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CDC 2011 Estimates: Methods

In 2011, Scallan et al. estimated the overall burden of foodborne illness caused by known and unspecified agents1.

This analysis included 31 pathogens known to cause foodborne illness and unspecified agents that cause acute gastroenteritis illnesses (AGI). Scallan et al. also estimated the number of hospitalizations and deaths caused by these illnesses.

Estimating US foodborne illnesses for 31 known foodborne pathogens

For each pathogen2, we gathered data from surveillance systems and corrected for underreporting and under-diagnosis. We then multiplied the adjusted number by the proportion of illnesses that was acquired in the United States (that is, not during international travel) and the proportion transmitted by food to yield an estimated number of illnesses that are domestically acquired and foodborne. Then, we added the estimates for each of the pathogens to arrive at a total, and used an uncertainty model to generate a point estimate and 90% credible interval (upper and lower limits) (Figure 1).

Figure 1. Estimating illnesses for pathogens known to cause foodborne illness, 2011*

Figure 1 is a diagram, depicting an equation used to estimate illnesses for pathogens known to cause foodborne illness for the year 2011. The equation is as follows: For each pathogen multiply the number of illnesses reported to surveillance system multiplied by the multiplier to correct for under-reporting multiplied by the pathogen-specific multiplier to correct for under-diagnosis multiplied by the estimated proportion  domestically acquired multipiled by the estimated proportion  transmitted through food. That results in the estimated number of domestically acquired foodborne illnesses due to each known pathogen, which is then added to the individual  pathogen estimates  summed. The final result is the estimated # of domestically acquired foodborne illnesses due to known pathogens.

*Probability distributions were used to model uncertainty in each of the data inputs. Point estimates were bounded by a 90% credible interval.

**For six of the 31 pathogens, no routine surveillance data were available so alternative approaches were used to estimate illnesses.

Estimating US foodborne illnesses for unspecified agents

Unspecified agents fall into four general categories:

  • Agents with insufficient data to estimate agent-specific burden
  • Known agents not yet recognized as causing foodborne illness
  • Microbes, chemicals, or other substances known to be in food whose pathogenicity is unproven
  • Agents not yet described

To estimate foodborne illnesses from unspecified agents, we used symptom-based data from surveys to estimate the total number of AGI and then subtracted the number of illnesses accounted for by known gastroenteritis pathogens. We then multiplied this number by the proportion of domestically acquired illnesses and of illnesses attributable to food, just as we did for the known agents. Finally, again as with the known-pathogens estimate, we used an uncertainty model to generate a point estimate and 90% credible interval (upper and lower limits) (Figure 2).

Foodborne illnesses due to chemicals that cause acute gastroenteritis are included in the estimate of illnesses due to unspecified agents. However, chemicals or unspecified agents that do not cause acute gastroenteritis are not included in the estimates.

Figure 2. Estimating foodborne illnesses due to unspecified agents, 2011*

Figure 2 is a diagram, depicting an equation used to estimate foodborne illness due to unspecified agents for the year 2011. The equation is as follows: Estimated number of acute gastro-enteritis illnesses (AGI) from population surveys multiplied by 2006 US population estimates minus Estimated number of illnesses due to 24 known foodborne pathogens that cause AGI. The result of that is then multiplied by Estimated proportion domestically acquired multiplied by Estimated proportion  transmitted through food which will result in Estimated number of domestically acquired foodborne illnesses due to unspecified agents.

*Probability distributions were used to model uncertainty in each of the data inputs. Point estimates were bounded by a 90% credible interval.

