Campylobacter jejuni Attribution with Multilocus Sequence Typing (MLST) and the Asymmetric Island Model Public

Abstract

Campylobacter is one of the leading causes of gastroenteritis in the United States, with C. jejuni accounting for 90% of those infections. C. jejuni is a widespread bacterial pathogen that is found in food, animal, and environmental sources. Using iSource software and MLST data, we can estimate the proportion and distribution of human isolates attributed to non-human sources. This was a retrospective study using 2,040 non-human C. jejuni isolates in North America from PubMLST and 789 human isolates from ten Foodborne Diseases Active Surveillance Network sites. We used seven constitutive genes for MLST schemes and linked them to isolate records to attribute human cases to our five categorized sources: poultry, meat, dairy environmental/animal contact, and water. The largest average proportion of human cases was attributed to poultry, accounting for 70% (95% confidence interval [CI]: 65-75%) while water had the smallest proportion (3%; 95% CI: 0–6%). The most likely order of the non-human sources that explained the most to the least number of human cases was: poultry, dairy, meat, environmental/animal contact, and water. Among the 228 isolates in our dairy source, 215 (94%) had a known pasteurization status, and all of these were raw or unpasteurized milk products from cows (215/228). Our work helps our understanding of the food and non-food sources of Campylobacter in North America using the genetic information of food, animal, and environmental isolates. Future attribution using just genetic information could help us refine the tools to link genetic human isolates to genetic source isolates via modeling techniques.

Table of Contents

BACKGROUND......................................................................................................... 1

METHODS.................................................................................................................. 2

Study Design.................................................................................................... 2

            Measures.......................................................................................................... 2

            Models and Analysis........................................................................................ 4

RESULTS..................................................................................................................... 5

DISCUSSION.............................................................................................................. 6

            Limitations..................................................................................................... 11

            Conclusions.................................................................................................... 13

REFERENCES........................................................................................................... 14

TABLES..................................................................................................................... 16

            Table 1: Distribution of source isolates in each category, before model attribution........................................................................................................ 16

            Table 2: Summaries of the posterior distribution of each source................... 17

            Table 3a: The most likely order of sources responsible for the most, second most, third most, etc. number of cases....................................................................... 18

            Table 3b: Probability that each source is responsible for the most, second most, third most, etc. number of cases....................................................................... 19

            Table 4: Most probable orderings and their posterior probabilities............... 20

FIGURES................................................................................................................... 21

            Figure 1: Histograms of the proportion of isolates attributable to animal, food and environmental sources......................................................................................... 21

            Figure 2: Trace plots of the proportion of isolates attributable to animal, food and environmental five sources demonstrating model convergence.......................... 22

            Figure 3: Estimated proportion of human cases attributable to animal, food and environmental sources................................................................................................ 23

            Figure 4: Probability of source for human cases............................................ 24

            Figure 5: Plots of migration and mutation probabilities in animal, food, and environmental samples, tracing evolutionary parameters using MCMC................... 25

            Figure 6: Graph of migration and mutation probabilities in animal, food, and environmental samples, tracing evolutionary parameters using MCMC........ 26

About this Master's Thesis

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School	Rollins School of Public Health
Department	Epidemiology
Subfield / Discipline	Epidemiology - MPH & MSPH
Degree	M.P.H.
Submission	Master's Thesis
Language	English
Research Field	Health Sciences, Epidemiology
Mot-clé	poultry model isolate food borne disease Campylobacter
Committee Chair / Thesis Advisor	Jenness, Samuel, Emory University
Committee Members	Bruce, Beau, CDC
Partnering Agencies	CDC

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