FAIRLEIGH DICKINSON UNIVERSITY SCHOOL OF NATURAL SCIENCES BIOL 3225 General Microbiology  Literature review paper and presentation: 15% Students are expected to write a literature review paper on a topic relevant to microbiology. The chosen topic may not cover an event more than 5 years old. You are encouraged to start your research paper as early in the semester as you possibly can. Your choice of topic may reflect your personal interests, support your career goals or nurture your inherent intuition and curiosity. Have enough time to gather literature, write, revise, revise some more, and turn in a scholarly paper. Maximum page limit is 10, double spaced, AMA (American Medical Association) format. - Presentations should be 7-10 minutes long and should include all pertinent information as per their literature review. The Scientific Literature Review  OBJECTIVES/RATIONALE Background research is a vital component of the scientific research process. The students will be able to locate, identify and critique key elements of scientific literature to discover what is known and what remains to be learned about a topic. Books and articles are categorized as either primary or secondary sources. It is always more desirable to use primary sources whenever possible. Primary sources are first-hand accounts of events Secondary sources are second-hand accounts. The competent researcher never relies on secondary sources but always reviews the primary source as a check against possible errors. The researcher then makes records of the sources studied and summarizes the pertinent information found in each. The most common and useful method for recording bibliographical information is to write the complete information for each publication on a separate 3X5 card (or file). These cards are kept in alphabetical order in a file to be a ready source to cite relevant works in the body of the research paper. The researcher must develop an orderly and systematic approach to coding their index cards. It is important to summarize an article or book using the same format each time. This will enable quick comparisons. For an article, examine the author’s credentials, scan the hypothesis, and focus on the methods of research used (how the sample was selected and the data was analyzed). Read the conclusion and summary. Retain sound and pertinent articles. To summarize and record the information, note author, title, and year of publication. • Title of article • Authors name(s) - all authors MUST be recorded. • Full reference – year of publication, FULL name of the journal or book, # of issue or edition and page numbers. • Summary of information of interest NOTE: no everything may be of importance to your research, concentrate only on the issues that are pertinent to your work.  REVIEWS For the past three or four years you have learned how to review a scientific paper, now is time to learn how to use this information in a more productive form. Scientist must keep up with the advances on their area of interest by constantly reading new publications. This will give them an overview of what is being accomplished by the scientific community. Each individual paper you read will give you a piece of the puzzle. During this exercise, you will learn how to put all the pieces of the puzzle together as a BIG PICTURE – Scientific Literature Review. ELEMENTS OF SCIENTIFIC LITERATURE Title short, specific, clear Introduction WHY are you doing this research?- state the propose of what you are expecting to find (Present tense), review the individual literature and compile what information already exists on this subject (background information reported by the papers you read regarding your topic) Materials & Methods HOW was the research carried out? (Past tense) (design, target population, treatment, analytical methods ---- brief explanation on how the different authors conducted their experiments) – compare their methods), please NOTE that this may not be appropriated for your research. Results WHAT kind of results were reported by the papers you read (past tense) again, this may not apply to your research or it could be combine with your discussion and conclusion. Discussion/Conclusions WHAT do the results published by the different researchers mean to you? (present tense) References / Literature cited Paper Guidelines: The project will be based on new literature, at least seven original research articles from scientific journals (primary source). Beside the new scientific literature (primary sources), background references like books, popular science magazines or older articles from science journals should be used to complete your work; to create the BIG PICTURE. (Minimum 10-12 references) The steps required for the completion of the project are: 1. Sign-up for a topic provided by your instructor or if you have a particular topic or interest, you may clear it with your instructor. Due (in class) by the 2nd week of class. Please note that no two person will be allow to research the same topic. • When deciding on a topic, you should ask yourself the question….. What do you want to know about this subject? * Once you define your topic, you will not be allowed to change it. • Find primary references – at least 7 original research scientific articles from reputable scientific journals (use the library services!). – NOTE: scientific reviews and mini-reviews are considered as secondary source. -- Copies of the scientific papers PDF’s must be e-mailed to the instructor for approval no later than September 23, 2018. late delivers will be penalized • NOTE that I cannot open any link! You must download the paper into your computer as a PDF file and then forward the PDF as an email attachment. 