Bacterial Pathogens, Viruses, and Foodborne Illness

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]

• USDA ARS Use of Data Science to Improve Food Safety [PDF, 21 pages]. Tatum Katz

•  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

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]

• 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