Evaluating Completeness of Foodborne Outbreak Reporting in the United States, 1998–2019
Abstract
:1. Introduction
2. Methods
2.1. Data Source
2.2. Data Preparation
- 26 variables generated by CDC personnel to track the reporting of electronic records (e.g., data recorder ID, local report date, CDC report date, etc.);
- 12 variables providing reporter contact information and optional comments written during reporting (e.g., recall comments, agency title, reporting site, etc.);
- 9 variables providing clarification responses to specific questions asked only for specific outbreaks (e.g., clarification of supply chain stage of contamination, questions regarding antimicrobial resistance testing, etc.); and
- 17 variables unavailable for the entire study period duration (e.g., illness attack rate, percentage of illnesses by age group, food contaminant infecting exposed persons, age percentage, etc.).
2.3. Crude Completeness Estimation
2.4. Measuring Temporal Changes in Completeness
2.5. Temporal Trend Analyses
3. Results
3.1. Outbreak Frequency and Completeness by Pathogen
3.2. Annual Completeness
3.3. Segemented and Seasonality Trend Analyses
4. Discussion
- Create a Standard Operating Procedure (SOP) to identify must-have variables, variables that are related to one another, and less-relevant variables. This SOP can assist in the streamlining of data cleaning procedures to identify true missingness, zero values, and information that is not applicable for an outbreak. Moreover, SOP can be used as a guideline to create NORS checkpoints to avoid missing information between related variables.
- Consider removing variables with consistently low completeness or conduct thorough investigation into the obstacles preventing adequate reporting these variables.
- Publicly report documentation explaining reasons for incomplete data; NORS has a rigorous data cleaning process that includes 30+ checkpoints for foodborne outbreaks. Outbreak data are reported as missing until all issues are solved [52]. Although incomplete outbreak reports cannot provide all information, these checkpoints and their completion may still be useful for researchers to study.
- In accordance with the Population Health Surveillance Theory, perform periodic system audits to evaluate data reporting procedure and data quality at the local level [53]. In addition, these periodic system audits can be used as an assessment to evaluate both workforce resource and laboratory testing capacities. For any local agency with low audit scores, the CDC can provide training materials, or relocate necessary recourses.
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Contaminant Name | Number of Outbreaks | Crude Completeness | Completeness Category | |||||
