patients with first episode of pulmonary tuberculosis in Kampala, in a setting with high TB incidence.

Infection with multiple MTB strains had little impact on the clinical course for individual patients. This is the first MIRU-VNTR-based study from in an East African country.

http://7thspace.com/headlines/366633/detection_of_multiple_strains_of_mycobacterium_tuberculosis_using_miru_vntr_in_patients_with_pulmonary_tuberculosis_in_kampala_uganda_.html

TUBERCULOSIS: Possible Persistence Switch for Tuberculosis

September 21st, 2010
 Possible Persistence Switch for Tuberculosis Found: Computer Model Finds Probable Genetic Mechanism for TB Dormancy
The bacteria that cause tuberculosis (TB), Mycobacterium tuberculosis, can transition into a dormant state to ward off attacks from antibiotics and the immune system. A new report from Igoshin and Tiwari in this month's issue of Physical Biology examines a network of genes that may make this possible. A computer model of the network showed it can act as a "persistence" switch that toggles the organism from a fast-growing to a slow-growing state.
"The molecular mechanisms that allow Mycobacterium tuberculosis to switch into this slow-growing, persistent state have been associated with genes that are activated when the microorganism is under stress," said Igoshin, senior author of the study and an assistant professor in bioengineering at Rice.
Tiwari, lead author of the study and a graduate student in Igoshin's lab, said, "We examined a stress-response network of genes that are found in both the TB bacterium and other closely related mycobacteria. We analyzed the role of multiple feedback loops in this network, and were eventually able to identify an ultrasensitive mechanism that works in combination with the feedback loops to form a switch. This switch can possibly activate transition to the persistent state."
The study was a collaborative effort between Igoshin's laboratory at Rice's BioScience Research Collaborative and the research groups of Gabor Balazsi at the University of Texas M.D. Anderson Cancer Center and Maria Laura Gennaro at the Public Health Research Institute of the New Jersey Medical School.
Scientists have long known that the TB bacterium has the ability to "hunker down" and go dormant under stressful conditions. Previous studies have confirmed that both the slow-growing and fast-growing forms of the bacteria have identical genes.
"The fact that the same organism can exist in two states at the same time in the same environment raises many questions," Igoshin said. "What is the basis for this bistability? What are the environmental cues that activate the switch?"
Other bacteria can switch between stable states as well, but Mycobacterium tuberculosis' ability to make this transition is one reason TB is such a widespread disease. As much as 30 percent of the world's population is believed to be infected with TB, which causes about 2 million deaths every year.
http://www.sciencemagnews.com/possible-persistence-switch-for-tuberculosis-found-computer-model-finds-probable-genetic-mechanism-for-tb-dormancy.html

TUBERCULOSIS: When It Comes to Fighting Tuberculosis, Genetic Balance May Be the Key

Why do some people exposed to the bacteria that causes tuberculosis (TB) get sick, while others completely resist the disease? Research published this year in the journal Cell suggests that it all comes down to balance.
Scientists from the University of Washington used a combination of zebrafish experiments and human genetics to identify how a precisely tuned level of inflammation allows the body to fight off Mycobacterium tuberculosis, the causative agent of TB, but not go overboard. These findings not only help explain why some people are hypersensitive to TB, but may also have important implications for prevention and cure of this disease caused by a bacterium that can be found in one third of the world’s population.
The researchers began by creating random mutations in zebrafish and then exposing the animals to Mycobacterium marinum, a close genetic relative of the human TB bacterium and a natural pathogen for the fish. The reactions of these genetically altered fish varied from completely resistant to extremely susceptible. Further analysis showed that much of this variability was due to the LTA4H gene, which regulates the balance between pro- and anti-inflammatory factors.
Armed with findings from their zebrafish experiments, the researchers then turned to humans. They examined whether variations in the human version of LTA4H, known from previous research to affect inflammation, also affected susceptibility to TB. They analyzed DNA from 692 Vietnamese people with TB and 759 healthy controls. They found that heterozygosity – having one pro-inflammatory version of the LTA4H gene and one anti-inflammatory version – was the best position to be in. For example, having one copy of an A and one copy of a G at rs1978331 was associated with with about 30% lower odds of having TB compared to people with either two As or two Gs. The people with AG at this SNP who did develop TB were less likely to die if their disease reached a severe state.
Brinkmann/Schaible, MPI for Infection Biology
A study of a group of people in Nepal who had been exposed to leprosy, another disease caused by a mycobacterium, showed the same protective effect of having one copy of an A and one copy of a G at rs1978331. There was no effect on actually contracting leprosy, but people with AG at this SNP were less likely to develop a severe case.
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Having two different versions of certain LTA4H variations seems to keep pro- and anti-inflammatory response mechanisms balanced. The authors suggest that when inflammation is inadequate (as may be the case when a person has two Gs at rs1978331), the risk of infection with TB or leprosy is high, as are the chances of severe disease and possibly death. On the other hand, when inflammation is excessive (as might happen with two As at rs1978331), tissue damage can occur, which can also lead to severe disease and death. The sweet spot in the middle, when there is neither too little nor too much inflammation, allows the body to adequately control and eventually clear an infection, without destroying itself in the process.
If the researchers’ hypothesis is true, if a balanced immune response to TB is best, this could explain why people with TB often improve when given anti-inflammatory immunosuppressive drugs alongside the standard antibiotic treatments.
The identification of the LTA4H variants opens the possibility for the development of new treatments for TB. In a press release, the senior author of the paper notes that because the same variations they identified in LTA4H have also been associated with heart disease, it’s possible that drugs that target this pathway in heart disease might be useful for treating TB too. Many strains of Mycobacterium tuberculosis have become resistant to standard treatments, so finding new ways to fight the disease is a priority. The new genetic findings may help researchers develop treatments that focus on helping a person’s immune system fight the infection, instead of attacking the pathogen directly.
About TuberculosisTB is a highly contagious disease that is spread through airborne droplets containing the bacterium. While the highest incidence rates occur in South-East Asia and Sub-Saharan Africa, about one third of the world is thought to be infected with the bacterium that causes TB, with a new infection occurring every second. However, not all infected people have active TB, which is characterized by a chronic cough with blood-tinged sputum, a fever, night-sweats, and weight loss. People with latent TB do not experience any symptoms and are not contagious. They simply respond positively to a TB skin test and have a 5-10% chance of developing active TB. HIV infection is the strongest risk factor for the development of active TB because it compromises the immune system.
Current methods of prevention and treatment for TB are complicated, at best. A vaccine against TB does exist – the BCG vaccine – however efficacy varies based on age, geography, TB type, and duration. Treatment for TB depends on resistance. Directly observed therapy (DOT) entails taking a strict regimen of drugs for about six months under supervision. Multidrug resistant strains of TB (MDR-TB) have developed in response to mismanaged treatment and require a different drug regimen. Extensively drug resistant TB (XDR-TB) is virtually untreatable.
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