2. Read the papers (followed guide provided in the beginning of this assignment) and look for additional scientific articles and background material (minimum 10 references should be included on your paper). • Prepare individual summary for each paper (like single pieces of a puzzle) write a two page “resume” in your own words for each reference. E-mail then to the instructor no later than October 6, 2018. – late delivers will be penalized 3. Compile all your information to give an overview of the studies done in a particular area of interest. “the entire puzzle” -4. Start writing your scientific literature review. First draft must be e-mailed to your instructor no later than 11:59pm October 27, 2018. • You may re-submit via e-mail working drafts until November 17. NO MORE DRAFTS WILL BE ACCEPTED AFTER THAT DAY. Make sure you have addressed all the recommendations and that your paper is free of grammatical errors and of good scientific quality as per the guide provided at the beginning of the assignment. • Points to remember: i. You are not to review each paper independently. DO NOT DESCRIBE INDIVIDUAL RESEARCHES, YOU MUST SUMMARIZE AND COMPARE ALL THE PAPERS. ii. You must compile all the information as a single unit iii. Don’t forget to cite in text what each author have to say. When citing in text use author(s) name(s) coma and year of publication. e.g. (Johnson, 2015) or (Johnson & Smith, 2016) or if more than two authors use (Willey et al., 2014) • It MUST include: o Title page -- (Title of your paper, your name and course number) o Introduction (background information reported by the papers you read regarding your topic) o Material & Methods if appropriate to your topic (brief explanation on how the different authors conducted their experiments) – compare their methods o Result / Discussion what do the results published by the different researchers mean to you. You may compare the data in tables, schemes or figures. BUT it has to be selfexplanatory and created by YOU. (do not copy them from the literature – that is considered plagiarism!) o Conclusion (what did you learn from your research) o Reference -- In text references and literature cited. In text references should be done by using the author(s) last name followed by a coma and the year of publication (ex. Johns, 2016; Johns & Willian, 2016; if more than three authors use the first authors name and et al. - Johns et al., 2016) End of the paper reference (literature cited) can be written as follow…Make sure to write the name of all authors here. -- do not use et al.! • Authors’ names (last name, Initial(s).and ; between the authors and before the last one)) Year of publication. Article title (capitalize only the first letter of the first word and proper nouns), Journal name (in italic), Volume number; full page numbers. o Li, B.; Li, W.; Chen, X.; Jiang, M.; and Dong, M. (2012). In vitro antibiofilm activity of the melanin from Auricularia auricula, an edible jelly mushroom. Annals of Microbiology, 62(4), 1523-1530. • Article in an online journal: Author(s) (same as above). Year Title. Journal Name; volume (issue NO.):inclusive pages. URL [provide the URL in this field; no need to use “URL:” preceding it]. Published [date]. Updated [date]. Accessed [date]. o Drake A.J., Smith A., and Betts P.R., (2002). Type 2 Diabetes in Obese White Children. Archives of Disease in Childhood 86(3), 207-208. http://vsearch.nlm.nih.gov/vivisimo/cgibin/query-meta?v:project=nlm-main-website&query=Archives+of+disease+in+childhood. Accessed April 5, 2016. o Langer, S., D. Schropp,, F. R. Bengelsdorf,, M. Othman, and M. Kazda. 