Clinical, Medical, & Public Health Microbiology

FAQ: Human Microbiome, January 2014



The human microbiome, the collection of trillions of microbes living in and on the human body, is not random, and scientists believe that it plays a role in many basic life processes.  As science continues to explore and better understand the identities and activities of the microbial species comprising the human microbiome, microbiologists hope to draw connections between microbiome composition, host genetic s, and human health.  FAQ: Human Microbiome addresses this growing area of research.







Teaching Materials:

Human Microbiome Infographic
Human Microbiome Trifold

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FAQ: West Nile Virus, July 2013

west nile  

Where does the virus come from? How is it spread? Can we predict when and where outbreaks will occur? What factors determine how sick a person will become if they are infected with West Nile virus?

To help answer the many questions people have about this multi-faceted virus, the American Academy of Microbiology has issued a new report entitled FAQ: West Nile Virus. The Academy convened twenty-two of the world’s leading experts on West Nile virus in March, 2013 to consider and answer some of the most frequently asked questions about West Nile virus. The resultant report provides non-technical, science-based answers to questions that people may have about the virus.


Teaching Materials
Microbes After Hours, YouTube video, "West Nile Virus"
Informational West Nile Virus Posters
West Nile Virus Brochure

MicrobeWorld Interview with Dr. Jorge Arias, an expert in vector-borne diseases

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FAQ: Influenza, April 2013


Where do new influenza viruses come from? How are they different from the influenza viruses that circulate every year? Why is vaccination so important? To help answer the many questions people have about this multi-faceted virus, the American Academy of Microbiology has issued a new report entitled FAQ: Influenza. The Academy convened twelve of the world’s leading experts on influenza in October, 2012 to consider and answer some of the most frequently asked questions about influenza. The resultant report provides non-technical, science-based answers to questions that people may have about the virus.



Teaching Materials 


Moving Targets: Fighting the Evolution of Resistance in Infections, Pests, and Cancer, March 2013



Concerned about antibiotic resistance? What if an insect pest becomes desensitized to the protective chemicals applied to crops? All kinds of living organisms have evolved mechanisms of resistance against the chemicals designed to control them – from bacteria, viruses, cancer cells to weeds. In the Academy of Microbiology’s newest, free report, explore the Darwinian principles underlying the evolution of resistance in these different biological communities and learn how experts in these fields have developed potentially discipline-spanning strategies of combatting them. 





Microbes in Pipes: The Microbiology of the Water Distribution System, January 2013



Non-microbiologists may assume that the goal of water utilities should be the elimination of all microbes from our drinking water. But the water we drink has never been sterile; perfectly safe water contains millions of non-pathogenic microbes in every glassful. Like every other human built environment, the entire water distribution system — every reservoir, every well, every pipe, and every faucet — is home to hundreds or thousands of species of bacteria, algae, invertebrates, and viruses, most of which are completely harmless to humans. In April, 2012, the American Academy of Microbiology convened a colloquium to assess what is known about the microbial inhabitants of the water distribution system and to propose goals for advancing our understanding of these communities in order to enhance the safety of our drinking water and the resilience of our water infrastructure.



Bringing the Lab to the Patient: Developing Point-of-Care Diagnostics for Resource Limited Settings, 2012



Easy-to-use, inexpensive point-of-care tests (POCTs) to diagnose infectious diseases are urgently needed in resource-limited settings where laboratory capacity is limited. Development and implementation of new POCTs requires coordinated efforts among the scientists and engineers designing the tests and the health care workers deploying them. Recognizing the need to connect these groups, the American Academy of Microbiology convened a colloquium in September 2011 to discuss how to develop POCTs that can be effectively integrated into resource limited settings. Based on that colloquium, this report identifies the POCTs that would make the biggest impact on health and the qualities they need to be effective in resource limited settings. The report also discusses systemic barriers to POCT deployment and recommends addressing these barriers in order to foster a more conducive environment for POCT development. The report is an example of the benefit of improved communication among the many groups that must work together to bring POCTs to the people that need them the most.

