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# Bacterial Pathogens, Viruses, and Foodborne Illness

Bacterial pathogens cause foodborne illness either by infecting the intestinal tissues of humans or by producing bacterial toxins that are transmitted by food. 

On this page, find links to articles, access research projects, watch or read USDA presentations, and identify external resources containing information about bacterial pathogens, viruses, and prions.

## Featured Resources

### Research Publications (Food Safety): Bacterial Pathogens

Research publications on bacterial pathogens from peer-reviewed journals.

Find Current Articles

### Books and Materials on Bacterial Pathogens in the NAL Catalog

National Agricultural Library's (NAL) searchable database for journal citations available to persons interested in information on bacterial pathogens.

Search NAL Catalog

### Research Projects: Bacterial Pathogens

The Food Safety Research Projects Database (RPD) contains information about research projects related to the study of bacterial pathogens.

Search for Projects

## Highlighted Salmonella Research

                    - The Grand Challenge: Salmonella Article [usda.gov]
                    -  The Grand Challenge: Salmonella Blog [usda.gov] 
                    -  The Chicken, the Egg, and Salmonella Article [usda.gov] 

A foodborne bacterial pathogen caused by Salmonellosis that affects the intestinal tract of humans.
                    - Response to Questions Posed by the Food Safety and Inspection Service: Enhancing Salmonella Control in Poultry Products [fsis.usda.gov]
                    - Egg Safety - Buying Eggs [ars.usda.gov] [PDF, 1 page]
                    - Egg Safety - Eating Eggs [ars.usda.gov] [PDF, 1 page]
                    - Egg Safety - Storing Eggs [ars.usda.gov] [PDF, 1 page]
                    - Egg Safety - Handling Eggs [ars.usda.gov] [PDF, 1 page]
                    - Salmonella and Salmonellosis [fsis.usda.gov]
                    - Salmonella Questions and Answers [fsis.usda.gov]
                    - Salmonella [cdc.gov]
                    - New Vaccine Fights Multiple Salmonella Types [ars.usda.gov]
                    - Preventing Foodborne Illness: Salmonella Typhi [ifas.ufl.edu]

##               Resources by Type of Bacteria          

Find information from federal and state governments, and cooperative extension programs about foodborne pathogens such as E. coli, Salmonella, Listeria monocytogenes, Cyclospora, and Hepatitis A.

## Selected External Resources on Foodborne Pathogens

Bacillus cereus is an aerobic spore-forming bacteria that is found in soil, vegetable, and many raw and processed food products.
                    - Fact sheet on Preventing Foodborne Illness: Bacillus cereus [nifa.usda.gov] [PDF, 335 KB]
                    - Bacteriological Analytical Manual Chapter 14: Bacillus cereus [fda.gov]
                    -  Learn about the sources of the organism, associated foods, microorgansims characteristics, and the disease and prevention of disease caused by Bacillus cereus [food.unl.edu] 
                    -  Bacillus cereus MLST Database [pubmlst.org] 

Campylobacter jejuni is a type of foodborne bacteria that is contracted by the consumption of undercooked poultry and unpasteurized milk products.
                    -  Campylobacter [fsis.usda.gov]         
                    -  Preventing Foodborne Illness: Campylobacteriosis[nifa.usda.gov] [PDF, 128 KB] 
                    -  Campylobacter (Campylobacteriosis) [cdc.gov] 
                    -  Campylobacter jejuni Multilocus Sequence Typing (MLST) [pubmlst.org] 
                    -  Campylobacter spp. [mpi.govt.nz] [PDF, 359 KB] 
                    -  Campylobacter [food.gov.uk] 

Clostridium botulinum may cause botulism toxicity which occurs from foods without adequate heat treatments or canning processes.  
                    -  National Botulism Surveillance [cdc.gov] 
                    -  Clostridium botulinum & Botulism [fsis.usda.gov] 
                    -  Botulism [cdc.gov] 
                    -  Preventing Foodborne Illness: Clostridium botulinum [ifas.ufl.edu] [PDF, 507 KB] 
                    -  National Botulism Surveillance Network [cdc.gov] 
                    -  Food Safety Wiki: Clostridum botulinum [cornell.edu] 

 

