Teresa Coque - Simposio Microbiología: Transmisión
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Los días 7 y 8 de mayo de 2015 organizamos en la Fundación Ramón Areces con la Fundación General CSIC el Simposio Internacional 'Microbiología: transmisión'. La "transmisión" en microbiología hace referencia al proceso por el que material genético es transferido de una célula a otra, de una población a otra. Es un proceso clave para entender el origen y la evolución de los seres vivos. El objetivo de esta reunión era conocer mejor la logística de la transmisión para ser capaces de modular o suprimir algunos procesos de transmisión dañinos.
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Teresa Coque - Simposio Microbiología: Transmisión
- 1. FOOD-TO-HUMANS BACTERIAL TRANSMISSION Teresa M. Coque Instituto Ramón y Cajal de Investigación Sanitaria, IRYCIS (Madrid, Spain) REDEEX Fundación Ramón Areces-Fundación Lilly May 7th-8th, 2015 1
- 2. Foods, Health and Disease 2 • Foods (Diet) are key players in the evolution of humans. • Foodborne infection (bacteria, virus, parasites) is a major cause of illness and death worldwide and it is a main issue of Food Microbiology. • The epidemiology of foodborne diseases is constantly changing as new foods and new opportunities for FD transmission.
- 3. Foods and Bacterial Transmission 3 How are bacteria transmitted and why? What mechanisms explain the transmission of bacterial agents at population level? The Shift in the paradigm of diagnostic methods
- 4. TRANSMISSION MECHANISMS • The Chain Model of Transmission • The Convergence Model (IOM, 2003) 4
- 5. The Chain Model of Transmission (CDC) It contains the key components that must be “linked” in order an infection to occur 5 the MECHANISM by which the agent is transmitted from the source to the host (e.g meat, water,…) HOW the agent enters the susceptible host (e.g., GI) WHERE the microbial agent multiplies and survives WHEN it is transmitted to the susceptible host HOW the agent exits the susceptible host (e.g., GI)
- 6. The Convergence Model of human-microbe interaction Lederberg, J., Hamburg, M. A., & Smolinski, M. S. (Eds.). (2003). Microbial Threats to Health:: Emergence, Detection, and Response. National Academies Press.; IOM, 2003 IOM, 2003 To set forth the principal factors involved in the threats’ emergence, take stock of existing measures for dealing with them, and specify what further investments were needed 6
- 7. • Thirteen individual factors—some reflecting the ways of nature, our ways of life—account for new or enhanced microbial threats • Microbial adaptation and change • Human susceptibility to infection • Climate and weather • Changing ecosystems • Economic development and land use • Human demographics and behaviour • Technology and industry • International travel and commerce • Breakdown of Public Health measures • Poverty and social inequealiity • War and famine • Lack of political will • Intent to harm IOM, 2003 The Convergence Model of human-microbe interaction (2) 7
- 8. • Thirteen individual factors—some reflecting the ways of nature, our ways of life—account for new or enhanced microbial threats • Microbial adaptation and change • Human susceptibility to infection • Climate and weather • Changing ecosystems • Economic development and land use • Human demographics and behaviour • Technology and industry • International travel and commerce • Breakdown of Public Health measures • Poverty and social inequealiity • War and famine • Lack of political will • Intent to harm IOM, 2003 The Convergence Model of human-microbe interaction (2) 8
- 9. Drivers and location of emergence events for zoonotic ID in humans from 1940-2005 Keesing, Nature 2010 9
