Science Needs for Microbial Forensics Developing Initial International Research Priorities (2014) / Chapter Skim
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4 Clinical and Forensic Approaches to Microbial Identification
4 Clinical and Forensic Approaches to Microbial Identification
Pages 79-96
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From page 79... ...
Dr. Dana Kadavy, Senior Microbiologist at Signature Science LLC, reviewed the microbial forensic process from systems and technical perspectives, described challenges in microbial forensics compared with the needs of clinical diagnostics and public health, and reviewed technologies applicable to identification of organisms for microbial forensics.
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From page 80... ...
Traditional microbiology and culture are the current gold standard in clinical diagnostics, but it is not always possible or practical to culture microbes in a forensic investigation. A capability needed in microbial forensics is sample processing to achieve desired sensitivity/accuracy in complex sample matrices, such as soil samples from forensic exhumations of graves linked to the Bosnian– Serbian war.
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From page 81... ...
Other platforms have attempted to increase this to as many as 20 fluorophores simultaneously, which would be a big advance in multiplex capability. Real-time qPCR is a rapid and sensitive nucleic acid signature detection technology that has proved effective in both clinical and microbial forensic applications.
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From page 82... ...
Mass spectrometry also is useful in identifying many non–nucleic acid chemical species that may provide clues to microbial identity, origins, and production processes. Proteins, peptides, lipids, carbohydrates, inorganic metals, and organic metabolites may provide information about an organism's source environment, how it was produced, and the level of sophistication of the preparation (Wahl et al., 2011)
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From page 83... ...
Microarray panels are available for microbial detection, SNP detection, and genome-wide association studies, gene expression, and protein presence and abundance. Laboratories that use a microarray reader for other purposes, such as oncology or infectious disease screening, could be leveraged by the development of custom chips that are directed to answering microbial forensic questions.
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From page 84... ...
For example, the same data run on two different systems -- the benchtop MPS (massively parallel sequencing) instruments, Personal Genome Machine™ or PGM (or Ion Torrent, Life Technologies)
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From page 85... ...
Kadavy suggested that investments in technology should be prioritized according to what is best for the common good. It is possible to leverage advancement that helps microbial forensics and public health simultaneously.
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From page 86... ...
He cited the example of the rapid response to the posting of the viral sequences of the H7N9 avian influenza by the Global Initiative on Sharing Avian Influenza Data (GISAID) by the Chinese CDC in March 2013.4 This process enabled Novartis, in partnership with a unit of the J
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From page 87... ...
INVESTIGATING INFECTIOUS DISEASES IN CLINICAL MEDICINE Professor Alemka Markotić shared her perspective as a scientist and a clinician who daily faces a variety of infectious diseases in patients and has used elements of microbial forensics to deal with public health outbreaks. She offered lessons learned through experience with zoonotic diseases -- diseases transmitted between animal species and from animals to humans -- which she believes could be useful to public health experts, clinicians, and microbial forensic investigators.
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From page 88... ...
Preparing for a biological threat event requires knowledge of pathogenic agents; a clinical picture of disease incubation, transmission mode, and treatment; knowledge of which molecular diagnostics and technologies to apply to which pathogen; and characterization of a usual versus an unusual outbreak (see Box 3-1)
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From page 89... ...
Molecular and phylogenetic analyses of viral nucleic acid sequences obtained from human and rodent samples confirmed an almost 100 percent similarity between the samples, which helped rule out the virus having been imported or deliberately created. The second major lesson learned was that molecular analysis enabled linking the human outbreak with a pathogen in a natural reservoir, rodents, in a specific geographic location.
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From page 90... ...
. Therefore, in addition to using multiplex technology to detect co-infection or multiple infections, the capability to measure immune response in unusual outbreaks or disease presentations should be developed.
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From page 91... ...
CDC spoke about how rapid developments in technology and clinical laboratory test methodologies are leading to culture-independent testing. He discussed the advantages and limitations of culture-independent tests from the clinical and public health perspectives, noting that his comments should not be assumed to reflect CDC policies.
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From page 92... ...
CDC. CDC and its partners in the State Public Health Laboratory network are working to develop higher resolution diagnostics, new rapid and standardized data collection methods, new analytical software, and improved environmental assessments (CDC, 2011)
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From page 93... ...
PERSPECTIVE OF A CLINICAL MICROBIOLOGIST IN THE PUBLIC HEALTH SECTOR Dr. Raymond Lin of the National University of Singapore offered a perspective on the challenges and issues clinical microbiologists who work in the public health sector face in terms of technology, policy, and legal issues.
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From page 94... ...
He tries to avoid being drawn into cases alleging, for example, that one person transmitted HIV to another person. The courts ask many questions, and Lin believes that public health lacks the manpower to spend time in court for such cases.
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From page 95... ...
Lin agreed with Morse in his concern that viral isolation has become almost a thing of the past in diagnostic labs. He believes that public health labs must make an effort to collect specimens of bacteria and viruses.
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