(U) National Research and Development Strategy for Microbial Forensics

This is the html version of the file http://www.ostp.gov/galleries/NSTC%20Reports/National%20MicroForensics%20R&DStrategy

%202009%20UNLIMITED%20DISTRIBUTION.pdf. 

Google automatically generates html versions of documents as we crawl the web.

Page 1

NATIONAL SCIENCE AND TECHNOLOGY COUNCIL

National Research and

Development Strategy

for Microbial Forensics 

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (1 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

Page 

2

National Strategy to Support Research in Microbial Forensics

Attribution Investigations and National Security 

Introduction

As described in NSPD-33 and HSPD-10, the essential pillars of the National Biodefense

Policy of the United States consist of: Threat Awareness, Prevention and Protection,

Surveillance and Detection, and Response and Recovery. As part of the “Surveillance and

Detection” pillar, “attribution” is specifically discussed with respect to biological attacks

and can also be used pertaining to an investigation of a planned attack. Attribution is the

investigative process by which the United States Government (USG) links the identity of

a perpetrator or perpetrators of illicit activity and the pathway leading to criminal activity.

Making a determination of attribution for a covertly planned or actual biological attack

would be the culmination of a complex investigative process drawing on many different

sources of information including technical forensic analysis of material evidence

collected during the course of an investigation of a planned attack or material evidence

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (2 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

2

resulting from an attack. During the course of an attribution investigation these sources of

information would generate many investigative leads and help draw connections between

places, events and a possible pool of suspects 1

. 

In addition to the traditional types of forensic evidence such as fingerprints, hair and

fibers and human DNA, forensic material collected as part of a biological attribution

investigation will yield unique types of microbiological evidence that are specific to the

nature of the potential attack or the attack itself. Examples of such microbiological

evidence could include; viable samples of the microbial agent, protein toxins, nucleic

acids, clinical specimens from victims, laboratory equipment, dissemination devices and

their contents, environmental samples, contaminated clothing, or trace evidence specific

to the process that produced and/or weaponized 2

the biological agent. 

A statistically sound scientific foundation supports the forensic capabilities used in

traditional criminal investigations to generate investigative leads, determine inclusion and

exclusion for questioned samples when compared to known references and establish

identity. Current capabilities to forensically characterize microbiological evidence in

support of an attribution investigation are limited primarily to detection and identification

which, while important, only begin to scratch the surface in terms of forensic

requirements for detailed characterization and comparative analyses. Microbial

Forensics 3

1 ‘Suspect’ in this context can refer to an individual, group or hostile nation state.

is the emerging interdisciplinary field of microbiology devoted to the

development, evaluation, validation, and application of methods to detect and fully

characterize microbial samples containing a biological agent or its components for the

purpose of statistically meaningful comparative analyses. These methods will provide

data for attribution investigations involving pathogens, toxins or other biological

2 “Weaponized”agents are those altered to enhance effectiveness as a weapon.

3 Microbial forensics has also been referred to as ‘bioforensics’ and ‘forensic microbiology.’

Page 

3

materials that are collected as part of an investigation of a planned or actual biocrime or

bioterrorism attack on people, animals or plants.

As a result of the Anthrax attacks in the fall of 2001, a considerable government

investment was made in the scientific analysis of evidence resulting from the attacks.

These investments did much to stimulate the field of microbial forensics and continue to

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (3 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

3

do so. However, microbial forensics is nonetheless still a nascent field facing broad and

complex scientific challenges. 

NSPD-33/HSPD-10 established the National Bioforensic Analysis Center (NBFAC)

within the Department of Homeland Security’s (DHS) National Biodefense Analysis and

Countermeasure Center (NBACC). The NBFAC, an internationally accredited laboratory,

is primarily operational in nature and is not focused solely on research and development.

Advancing the field of microbial forensics to provide the NBFAC and other US

Government organizations with robust capabilities to detect, identify and characterize

biological agents will require a sustained investment in multidisciplinary basic research,

focused technology development and robust method validation. 

Purpose:

The purpose of the National Strategy to Support Microbial Forensic Research is to guide

and focus the research efforts of the US Government to advance the discipline of

microbial forensics and provide the nation with the most scientifically sound and

statistically defensible capability to provide scientific data to support attribution

investigations of a potential or actual biological attack. The Strategy has three primary

goals: 

I. Develop a strategic microbial forensics research agenda that will produce a national

microbial forensic capability that is ultimately capable of high confidence, robust

detection, characterization and comparison of biological agents in forensic samples. 

II. Promote interagency communication, coordination and information sharing on

microbial forensics research and development efforts.

III. Develop effective interagency education and training on microbial forensics

designed to inform policymakers and scientific and technical personnel.