---|---|---|---|---|---|---|---|---|
per Outbreak | per Variable | 1 | 2 | 3 | 4 | 5 | ||
All Outbreaks | 22,792 | 59.45 | 53.65 | 98.45 | 81.00 | 52.48 | 29.01 | 14.46 |
Multiple Etiologies | 779 | 64.54 | 60.19 | 98.61 | 87.72 | 60.09 | 34.91 | 25.56 |
Unknown Etiologies | 7401 | 51.22 | 46.06 | 96.42 | 75.19 | 40.60 | 18.46 | 7.60 |
Bacterial Pathogens | ||||||||
Salmonella | 2872 | 58.94 | 53.90 | 97.16 | 77.20 | 52.12 | 27.08 | 22.41 |
Clostridium | 944 | 62.37 | 56.90 | 98.83 | 85.91 | 59.62 | 32.99 | 13.91 |
Escherichia | 649 | 58.69 | 56.18 | 97.69 | 75.28 | 51.29 | 30.69 | 32.07 |
Staphylococcus | 625 | 56.02 | 49.69 | 98.84 | 78.39 | 48.04 | 21.57 | 9.29 |
Campylobacter | 510 | 62.93 | 58.76 | 98.25 | 83.53 | 60.44 | 39.52 | 18.61 |
Bacillus | 376 | 59.69 | 53.95 | 98.30 | 82.50 | 55.27 | 31.13 | 9.84 |
Vibrio | 220 | 67.38 | 66.18 | 98.09 | 84.57 | 64.32 | 44.25 | 27.67 |
Shigella | 195 | 53.61 | 48.23 | 97.08 | 74.77 | 46.32 | 18.78 | 7.92 |
Listeria | 95 | 57.63 | 52.45 | 97.49 | 68.12 | 44.18 | 34.81 | 17.79 |
Yersinia | 17 | 50.83 | 49.33 | 97.15 | 69.75 | 38.69 | 17.23 | 10.11 |
Brucella | 6 | 61.39 | 59.13 | 99.07 | 78.57 | 63.96 | 32.14 | 6.25 |
Streptococcus | 5 | 65.87 | 65.90 | 100.00 | 79.05 | 69.25 | 45.71 | 23.75 |
Enterococcus | 1 | 74.42 | 73.03 | 100.00 | 100.00 | 85.00 | 57.14 | 6.25 |
Other—Bacterium | 138 | 57.87 | 54.66 | 98.00 | 88.34 | 51.53 | 27.83 | 10.55 |
Subtotal | 6653 | 59.55 | 54.59 | 97.81 | 79.40 | 53.59 | 29.31 | 19.54 |
Viral Pathogens | ||||||||
Norovirus | 6416 | 60.36 | 54.54 | 98.52 | 85.03 | 56.77 | 25.19 | 13.90 |
Hepatitis | 103 | 47.08 | 44.13 | 96.55 | 62.23 | 34.07 | 19.73 | 8.00 |
Rotavirus | 15 | 55.54 | 52.22 | 97.01 | 76.83 | 48.11 | 23.67 | 13.33 |
Sapovirus | 15 | 73.41 | 66.79 | 96.30 | 91.75 | 67.84 | 33.33 | 42.75 |
Astrovirus | 2 | 58.43 | 57.02 | 100.00 | 88.10 | 51.25 | 17.86 | 9.38 |
Other—Virus | 102 | 45.59 | 38.64 | 97.26 | 67.65 | 29.86 | 2.84 | 0.88 |
Subtotal | 6653 | 59.95 | 54.11 | 98.46 | 84.41 | 56.01 | 24.77 | 13.68 |
Parasitic Pathogens | ||||||||
Cyclospora | 112 | 70.58 | 72.49 | 98.54 | 85.63 | 67.79 | 62.10 | 46.95 |
Cryptosporidium | 32 | 61.59 | 60.36 | 96.30 | 78.13 | 59.90 | 32.59 | 21.48 |
Trichinella | 23 | 62.58 | 61.01 | 97.54 | 84.89 | 55.04 | 41.30 | 13.32 |
Giardia | 22 | 53.63 | 48.42 | 98.94 | 71.65 | 45.70 | 13.86 | 10.43 |
Toxoplasma | 3 | 85.37 | 85.86 | 100.00 | 100.00 | 88.75 | 76.19 | 56.25 |
Anisakis | 1 | 44.57 | 43.07 | 100.00 | 57.14 | 36.67 | 7.14 | 0.00 |
Other—Parasite | 2 | 41.96 | 38.86 | 100.00 | 52.38 | 27.92 | 0.00 | 0.00 |
Subtotal | 195 | 66.05 | 64.10 | 98.15 | 82.47 | 61.69 | 43.00 | 33.32 |
Chemicals and Toxins | ||||||||
Scombroid toxin/ Histamine | 505 | 58.51 | 55.08 | 98.31 | 83.88 | 48.66 | 29.48 | 12.13 |