 Clostridium perfringens is a bacterium found on raw meat, poultry, and prepackaged meats.
                    -  Prevent Illness from C. perfringens [cdc.gov] 
                    -  Risk Assessment for Clostridium perfringens in Ready-to-Eat and Partially Cooked Meat and Poultry Products [fsis.usda.gov] 
                    -  Food Safety Wiki: Clostridium perfringens, foodborne [cornell.edu] 
                    -  Preventing foodborne Illness Associated with Clostridium perfringens [ifas.ufl.edu] [PDF, 251 KB] 

Escherichia coli (E. coli) 0157:H7 is a type of pathogenic bacteria from the Shiga Toxin Producing E. coli (STEC) family which is produced from contaminated food and water.
                    - Escherichia coli O157:H7 and other Shiga toxin-producing E. coli (STEC)[fsis.usda.gov ]
                    - E. coli Factsheet [who.int]
                    -  Microbiological Testing Program for Escherichia coli O157:H7 and non-O157 Shiga toxin-producing Escherichia coli (STEC) [fsis.gov] 
                    -  E. coli [cdc.gov] 
                    -  E.coli [food.gov.uk] 

Listeria monocytogenes may cause listeriosis through the consumption of contaminated food products despite refrigeration.
                    - Listeria Monocytogenes [fsis.usda.gov]
                    - Preventing Foodborne Illness: Listeriosi [ifas.ufl.edu]
                    - Control of Listeria monocytogenes in Ready-To-Eat Foods: Guidance for Industry [fda.gov]
                    - Verification Activities for the Listeria monocytogenes (Lm) Regulation and the Ready-to-Eat (RTE) Sampling Program [fsis.usda.gov]
                    - Verification Procedures for Enforcement, Investigations and Analysis Officers (EIAOs) for the Listeria monocytogenes (Lm) Regulation and Routine Risk-Based Listeria monocytogenes (RLm) Sampling Program [fsis.usda.gov]

Resources from reports and government websites describes microbial ecology which is how biofilms are formed from various types of bacteria. 
                    - Biofilms of Dairy Farms [extension.psu.edu]
                    -  Biofilm and Food Safety: What is Important to Know [askbioexpert.com] 
                    -  Food Safety: Biofilm Formation and Removal [stellarfoodforthought.net] 

Shigella is a common intestinal disease in humans caused by the bacteria Shigellosis.
                    - New Test Detects All Known Shiga Toxins [ars.usda.gov]
                    - Shigella – Shigellosis [cdc.gov]
                    - Shiga Toxin E. coli Detection Differentiation Implications for Food Safety [ifas.ufl.edu]
                    - MedlinePlus Medical Encyclopedia: Shigella enteritis [medlineplus.gov]
                    - Preventing Foodborne Illness: Shigellosis [ifas.ufl.edu]

Staphylococcus aureus is a bacteria that resides in the nasal passages of humans.
                    - Bacteriological Analytical Manual Staphylococcus aureus [fda.gov]
                    - Staphlococcus Aereus [health.govt.nz]
                    - Staphlococcus (Staph) Food Poisoning [cdc.gov]
                    - Staphlococcus Aereus Toxin Formation in Hydrated  Battered Mixes A Biological Hazard [fda.gov]
                    - Staphlococcus Aereus [sanger.ac.uk]

The pathogenic bacteria that causes cholera in humans is Vibrio cholerae.
                    - Bacteriological Analytical Manual Online, Chapter 9: Vibrio [fda.gov]
                    - Cholera - Vibrio cholerae infection [cdc.gov]
                    - Vibrio Species Causing Vibriosis [cdc.gov]
                    - Travelers' Health - Yellow Book: Cholera [cdc.gov]
                    - Food Safety Wiki: Vibrio cholerae, toxigenic [cornell.edu]

Vibrio parahaemolyticus causes an illness in humans who consume raw seafood, especially crab and oysters.
                    - ARS Research Helps Make Oysters Safer [ars.usda.gov]
                    - Vibrio Species Causing Vibriosis [cdc.gov]
                    - Preventing Foodborne Illness: Vibrio parahaemolyticus [ifas.ufl.edu] [PDF, 496 KB]
                    - Bacteriological Analytical Manual Online, Chapter 9: Vibrio [fda.gov]
                    - Compendium of Fish and Fishery Product Processes, Hazards, and Controls Chapter 20:Vibrio spp. [seafood.oregonstate.edu] [PDF, 270.89 KB]

