Pathogen genomic sequencing
Pathogen genomic sequencing refers to the techniques used to determine the linear order of nucleotides in the genomes of disease-causing microorganisms, including viruses, bacteria, and fungi. This process plays a critical role in microbial forensics, which helps enhance epidemiological studies by providing detailed characterizations of pathogens that can be used as evidence in legal cases. By utilizing methods such as polymerase chain reaction (PCR) and genomic sequencing, forensic scientists can trace the origins of pathogens involved in biocrimes and identify the individuals or organizations responsible for their dissemination. Notable pathogens studied through sequencing include those causing tuberculosis, plague, and anthrax, all of which pose significant health threats worldwide. The preservation and analysis of pathogen samples, especially in sensitive situations, follow specific protocols to ensure accurate forensic outcomes. Significant advances in sequencing technology, such as the comprehensive characterization of the human genome, have facilitated improvements in the understanding of microbial genomes and their implications for public health. Ultimately, pathogen genomic sequencing is essential for managing emerging infectious diseases and enhancing public safety.
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Pathogen genomic sequencing
DEFINITION: Techniques used to determine the linear order of monomers (small molecules such as nucleotides) that can be linked together to form polymers, mainly nucleic acids, found in the genomes of disease-causing microbes such as certain viruses, bacteria, and fungi.
SIGNIFICANCE: Microbial forensics, the branch of forensic science that deals with microorganisms, extends the scope of epidemiology by going into greater detail to characterize pathogens for use as possible evidence in legal proceedings. The sequencing of pathogens is an especially important technique in forensic science as it pertains to increasingly dangerous global scourges of infectious emerging diseases.
Using a triad of techniques—polymerase chain reaction (PCR) and genomic sequencing followed by phylogenetic studies, which infer relationships among microbial strains—forensic scientists have the ability to determine the origin of a disease-causing agent, or pathogen, used in a biocrime and to determine who or what organization was responsible for its dissemination. In 2000, the human genome was characterized through sequencing techniques; this accomplishment revolutionized molecular biology. The comparatively small viral genomes of human immunodeficiency virus (HIV), hantaviruses, and Haemophilus influenzae have been elucidated through sequencing, as have the larger genomes of bacteria, including Mycobacterium tuberculosis (TB) and its drug-resistant strains, Yersinia pestis (plague), Mycobacterium leprae (leprosy or Hansen’s disease), Salmonella typhi (typhus), Bacillus anthracis (anthrax), and Neisseria meningitidis (meningitis). All of these pathogens are considered threats to global health.
The techniques used by forensic scientists in the collection, handling, shipping, and preservation of potential pathogens are different from those employed for nonpathogenic samples. Forensic microbial analysis is based on a technique that identifies tandemly repeated sequences within the pathogen’s genome. (Tandem repeats are repetitive sequences consisting of two or more nucleotides that serve as genetic markers and are frequently used to establish attribution—the source of a pathogen—in legal proceedings.)
After an unknown attacker sent letters containing B. anthracis to addresses in New York City, Washington, DC, and Boca Raton, Florida, in the fall of 2001, careful preservation of initial and follow-up samples of the contents of the envelopes allowed forensic scientists to identify the Ames strain of B. anthracis as the specific pathogen used in the attacks. Before the entire genome was sequenced, the sample in question was compared with natural strains of B. anthracis; this comparison narrowed the possible source to a human-made strain of anthrax as opposed to one that might be found in nature. Further comparison to attribute the Ames strain to this biocrime was possible because the first strain, isolated from a victim in Florida (the index case), and the strains isolated from other victims as well as those found in anthrax spores recovered in the letters had previously been collected and preserved according to microbial forensic guidelines.
Specialized facilities, such as the J. Craig Venter Institute (JCVI), have been established to enable microbial forensic analysts to ascertain the entire genomic sequences of about five million bases of B. anthracis so as to identify polymorphisms (variations in sequences) that serve as genomic signatures. In late 2007, the National Institute of Allergy and Infectious Diseases announced that twenty-eight hundred human and avian isolates had been completely sequenced and were publicly accessible.
Bibliography
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