Science Needs for Microbial Forensics Developing Initial International Research Priorities (2014) / Chapter Skim
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2 Microbial Science: Ecology, Diversity, and Characterizing the Microbial World
2 Microbial Science: Ecology, Diversity, and Characterizing the Microbial World
Pages 35-58
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From page 35... ...
In the last 20 years, technological advances have made it possible to explore a microbial world that has proven vastly more extensive, important, and diverse than previously imagined. Analyses of microbial communities in the soil, in the ocean, and even in the human body have shown that previ ous methods detected only a tiny percentage of the different microbes in these environments.
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From page 36... ...
Although the biology of the small fraction of bacteria and viruses that are pathogenic to human beings, livestock and companion animals, and crop or forestry plants is somewhat better known and understood, there is still much to be learned about their evolution, how many strains of pathogen species exist in nature, what their distribution is throughout the world, and how this distribution affects, and is affected by, ecological conditions. BIOSURVEILLANCE Biosurveillance is "the process of active data-gathering with appropriate analysis and interpretation of biosphere data that might relate to disease activity and threats to human or animal health -- whether infectious, toxic, metabolic, or otherwise, and regardless of intentional or natural origin -- in order to achieve early warning of health threats, early detection of health events, and overall situational awareness of disease activity" 1 The study of evolutionary relatedness among various groups of organisms through molecular sequencing data and morphological data matrices.
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From page 37... ...
adopted revisions to the International Health Regulations (IHR) , changing the basis for reporting disease outbreaks from a list of specific diseases to a set of characteristics that constitute a "Public Health Emergency of International Concern." The IHRs reflect more than a decade of international effort to achieve global consensus on the need to improve disease surveillance capacities and to accept international requirements to do so in a timely manner.
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From page 38... ...
For example, the Global Public Health Intelligence Network (GPHIN) , which was originally developed by Public Health Canada in collaboration with WHO, continuously searches media sources for information about infectious disease outbreaks.
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From page 39... ...
. accelerate progress toward a world safe and secure from infectious disease threats and to promote global health security as an international security priority, to • Prevent and reduce the likelihood of outbreaks -- natural, acciden tal, or intentional; • Detect threats early to save lives; 11 http://www.glews.net/; accessed April 6, 2014.
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From page 40... ...
Such information would help microbial forensics investigators to better understand the context of an active outbreak and better interpret microbial forensics findings. The rest of this chapter explores several actual microbial forensics cases to illustrate the techniques that have been developed over the last 10-12 years, some of the relationships between public health and microbial forensics, and the unmet needs that remain in the area of understanding microbial ecology, diversity, and characterization of strains and other genetic variants.
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From page 41... ...
. Very early in the investigation the anthrax spores in the letters and the environmental and clinical isolates were identified as the "Ames strain" by Dr.
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From page 42... ...
Thus, although the identification of the Ames strain narrowed the possibilities, making the source likely to be a laboratory that had access to the strain, MLVA was insufficient to identify its source unequivocally. The evidence, therefore, needed to be more painstakingly examined for additional unique and distinguishing genetic and other features that could be compared to samples obtained from laboratories holding the Ames strain to narrow the search for the source and perpetrator(s)
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From page 43... ...
Nevertheless, the analysis of the repository samples using the then newly created assays eventually led the FBI to focus attention on a particular flask at USAMRIID containing a spore preparation known as RMR-1029. In addition, physical science analytical approaches, such as scanning transmission electron microscopy, energy-dispersive X-ray analysis, carbon dating by accelerator mass spectrometry, and inductively coupled plasma-optical emission and mass spectrometry, were used to try to determine the chemical and elemental profiles of the spore powders (NRC, 2011)
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. When it is concluded that something is not the same -- not the Ames strain -- based on the evolutionary models and assays, these conclusions are very strong.
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From page 45... ...
Links to the Japanese terrorist group and the Russian and Iraqi biological weapons programs were therefore ruled out. Keim named the following as the key challenges associated with the anthrax letters investigation: 1.
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Richard Vipond, Operations Manager for the Rare and Imported Pathogens Laboratory at Porton Down in the United Kingdom, reviewed the forensic work employed during a 2009-2010 anthrax outbreak involving contaminated heroin (Price et al., 2012; Vipond presentation, 2013)
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From page 47... ...
Vipond does not believe that the heroin-related anthrax outbreak represented a biocrime or bioterrorist attack. One argument against the outbreak being due to bioterrorism is that drug users are not an ideal target population for capturing the public's interest.
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From page 48... ...
For some microorganisms, ecological diversity is high because the organisms may inhabit ecological niches in soil, the ocean, and even in the human body, in which there are 10 times the number of microbial cells as human cells (Koeppel et al., 2008)
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V parahaemolyticus is a highly diversified pathogen in which high-frequency homologous recombination leads to a radiated phylogenetic relationship.
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They have performed WGS on single strains and employed comparative genomics to understand pathogen diversity, using SNP analysis to understand the transmission of Y pestis through history and the phylogenetic differences in strains.
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National Institutes of Health established a major project on the Human Microbiome and there are comparable European programs in existence. These efforts have produced vast quantities of new information on the bacteria, viruses, and microbial eukaryotes living in or on the human body (e.g., see Human Microbiome Jumpstart Reference Strains Consortium, 2010)
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From page 52... ...
anthracis, are still incomplete, and there is as yet no worldwide repository of information on pathogen species and strains or any coordinated effort to develop information exchange mechanisms. John Clements pointed out that if public health agencies are not routinely collecting surveillance data (e.g., on influenza cases)
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From page 53... ...
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From page 54... ...
But it also suggested that one might be able to use gene content, instead of just nucleotide sequences, for forensic characterization because the gene content appears to be evolving almost as fast, if not faster, than the nucleotides. Darling related information about a joint pilot project by the University of California, Davis and the JGI, that sought to characterize the genetic diversity of microbial organisms worldwide.15 As noted earlier, if one wishes to build a database of background information about different microbial ecosystems around the globe, an understanding of what exists is needed.
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From page 55... ...
However, metagenomic data do not satisfy these requirements because the data frequently contain small nonoverlapping fragments of each organism's gene sequence. Two inferential approaches that can be used to create phylogenetic trees from metagenomic data include phylogenetic placement, in which the read fragments are "mapped" into a reference phylogeny tree; and co-estimating the read clusters.
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From page 56... ...
THE ISSUE OF DATA SHARING Even if there is a major effort to characterize microbial diversity comprehensively through nucleic acid sequencing, unless the data that are collected are shared in such a way that scientists around the world have access to them, they will not provide optimal benefit for either public health or microbial forensics. During the discussion following the workshop session on microbial ecology and diversity, various workshop participants pointed out a variety of problems involved with data sharing.
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From page 57... ...
Yang stated that the decision to share is not always left up to the scientists, who are not always permitted to publish everything. Yang said that the worldwide scientific community could press governments to address the need for data sharing, given the bioweapons context, citing the needs of public health and microbial forensics.
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