Vibrio vulnificus flourishes in warm seawater where oysters and raw seafood thrive.
                    - ARS Research Helps Make Oysters Safer [ars.usda.gov]
                    - Vibrio Species Causing Vibriosis [cdc.gov]
                    - Preventing Foodborne Illness: Vibrio vulnificus [ifas.ufl.edu] [PDF, 116 KB]
                    - Fact Sheet: Vibrio vulnificus [clemson.edu]
                    - Bacteriological Analytical Manual Online, Chapter 9: Vibrio [fda.gov]

Illnesses caused by Yersinia enterocolitica occurs when it is present in raw pork meat. 
                    -  Yersiniosis and Chitterlings: Tips to Protect You and Those You Care for from Foodborne Illness [fsis.usda.gov] 
                    -  Preventing Foodborne Illness: Yersiniosis [ifas.ufl.edu] [PDF, 605 KB] 
                    -  Yersinia enterocolitica (Yersiniosis) [cdc.gov] 
                    -  Fact Sheet: Yersinia enterocolotica [meatpoultryfoundation.org] 
                    -  Bacteriological Analytical Manual Online, Chapter 8 Yersinia enterocolitica [fda.gov] 

## Meet the Experts

**Rapid inactivation of Taxoplasma gondibradyzoites in dry cured sausage** (Introductory Video)

Investigators: John Luchansky, PhD, Anna Porto-Fett, PhD

Date: 2020

View full-length video of Dr. Niemira speaking about rapid inactivation of Taxoplasma gondibradyzoites in dry cured sausage [youtube.com]

## What's in Your Water?

**What's in Your Water?** 

Investigators: Manan Sharma, PhD

Date: 2020

## Biological Soil Amendments

**Biological Soil Amendments**

Investigators: Manan Sharma, PhD

Date: 2020

 

## Bacterial Pathogens Presentations

                    -   USDA ARS Integrated Pathogen Modeling Platform [PDF, 59 pages] . Lihan Huang 

                    -  Advanced Methods for Predictive Modeling of Growth of C. perfringens in Cooked Meats during Cooling [PDF, 14 pages]. Lihan Huang 
                    -  Salmonella Infantis persistence in U.S. poultry and analysis of the plasmid carrying the CTX-M-65 ESBL GENE [PDF, 22 pages]. Jonathan Frye 

                    - Characterization and Mitigation of Bacterial Pathogens in the Fresh Produce Production and Processing Continuum [PDF, 22 pages] . Jitu Patel, Xiangwu Nou, Manan Sharma, Pat Millner, Yaguang Luo
                    - Integration of Multiple Interventions to Enhance Microbial Safety, Quality, and Shelf-life of Foods [PDF, 29 pages] . Sudarshan Mukhopadhyay
                    - Campylobacter jejuni and Chicken Livers: Real World Problems in Need of Real World Solutions [PDF, 16 pages] . Nereus “Jack” Gunther
                    - Development of Predictive Microbial Models for Food Safety using Alternate Approaches [PDF, 119 pages] . Lihan Huang 
                    - Ecology and Detection of Human Pathogens in the Produce Production Continuum [PDF, 44 pages] . Lisa Gorski, Maria Brandl, Michael Cooley, Michelle Carter, Peng Tian 
                    - Production and Processing Intervention Strategies for Poultry Associated Foodborne Pathogens [PDF, 42 pages] . R. Jeff Buhr, Doug E. Cosby, Nelson A. Cox, Arthur Hinton 
                    - Identification of the Ecological Niches and Development of Intervention Strategies to Reduce Pathogenic Foodborne Pathogens in Poultry [PDF, 40 pages] . Michael Kogut, Kenneth Genovese, Christina Swaggerty, Haiqi He, Toni Poole, Michael Hume
                    - Characterization, inactivation, and control of Extra-intestinal Pathogenic Escherichia coli in poultry meat [PDF, 69 pages] . Christopher Sommers, Aixia Xu, Shiowshuh Sheen 
                    - Development of Alternative Intervention Technologies for Fresh or Minimally Processed Foods [PDF, 56 pages] . Brendan Niemira 
                    - Molecular Characterization of Foodborne Pathogens Research Unit [PDF, 20 pages] . Yanhong Liu 
                    - Rapid Optical Detection Methods for Foodborne Pathogens [PDF, 48 pages] . Bosoon Park, Seung-Chul Yoon, Gary Gamble, Kurt Lawrence 
                    - Development of Portable Detection and Quantification Technologies for Foodborne Pathogens [PDF, 77 pages] . Andrew G. Gehring, Cheryl M. Armstrong, Joseph A. Capobianco, Yipping He, George C. Paoli
                    - Radio Frequency Pasteurization of Shell Eggs through the Development of Commercial Prototypes of Continuous Equipment for Multiple Eggs [PDF, 19 pages] . David Geveke