2014. Dynamics of biofilm formation during anaerobic digestion of organic waste. Anaerobe 29 , p 44-51. http://dx.doi.org/10.1016/j.anaerobe.2013.11.013. Accessed April 5, 2016 • When citing data from a Web site, include the following elements, if available, in the order shown below: Author(s), if given (often, no authors are given). Title of the specific item cited (if none is given, use the name of the organization responsible for the site). Name of the Web site. URL [provide URL and verify that the link still works as close as possible to publication]. Published [date]. Updated [date]. Accessed [date]. o Living With Type 1 Diabetes. Diabetes.org. http://www.diabetes.org/living-withdiabetes/recently-diagnosed/living-with-type-1-diabetes.html. Published February 9, 2015. Accessed April 7, 2015. o Why Immunize? cdc.gov. http://www.cdc.gov/vaccines/vac-gen/why.htm. Updated September 23, 2014. Accessed April 7, 2015. o Yale University. Science Daily. http://www.sciencedaily.com/relesases/2015/01/1501733950. Published January 7, 2015. Accessed April 5, 2015. • When referring to an entire book, not pages or specific sections, use the following format: References should include the last name and first and middle initials of the author(s), italicized title case format for all titles (capitalize all words except prepositions such as of, between, through), articles (such as a, the, and an), and conjunctions (such as but, and, or; however, capitalize them if they begin the title or the subtitle) the city and state of publication, the publisher, and the year of publication/creation. o Silverstein A., Silverstein V.B., Nunn L.S. Cancer. Minneapolis, MN: Twenty-First Century Books; 2006. o Maul-Mellott, S.K. and Adams, J.N. Childhood Cancer: A Nursing Overview. Boston, MA: Jones and Bartlett; 1987. o Willey,J. M., L. M. Eherwood and C. J. Woolverton. Prescott’s MICROBIOLOGY 9th. Edition. McGraw-Hill. 2014. • Chapters from books should be capitalized in the same format as journal articles (sentence case format) and should not use quotation marks. Additionally, inclusive page numbers for the each chapter should be provided. The title of the book, however, should be title cased and italicized, following the print book format. A colon should follow the publication date and no space should be provided between the colon or the page number(s) and hypen. o Yagyu, S. and Iehara, T. MYCN nonamplified neuroblastoma: Detection of tumor-derived cellfree DNA in serum for predicting prognosis of neuroblastoma. In Hayat MA, ed. Pediatric Cancer Diagnosis, Therapy, and Prognosis. Dordrecht, NY: Springer; 2013:11-17. 5. You must prepare the material to be presented to your classmates. All Presentations (ppt, prezi, etc.. and an one page summary) regardless of your presentation date are due via e-mail to your instructor on November 25, 2018 NO EXCEPTIONS. Points will be deducted for late submissions  You will be presenting your topic during the class schedule time (based on the topic) and credit will be given for the presentation and for answered questions.  Presentations should be 7-10 min. long and should include all pertinent information as per their literature review.  A summary (one page) of your presentation should be prepared and e-mailed to your instructor before your presentation date for distribution to your classmates. All presentation materials will be included in your final examination. 6. Final paper is to be submitted via Safe-Assignment by 11:59PM DECEMBER 1, 2018- Once you submit it via Safe-assignment, you can no longer re-write it or fix it. EVALUATION OF THE PROJECT (15%) • • • • • Primary references delivered on time (1 pt each) Two page summary for each reference (2 pts each) First draft complete and delivered on time Final paper o Paper depth o Format o Spelling, paragraph and sentence structure, grammar and punctuation Oral presentation o One page summary o Presentation content o Timing + Question and answers Penalties: • Late submission(s) • No approved topic or literature • No drafts • No oral presentation 30pts 5pts 5pts 5pts 10pts 5pts - 50% of original pts. - 50 pts - 25 pts - 30 pts. 10pts 20pts 10pts 40pts 20pts SAMPLE LITERATURE REVIEW Prion propagation and their effect in humans Introduction Prions cause diseases like Creutzfeldt-Jakob disease (CJD), Gerstmann-Strässler-Scheinker syndrome (GSS), kuru, and fatal familial insomnia in humans (Barbisin et al. 2014). Diseases caused by prions in animals include bovine spongiform encephalopathy (BSE), also known as Mad Cow Disease, in cattle (Strom et al. 2014), scrapie in sheep, chronic wasting disease (CWD) in cervids (which includes deer), transmissible mink encephalopathy, and feline spongiform encephalopathy (Barbisin et al. 2014). Prion diseases are both fatal and currently incurable. These neurodegenerative diseases are collectively referred to as transmissible spongiform encephalopathies (TSEs). Prions cannot be seen by the naked eye and are naturally found in cells as normal, functional proteins. Their microbiological influence affects organisms on the cellular level, with neurons as the primary focus for most studies……………………….. Materials and Methods The researchers, Krejciova et al.