Ciguatoxin | 349 | 61.97 | 59.12 | 98.74 | 84.84 | 49.61 | 41.98 | 13.39 |
Mycotoxins | 35 | 62.78 | 57.25 | 98.24 | 88.03 | 58.27 | 26.57 | 10.59 |
Paralytic shellfish poison | 17 | 56.43 | 54.45 | 94.77 | 80.95 | 44.94 | 25.63 | 11.40 |
Heavy metals | 9 | 51.10 | 44.35 | 100.00 | 79.37 | 35.94 | 4.44 | 0.00 |
Cleaning agents | 8 | 57.72 | 55.35 | 100.00 | 70.24 | 54.43 | 33.93 | 5.47 |
Neurotoxic shellfish poison | 7 | 57.44 | 54.86 | 100.00 | 82.31 | 46.99 | 17.35 | 10.71 |
Pesticides | 4 | 64.24 | 63.20 | 100.00 | 95.24 | 70.00 | 28.57 | 1.56 |
Puffer fish tetrodotoxin | 3 | 62.65 | 60.54 | 99.79 | 92.06 | 57.92 | 33.33 | 2.08 |
Amnesic shellfish poison | 1 | 66.57 | 64.33 | 100.00 | 95.24 | 51.25 | 57.14 | 6.25 |
Monosodium glutamate (MSG) | 1 | 57.36 | 55.43 | 100.00 | 95.24 | 56.67 | 0.00 | 0.00 |
Other—Chemical/Toxin | 172 | 56.37 | 50.73 | 98.65 | 83.19 | 47.95 | 23.76 | 7.83 |
Subtotal | 1111 | 59.34 | 53.09 | 98.49 | 84.10 | 48.81 | 30.38 | 11.26 |
Yearly % Change (eFORS) | Monthly Outbreaks Jan’09 | Yearly % Change (NORS) | |||||||
---|---|---|---|---|---|---|---|---|---|
Group | Estimate | LCI | UCI | Estimate | LCI | UCI | Estimate | LCI | UCI |
All pathogens | −0.048 ** | −0.060 | −0.036 | 75.25 | 71.27 | 79.45 | −0.0024 | −0.012 | 0.012 |
Norovirus | 0.048 ** | 0.024 | 0.060 | 30.01 | 26.47 | 34.01 | −0.036 ** | −0.06 | −0.012 |
Salmonella | −0.012 | −0.036 | 0.000 | 9.96 | 8.82 | 11.24 | 0.012 | 0.000 | 0.036 |
Clostridium | −0.048 ** | −0.072 | −0.024 | 3.18 | 2.76 | 3.64 | −0.0036 | −0.024 | 0.024 |
Unknown Etiology | −0.096 ** | −0.108 | −0.084 | 21.92 | 20.36 | 23.61 | −0.036 ** | −0.048 | −0.024 |
Multiple Etiology † | −0.048 ** | −0.072 | −0.012 | 2.47 | 2.07 | 2.95 | 0.072 ** | 0.036 | 0.096 |
Category | Estimated % Completeness at the Point of System Changing | Estimated Effect Associated with Outbreak Counts | Estimated % Completeness Change in eFORS Time | Estimated % Completeness Change in NORS Time | ||||
---|---|---|---|---|---|---|---|---|
Estimate | Std. Error | Estimate | Std. Error | Estimate | Std.Error | Estimate | Std. Error | |
All Pathogens | ||||||||
1 | 97.943 ** | 0.161 | −0.017 * | 0.005 | −0.002 | 0.002 | 0.001 | 0.002 |
2 | 87.826 ** | 0.489 | −0.080 ** | 0.016 | 0.160 ** | 0.006 | 0.036 ** | 0.006 |
3 | 67.491 ** | 0.531 | −0.228 ** | 0.017 | 0.304 ** | 0.007 | 0.078 ** | 0.007 |
4 | 26.317 ** | 0.781 | −0.142 ** | 0.026 | 0.197 ** | 0.01 | 0.328 ** | 0.01 |
5 | 5.459 ** | 0.499 | −0.038 | 0.016 | 0.031 ** | 0.006 | 0.396 ** | 0.006 |
Norovirus | ||||||||
1 | 97.913 ** | 0.276 | 0.033 ** | 0.007 | 0.005 | 0.003 | −0.009 ** | 0.003 |
2 | 87.420 ** | 1.13 | 0.052 | 0.029 | 0.155 ** | 0.011 | 0.025 * | 0.011 |
3 | 67.965 ** | 1.098 | −0.058 * | 0.028 | 0.339 ** | 0.011 | 0.072 ** | 0.011 |
