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Microbes in Court: The Emerging Field of Microbial Forensics

Abigail A. Salyers


Microbial forensics is a relatively new field that can help in solving cases such as:

  • bioterrorism attacks
  • medical negligence
  • outbreaks of foodborne diseases

January 2004


Microbial forensic data must hold up to the scrutiny of scientists as well as judges and juries. Source: Microsoft Images.

Editor’s Note: This article is comprised of excerpts from a comprehensive, original paper on microbial forensics by Abigail A. Salyers. The paper is also provided on this website as a supplement to this article.

What is microbial forensics?

Microbes as weapons is not a new concept.

You have probably heard of commonly used forensic methods such as the analysis of striations on bullets to identify the gun used to commit a crime. But what if a microbe is the weapon of choice, as can occur if a bioterrorist comes to town? Microbes as weapons is not a new topic. There have been reported cases, for example of HIV-infected people intentionally infecting others.

Microbes have been involved in medical negligence and foodborne diseases, for example.

Moreover, microbes can be involved in cases of medical negligence in which a surgeon or nurse causes a patient to contract a post-surgical or other hospital-acquired infection due to inadequate hygiene. There is currently a lawsuit making its way through the Scottish courts against a hospital alleging that inadequate hygiene resulted in the death of a patient.1 It is also conceivable that outbreaks of foodborne disease could spawn lawsuits alleging either negligence or intentional contamination. Tracing the infecting microbe to the company and person(s) of origin will be critical in such cases.

Molecular techniques have been used for years to trace microbial diseases.

Microbial forensics is the term that is applied to this new type of forensic analysis. Molecular techniques have been used for years to trace outbreaks of microbial diseases, a practice called molecular epidemiology. In fact, there are currently surveillance systems that store and make available DNA fingerprints for microbes that are likely to be involved in hospital-acquired infections and foodborne infections (e.g., PulseNet of the U.S. Centers for Disease Control [CDC], a surveillance system for tracking infections such as Salmonella).2 Although these surveillance systems are still only a few years old, they are rapidly growing in sophistication.

What distinguishes microbial forensics from molecular epidemiology is that microbial forensic data must hold up not only to the scrutiny of scientists in the health care community, but also to the scrutiny of judges and juries. Nonetheless, work done to date on microbial epidemiology will provide an invaluable starting point for the additional work that needs to be done to make microbial forensics ready for its day in court.

The 2001 mail-delivered anthrax attack brought microbial forensics to the fore.

The bioterrorism connection

A good example of the problems that need to be solved is provided by the response to the anthrax attack of 2001, in which spores of the bacterium Bacillus anthracis, the cause of anthrax, were disseminated via the mail.3 The effects of this crime extended far beyond the deaths of the 5 people who died of inhalation anthrax.

If a suspect is ever arrested and charged with perpetrating the anthrax attack, spores will be an important part of the physical evidence.

Prosecuting an anthrax suspect would present challenges.
  • Prosecutors will have to prove that spores isolated from the suspect’s home or laboratory are in fact THE spores, the ones introduced into the envelopes and mailed.
  • The problem with making such a case is that spores of B. anthracis are found widely in soil, especially farm soil in the southern U.S. So the prosecution will have to prove that any spores submitted as evidence were the spores used in the attack and not simply spores that had been tracked into a house or laboratory from a nearby field.

The problem

Proving the assertion that the spores introduced as evidence were the ones used to contaminate the envelopes used in the anthrax bioattack may not be as easy as a laboratory scientist, who is familiar with DNA-based molecular epidemiology methods, might think.

Isolating the exact anthrax strain may prove difficult.
  • Spores of different strains of B. anthracis and of the vegetative (actively dividing) form of the bacteria, unlike diatoms, look very much alike.
  • In fact, different strains of B. anthracis are also very similar to each other at the genome sequence level.
  • Given that the error rate for DNA sequencing is not zero, proving that a particular isolate of B. anthracis is the same as the strain used in the bioattack may prove to be difficult.

So, if the assertion to be proven is that the spores found in the home or laboratory of a suspect are the same as those mailed in the envelopes, questions about the meaning of slight variations in test results will have to be answered.

The beginning of a solution — the scientific community responds

The response of the scientific community to the challenge of the hoped-for anthrax court cases provides a good illustration of how scientists proceed in such cases.