(2014), simulated PrP conversion from the normal form to the abnormal form (that would normally occur in cells) in vitro using a technique called protein misfolding cyclic amplification (PMCA). PMCA works by incubating normally folded protein mixed with a small amount of misfolded protein. Then the conversion is sped up with a blast of ultrasound. The cycle is repeated until the desired end result is achieved (Zou & Pierluigi, 2012)……………….. Barbisin et al. (2014) were also concerned about humans becoming infected with prions. They had worked under certain assumptions. The primate Macaca fasicularis is known to be a good research subject for the understanding prion diseases inflicting humans………. Another group of scientists (Belay et al. 2015) found that prion studying from RNA studies had problems in maintaining RNA integrity, specifically from the heat produced using a rotating biopsy stamp when extracting cells…………………………………………………... Results/Discussion The findings of these studies indicate that prions continue to boggle the minds of researchers. These studies do, however, give more insight to the capabilities of TSE-related prions……………………………. Conclusion Researchers Krejciova et al. (2014) have concluded that prions from cattle infected with BSE can effectively afflict sheep of certain genotypes. However, the prion types found in these sheep have lost the capability to infect humans…………. Ultimately the ways prions propagate and influence cells and other microbes continues to elude researchers. The current level of knowledge surrounding prions highlights that there is little information on how to protect livestock and people from TSEs and other prion related neurodegenerative disorders………. Literature cited: Barbisin, M., Silvia Vanni, Ann-Christin Schmädicke, Judith Montag, Dirk Motzkus, Lennart Opitz, Gabriela Salinas-Riester, Giuseppe Legname (2014) Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)infected cynomolgus macaques BMC Genomics. 2014; 15: 434. Published online 2014 Jun 5. doi: 10.1186/14712164-15-434 9/22/2018 World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseas… World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis Martyn D. Kirk , Sara M. Pires, Robert E. Black, Marisa Caipo, John A. Crump, Brecht Devleesschauwer, Dörte Döpfer, Aamir Fazil, Christa L. Fischer-Walker, Tine Hald, Aron J. Hall, Karen H. Keddy, Robin J. Lake, Claudio F. Lanata, Paul R. Torgerson, Arie H. Havelaar, Frederick J. Angulo Published: December 3, 2015 https://doi.org/10.1371/journal.pmed.1001921 Correction 23 Dec 2015: Kirk MD, Pires SM, Black RE, Caipo M, Crump JA, et al. (2015) Correction: World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis. PLOS Medicine 12(12): e1001940. https://doi.org/10.1371/journal.pmed.1001940 | View correction Abstract Background Foodborne diseases are important worldwide, resulting in considerable morbidity and mortality. To our knowledge, we present the first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases. Methods and Findings We synthesized data on the number of foodborne illnesses, sequelae, deaths, and Disability Adjusted Life Years (DALYs), for all diseases with sufficient data to support global and regional estimates, by age and region. The data sources included varied by pathogen and included systematic reviews, cohort studies, surveillance studies and other burden of disease assessments. We sought relevant data circa 2010, and included sources from 1990–2012. The number of studies per pathogen ranged from as few as 5 studies for bacterial intoxications through to 494 studies for diarrheal pathogens. To estimate mortality for Mycobacterium bovis infections and morbidity and mortality for invasive non-typhoidal Salmonella enterica infections, we excluded cases attributed to HIV infection. We excluded stillbirths in our estimates. We estimate that the 22 diseases included in our study resulted in two billion (95% uncertainty interval [UI] 1.5–2.9 billion) cases, over one million (95% UI 0.89–1.4 million) deaths, and 78.7 million (95% UI 65.0–97.7 million) DALYs in 2010. To estimate the burden due to contaminated food, we then applied proportions of infections that were estimated to be foodborne from a global expert elicitation. Waterborne transmission of disease was not included. We estimate that 29% (95% UI 23–36%) of cases caused by diseases in our study, or 582 million (95% UI 401–922 million), were transmitted by contaminated food, resulting in 25.2 million (95% UI 17.5–37.0 million) DALYs. Norovirus was the leading cause of foodborne illness causing 125 million (95% UI 70–251 million) cases, while Campylobacter spp. caused 96 million (95% UI 52–177 million) foodborne illnesses. Of all foodborne diseases, diarrheal and invasive infections due to non-typhoidal S. enterica infections resulted in the highest burden, causing 4.07 million (95% UI 2.49–6.27 million) DALYs. Regionally, DALYs per 100,000 population were highest in the African region followed by the South East Asian region. Considerable burden of foodborne disease is borne by children less than five years of age. Major limitations of our study include data gaps, particularly in middle- and high-mortality countries, and uncertainty around the proportion of diseases that were foodborne. Conclusions Foodborne diseases result in a large disease burden, particularly in children. Although it is known that diarrheal