4 | 22.537 ** | 1.9 | 0.039 | 0.049 | 0.219 ** | 0.019 | 0.273 ** | 0.019 |
5 | 3.493 * | 1.114 | 0.028 | 0.029 | 0.034 * | 0.011 | 0.383 ** | 0.011 |
Salmonella | ||||||||
1 | 97.946 ** | 0.388 | −0.035 | 0.027 | 0.003 | 0.004 | −0.007 | 0.004 |
2 | 80.611 ** | 1.229 | −0.014 | 0.084 | 0.138 ** | 0.013 | 0.045 ** | 0.013 |
3 | 61.927 ** | 1.263 | −0.139 | 0.086 | 0.254 ** | 0.014 | 0.068 ** | 0.014 |
4 | 21.740 ** | 1.609 | −0.188 | 0.11 | 0.150 ** | 0.017 | 0.331 ** | 0.018 |
5 | 9.286 ** | 1.253 | −0.071 | 0.086 | 0.021 | 0.014 | 0.432 ** | 0.014 |
Clostridium | ||||||||
1 | 97.777 ** | 0.537 | 0.231 * | 0.111 | 0.002 | 0.006 | 0.001 | 0.006 |
2 | 95.423 ** | 1.413 | −0.245 | 0.292 | 0.190 ** | 0.017 | −0.011 | 0.016 |
3 | 73.487 ** | 1.536 | 0.057 | 0.317 | 0.347 ** | 0.018 | 0.066 ** | 0.017 |
4 | 31.267 ** | 2.325 | −0.584 | 0.48 | 0.212 ** | 0.027 | 0.417 ** | 0.026 |
5 | 0.335 | 1.465 | 0.479 | 0.303 | 0.028 | 0.017 | 0.445 ** | 0.016 |
Unknown Etiology | ||||||||
1 | 96.679 ** | 0.45 | −0.092 ** | 0.017 | −0.048 ** | 0.006 | 0.029 ** | 0.005 |
2 | 85.505 ** | 0.919 | −0.088 * | 0.034 | 0.160 ** | 0.013 | 0.068 ** | 0.009 |
3 | 55.788 ** | 1.119 | 0.076 | 0.042 | 0.368 ** | 0.016 | 0.085 ** | 0.011 |
4 | 18.537 ** | 1.82 | 0.12 | 0.068 | 0.225 ** | 0.026 | 0.249 ** | 0.018 |
5 | 3.826 ** | 0.914 | 0.044 | 0.034 | 0.060 ** | 0.013 | 0.297 ** | 0.009 |
Multiple Etiology | ||||||||
1 | 97.870 ** | 0.501 | 0.270 * | 0.101 | 0.002 | 0.007 | −0.012 | 0.006 |
2 | 88.028 ** | 1.940 | 1.189 * | 0.391 | 0.138 ** | 0.026 | −0.041 | 0.025 |
3 | 71.680 ** | 1.775 | −0.580 | 0.358 | 0.335 ** | 0.024 | 0.049 * | 0.023 |
4 | 22.670 ** | 2.225 | −0.776 | 0.448 | 0.168 ** | 0.030 | 0.380 ** | 0.028 |
5 | 1.809 | 1.459 | 0.222 | 0.294 | 0.022 | 0.020 | 0.496 ** | 0.019 |
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Zhang, Y.; Simpson, R.B.; Sallade, L.E.; Sanchez, E.; Monahan, K.M.; Naumova, E.N. Evaluating Completeness of Foodborne Outbreak Reporting in the United States, 1998–2019. Int. J. Environ. Res. Public Health 2022, 19, 2898. https://doi.org/10.3390/ijerph19052898
Zhang Y, Simpson RB, Sallade LE, Sanchez E, Monahan KM, Naumova EN. Evaluating Completeness of Foodborne Outbreak Reporting in the United States, 1998–2019. International Journal of Environmental Research and Public Health. 2022; 19(5):2898. https://doi.org/10.3390/ijerph19052898
Chicago/Turabian StyleZhang, Yutong, Ryan B. Simpson, Lauren E. Sallade, Emily Sanchez, Kyle M. Monahan, and Elena N. Naumova. 2022. "Evaluating Completeness of Foodborne Outbreak Reporting in the United States, 1998–2019" International Journal of Environmental Research and Public Health 19, no. 5: 2898. https://doi.org/10.3390/ijerph19052898