FAQ: Adult Vaccines: A Grown Up Thing to Do, March 2012



Because vaccines have been so successful at controlling diseases like smallpox and polio in the United States, we often take our relatively epidemic-free world for granted. But less than a lifetime ago, these diseases and others were still real threats to health. Despite vaccines’ successes, many people do not know how vaccines work, or that they are not just important for children, but adults too. On December 6th, 2011, the American Academy of Microbiology convened a panel of experts to help explain how vaccines protect us from disease and what vaccination options are available to adults. The report also provides insights into the history of vaccines, why they are so safe, and why adults need to stay up to date on vaccines - to protect their health, and the health of their loved ones.




Teaching Materials

Adult Vaccination brochure to use at your office or classroom
Adult Vaccination brochure-Spanish Translation


FAQ: E. Coli: Good, Bad, and Deadly, November 2011



News headlines often paint E. coli as a vicious bacterium, capable of causing disease and death to those unfortunate enough to ingest it. But that is only a tiny minority of E. coli, and a very small part of the story of this remarkable bacterium; its relationship to human health and the food we eat is much more complex. Not all E. coli are bad - in fact most are not - and some are even beneficial. On September 1st 2011, the American Academy of Microbiology convened an expert panel of microbiologists, food safety experts, and bacteriologists to develop a more accurate picture of this often maligned bacterium. This report, the product of that meeting, tells the larger story of E. coli: its role in human health, in food, and even in our understanding of our own biology.




Teaching Materials

ASM Curriculum Guidelines Description

The Secret Lives of E. coli teaching poster

The Secret Lives of E. coli teaching poster-Spanish Translation


Global Food Safety: Keeping Food Safe from Farm to Table, 2010



“Global Food Safety: Keeping Food Safe from Farm to Table,” is based on a colloquium convened by the Academy in 2009. This report reviews the current state of affairs in microbiological food safety around the world. It is extremely challenging to know how many people are made sick by food, which foods are at fault, which pathogens are most widespread or dangerous, and where those pathogens entered the food production system. In such a situation, where should research, prevention and education efforts be directed? In this report, each step in our complicated food production and supply system is described, highlighting key points of vulnerability, and making it clear that providing safe food is a shared responsibility.

Applications of Clinical Microbial Next-Generation Sequencing, February 2016


Next-generation sequencing (NGS) has the capacity to provide crucial clinical benefits in patient care, patient outcomes, and public health, however, clinical laboratories must find ways to overcome operational, technical, regulatory, and strategic challenges in order to effectively employ NGS-based diagnostic tests. The Academy convened a colloquium on this topic in April 2015. Beyond the potential lifesaving impact of NGS methodologies, the report examines the main deterrents and shortcomings of the technology such as the data analysis and management pipelines, regulatory concerns and reimbursement issues, and the creation and maintenance of curated and secure databases. The report, titled Applications of Clinical Microbial Next-Generation Sequencing provides recommendations and suggestions for combating these current limitations to implementing NGS in clinical settings. 



Harnessing the Power of Microbes as Therapeutics: Bugs as Drugs



Bacteria and viruses are not always categorized as harmful microorganisms. In fact, these groups of microbes can be beneficial and can actively participate in many biological processes. With the perception of microorganisms being our partners, research is now being conducted to use microbes to treat disease and enhance human health. Some viruses and species of bacteria can be targeted to kill cancer cells while others can be deployed to replicate in and kill tumors. The Academy convened a colloquium in April 2014 in San Diego, CA to discuss the vast potential of microbes as supplements to existing therapies against infectious and chronic diseases. The product of those discussions was the full report, Harnessing the Power of Microbes as Therapeutics: Bugs as Drugs.

Antibiotic Resistance: An Ecological Perspective on an Old Problem, September 2009



According to the report, it is possible to co-exist with resistance by- developing new strategies to prevent resistance from spreading and, where it already exists, identify the strains we need to protect against; find new ways to treat resistance infections effectively in patients; and manage reservoirs of antibiotic strains in the environment. The report summarizes the current scientific understanding of antibiotic resistance, the scope of the problem, and methods at our disposal for detecting emergence and preventing spread. The knowledge gaps about the prevalence of resistant strains and resistant infections are highlighted as are the unique problems and challenges in developing countries.