diseases are a major burden in children, we have demonstrated for the first time the importance of contaminated food as a cause. There is a need to focus food safety interventions on preventing foodborne diseases, particularly in low- and middle-income settings. Editors' Summary Background Foodborne diseases are responsible for a large burden of illness (morbidity) and death (mortality) in both resource-rich and resource-poor countries. More than 200 diseases can be transmitted to people through the ingestion of food contaminated with microorganisms (bacteria, viruses, and parasites) or with chemicals. Contamination of food can occur at any stage of food production—on farms where crops are grown and animals raised, in factories where food is processed, and during food storage and preparation in shops, restaurants and the home. Contamination can arise because of pollution of the water, soil or air or through poor food-handling practices such as failing to wash one’s hands before preparing food. Many foodborne diseases (for example, norovirus, Escherichia coli, and campylobacter infections) present with gastrointestinal symptoms—stomach cramps, https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001921 1/14 9/22/2018 World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseas… diarrhea, and vomiting. However, some foodborne illnesses cause symptoms affecting other parts of the body and some have serious sequelae (abnormal bodily conditions or diseases arising from a pre-existing disease). For example, infection with some strains of E. coli can lead to kidney failure. Why Was This Study Done? Accurate regional and global estimates of the disease burden of foodborne illnesses are needed to guide governmental and international efforts to improve food safety. However, estimates of the number of cases of foodborne illness, sequelae, deaths, and disability adjusted life years (a DALY represents the disease-related loss of one year of full health because of premature death or disability; DALYs provide a measure of the burden of a disease) are only available for a few countries. Consequently, in 2007, the World Health Organization (WHO) established the Foodborne Disease Burden Epidemiology Reference Group (FERG) to estimate the global and regional burden of disease attributable to foodborne illnesses. Here, researchers involved in one of the constituent task forces of FERG—the Enteric Diseases Task Force—undertake a data synthesis (the combination of information from many different sources) to provide global and regional estimates of the disease burden of several important foodborne bacterial, protozoal (parasitic), and viral diseases. What Did the Researchers Do and Find? The researchers combined national estimates of foodborne diseases and data from systematic reviews (studies that identify all the research on a given topic using predefined criteria), national surveillance programs, and other sources to estimate the number of illnesses, sequelae, deaths and DALYs globally and regionally for 22 diseases with sufficient data to support such estimations. Together, these 17 bacterial infections, two viral infections, and three protozoal infections caused 2 billion cases of illness, more than 1 million deaths, and almost 80 million DALYs in 2010. Using information on the proportions of infections considered to be foodborne by expert panels, the researchers estimated that nearly a third of these cases of illness (582 million cases), resulting in 25 million DALYs, were transmitted by contaminated food. Notably, 38% of the cases of foodborne illness, 33% of deaths from these diseases, and 43% of the disease burden from contaminated food (11 million DALYs) occurred in children under 5 years old. The leading cause of foodborne illness was norovirus (125 million cases), closely followed by campylobacter (96 million); diarrheal and invasive infections caused by non-typhoidal Salmonella enterica infections caused the largest burden of disease (4.07 million DALYs). Finally, the burden of foodborne illness was highest in WHO’s African region. What Do These Findings Mean? The lack of reliable data on the 22 illnesses considered in this analysis for many regions of the world, including some of the most populous regions, and uncertainty about the proportion of the cases of each illness that is foodborne may limit the accuracy of these findings. Nevertheless, these results provide new information about the regional and global disease burden caused by foodborne illnesses. In particular, these estimates reveal an unexpectedly high disease burden caused by foodborne illnesses among young children. Thus, although children under the age of 5 years represent only 9% of the global population, nearly half of the disease burden from contaminated food may occur in this age group. Overall, the findings of this study suggest that governments and international agencies should prioritize food safety to prevent foodborne illness, particularly among young children, and highlight the need to identify effective food hygiene interventions that can be implemented in low- and middle-income countries. Additional Information This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx.doi.org/10.1371/journal.pmed.1001921.  