Displaying and Analyzing Mycobacterium Tuberculosis Data
Displaying and Analyzing Mycobacterium Tuberculosis Data
Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction-based method of DNA fingerprinting the Mycobacterium tuberculosis complex. We examined spoligotype data using a bioinformatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gain insights into the global dissemination of strains of tuberculosis. Logo analysis of spoligotyping data provides a simple way to describe a fingerprint signature and may be useful in categorizing unique spoligotypes patterns as they are discovered. Large databases of DNA fingerprint information, such as those from the U.S. National Tuberculosis Genotyping and Surveillance Network and the European Concerted Action on Tuberculosis, contain information on thousands of strains from diverse regions. The description of related spoligotypes has depended on exhaustive listings of the individual spoligotyping patterns. Logo analysis may become another useful graphic method of visualizing and presenting spoligotyping clusters from these databases.
The process of DNA fingerprinting Mycobacterium tuberculosis isolates provides epidemiologists with data for investigating transmission and confirming laboratory cross-contamination. When personnel and resources are available, strains from all newly diagnosed cases of tuberculosis (TB) are fingerprinted. Interpreting the data from these sentinel surveillance studies can be challenging. TB can be latent for decades before resulting in active disease. The best method for examining M. tuberculosis complex genotyping data gathered over just a few years is still in question.
The genotyping of M. tuberculosis complex has been undertaken in the United States in directed studies and in sentinel surveillance. Since 1992, M. tuberculosis complex DNA fingerprinting for isolates has been available to U.S. Departments of Health and TB Control Offices to investigate cases of suspected TB transmission and suspected laboratory cross-contamination. At the same time, sentinel surveillance of select regions was used to evaluate if genotyping every new patient isolate from a particular region was useful. Although direct DNA fingerprinting studies are relatively simple to design, we are still learning how best to use in toto the large and diverse databases generated by sentinel surveillance studies from multiple laboratories. Previous studies have used DNA fingerprinting methods to understand the development and spread of subspecies of the M. tuberculosis complex, such as Mycobacterium africanum, M. bovis, and the W-Beijing family.
Analyzing the spread and evolution of M. tuberculosis complex strains is more complicated because of the long incubation of disease and relatively short-term collection of data (approximately 10 years). We examine whether bioinformatic tools can help in analyzing the data collected. Bioinformatics uses sophisticated analyses of large amounts of genetic information to clarify the relationships between species, explain the evolution of groups of genes, and assemble information from genome sequencing projects. Bioinformatic analysis involves searching nucleic acid or protein sequence information for previously unrecognized motifs that may signal previously unrecognized regions of interest. Spoligotype analysis is a form of DNA sequencing by hybridization. Several groups have used some of these novel analytical tools to examine M. tuberculosis complex genotyping. Sequence logo analysis can find motifs in potentially related nucleic acid or protein sequences. Logo analysis combines these data on a graphic that illustrates the location and degree of sequence conservation in the selected sequences. We applied sequence logo analysis to find motifs based on the presence or absence of specific spacer sequences. We also evaluated the usefulness of logo analysis in examining phylogenetic relationships of the M. tuberculosis complex direct repeat (DR) locus and its potential as a simple graphic method presenting grouped spoligotyping data.
We suggest using the sequence logo technique to understand the distribution of each spacer sequence used in the spoligotype assay. This information is useful in improving or redesigning the spoligotype assay by showing the degree of differentiation achieved with each spacer sequence.
Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction-based method of DNA fingerprinting the Mycobacterium tuberculosis complex. We examined spoligotype data using a bioinformatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gain insights into the global dissemination of strains of tuberculosis. Logo analysis of spoligotyping data provides a simple way to describe a fingerprint signature and may be useful in categorizing unique spoligotypes patterns as they are discovered. Large databases of DNA fingerprint information, such as those from the U.S. National Tuberculosis Genotyping and Surveillance Network and the European Concerted Action on Tuberculosis, contain information on thousands of strains from diverse regions. The description of related spoligotypes has depended on exhaustive listings of the individual spoligotyping patterns. Logo analysis may become another useful graphic method of visualizing and presenting spoligotyping clusters from these databases.
The process of DNA fingerprinting Mycobacterium tuberculosis isolates provides epidemiologists with data for investigating transmission and confirming laboratory cross-contamination. When personnel and resources are available, strains from all newly diagnosed cases of tuberculosis (TB) are fingerprinted. Interpreting the data from these sentinel surveillance studies can be challenging. TB can be latent for decades before resulting in active disease. The best method for examining M. tuberculosis complex genotyping data gathered over just a few years is still in question.
The genotyping of M. tuberculosis complex has been undertaken in the United States in directed studies and in sentinel surveillance. Since 1992, M. tuberculosis complex DNA fingerprinting for isolates has been available to U.S. Departments of Health and TB Control Offices to investigate cases of suspected TB transmission and suspected laboratory cross-contamination. At the same time, sentinel surveillance of select regions was used to evaluate if genotyping every new patient isolate from a particular region was useful. Although direct DNA fingerprinting studies are relatively simple to design, we are still learning how best to use in toto the large and diverse databases generated by sentinel surveillance studies from multiple laboratories. Previous studies have used DNA fingerprinting methods to understand the development and spread of subspecies of the M. tuberculosis complex, such as Mycobacterium africanum, M. bovis, and the W-Beijing family.
Analyzing the spread and evolution of M. tuberculosis complex strains is more complicated because of the long incubation of disease and relatively short-term collection of data (approximately 10 years). We examine whether bioinformatic tools can help in analyzing the data collected. Bioinformatics uses sophisticated analyses of large amounts of genetic information to clarify the relationships between species, explain the evolution of groups of genes, and assemble information from genome sequencing projects. Bioinformatic analysis involves searching nucleic acid or protein sequence information for previously unrecognized motifs that may signal previously unrecognized regions of interest. Spoligotype analysis is a form of DNA sequencing by hybridization. Several groups have used some of these novel analytical tools to examine M. tuberculosis complex genotyping. Sequence logo analysis can find motifs in potentially related nucleic acid or protein sequences. Logo analysis combines these data on a graphic that illustrates the location and degree of sequence conservation in the selected sequences. We applied sequence logo analysis to find motifs based on the presence or absence of specific spacer sequences. We also evaluated the usefulness of logo analysis in examining phylogenetic relationships of the M. tuberculosis complex direct repeat (DR) locus and its potential as a simple graphic method presenting grouped spoligotyping data.
We suggest using the sequence logo technique to understand the distribution of each spacer sequence used in the spoligotype assay. This information is useful in improving or redesigning the spoligotype assay by showing the degree of differentiation achieved with each spacer sequence.