- 10. Temporal changes in foodborne outbreaks 1950´s-1970´s • High attack rates (ID50) • Short incubation periods • Locally defined • Small number of persons • Staphylococcus, • C. perfringens 1990´s- • Low infectivity (ID1000) • No outbreaks • Widespread • Large number of persons • Salmonella, • Campylobacter, • E. coli O157, • Listeria monocytogenes 10 Hedberg et al, CID 1994; Food Microbiology:fundamentals and Frontiers 4th ed. Doyle and Buchanan ed 2014
- 11. Mortality and morbility due to Food commodities in the US (1998-2008) Painter et al, EID 2013 Bacillus cereus Clostridium botulinum E. coli STEC, 0157 Salmonella (Java, Newport, Typhi, paratyphi) Clostridium perfringens Campylobacter Listeria Salmonella enteritidis Salmonella Heidelberg SGA Yersinia enterocolitica Staphylococci Vibrio Aeromonas AQUATIC LAND PLANTS 11
- 12. Mortality and morbility due to Food commodities in the US (1998-2008) Painter et al, EID 2013 12 Increase of Salmonellosis, shigellosis New emerging pattern: Widespread-No Outbreaks- Temporal clustering Delay in recognition made difficult to trace the source
- 13. Changes In Diet and Diet Habits 13 Hedberg et al, CID 1994 • Changes in food types • Food service establishments (73,000-150,000) • New methods of food production • (networks of distribution)
- 14. Land Use and Agriculture The sudden increase in Leafy Vegetables Outbreaks Consumption modestly increased (16 lb per capita in 1973 to 17 lb in 2011) Changes in types (headlettuce decreased from 20·8 to13·2 lb in 2012, while the romaine and leaf lettuce increased from 3 lb per capita in 1985 to10·7 lb in 2012) Herman and Gould, Epidemiology and Infection, 2015 14
- 15. Rising Demand for Meat 15
- 16. 16
- 17. The Footprint of Meat Eshel et al, PNAS July 21 2014; Kunzig, National Geographic 2014 FEED needed > 3 times that needed for pork. LAND Beef cattle production accounts for almost 90 percent of the land used for raising livestock in the USA acreage that includes pasture as well as cropland for growing feed. WATER needed > 3 times that needed for all the other livestock. Dairy cows required much less EMISSIONS Greenhouse gases from cattle production are 40% methane, burped by cattle from their specialized stomachs. Cattle fed only grass belch more than those eating grass and feed. 17
- 18. The Next Green Revolution 18
- 19. Changing Ecosystems 19 Jones et al, PNAS 2013: Gu et al, PlosOne, 2011; Potnis et al, AEM 2014; Ottensen, BMC Microbiol 2013 • Forest fragmentation and Expansion of ecotones: transmission between non-human primates, livestock and humans (E. coli in Uganda) • Fertilizers and pesticides can contaminate plants with pathogens Increases persistence of Salmonella in plants associated with plant pathogens (Xanthomonas perforans) • Bushmeat and ilegal wildlife animals trade 55million pounds of bushmeat low into the U.S.each year – most of it arriving at New York City, Miami or Los Angeles from China, Nigeria, Hong-Kong Nonhuman primate bushmeat specimens confiscated at US airports.
- 21. Transmission dynamics is the population-level view of transmission of microbial agents with the occurrence of infectious disease cases. • Ro (reproductive number) the average number of secondary infections produced by a single primary infection introduced into a large population of previously unexposed hosts. • Io is the number of primary cases of infection introduced into the human population from an external source Woolhouse, Trends Microbiology 2002; Woolhouse, EID 2005; Aragon and Reingold, 2011 Ro < 1, the no of new cases will decline and eventually go to zero Ro ≈1, the no of new cases will assume a steady state. Outbreak size is determined by the number of introductions Ro > 1, the no of new cases will increase (growing epidemic). Outbreak size is determined by the size of susceptible population Transmission dynamics 21