The anthrax case illustrated the need for procedural standards.
  • One thing was very clear from the outset — that too little attention had been paid previously to microbial forensics.
  • This realization caused scientists to start back at the very beginning, by meeting to identify what information is available, what research remains to be done, and how to proceed as expeditiously as possible.
  • Paul Keim, a leader in the early development of DNA-based methods for identifying individual strains of B. anthracis, set the process in action when he approached the American Academy of Microbiology (AAM) about convening a meeting of experts to consider the subject.4

The American Academy of Microbiology is an organization that has a long history of assembling small groups of experts and challenging them to define the future needs for work in a new area of microbiology and was thus the obvious organization to spearhead such an effort. A group of 35 scientists with expertise that might be able to help answer the question of what needs to be done to validate tests that could be put to forensic use was identified by the AAM and met in June 7-9, 2002, in a bucolic setting in Burlington, Vermont. The author of this article was one of the attendees.

The American Academy of Microbiology provided recommendations for microbial forensics in a recent report.

For the first time in the history of these AAM-organized meetings, three scientists from the FBI were included. The FBI scientists, all of whom had had direct involvement in investigation of the anthrax case, helped provide the occasional reality check, as other scientists not familiar with work in the field grappled with the question of how to establish standards for evidence collection and for analysis and interpretation of the plethora of new molecular tests, more of which are being published every month. The anthrax attack was not the only example of the possible use of microbial forensics considered by the group of AAM experts. Other examples included intentional contamination of others by HIV-positive individuals and outbreaks of hospital-acquired or foodborne disease. Understandably, however, the anthrax bioattack dominated the discussion.

“Microbial Forensics: A Scientific Assessment,” the report of the conclusions reached by this group of experts, has now been published by the American Academy of Microbiology.5 (See “article references” at the end of this article for information on how to obtain a copy of this report.)

Standards should be developed for specimen collecting/ analyzing and quality control.

Identification of key challenges and recommendations for finding solutions

Challenge #1: Collecting specimens at the attack site

The first challenge is proper collection of evidence at a site where the release of an infectious microbe is suspected.

Challenge #2: Recognizing that an attack is occurring and diagnosing the disease

In the case of the anthrax bioattack, the agent responsible was identified almost immediately. In other cases of intentional disease transmission, the identity of the microbe being used in the attack may not be apparent so quickly. This is where physicians and other health care workers come in. The physicians are the ones who will recognize, diagnose and treat infected patients.

Challenge #3: Analysis of specimens

The next challenge is the analysis of the specimens collected by first responders and by microbiologists subsequently sent to the site.

Challenge #4: Validation — quality assurance and control

The next challenge is, in some ways, the most formidable one, rigorously validating each analytical method by establishing its limitations, its sensitivity, and its reliability. Also important is the robustness of a method — the assurance that the method can be used successfully in many different laboratories and field conditions, always giving the same results. The credibility of analytical results relies absolutely on proof that the analytical procedure has been thoroughly vetted by experts.

Is all this effort worth the cost?

Bioattack preparedness will help in cases of natural or intentional outbreaks of disease.

You do not have to be an expert to realize that the research described in the forgoing material will cost a lot of money. Not only will it be expensive to solve these problems for B. anthracis but also, if full preparedness is the goal, it will be necessary to go through the same process for other agents that might be used in a bioterror attack. What is the taxpayer getting for this large expenditure of money, especially if no further attacks occur?

  • One possible benefit is that having a well-prepared response plan in place might deter at least some potential terrorists.
  • Perhaps the main benefit, however, is that much of the outcome would also be applicable to tracing natural outbreaks of disease.
  • Also, there have been cases in which infected people have intentionally infected others and such cases may well end up in court.

True, specific tests for B. anthracis or Variola (the smallpox virus) would not themselves be of much use, but the development of procedures for reliable collection and storing of microbial specimens and for QA/QC (quality assurance/control) of new molecular tests for identifying and tracking a disease outbreak could be very beneficial in many different infectious disease situations. If, for example, there was a sudden cluster of cases of a disease like Ebola, having a plan for a rapid and effective response could quickly limit the spread of the disease.

Scientists are used to freely communicating their research.

Communicating research results

Application of research done on responses to bioattacks to natural disease outbreaks is not a guaranteed benefit, however. Scientists who work in the areas of epidemiology and diagnosis of infectious diseases have always had a tradition of free communication with each other through speeches at open meetings and publication of papers in widely disseminated journals. By contrast, the scientists and politicians who have controlled much of the research on bioterrorism and biodefence have become accustomed to a security system that controls information flow and classifies much of the information obtained.

That is usually not the case with those responsible for protecting the public against bioattacks.

If those who are responsible for protecting the public against bioattacks insist on keeping most of their discoveries out of the public domain, the public will not be well served. The free communication of scientific findings, free of government censorship, has been proven to be an essential precondition for scientific progress. Also, if an analytical method, for example, is going to be useful in gathering evidence that may be used in court, it must be made available to law enforcement personnel and to lawyers and juries. That is, it will have to become public information.

Secrecy could limit research in disease situations that are not bioattacks.