The World Health Organization provides information about foodborne diseases, food safety and the estimation of the global burden of foodborne diseases (available in several languages)  The US National Institute of Allergy and Infectious Diseases provides detailed information about several foodborne illnesses  The US Centers for Disease Control and Prevention provides information about foodborne disease outbreaks in the US and elsewhere and information about food safety in the US  The UK National Health Service Choices website provides information about food poisoning (another name for foodborne illness) and about food safety  STOP Foodborne Illness STOP Foodborne Illness, a US non-profit public-health organization, provides personal stories about foodborne illness Citation: Kirk MD, Pires SM, Black RE, Caipo M, Crump JA, Devleesschauwer B, et al. (2015) World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis. PLoS Med 12(12): e1001921. https://doi.org/10.1371/journal.pmed.1001921 Academic Editor: Lorenz von Seidlein, Mahidol-Oxford Tropical Medicine Research Unit, THAILAND Received: March 20, 2015; Accepted: November 3, 2015; Published: December 3, 2015 Copyright: © . 2015 World Health Organization. This is an open access article distributed under the Creative Commons Attribution IGO License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/3.0/igo/. This article should not be reproduced for use in association with the promotion of commercial products, services or any legal entity. Data Availability: All relevant data are within the paper and its Supporting Information files. https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001921 2/14 9/22/2018 World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseas… Funding: This study was commissioned and paid for by the World Health Organization (WHO). Copyright in the original work on which this article is based belongs to WHO. The authors have been given permission to publish this article. We acknowledge the support from the Bill & Melinda Gates Foundation that funded CFL, CFW, and REB through the Child Health Epidemiology Reference Group (CHERG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The findings and conclusions of this report are those of the authors and do not necessarily represent the official views, decisions or policies of the World Health Organization, US Centers for Disease Control and Prevention, the Department of the Navy, Department of Defense, the US Government or other institutions listed. CFL, AJH, and FJA are employees of the US Government. MDK, REB, MC, BD, DD, AF, TH, KHK, RL, CFL, PRT, AHH, and FJA serve as members of the World Health Organization advisory body—the Foodborne Disease Epidemiology Reference Group—without remuneration. MDK is a member of the Editorial Board for PLOS ONE. PRT is a member of the Editorial Board for PLOS Neglected Tropical Diseases. Introduction Foodborne diseases are globally important, as they result in considerable morbidity, mortality, and economic costs [1,2]. Many different diseases, including those due to bacteria, viruses, parasites, chemicals, and prions, may be transmitted to humans by contaminated food [3]. Outbreaks and sporadic cases of foodborne disease are regular occurrences in all countries of the world. In recent decades, globalization of the food supply has also meant that pathogens causing foodborne diseases are rapidly transported across international borders [4]. Foodborne disease outbreaks have led to adverse impacts on trade and food security [5,6]. In response to foodborne diseases, national governments and international bodies have established elaborate systems to control and improve food safety [7]. Recognizing that contaminated food is an important cause of human disease, estimates of disease burden of the various foodborne diseases has been sought to enable advocacy for improved food safety and to assist governments to prioritize efforts for enhancing food safety. Although several countries have estimated the number of cases, sequelae, deaths, and Disability Adjusted Life Years (DALYs) resulting from foodborne diseases at the national level, most have not [8]. Furthermore, global and regional estimates of the burden of foodborne diseases have not been available [1,2]. In 2007, the World Health Organization (WHO) established the Foodborne Disease Burden Epidemiology Reference Group (FERG) to estimate the global and regional burden of disease attributable to food from all causes [9]. FERG consists of thematic task forces to estimate the human health burden of (1) enteric bacterial and viral infections, (2) parasitic infections, and (3) illnesses due to chemicals and toxins. The Director General of WHO nominated