This Strategy shall form the framework of an interagency implementation plan that will

begin to address research and interagency communications issues that are required for an

enduring national capability in microbial forensics. 

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (4 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

Page 

4

________________________________________________________________________

Goal I. Develop a Strategic Microbial Forensics Research Agenda that will

Produce an Enduring National Microbial Forensic Capability that Supports

Sensitive Detection, Characterization and High Confidence Comparison of

Biological Agents and or Their Components in Forensic Samples.

A directed strategic microbial forensics research agenda that meets the requirements

delineated by those government agencies conducting attribution investigations will guide

investment to build a microbial forensic capability consisting of both genomic and nongenomic approaches for the forensic characterization and analysis of microbiological

evidence supporting an attribution investigation of a potential or actual biocrime or

bioterrorism attack. An effective microbial forensic capability must include reliable,

rigorous and sensitive techniques to collect forensic samples, detect and identify

forensically relevant “signatures”, and fully characterize forensic evidence. Additionally,

a microbial forensic capability must be able to address the requirement to conduct

comparative sample analyses in order to query known and questioned samples and draw

inferences relating to the process used to produce a pure sample, the provenance of a

sample or relatedness between samples. Rigorous quality standards must be applied at

every level of the forensic process from sample collection, through sample analysis and

data analysis to the reporting and the interpretation of results. In order to meet these

challenges in microbial forensics, a number of research goals will have to be achieved. In

some of these areas there is ongoing work while in other areas there is very little. This

strategy serves to highlight important areas for research and provide recommendations

for action in those areas based upon requirements of those conducting attribution

investigations.

Objectives: Continue to expand national microbial forensic capabilities and develop new

capabilities in the following areas: A.) sample collection, processing, preservation, and

recovery and concentration of microbial pathogens and signatures from collected samples

B.) sensitive signature detection and characterization C.) orthogonal methods for

conducting forensic comparisons between samples to include the basic scientific

research, which is required to build the foundational supporting data that will enable

forensic comparisons to be made and interpreted, D.) validation of existing technologies

for new application to microbial forensic problems, development of new technologies,

and development of new bioinformatics analysis tools and creation of new theoretical

frameworks for data analysis and interpretation. 

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (5 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

4

Page 

5

A. Sample Collection, Processing, Preservation and Recovery and Concentration of

Microbial Pathogens and their Signatures from Collected Samples for Microbial

Forensic Analyses

Actions: 

1. Collect and evaluate all the work conducted across the US Government and

academic sectors that has focused on the collection of microbial samples,

preservation, recovery and concentration of microbial agents and their signatures

from collected samples and use the results of the evaluation to identify current

research gaps and consolidated research efforts to avoid duplication.

2. Develop and improve methods for the collection, processing, preservation and

recovery of microbial agents and their signatures from microbial forensic samples

that do not interfere with subsequent forensic analyses of the sample. 

2.1. Methods are needed to collect, process, and recover a wide range of human,

animal, and agricultural microbial agents from a broad range of common

surfaces, matrix types and sample collection devices.

2.2. Methods are needed for the collection of trace microbial forensic evidence

applicable to the recovery of viable organisms and non-viable trace signatures

from a variety of sample collection environments. 

2.3. An interagency working group shall be identified or, if none exists, formed, to

develop scientifically acceptable standards of performance and the path to

validate the approaches.

B. Microbial Forensic Signature Development, Detection, and Characterization for

Known, Emerging, Enhanced, Genetically Engineered Advanced and Synthetically

Derived de novo Agents:

Actions:

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (6 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

5

1. From among the total spectrum of human, animal, and agricultural pathogens,

construct a prioritized list of microorganisms and toxins of biological origin that are

assessed to be of high consequence in terms of actual threat or perceived existing

vulnerability. Use the list to drive directed forensic assay development. 

2. Develop sensitive and broad detection capabilities using both traditional

microbiological culture, molecular (nucleic acid - based/ protein-based) and

immunological detection and next generation technologies for the identification,

characterization and comparison of all identified human and agricultural bio-threat

pathogens and toxins including, new emerging microbial agents, enhanced microbial

agents and advanced microbial agents to include a capability for de novo or

synthetically derived microbial agents. 

Page 

6

3. For additional levels of forensic characterization identify applicable phenotypic

approaches such as, metabolomics, metabolic phenotype profiling techniques,

serotyping, carbohydrate cell surface profiling, Membrane Fatty Acid Analysis

(MIDI) and phage-typing that are useful across the range of human and agricultural

bio-threat agents. Assess the limits of and utility those approaches as forensic tools.