                    - Progress of Rapid Optical Detection Methods for Foodborne Pathogens [PDF, 26 pages] . Bosoon Park 
                    - Characterization, inactivation, and control of Extraintestinal Pathogenic Escherichia coli in poultry meat [PDF,26 pages] . Christopher Sommers 
                    - MetagenomeTRAKR: Using metagenomic approaches for pathogen detection and description of food and agricultural microbiomes [PDF, 67 pages] . Andrea Ottesen 
                    - Foodborne Toxin Detection and Prevention Research Unit [PDF, 28 pages] . Larry Stanker 
                    - FSIS Update: Chicken Liver [PDF, 17 pages] . Karen Becker 
                    - Recovery, Characterization, and Control of Salmonella spp. in/on Chicken Liver and in Pâté Made with Chicken Liver [PDF, 16 pages] . John Luchansky, Anna Porto-Fett, YangJin Jun 
                    - nBPW Research Update [PDF, 12 pages] . Gary Gamble, Arthur Hinton, Mark Berrang 
                    - The nBPW Factor [PDF, 22 pages] . Stevie Hretz 
                    - Prevalence and MLST subtypes of Campylobacter in retail chicken livers [PDF, 17 pages] . Mark Berrang 
                    - Characterization of virulence potencies associated with the expression of Shiga toxin subtypes using cell-based assays & Mass spectrometry [PDF, 34 pages] . Clifton Fagerquist, Beatriz Quiñones 

                    - Antimicrobials to Control Foodborne Pathogens on Cantaloupe (Salmonella, E. coli, L. monocytogenes) [PDF, 23 pages] . Jitu Patel 
                    - A Screening Tool for Bacterial Pathogens and Indicators (Listeria, Vibrio, Salmonella, STEC, Bacillus, Campylobacter) [PDF, 27 pages] . Arun K. Bhunia 
                    - Ecology and Detection of Human Pathogens in the Produce Production Continuum (Campylobacter jejuni and E. coli) [PDF, 29 pages] . Lisa Gorski, Maria T. Brandl, Michelle Q. Carter, Michael B. Cooley, Subbarao Ravva, Peng Tian, Vivian C. Wu 
                    - Listeria Monocytogenes Market Basket Survey: Pathogen Presence and/or Viability on Foods and in Retail Stores [PDF, 36 pages] . John B. Luchansky, Anna C. Porto-Fett, James Lindsay, Yuhuan Chen, Sherri Dennis, Jane Van Doren, Mickey Parish, Janell Kause, Michelle Catlin, Nate Bauer, Bill Shaw, Denise Eblen, Jee Lee 
                    - Antimicrobial Containers for Enhancing Food Safety and Extending Food Shelflife [PDF, 67 pages] . Zhonglin (Tony) Jin 
                    - NIFA Food Safety Portfolio: An Overview (Campylobacter, Salmonella) [PDF, 37 pages] . Max Teplitski 
                    - Preventing Pathogen Cross-Contamination during Fresh-cut Produce Wash Operation [PDF, 18 pages] . Yaguang (Sunny) Luo
                    - Food Safety Intervention Technologies (E. coli, Salmonella, Listeria) [PDF, 62 pages] . Joshua Gurtler, Dike O. Ukuku, Modesto Olanya, Bassam Annous, Brendan Niemira, Joseph Sites 
                    - Assessing Microbial Quality in Irrigation Water Sources [PDF, 18 pages] . Yakov Pachepsky, Daniel Shelton 
                    - Response of Salmonella to Poultry-Relevant Challenge by Heat, Acid, and Pressure [PDF, 15 pages] . John B. Luchansky, Anna C. Porto-Fett 
                    - Interventions for Shell Eggs [PDF, 29 pages] . David Geveke 
                    - Susceptibility of Salmonella to Biocides Used in Processing and its Relationship to Antimicrobial Resistance [PDF, 20 pages] . Jonathan G. Frye, Charlene R. Jackson

##               Resources by Type of Viruses and Prions          

Foodborne and waterborne pathogens such as Trichinella and Cyclospora, as well as virus and prions that cause Avian Influenza (bird flu), Bovine spongiform encephalopathy (mad cow disease), Norwalk and Hepatitis A.