For these reasons, many scientists are concerned that classifying information about analytical methods will severely limit its use in disease situations that are not bioattacks. There is currently a debate underway about what types of microbiology research results should be published freely. Leading scientific societies such as the American Society for Microbiology and the National Academies of Science have come out in support of free publication of any scientific results that have not been classified, but not all people, especially politicians, agree with this stance.

Editor’s Note: This article is comprised of excerpts from a comprehensive, original paper on microbial forensics by Abigail A. Salyers. The paper is also provided on this Web site as a supplement to this article.

Abigail A. Salyers, Ph.D., is Professor of Microbiology at the Department of Microbiology, University of Illinois at Urbana-Champaign. She received her Ph.D. from George Washington University in 1969 and an Honorary Doctorate from ETH University (Zurich, Switzerland) in 2001. Her publishing credits include co-editor of the best-selling textbook Bacterial Pathogenesis (American Society of Microbiology, 2002) and co-writer of Microbiology: Diversity, Disease, & the Environment (John Wiley & Sons, 2000). Dr. Salyers was President of the American Society of Microbiology for the 2001-2 term.

Microbes in Court: The Emerging Field of Microbial Forensics

“Microbial Forensics: A Scientific Assessment”

This 2002 report, discussed in Dr. Salyers’ article, was published by the American Academy of Microbiology in early 2003 and is available to the public on their web site.

BioScience Article

“Crime Scene Genetics: Transforming Forensic Science through Molecular Technologies.”
According to Melissa Lee Phillips (BioScience, June 2008), advances in DNA technology over the past 25 years have led to spectacularly precise forensic identification techniques, although some applications have also unleashed controversies regarding genetic privacy. Current molecular forensic work is pushing these technologies even further by analyzing extremely damaged DNA and by introducing RNA techniques to forensics. Read the abstract, or log in to purchase the article.

### A microbial genomics primer
An overview of the international efforts to sequence microbial genomes, potentially unlocking beneficial applications in bioremediation, climate change, biotechnology, energy production.

“Microbial Forensics: Cross-examining Pathogens”

Microbial forensics is devoted to tracing the source of a pathogen using a sophisticated system of molecular markers — the high-tech bio version of fingerprinting. This 14 June 2002 Science magazine article (Vol. 296), provides an overview, tied into the recent U.S. anthrax situation.

“When the FBI Asks, Should Scientists Tell?”

This article in The Scientist examines ethical issues related to scientists working with dangerous pathogens (1/02).

Pathogen genomics

General information (fact sheets & brochures), articles, reports, research news, and activities. From the Division of Microbiology & Infectious Diseases of the US National Institutes of Health.

Forensic science resources

A list of links to various resources, e.g., crime scene investigation, forensic DNA analysis, and forensic chemistry & toxicology.

Sociedad Española de Microbiología

“The Spanish Society for Microbiology (SEM) was founded in 1946 to gather scientists interested in the development of microbiology both in the basic and the applied fields.”

Microbiology glossary

Definitions of microbiology terms & abbreviations, e.g., antibody, decontamination, and sepsis.

Read a book

The second edition of the best-selling textbook Bacterial Pathogenesis (Editors Abigail A. Salyers & Dixie D. Whitt) brings together the recent advances in our understanding of how bacteria cause disease and includes introductory chapters that provide the scientific background necessary for exploring the bacterial diseases covered in the book. American Society for Microbiology, January 2002; ISBN: 155581171X

American Society for Microbiology (ASM) and American Academy of Microbiology (AAM)

News, meeting notices, and publications for microbiology students and professionals. You can sign up for e-mail alerts. “The American Academy of Microbiology is the honorific leadership group within the American Society for Microbiology, the world’s oldest life science organization.”

Class Activities

  1. The Scotsman. May 27, 2003. “Our hospitals have to clean up their act” by Tanya Thompson. (accessed 9/10/03)
  2. Centers for Disease Control and Preventions’s PulseNet site (the U.S. National Molecular Subtyping Network for Foodborne Disease Surveillance.:
  3. Morbidity and Mortality Weekly Report. November 16, 2001. “Update: Investigation of Bioterrorism-Related Anthrax, 2001.” From US Center for Disease Control and Prevention.
  4. Los Angeles Times. Dec. 17, 2001. “Paul Keim: Anthrax’s Dogged Detective” by Rosie Mestel. Reprinted on the University of California in Los Angeles (UCLA. web site) (accessed 12/15/03)
  5. “Microbial Forensics: A Scientific Assessment,” a report published by the American Academy of Microbiology in early 2003, based on events in 2002, is available to the public on their web site. This report contains a comprehensive list of reliable references that were used in this article and which are suitable for those who wish to read further material on the subject. (accessed 9/10/03)


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