C-EnterNet 2009 Annual Report

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National Integrated Enteric Pathogen Surveillance Program

Table of Contents

• Acknowledgments
• Executive Summary
  • List of Figures
  • List of Tables
• 1. Introduction
• 2. Human Case Summary
  • 2.1 Overview of Human Cases
  • 2.2 Outbreak-related Cases
  • 2.3 Travel-related Cases
  • 2.4 Endemic Cases
• 3. Campylobacter
  • 3.1 Human Cases
  • 3.2 Exposure Surveillance
  • 3.3 Temporal Distribution of Campylobacteriosis
  • 3.4 Summary of Campylobacter Results
• 4. Salmonella
  • 4.1 Human Cases
  • 4.2 Exposure Surveillance
  • 4.3 Advanced Subtype Comparison
  • 4.4 Temporal Distribution
  • 4.5 Summary of Salmonella Results
• 5. Pathogenic E. coli
  • 5.1 Human Cases
  • 5.2 Exposure Surveillance
  • 5.3 Temporal Distribution
  • 5.4 Summary of Pathogenic E. coli Results
• 6. Yersinia
  • 6.1 Human Cases
  • 6.2 Exposure Surveillance
  • 6.3 Summary of Yersinia Results
• 7. Listeria
  • 7.1 Human Cases
  • 7.2 Exposure Surveillance
  • 7.3 Summary of Listeria monocytogenes Results
• 8. Parasites
  • 8.1 Giardia
    • 8.1.1 Exposure Surveillance
  • 8.2 Cryptosporidium
    • 8.2.1 Exposure Surveillance
  • 8.3 Cyclosporiasis
  • 8.4 Amoebiasis
• 9. Shigella
  • 9.1 Human Cases
  • 9.2 Exposure Surveillance
• 10. Viruses
  • 10.1 Human Cases
  • 10.2 Exposure Surveillance
• 11. Temporal Variations
  • 11.1 Temporal Variations in Enteric Disease Incidence
  • 11.2 Temporal Variations in Exposure Source
  • 11.3 Association between temporal variations in human incidence and in contamination of exposure sources
• 12. Source Attribution
• APPENDIX A: Laboratory Testing
• APPENDIX B: Questionnaire Results
• APPENDIX C: Method Changes in 2009
• APPENDIX D: Retail Enumeration Results
• APPENDIX E: Sources Cited

List of Figures

• Figure 2.1: Relative proportion of enteric diseases reported in Sentinel Site 1 in 2009 (all cases)
• Figure 3.1: Incidence rates of endemic campylobacteriosis in Sentinel Site 1 by gender and age group 2009
• Figure 3.2: Temporal distribution of human endemic Campylobacter cases in Sentinel Site 1 reported in 2009 by month of onset
• Figure 3.3: Monthly distribution of Campylobacter jejuni contamination from all sources and incidence of human cases in Sentinel Site 1 in 2009
• Figure 4.1: Incidence rates of endemic salmonellosis cases by gender and age group in Sentinel Site 1 in 2009
• Figure 4.2: Temporal distribution of human endemic salmonellosis cases in Sentinel Site 1 reported in 2009
• Figure 4.3: Temporal distribution of Salmonella detected in human endemic cases, untreated surface water and retail meat samples in Sentinel Site 1 in 2009
• Figure 5.1: Incidence rates of endemic E. coli O157:H7 in Sentinel Site 1 by gender and age group in 2009
• Figure 6.1: Incidence rates of endemic Yersinia infection by gender and age group in Sentinel Site 1 in 2009
• Figure 8.1: Incidence rates of endemic giardiasis cases by gender and age group in Sentinel Site 1 in 2009
• Figure 8.2: Monthly distribution of Giardia cases and detection in untreated surface water sampled in Sentinel Site 1 in 2009
• Figure 8.3: Incidence rates of endemic cryptosporidiosis cases by gender and age group in Sentinel Site 1 in 2009
• Figure 8.4: Monthly distribution of Cryptosporidium cases and detection in untreated surface water sampled in Sentinel Site 1 in 2009
• Figure 8.5: Incidence rates of endemic amoebiasis cases by gender and age group in Sentinel Site 1 in 2009
• Figure 11.1: Monthly counts (based on onset dates) of sporadic, non travel-related cases reported in Sentinel Site 1 from June 2005 to December 2009 for selected enteric diseases and the smoothed predicted counts according to a fitted negative binomial regression model
• Figure 11.2: Changes in annual incidence rates of sporadic, non travel-related cases of reportable enteric diseases over the years relative to the first full year of enhanced surveillance implementation in Sentinel Site 1 (2006)
• Figure 11.3: Changes (with 95% confidence interval) in annual incidence rates between the year 2009 and the first 3 full years of the enhanced surveillance implementation in Sentinel Site 1 (2006-2008, inclusive) for sporadic, non travel-related cases of reportable enteric diseases
• Figure 11.4: Changes (with 95% confidence interval) in annual incidence rates between the year 2009 and the first 3 full years of the enhanced surveillance implementation in Sentinel Site 1 (2006-2008, inclusive) for sporadic, non travel-related cases of reportable enteric diseases
• Figure 11.5: Annual variations in pathogens detected from manure samples in Sentinel Site 1, 2006-2009
• Figure 11.6: Proportion by year (with 95% confidence interval) of positive untreated surface water samples tested by culture method for selected enteric pathogens in Sentinel Site 1 between June 2005 and December 2009
• Figure 11.7: Proportion by quarter (with 95% confidence interval) of positive untreated surface water samples tested for selected enteric pathogens by culture method in Sentinel Site 1 between Summer 2005 and Fall 2009  (winter: December to February; spring: March to May; summer: June to August; fall: September to November)
• Figure 11.8: Proportion by year (with 95% confidence interval) of retail meat positive for selected enteric pathogens in Sentinel Site 1, June 2005 to December 2009
• Figure 11.9: Proportion by quarter (with 95% confidence interval) of retail meats positive for selected enteric pathogens in Sentinel Site 1 between June 2005 and November 2008 (winter: December to February; spring: March to May; summer: June to August; fall: September to November)
• Figure 11.10: Comparative evolution of the temporal changes over time in the human incidence and some selected exposure source contamination for Campylobacter and for Salmonella