members of the FERG following an open call for applications to governments, in the scientific press, and through global networks [1]. The Enteric Diseases Task Force (EDTF) of the FERG comprised 14 experts in the epidemiology of viral, bacterial and parasitic infections transmitted by food, and was supported by various resource advisors who were expert in various aspects of infectious disease transmission. Methods In this study, the EDTF estimates the global and regional disease health burden in 2010 resulting from the most common foodborne diseases. For a glossary of terms used in this paper see S1 Text. FERG EDTF reviewed the epidemiology of all bacterial and viral diseases potentially transmitted by food and identified those for inclusion based on public health importance and data availability. We excluded enteroaggerative Escherichia coli, Vibrio parahaemolyticus, V. vulnificus, and Yersinia spp., which are infrequent causes of foodborne diseases, due to a lack of sufficient data for global estimation, ie–not commonly reported in systematic reviews of etiological agents of diarrhea [10]. After excluding these agents, we included 19 bacterial or viral diseases in our study. Of these 19 diseases, four are distinct manifestations of Salmonella enterica infection: invasive infections due to S. enterica serotype Typhi (Salmonella Typhi); invasive infections due to S. enterica serotype Paratyphi A (Salmonella Paratyphi A); invasive infections due to non-typhoidal S. enterica (iNTS); and diarrheal disease due to non-typhoidal S. enterica (NTS). We then determined that our approach for estimating the burden for diarrheal diseases could also be applied to protozoal diseases and included 3 protozoal diseases. Diarrhea is a dominant feature for 14 of these diseases—ten caused by bacteria, three by protozoa, and one by a virus. One or more extra-intestinal manifestations including bacteremia, hepatitis, and meningitis are the dominant feature for the other eight diseases—seven caused by bacteria and one caused by a virus. To identify data for estimation of incidence, mortality and sequelae for different agents, we conducted literature reviews to identify relevant studies, consulted with academics and expert committees, and evaluated systematic reviews that were conducted circa 2010. Where data sources were not available, the EDTF recommended that WHO commission systematic reviews into incidence and outcomes of specific agents, which were subsequently published in the peer-reviewed literature [11–22]. Where multiple data sources were available for a single agent, the EDTF made decisions to use the most contemporaneous and comprehensive sources, or incorporate both into the estimation process. In the following sections, we outline how we synthesized data in accordance with a documented framework reported elsewhere [23]. Table 1 summarizes our approach, while S2 Text provides a comprehensive description of the methods and distribution for all parameters used for estimating cases, sequelae, deaths and DALYs for each of the 22 diseases. https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001921 3/14 9/22/2018 World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseas… Table 1. Summary of enteric pathogens included and methods of estimating incidence of infection. For more information, see S2 Text. https://doi.org/10.1371/journal.pmed.1001921.t001 Estimating Cases, Sequelae, and Deaths for Diarrheal Diseases For diarrheal diseases caused by Campylobacter spp., Cryptosporidium spp., Entamoeba histolytica, enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Giardia lamblia, norovirus, NTS, and Shigella spp., national estimates of foodborne diseases were only available from a limited number of countries. We therefore used two approaches, documented in Pires et al. [11], depending on the level of development of the country. The first approach, based on national estimates of the incidence of foodborne diseases from seven studies published between 2005–2014, was applied to the 61 countries in low-mortality (European Region (EUR) and other subregion A [27]) countries [3,28–35]. For countries with national estimates of incidence and mortality, we used these data. We used the median and associated uncertainty intervals for diarrheal diseases for the subregion to estimate incidence and mortality of diarrheal diseases for other countries within the subregion without national data [10]. The second approach was applied to the remaining 133 countries not in EUR or other subregion A categories (see S1 Text for a country list by subregion). For this approach, we modified the WHO Child Health Epidemiology Reference Group (CHERG) method to estimate diarrheal incidence and mortality for all age groups [10]. First, we estimated the overall incidence of diarrhea from all causes (i.e., “envelope” of diarrheal incidence) for 2010 by combining estimates of diarrheal incidence for children
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