- 22. Transmission dynamics: Determinants of the outbreak size Woolhouse, Trends Microbiology 2002; Woolhouse, EID 2005 Ro (reproductive number) the average number of secondary infections produced by a single primary infection introduced into a large population of previously unexposed hosts. Im is the fraction of total population. Io is the number of primary cases of infection introduced into the human population from an external source. Most foodborne bacterial pathogens are NOT highly transmissible within human populations and NOT cause major epidemics The curves are obtained from a modified version of the Kermack-McKendrick equation 22
- 23. Transmission Containment Designing and implementing transmission containment interventions involves three steps: 1. Identify control points 2. Derive control strategies 3. Design and implementing control measures 23
- 24. Identification of foodborne pathogens by WGS: shift in the paradigm 24
- 25. Bacterial Diagnostics: traditional approaches 25 Didelot, Nat Rev Gen 2014
- 26. 26 Didelot, Nat Rev Gen 2014 Bacterial Diagnostics: New approaches Very few examples, rarely on real-time
- 27. 27 Courtesy of Marc Allard at FDA
- 28. Genomics for diagnosis and surveillance is a global issue • Fast and efficient implementation at the global level • Sharing data in real-time • Availability of IT-infrastructures • Technical gaps • QA/QC • Political and ethical barriers 28
- 29. 29 Courtesy of Marc Allard at FDA
- 30. 30
- 31. 31 Courtesy of Mark Allard at FDA
- 32. 32 Real-time diagnosis of outbreaks
- 33. 33
- 34. 34
- 35. 35 Real-time diagnosis of outbreaks
- 36. 36 Surveillance
- 38. 38
- 39. 39
- 40. 40
- 41. Technical gaps Procedure for analysis Need for harmonisation • Gene by gene following by SNPs • Need standarisation for each species • Kmer followed by SNPs • Species independent • Novel taxonomy 41 • Gene by gene analysis • rMLST, 16SRNA, MLST • Traditional nomeclature • The entire sequence • k-mer • SNPs
- 42. 42
- 44. 44
- 45. FOOD-TO-HUMANS BACTERIAL TRANSMISSION Teresa M. Coque Instituto Ramón y Cajal de Investigación Sanitaria, IRYCIS (Madrid, Spain) REDEEX Fundación Ramón Areces-Fundación Lilly May 7th-8th, 2015 45
- 46. Timeline showing some of the temporal intersections of diet, natural selection and one of the many changes in human morphology Courtney C. Babbitt et al. Proc. R. Soc. B 2011;278:961-969 The Evolution of Diet Emergence of contagious diseases, often of animal origin Introduction in naive populations 46
Notas del editor
- First, I will review infectious disease transmission mechanisms. How are bacteria transmitted and why? Second, we review infectious disease transmission dynamics. At the populationlevel, what mechanisms explain the transmission of microbial agents and the appearance of infectious cases? How do infec-tious cases interact with susceptible hosts? Third, we reviewtransmission containment.From our study of transmission dy- namics, we identify transmission CONTROL POINTS FOR PREVENTING AND CONTROLLING ID. We will use these control points to guide the development of appropriate control mea- sures. This process helps us to evaluate the success or failure of our control measures.
- The Chain Model of infectious diseases contains the key components that must be “linked” in order for an infection to occur. First, there is a susceptible host. Second, there is a microbial agent capable of adhering, entering, infecting, and causing disease in the susceptible host. In its natural settings, the microbial agent multiplies and survives in a RESERVOIR. The SOURCE is where the microbial agent is when it is transmitted to the susceptible host. The The MODE OF TRANSMISSION is the mechanism by which the agent is transmitted from the source to the host (e.g., the PORTAL OF ENTRY is how the agent enters the susceptible host (e.g., respiratory tract, gas- trointestinal tract, genitourinary tract, skin).