4. Develop sensitive and specific forensic assays that can detect, identify and quantitate

the amount of biologically active toxin of biological origin 4 present in a variety of

commonly encountered environmental and food matrix types.

5. Develop sensitive and specific physical/chemical analytic capabilities that are

capable of additional exploitation of evidentiary samples to identify and characterize

preparation and process related signatures associated with microbial forensic samples.

6. Develop libraries of standard microbiological reference materials required, for the

development and validation of microbial forensic methods, and for forensic

comparisons to known isolates. Reference standards must be made available to assay

developers and any independent assay validation group. Reference material must be

well curated to insure the quality of the reference product used for comparative

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (7 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

6

analyses. 

C. Forensic Sample Comparison and Generation of the Required Supporting

Foundational Data.

Actions:

1. Develop and execute a theoretical framework and set of forensic interpretation

guidelines to define what is meant by a genetic “match” when comparing the genetic

sequence of microbiological samples across the spectrum of microbial agents to

include known agents, emerging agents, enhanced agents, advanced agents and de

novo synthetic agents.

2. Engage experts in the fields of microbial ecology, epidemiology, and agriculture to

help develop approaches to understand the spectrum of natural diversity and

endemicity, of microbial agents that would be informative for forensic purposes and

sample comparisons.

3. Conduct a survey of all currently available full genome sequences from microbial

agents to include pathogens and near neighbor to assess if the number and diversity is

4

The phrase Toxin of biological origin in this context refers to any toxic substance which is produced by a

microorganism, plant, animal, insect or fungus that is dangerous to humans or agriculture and of biological weapons

proliferation concern. Examples include but are not limited to ricin, botulinum toxin, and bioregulatory peptides.

Page 

7

adequate for forensic purposes in terms of assay development, characterization, assay

validation or interpretation of genetic comparisons. Based on the survey recommend

additional strains for whole genome sequencing.

4. Develop and validate non-genetic orthogonal methods to conduct sample matching

of microbial forensic samples from an investigation of a planned or actual biological

crime or attack.

5. Continue to support a comprehensive research program on understanding genetic

diversity in microbial populations and communities as it relates to both bacteria and

viruses. Focus research on the forensics implications associated with bacterial and

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (8 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

7

viral population dynamics and environmental effects to genetic stability, gene

transfer, mutation rates and other phenomena affecting the genome.

D. Leverage of existing and next generation genomic and non genomic technologies

for new application to microbial forensic problems, development of new

technologies, and creation of bioinformatics analysis tools and new theoretical

frameworks and models for data analysis and interpretation.

Actions:

1. Continue to support the development of rapid and cost-effective high throughput

sequencing and closure technologies that can be used to generate high confidence

whole genome sequence data and genetic variation data for any known and unknown

microorganism.

2. Continue to develop a specific bioinformatics genetic toolbox for microbial

forensics, which addresses the unique requirements of forensic genetic comparisons. 5

3. Conduct a market survey of microarray and mass spectroscopy and other high

throughput technologies that might be appropriate for forensic applications to identify

the most promising candidate technologies, approaches, suppliers and types of

systems (nucleic acid and protein-based). As part of the survey, address the a)

maturity of the technology, b) experience of the producer, c) type of forensic

application for which the platform is appropriate, d) cost and, e) possible lifespan of

the technology, and f) benefit of the technology over traditional RT-PCR/Sanger

methods.

4. Continue to support other genomic and non genomic high throughput technologies

that can be applied to microbial forensic capabilities including DNA microarrays,

proteomics, metabolomics, glycomics and lipodomics that provide increased

sensitivity, specificity, and robustness over traditional methods. 

5

See “Microbial Forensics Implementation Plan elements 2.1-2.9. 

Page 

8

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:ww...microbial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (9 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

5. Develop a strategic roadmap for the integration of microbial forensics metadata into

a unified, web based, relational information system that provides both researchers and

operations personnel rapid access to robust microorganism details for forensics

interpretation. Roadmap should focus on current systems candidates, integration

specifications, requirements data, life cycle hosting IT support, and management

concept.

6. Develop statistical approaches and bioinformatics models that are capable of

incorporating diverse analytic results (genetic, phenotypic and physical/chemical)

into forensic comparisons and building networks and models to help investigators

draw inferences regarding sample relatedness with described confidence intervals.

________________________________________________________________________

Goal II. Promote Interagency Communication, Coordination and Information

Sharing on Microbial Forensics Research and Development.