**Estimated proportions were based on the 24 known pathogens that cause acute gastroenteritis illnesses.

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Estimating hospitalizations and deaths from US foodborne illnesses due to known pathogens


For each known pathogen with surveillance data available, we multiplied the estimated number of reported illnesses (after correcting for underreporting) by the pathogen-specific hospitalization and death rate from surveillance data, surveys, or outbreak data. Because some people with illnesses that were not laboratory-confirmed would also have been hospitalized and died, we doubled the estimates to correct for under-diagnosis. We multiplied the adjusted hospitalization and death estimates by the proportion of illnesses that were acquired within the United States (vs. international travel-related) and the proportion transmitted by food. Finally, we used an uncertainty model to generate a point estimate and 90% credible intervals for both hospitalizations and deaths (Figures 3 and 4).

Figure 3. Estimating hospitalizations from foodborne illnesses due to known pathogens, 2011*

Figure 3 is a diagram, depicting an equation used to estimate hospitalizations from foodborne illnesses due to known pathogens for the year 2011. The equation is as follows: Estimated number of illnesses reported to surveillance system (after correcting for under-reporting), multiplied by the proportion of persons hospitalized, multiplied by 2 to correct for under-diagnosis, multiplied by estimated proportion  domestically acquired, multiplied by estimated proportion  transmitted through food. This results in the estimated number of hospitalizations from domestically acquired foodborne illnesses due to known pathogens.

*Probability distributions were used to model uncertainty in each of the data inputs. Point estimates were bounded by a 90% credible interval.

Figure 4. Estimating deaths from foodborne illnesses due to known pathogens, 2011*

Figure 3 is a diagram, depicting an equation used to estimate deaths from foodborne illnesses due to known pathogens for the year 2011. The equation is as follows: Estimated number of illnesses reported to surveillance system (after correcting for under-reporting), multiplied by the proportion of persons who died, multiplied by 2 to correct for under-diagnosis, multiplied by estimated proportion  domestically acquired, multiplied by estimated proportion  transmitted through food. This results in the estimated number of deaths from domestically acquired foodborne illnesses due to known pathogens.

*Probability distributions were used to model uncertainty in each of the data inputs. Point estimates were bounded by a 90% credible interval.

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Estimating hospitalizations and deaths from US foodborne illnesses due to unspecified agents


To estimate hospitalizations, we applied the average hospitalization rate for all AGI, determined from survey data for 2000–2006, to 2006 US population estimates and subtracted the estimated number of hospitalizations caused by the 24 known pathogens that cause AGI. For deaths, we determined the death rate for acute gastroenteritis illnesses from US death certificates (specifically, multiple-cause-of-death data) for 2000–2006 and applied that rate to the 2006 US population estimate. We then subtracted the estimated number of deaths from the 24 known gastroenteritis pathogens. For both hospitalizations and deaths, we multiplied the overall number by the proportion of hospitalizations and deaths from the 24 known gastroenteritis pathogens that was domestically acquired and foodborne.  Finally, we used an uncertainty model to generate a point estimate and 90% credible intervals (Figures 5 and 6).

Figure 5. Estimating hospitalizations from foodborne illnesses due to unspecified agents, 2011*

Figure 5 is a diagram, depicting an equation used to estimate hospitalizations from foodborne illnesses due to unspecified agents for the year 2011. The equation is as follows: Hospitalization rate for acute gastroenteritis illness from population surveys, multiplied by 2006 US population estimates, minus number of hospitalizations due to 24 known foodborne pathogens that cause acute gastroenteritis illness. The result of that is then multiplied by the estimated proportion domestically acquired, multiplied by estimated proportion  transmitted through food. This results in the estimated number of hospitalizations from domestically acquired foodborne illnesses due to unspecified agents.

*Probability distributions were used to model uncertainty in each of the data inputs. Point estimates were bounded by a 90% credible interval.

Figure 6. Estimating deaths from foodborne illnesses due to unspecified agents, 2011*

Figure 6 is a diagram, depicting an equation used to estimate deaths from foodborne illnesses due to unspecified agents for the year 2011. The equation is as follows: Death rate for acute gastroenteritis illness from US multiple cause-of-death data, multiplied by 2006 US population estimates, minus number of deaths due to 24 known foodborne pathogens that cause acute gastroenteritis illness. The result of that is then multiplied by the estimated proportion domestically acquired, multiplied by estimated proportion transmitted through food. This results in the estimated number of deaths from domestically acquired foodborne illnesses due to unspecified agents.