- In March, 2003, the “Convergence model of human-microbe interaction” was published by the Institute of Medicine (IOM), Committee on EmergingMicrobial Threats to Health in the 21st Century. The committee’s assignment was to set forth the principal factors involved in the threats’ emergence, take stock of existing measures for dealing with them, and specify what further investments of fiscal and political capital are needed Thirteen individual factors—some reflecting the ways of nature, most of them reflecting our ways of life—account for new or enhanced microbial threats. ANY OF THESE FACTORS ALONE CAN TRIGGER PROBLEMS, BUT THEIR CONVERGENCE CREATES ESPECIALLY HIGH-RISK ENVIRONMENTS WHERE INFECTIOUS DISEASES MAY READILY EMERGE, OR RE-EMERGE, AFFLICTING INDIVIDUALS AND SOCIETIES alike while posing particular challenges for the medical and public health communities that must face these situations at the front lines. It’s conceivable, in fact, that in certain places microbial “perfect storms” could occur—convergences of several factors—and unlike meteorological perfect storms, the events would not be on the order of once-in-a-century, but frequent. Epidemiologists can think of this model as an updated ver-sion of the agent-host-environment model of infectious diseasecausation, also referred to as the “epidemiologic triad” [20].However, the Convergence model provides important detail.More specifically, the IOM Committee considered the follow-ing individual factors as major contributors to the emergenceand re-emergence of microbial threats to health:• Microbial adaptation and change;• Human susceptibility to infection;• Climate and weather;• Changing ecosystems;• Economic development and land use;• Human demographics and behavior;• Technology and industry;• International travel and commerce;• Breakdown of public health measures;• Poverty and social inequality;• War and famine;• Lack of political will; and .
- In March, 2003, the “Convergence model of human-microbe interaction” was published by the Institute of Medicine (IOM), Committee on EmergingMicrobial Threats to Health in the 21st Century. The committee’s assignment was to set forth the principal factors involved in the threats’ emergence, take stock of existing measures for dealing with them, and specify what further investments of fiscal and political capital are needed Thirteen individual factors—some reflecting the ways of nature, most of them reflecting our ways of life—account for new or enhanced microbial threats. ANY OF THESE FACTORS ALONE CAN TRIGGER PROBLEMS, BUT THEIR CONVERGENCE CREATES ESPECIALLY HIGH-RISK ENVIRONMENTS WHERE INFECTIOUS DISEASES MAY READILY EMERGE, OR RE-EMERGE, AFFLICTING INDIVIDUALS AND SOCIETIES alike while posing particular challenges for the medical and public health communities that must face these situations at the front lines. It’s conceivable, in fact, that in certain places microbial “perfect storms” could occur—convergences of several factors—and unlike meteorological perfect storms, the events would not be on the order of once-in-a-century, but frequent. Epidemiologists can think of this model as an updated ver-sion of the agent-host-environment model of infectious diseasecausation, also referred to as the “epidemiologic triad” [20].However, the Convergence model provides important detail.More specifically, the IOM Committee considered the follow-ing individual factors as major contributors to the emergenceand re-emergence of microbial threats to health:
- In March, 2003, the “Convergence model of human-microbe interaction” was published by the Institute of Medicine (IOM), Committee on EmergingMicrobial Threats to Health in the 21st Century. The committee’s assignment was to set forth the principal factors involved in the threats’ emergence, take stock of existing measures for dealing with them, and specify what further investments of fiscal and political capital are needed Thirteen individual factors—some reflecting the ways of nature, most of them reflecting our ways of life—account for new or enhanced microbial threats. ANY OF THESE FACTORS ALONE CAN TRIGGER PROBLEMS, BUT THEIR CONVERGENCE CREATES ESPECIALLY HIGH-RISK ENVIRONMENTS WHERE INFECTIOUS DISEASES MAY READILY EMERGE, OR RE-EMERGE, AFFLICTING INDIVIDUALS AND SOCIETIES alike while posing particular challenges for the medical and public health communities that must face these situations at the front lines. It’s conceivable, in fact, that in certain places microbial “perfect storms” could occur—convergences of several factors—and unlike meteorological perfect storms, the events would not be on the order of once-in-a-century, but frequent. Epidemiologists can think of this model as an updated ver-sion of the agent-host-environment model of infectious diseasecausation, also referred to as the “epidemiologic triad” [20].However, the Convergence model provides important detail.More specifically, the IOM Committee considered the follow-ing individual factors as major contributors to the emergenceand re-emergence of microbial threats to health:• Microbial adaptation and change;• Human susceptibility to infection;• Climate and weather;• Changing ecosystems;• Economic development and land use;• Human demographics and behavior;• Technology and industry;• International travel and commerce;• Breakdown of public health measures;• Poverty and social inequality;• War and famine;• Lack of political will; and .
