A Permutation Test of Genetic Association between Salmonella Isolated On-farm and At-abattoir using Amplified Fragment Length Polymorphism

Date
2014-01-01
Authors
Du, Yingzhou
Wang, Chong
Liu, Peng
Journal Title
Journal ISSN
Volume Title
Publisher
Altmetrics
Authors
Wang, Chong
Person
Research Projects
Organizational Units
Journal Issue
Series
Abstract

Pork and pork products have been identified as a significant source of Salmonella infection, which is a major public health concern. The contamination of Salmonella on pork can happen both on farms (before slaughter) and at abattoirs (after slaughter). Salmonella isolates were collected from both feces on farms and lymph nodes in the abattoir to determine if contamination at abattoirs can be linked back to the farms of origin. Molecular subtyping of the isolated Salmonella was performed using amplified fragment length polymorphism (AFLP), a Polymerase chain reaction-based, high-throughput, relatively inexpensive method. In this paper, we develop a permutation test for the genetic association of Salmonella isolated on-farm and at-abattoir using the AFLP data. Simulation studies show that the proposed permutation test controls the type I error rate appropriately as well as possesses high power. An application of the proposed permutation test to the real Salmonella ALFP data results in a p-value of 0.038 which shows strong evidence of association between Salmonella isolated on-farm and at-abattoir.

Description

This article is from Biometrics & Biostatistics 5 (2014); 204, doi: 10.472/2155-6180.1000204. Posted with permission.

Keywords
ALFP, Genetic association, Permutation test, Salmonella
Citation
DOI
Collections