In addition to a strong research agenda to develop microbial forensic methods, the second

goal of this strategy is to facilitate interagency cooperation to spur the development of the

field as a whole. Interagency communication, coordination, and collaboration will be the

key to developing an enduring national capability in microbial forensics to support

attribution investigations. A diverse group of federal stakeholders have a shared interest

in the development of microbial forensics to support a range of attribution investigations

and these shared interests and activities must translate to concerted action and

cooperation. The developing field of microbial forensics faces broad scientific challenges

that require sustained research and resource commitment. Only strong interagency

partnerships will ensure the development of a powerful microbial forensic investigative

capability to support attribution investigations. Microbial forensics stands to benefit by

leveraging existing government biodefense programs wherever relevant. Assessing the

areas of opportunity that could be leveraged for microbial forensic development is an

important part of the interagency collaboration that is needed.

Objectives: Improve interagency communication, coordination, and information sharing. 

A.) establish and draft terms of reference and a charter for a formal Interagency

Microbial Forensics Advisory Board (IMFAB) and B.) develop a National Archive and

Resource for Forensically-Important Pathogen Strain Collections to serve microbial

forensics.

A. Establish and draft terms of reference and a charter for a formal Interagency

Microbial Forensics Advisory Board (IMFAB). The IMFAB shall:

1. Identify the microbial forensic analytical requirements from relevant government

stakeholders to support attribution investigations. 

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:w...icrobial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (10 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

8

Page 

9

2. Review and update the National Strategy for Microbial Forensics Research and

Development annually and align this strategy with microbial forensic analytical

requirements from government stakeholders.

3. Develop an agreed upon interagency lexicon of microbial forensics terms based upon

current understanding and state of the art in the field that is to be published as a

position paper with the lexicon.

4. Support coordination and collaboration on microbial forensics research efforts.

5. Guarantee high quality research and development

6. Establish and sponsor an in depth periodic interagency peer review mechanism to

complement the research agenda and inform resource allocations relevant to the

strategy. The IMFAB shall select the members of the review panel to include

government scientists and non-government scientists with the appropriate clearance

levels to participate in these reviews.

7. Design and sponsor periodic objective capabilities assessments based on interagency

exercises that incorporate realistic scenarios and sample sets to generate forensic data

from which inferences can be drawn and be graded against the scenario. 

8. Provide recommendations and expert advice to the National Archive and Resource

for Forensically Important Pathogen Strain Collections.

9. Conduct professional outreach and engage existing interagency and outside scientific

working groups and professional societies, as needed, to further the development of

microbial forensics capabilities.

B. Develop a National Archive and Resource for Forensically-Important Pathogen

Strain Collections to serve microbial forensics.

1. Convene interagency stakeholders to identify their requirements for a National

Archive and Resource for Forensically – Important Pathogen Strain Collections and

coordination with existing collections of microorganisms. 

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:w...icrobial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (11 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

9

2. Develop a national pathogen strain management system that uses existing resources

and paradigms, in as much as possible, to best serve the interests of stakeholder

agencies and ensure the fullest participation of the biodefense, research, and

microbial forensics communities.

3. Establish a Microbial Forensic Resource Center (MFRC) that can support the

requirements of assay development and validation by providing reference standards

as per Goal I, Objective B.6 of the Research and Development Strategy. 

Page 

10

Goal III. Develop Effective Interagency Education and Training on Microbial

Forensics Designed to Inform Policymakers and Scientific and Technical Personnel

In order to better inform national security professionals, policymakers, the analytic and

interested scientific communities to the complexities of microbial forensic analysis, a

system of education and training is required. The educational focus will occur at two

levels. The first level of education would consist of a broad overview for those

individuals for whom an awareness of important forensic issues and their implications is

all that is required. The next level of training shall focus, in depth, on the scientific

challenges and complexities inherent to forensic analysis of microorganisms. Together

both levels of education will form a core curriculum that will inform consumers and serve

to produce a more informed core of analytic professionals.

Objectives: Establish and develop a core curriculum of training courses that will

provide: A.) high level overview of the microbial forensics discipline and the challenges

of forensic analysis and B.) “in depth” technical courses on the types of analyses used

and the limitations and challenges inherent to them.

Actions:

1. Develop a core course which introduces the field of microbial forensics at a high

level, appropriate for non-technical professionals.

2. Develop a core training program on specific technical topics relevant to microbial

forensics. 

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:w...icrobial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (12 of 13)3/11/2010 7:36:36 AM
(U) National Research and Development Strategy for Microbial Forensics

10

3. Develop and deliver courses in microbial forensics relevant topics, such as, PCR

methods, next generation sequencing technology, comparative genomics,

bioinformatics and microbial ecology. 

http://74.125.113.132/search?q=cache:-TuDGVkAoaoJ:w...icrobial+forensics%22+.pdf&cd=3&hl=en&ct=clnk&gl=us (13 of 13)3/11/2010 7:36:36 AM