Warning signs and mitigation strategies for the Avian influenza, commonly known as the bird flu.
                    -  Avian Influenza [aphis.usda.gov] 
                    -  Avian Influenza [usda.gov] 
                    -  Information on Avian Influenza [cdc.gov] 
                    -  Statement on Food Safety Considerations of Novel H1N1 Influenza Virus Infections in Human [efsa.onlinelibrary.wiley.com] 

Information about Bovine spongiform encephalopathy (BSE), also known as mad cow disease.
                    - All About BSE (Mad Cow Disease) [fda.gov]
                    - Bovine Spongiform Encephalopathy [aphis.usda.gov]
                    - Creutzfeldt-Jakob Disease, Classic (CJD) [cdc.gov]
                    -  Variant Creutzfeldt-Jakob Disease (vCJD) [cdc.gov] 

Global food and agriculture updates related to COVID-19. 
                    - Food Supply Chain [usda.gov]  
                    - SARS-CoV-2 Virus Transmission [foodsafety.ces.ncsu.edu ]
                    - COVID-19 (Novel Coronavirus) [ifas.ufl.edu]
                    - United Nations FAO COVID-19 updates affecting global food and agriculture [fao.org]

 Cyclospora is a parasite that can cause intestinal distress when consumed through contaminated water or food products.
                    - Preventing Foodborne Illness: Cyclospora cayetanensis [ifas.ufl.edu]
                    - Traveler's Health - Cyclospora [cdc.gov]
                    - Parasites - Cyclosporiasis (Cyclospora Infection) [cdc.gov]
                    - Food Safety Wiki: Cyclospora cayentanensis [cornell.edu]

The cause of a gastrointestinal disease from unsafe food handling practices or unsanitary drinking water that are contaminated with the parasite Giardia. 
                    - Parasites - Giardia [cdc.gov]
                    - DPDx - Laboratory Identification of Parasites of Public Health Concern - Giardiasis [cdc.gov]
                    - Giardiasis [amboss.com]
                    - Giardiasis[vdh.virginia.gov]

Hepatitis A is a contagious disease that is contracted through the consumption of contaminated water or food products.
                    - Viral Hepatitis - Hepatitis A [cdc.gov]
                    - BAM Chapter 26 and Appendices: Concentration, Extraction and Detection of Enteric Viruses from Food [fda.gov]
                    - Hepatitis A [fmi.org]
                    - Hepatitis A Information Guide for Food Retail [fmi.org]
                    - Food Safety Wiki: Hepatitis A [cornell.edu]

A highly contagious virus that can be contracted through contact surfaces by Norovirus. 
                    - Preventing Foodborne Illness: Norovirus [ifas.ufl.edu] [PDF, 777 KB]
                    - Norovirus Outbreak Attribution [nifa.usda.gov] [PDF, 1 MB]
                    - Norovirus, Cultured. [nifa.usda.gov] [PDF, 1.73 MB]
                    - Norovirus [cdc.gov]
                    -  About Norovirus [food.gov.uk] 

Trichinella occurs from parasitic roundworms in pork or meat products that are undercooked. 
                    - Trichinellosis Surveillance - United States, 2008-2012 [cdc.gov]
                    - Parasites - Trichinellosis (also known as Trichinosis) [cdc.gov]

## Viruses and Prions Presentations

                    - Advance the Development of Technologies for Detecting and Determining the Bioavailability of Toxins that Impact Food Safety and Food Defense [PDF, 66 pages] . Luisa Cheng 
                    - Improve Analytical Technologies for Detection of Foodborne Toxins and Their Metabolites [PDF, 31 pages] . Chris Maragos, Mark Busman, Mike Appell, Zakir Hossain
                    - Novel Methods for Controlling Trichothecene Contamination of Grain and Improving the Climate Resilience of Food Safety and Security Programs [PDF, 40 pages] . Martha Vaughan, Susan McCormick, Guixia Hao, Matt Bakker, Robert Proctor, Todd Ward 

                    - #1 Noroviruses (NoV) & Hepatitis A [PDF, 17 pages] . David Kingsley 
                    - Botulinum Neurotoxin – Detection and Bioavailability Research [PDF, 33 pages] .Larry Stanker

## Page Content Curated By

Food Safety Research Information Office (FSRIO)