- We will focus in the influence of these factors on the foodborne infections. For ths, I will use data from outbreks in the last 2 decades
- Using data from outbreak-associated illnesses for 1998–2008, Painter et al estimated annual US food- borne illnesses, hospitalizations, and deaths attributable to different foods classified in 17 food commodities Human behavioral changes, driven by increasingpopulation, economic and technological development, and theassociated spatial expansion of agriculture, are creating novel aswell as more intensive interactions between humans, livestock,and wildlife. Most bacterial illnesses were attributed to dairy (18%),poultry (18%), and beef (13%) commodities
- Using data from outbreak-associated illnesses for 1998–2008, Painter et al estimated annual US food- borne illnesses, hospitalizations, and deaths attributable to different foods classified in 17 food commodities Human behavioral changes, driven by increasingpopulation, economic and technological development, and theassociated spatial expansion of agriculture, are creating novel aswell as more intensive interactions between humans, livestock,and wildlife. Most bacterial illnesses were attributed to dairy (18%),poultry (18%), and beef (13%) commodities
- Because some types of lettuceare more likely to be contaminated in the field or dur-ing harvest, these changes could have increased therisk of consumer exposure to contaminated leafygreens. and other changes in packaging, pro-cessing, and distribution have extended the shelf life ofleafy vegetables to make them more availablethroughout the year
- Appetite for meat is growing as the developing world becomes more prosperous. But meat—especially beef—can be polarizing, on health, environmental, and ethical grounds. Chicken outpaced beef in the U.S. in 2010. Total U.S. meat consumption peaked in the mid-2000s and has declined ever since. Argentina’s famous appetite for beef has fallen because of cholesterol consciousness and economic downturns. In countries where meat is a newly affordable option, animal protein is a boon, not a debate. But by 2050, when the world’s population is expected to surpass nine billion, crop production will need to double to provide feed for livestock as well as direct human consumption.
- Beef cattle production accounts for almost 90 percent of the land used for raising livestock in the United States, acreage that includes pasture as well as cropland for growing feed. Irrigating land for cattle feed uses almost three times as much water as all the other foods here combined. Dairy cows require much less, and their products contribute the most calories to U.S. diets EMISSIONS Greenhouse gases from cattle production are 40 percent methane, burped by cattle from their specialized stomachs. Cattle fed only grass belch more than those eating grass and feed.
- La Revolución Verde (1960-90) fue una campaña dirigida por centros de investigación agrícolas internacionales con la meta de modernizar la agricultura en los países en vías de desarrollo.
- Current methods for characterizinsing foodborne pathogens in a PH lab should improve in speed, cost and sensitivity. Arecent review
- The genomic epidemiological database for global identification of microorganisms is a platform for STORING WGS data of microorganisms, for the IDENTIFICATION of relevant genes and for the COMPARISON OF GENOMES to detect outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.
- A timeline showing some of the temporal intersections of diet, natural selection and one of the many changes in human morphology. Green bars indicate the temporal range on which different methods for scanning for selection are optimized to identify relevant changes in the genome (reviewed in [111]). Blue bars indicate the times in which there is evidence for shifts in human dietary intake [6,17,28,36,112,113]. The coloured bubbles are a general schematic of the time and range in size of cranial capacity found in various hominin species adapted from Schoenemann [27] with additional data from White et al. [114]. Since prehistoric time, major changes in human disease bur- den, spatial distribution, and pathogen types have arisen largely owing to human activity. The change from small hunter-gatherer to large agricultural communities was associated with the emergence of human contagious diseases, many of which areof animal origin. Travel and colonization facilitated the in-troduction of disease to naïve populations. In the last century,improved nutrition and hygiene and the use of vaccines andantimicrobials reduced the infectious disease burden. However,in recent decades, increasing global travel and trade, expandinghuman and livestock populations, and changing behavior havebeen linked to a rise in disease emergence risk and the potentialfor pandemics (1–3).