*Probability distributions were used to model uncertainty in each of the data inputs. Point estimates were bounded by a 90% credible interval.

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Data Sources for the 2011 Estimates

We used five general types of data sources to create the 2011 estimates:

Active surveillance: (public health officials actively gather data from state and local health departments, laboratories, hospitals, etc.)

  • Foodborne Diseases Active Surveillance Network (FoodNet)

Passive surveillance: (public health officials rely on state and local health departments, laboratories, hospitals, etc. to report data to surveillance systems)

  • National Notifiable Diseases Surveillance System (NNDSS)
  • National Tuburculosis Surveillance System (NTSS)
  • Public Health Laboratory Information System
  • Cholera and other Vibrio Illness Surveillance System (COVIS)

Outbreak surveillance:  

  • Foodborne Disease Outbreak Surveillance System

Surveys:

  • FoodNet Population Survey
  • FoodNet Laboratory Survey
  • National Ambulatory Medical Care Survey (NAMCS)
  • National Hospital Ambulatory Medical Care Survey (NHAMCS)
  • National Hospital Discharge Survey (NHDS)
  • National Health and Nutrition Survey (NHANES)
  • Nationwide Inpatient Sample (NIS)

Vital (Government) Statistics

  • Multiple-cause-of-death data (from US death certificates)
  • US Census

Tables 6a and 6b from Scallan et al. provide detailed descriptions of the data sources. Please visit the links below to view these tables.

Table 6a. Data sources used to estimate illnesses, hospitalizations, and deaths due to known foodborne pathogens in the United States, 2011 (from Scallan et al.)

Table 6a. Data sources used to estimate illnesses, hospitalizations, and deaths due to known foodborne pathogens in the United States, 2011 (from Scallan et al.)

Data Source Data Pathogen(s) Geographic Coverage Time Frame Adjustments
Cholera  and  Other  Vibrio  Illness  Surveillance  System  (COVIS)*  Number  of  case-patient  reports,  proportion  hospitalized,  proportion  who  died Vibrio  cholerae,  toxigenic;  Vibrio  vulnificus;  Vibrio  parahaemolyticus;  other  Vibrio  spp. United  States 2000–2007 Underreporting;  Under-diagnosis 
Foodborne  Diseases  Active  Surveillance  Network  (FoodNet)  Number  of  laboratory-confirmed  illnesses,  proportion  hospitalized,  proportion  who  died Campylobacter  spp.;  Cryptosporidium  spp.;  Cyclospora  cayetanensis;  Shiga  toxin–producing  Escherichia  coli  O157;  Shiga  toxin-producing  E.coli  non-O157;  Listeria  monocytogenes;  non-typhoidal  Salmonella;  Salmonella  serotype  Typhi;  Shigella  spp.;  Yersinia  enterocolitica FoodNet  sites 2005–2008 Geographical  coverages§;  Under-  diagnosis
Foodborne  Disease  Outbreak  Surveillance  System  (FDOSS) Number  of  foodborne  outbreak-associated  illnesses Bacillus  cereus;  Clostridium  perfringens;  Enterotoxigenic  Escherichia  coli;  Staphylococcus  aureus;  Streptococcus  spp.Group  A United  States 2000–2007;  (Streptococcus  spp.,Group  A  1996–2007) Underreporting;  Under-diagnosis
Proportion  hospitalized  and  proportion  who  died  in  foodborne  outbreaks Bacillus  cereus;  Clostridium  perfringens;  Enterotoxigenic  Escherichia  coli;  Staphylococcus  aureus;  Streptococcus  spp.,  Group  A;  Clostridium  botulinum;  Trichinella  spp. United  States 2000–2007;  (Streptococcus  spp.,Group  A1981–2007) Under-diagnosis
Nationwide Inpatient  Sample  (NIS) Hospitalization  rate Giardia  intestinalis  (ICD-9-CM  code  007.1),  Toxoplasma  gondii  (ICD-9-CM  codes  130.0-9) Sample  of  discharge  records  from  US  hospitals 2000–2006 Weighted  to  give  national  estimates  according  to  Healthcare  Cost  and  Utilization  Project  (HCUP)  criteria;  Under-diagnosis(Giardia  intestinalis  and  Toxoplasma  gondii
Death  rate Giardia  intestinalis  (ICD-9-CM  code  007.1),  Toxoplasma  gondii  (ICD-9-CM  codes  130.0-9) Sample  of  discharge records  from  US  hospitals