Mycobacterium avium paratuberculosis: Infrequent Human Pathogen or Public Health Threat? August 2008



Prepared by Carol Nacy and Merry Buckley.

People with Crohn’s disease (CD) are seven-fold more likely to have in their gut tissues the bacterium that causes a digestive-tract disease in cattle called Johne’s disease. The role this bacterium may or may not play in causing CD is a top research priority. This report points out that the cause of Crohn’s disease is unknown, and the possible role of this bacterium, which could conceivably be passed up the food chain to people, has received too little attention from the research community.


Probiotic Microbes: The Scientific Basis, June 2006



Prepared by Richard Walker and Merry Buckley.

This report details how beneficial microbes could represent the future of medicine, with the potential to treat a variety of diseases in humans and animals from diarrhea and eczema to gum disease and autoimmune disorders.








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Vaccine Development: Current Status and Future Needs, October 2005



Prepared by James Kaper, Rino Rappuoli, and Merry Buckley.

This report outlines the challenges society needs to confront in order to combat plagues of the 21st Century, and provides recommendations to overcome obstacles that prevent the best use of existing vaccines.

Microbial Triggers of Chronic Human Illness, April 2005



Prepared by Kathryn M. Carbone, Ronald B. Luftig, and Merry Buckley.

Details how the increase aging populations in the United States and throughout the developed world, appears to correlate with a switch from acute infectious diseases to chronic diseases as the major cause of morbidity and mortality. The report also recommends new criteria be developed for evaluating the strength of association between microbes and chronic illness.

The Genomics of Disease-Causing Organism: Mapping a Strategy for Discovery and Defense, July 2004


Prepared by Merry Buckley.

This report details the study of pathogenesis and how far we have come to having a complete understanding of pathogenesis and a phylogenetic framework for understanding the phenomenon.

Microbial Forensics: A Scientific Assessment, 2003



Prepared by Paul Keim.

Surveys this new field and makes recommendations about how to move it forward.

Resolving the Global Burden of Gastrointestinal Illness: A Call to Action, 2002



Prepared by Pierre Payment and Merry S. Riley.

Looks at incidence, severity, and duration and discusses routes of transmission of gastrointestinal disease around the world. Recommends future directions for the clinical arena, research, education, disease prevention, and communication.

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Antimicrobial Resistance: An Ecological Perspective, 2002



Synthesizes conclusions reached by working groups at 1999 colloquium. Takes a broad view of the problem of increasing resistance to antimicrobials and its consequences for human, animal, and environmental health. Provides an overview of the current situation and offers specific recommendations for scientific research, surveillance programs, and education effor

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Bioterrorism Threats to Our Future, 2001 (Available online only)



Prepared by James W. Snyder and William Check.

The Academy joined with the American College of Microbiology to examine the central roles of professional microbiologists and clinicians in recognizing the occurrence of possible bioterrorism events. Issues of medical laboratory and practitioner training, emergency preparedness plans, public education, collaboration, and communication across health care and law enforcement agencies from the local to the federal level are discussed.

Health, Climate and Infectious Disease: A Global Perspective, 2001



Prepared by Joan B. Rose, Anwar Huq, and Erin K. Lipp.

Takes a look at the combined advances in microbiology, meteorology, climatology, epidemiology, oceanography, ecology, medicine, and space science that are shedding light on the intricate connections between weather, oceans, and emerging and re-emerging diseases. Makes specific recommendations for future data collection, research collaboration, risk assessment, and the use of technology and molecular techniques.

Climate, Infectious Disease and Health: An Interdisciplinary Perspective, 1998


Prepared by Rita R. Colwell, and Jonathan A. Patz. 

Discusses research issues relating to the effects of climate on the incidence and distribution of infectious disease. Addresses specific infectious diseases and offers recommendations for future research.

The Scientific Future of DNA for Immunization, 1997



Prepared by Harriet L. Robinson, Harold S. Ginsberg, Heather L. Davis, Stephen A. Johnston, and Margaret A. Liu. 

Provides in-depth analysis of relevant issues and outlines a strategy for funding and coordinating a massive research effort to increase knowledge about the mechanism of genetic immunizations and to identify potential applications.