List of Tables

• Table 2.1: Number of cases and incidence rates per 100,000 person-years of laboratory-confirmed enteric diseases in Sentinel Site 1 in 2009
• Table 2.2: Site of isolation of pathogens detected in laboratory-confirmed cases reported in Sentinel Site 1 in 2009 (including outbreak, international travel-related and endemic)
• Table 2.3: Travel-related cases in Sentinel Site 1 in 2009
• Table 3.1: Campylobacter detection and speciation data (culture-based methods) from integrated surveillance activities in Sentinel Site 1 in 2009
• Table 4.1: Salmonella detection and serotyping data (culture-based methods) from the integrated surveillance activities in Sentinel Site 1 in 2009
• Table 4.2: Integrated comparison of Salmonella Typhimurium phage types for 2009 in Sentinel Site 1 (2005-2008 results in brackets)
• Table 4.3: Integrated comparison of Salmonella Enteritidis phage types for 2009 in Sentinel Site 1 (2005-2008 results in brackets)
• Table 4.4: Integrated comparison of Salmonella Heidelberg phage types for 2009 in Sentinel Site 1 (2005-2008 results in brackets)
• Table 4.5: Integrated comparison of Salmonella Heidelberg PFGE patterns for 2009 in Sentinel Site 1(2005-2008 results in brackets)
• Table 5.1: Verotoxigenic E. coli detection data from the integrated surveillance activities in Sentinel Site 1 in 2009
• Table 5.2: PFGE results for E. coli O157:H7 for all components, including human travel-related cases in Sentinel Site 1 in 2009 (values in brackets refer to results from 2005-2008 for comparison)
• Table 6.1: Yersinia detection and speciation data from the integrated surveillance activities in Sentinel Site 1 in 2009
• Table 7.1: Listeria monocytogenes detection data from the integrated surveillance activities in Sentinel Site 1 in 2009
• Table 7.2: Listeria monocytogenes serotype data from the integrated surveillance activities in Sentinel Site 1 in 2009 (values in brackets refer to 2005-2008 data for comparisons)
• Table 7.3: Listeria monocytogenes PFGE data from the integrated surveillance activities in Sentinel Site 1 in 2009 (values in brackets refer to 2005-2008 data for comparison)
• Table 8.1: Giardia detection and sub-typing data for the integrated surveillance activities in Sentinel Site 1 in 2009 (values in brackets refer to data from 2005-2008)
• Table 8.2: Cryptosporidium detection and sub-typing data for the integrated surveillance activities in Sentinel Site 1 in 2009 (values in brackets refer to data from 2005-2008)
• Table 8.3: Cyclospora detection and sub-typing data for retail sampling in Sentinel Site 1 in 2009
• Table 9.1: Shigella detection in human cases and on retail food (bagged leafy greens) in Sentinel Site 1 in 2009
• Table 10.1: Norovirus detection on retail food (bagged leafy greens) in Sentinel Site 1 in 2009
• Table 10.2: Rotavirus detection on retail food (bagged leafy greens) in Sentinel Site 1 in 2009
• Table 12.1: C-EnterNet plan and achievements with regards to Source Attribution in 2009

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