2000–2006

Under-diagnosis

National  Health  and  Nutrition  Examination  Survey  (NHANES)

Seroprevalence

Toxoplasma  gondii 

United  States 1999–2004 Rate  of  infection  over  time  and  percentage  symptomatic 
National  Notifiable  Diseases  Surveillance  System  (NNDSS) Number  of  case-patient  reports Brucella  spp.;  Clostridium  botulinum  (foodborne);  Trichinella  spp.;  Hepatitis  A;  Giardia  intestinalis United  States 2000–2007 (2002–2007  for Giardia  intestinalis)# Underreporting;  Under-diagnosis
Hospitalization  rate Hepatitis  A United  States 2000–2007  Under-diagnosis
National  Tuberculosis  Surveillance  System  (NTSS) Number  of  tuberculosis  case-patient  reports,  proportion  who  died Mycobacterium  bovis United  States 2004–2007 Percentage  of  tuberculosis  cases  attributable  to  M.bovis;  under-diagnosis 
US  Census Population  estimates Astrovirus,  rotavirus,  sapovirus United  States 2006 75%  of  children  experience  an  episode  of  clinical  illness  by  5  years  of  age
Various  acute  gastroenteritis  data  sources  (see  Table  6b) Acute  gastroenteritis  illnesses,  hospitalizations,  and  deaths Norovirus See Table 6b See Table 6b Fraction  of  acute  gastroenteritis  attributable  to  norovirus

* Passive surveillance from COVIS was used in preference to active surveillance from FoodNet for Vibrio spp. because most illnesses are reported by Gulf States (Florida, Alabama, Louisiana, Texas) that are not included in the FoodNet surveillance area.

Beginning in 2000, there were 10 FoodNet sites. In 2008, the population of these sites was 46 million persons, 15% of the US population.

§ Incidence of laboratory-confirmed illnesses in FoodNet from 2004 to 2007 was applied to the 2006 US Census population estimates.

Data from FDOSS on Streptococcus spp., Group A were included from 1996 to 2007 for illnesses and from 1981 to 2007 for hospitalizations and deaths because of a paucity of data (Appendix 1 and 3).

# Giardia intestinalis became nationally notifiable in 2002.

Table 6b. Data sources used to estimate illnesses, hospitalizations, and deaths due to acute gatroenteritis in the United States, 2011 (from Scallan et al.)

Table 6b. Data sources used to estimate illnesses, hospitalizations, and deaths due to acute gatroenteritis in the United States, 2011 (from Scallan et al.)

Data source Data Definition Geographic coverage Time frame
FoodNet  Population  Survey Rate  of  illness  Average  annual  rate  of  acute  gastroenteritis  was  derived  by  multiplying  the  average  monthly  prevalence  by  12,  where  an  episode  of  acute  gastroenteritis  was  defined  as  diarrhea  (≥3  loose  stools  in  24  hours)  or  vomiting  in  the  past  month  with  both  lasting  >1  day  or  resulting  in  restricted  daily  activities.  Persons  with  a  chronic  condition  in  which  diarrhea  or  vomiting  was  a  major  symptom  and  persons  with  concurrent  symptoms  of  cough  or  sore  throat  were  excluded. FoodNet  sites 2000–2001,  2002–2003,  2006–2007
Death  certificates  --  Multiple-cause-of-death  data  from  the  National  Vital  Statistics  System Death  rate Norovirus;  Acute  gastroenteritis  deaths  were  identified  from  the  underlying  or  contributing  cause  of  death  classified  by  ICD-10  diagnostic  codes  A00.9–A08.5  (infectious  gastroenteritis  of  known  cause)  A09  (diarrhea  &  gastroenteritis  of  presumed  infectious  origin);  and  K52.9  (noninfectious  gastroenteritis  &colitis,  unspecified);  excluding  A04.7  (enterocolitis  due  to  Clostridium  difficile)  &  A05.1  (botulism) United  States 2000–2006
National  Ambulatory  Medical  Care  Survey  (NAMCS);  National  Hospital  Ambulatory  Medical  Care  Survey  (NHAMCS) Hospitalization  rate  Norovirus;  Acute  gastroenteritis  hospitalizations  were  identified  from  patient  visits  to  clinical  settings,  including  physician  offices,  hospital  emergency  and  outpatient  departments  with  a  diagnosis  of  infectious  enteritis  ICD-9-CM  diagnostic  codes  001–008  (infectious  gastroenteritis  of  known  cause);  009  (infectious  gastroenteritis);  558.9  (other  and  unspecified  noninfectious  gastroenteritis  and  colitis),  or  787.9  (other  symptoms  involving  digestive  system:  diarrhea);  [excluding  008.45  (Clostridium  difficile  colitis)  and  005.1  (botulism)]  or  reason  for  visit  classification  codes  for  diarrhea  (1595)  or  gastrointestinal  infection  (1540)  resulting  in  hospitalization. Nationally  representative  sample  of  US  clinical  settings 2000–2006
Nationwide  Inpatient  Sample  (NIS) Hospitalization  rate Norovirus;  Acute  gastroenteritis  hospitalizations  were  identified  from  discharges  with  one  of  the  first  three  listed  diagnoses  classified  by  ICD-9-CM  diagnostic  codes  001–008  (infectious  gastroenteritis  of  known  cause);  009  (infectious  gastroenteritis);  558.9  (other  and  unspecified  noninfectious  gastroenteritis  and  colitis),  or  787.9  (other  symptoms  involving  digestive  system:  diarrhea);  excluding  008.45  (Clostridium  difficile  colitis)  and  005.1  (botulism) Sample  of  discharge  records  from  US  hospitals 2000–2006

National  Hospital  Discharge  Survey  (NHDS)

Hospitalization  rate Norovirus.  Acute  gastroenteritis  hospitalizations  were  identified  from  discharges  with  one  of  the  first  three  listed  diagnoses  classified  by  ICD-9-M  diagnostic  codes  001–008  (infectious  gastroenteritis  of  known  cause);  009  (infectious  gastroenteritis);  558.9  (other  and  unspecified  noninfectious  gastroenteritis  and  colitis),  or  787.9  (other  symptoms  involving  digestive  system:  diarrhea);  excluding  008.45  (Clostridium  difficile  colitis)  and  005.1  (botulism) Nationally  representative  sample  of  discharge  records  from  US  hospitals  2000–2006

Beginning in 2000, there were 10 FoodNet sites. In 2008, the population of these sites was 46 million persons, 15% of the US population.

Codes for other and unspecified noninfectious gastroenteritis and colitis were included because infectious illnesses of unknown etiology are sometimes coded as noninfectious.

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References

1In the Mead et al. paper, unspecified agents were referred to as unknown agents.

2For 6 of the 31 known pathogens, no routine surveillance data were available so alternative approaches were used to estimate illnesses.

 
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