Genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s

Jean Guard,Guojie Cao,Yan Luo,Joseph D Baugher,Sherrill Davison,Kuan Yao,Maria Hoffmann,Guodong Zhang,Nathan Likens,Rebecca L Bell,Jie Zheng,Eric Brown,Marc Allard

doi:10.1016/j.ygeno.2019.04.005

Abstract

A total of 91 draft genome sequences were used to analyze isolates of Salmonella enterica serovar Enteritidis obtained from feral mice caught on poultry farms in Pennsylvania. One objective was to find mutations disrupting open reading frames (ORFs) and another was to determine if ORF-disruptive mutations were present in isolates obtained from other sources. A total of 83 mice were obtained between 1995–1998. Isolates separated into two genomic clades and 12 subgroups due to 742 mutations. Nineteen ORF-disruptive mutations were found, and in addition, bigA had exceptional heterogeneity requiring additional evaluation. The TRAMS algorithm detected only 6 ORF disruptions. The sefD mutation was the most frequently encountered mutation and it was prevalent in human, poultry, environmental and mouse isolates. These results confirm previous assessments of the mouse as a rich source of Salmonella enterica serovar Enteritidis that varies in genotype and phenotype.

Highlights

Salmonella enterica serovar Enteritidis (SE) is a long-standing public health concern in the US (1); salmonellosis can result in hospitalization or death of infants, the elderly, and those with compromised immune systems (2, 3)
Understanding the evolutionary relationships among SE isolates from mice, poultry, environmental surfaces, and clinical cases is important both for outbreak investigations and for identifying strains with genetic markers for virulence or capacity for rapid host adaptation, such as mutations in the mismatch repair gene mutS that can contribute to rapid evolution in immunocompromised hosts (11)
CFSAN051866_spleen_1996_FarmVII_SCA, which provides the following details: this bacterium was isolated from a mouse spleen in 1996, that mouse came from Farm VII, and the isolate fits within single nucleotide polymorphisms (SNPs) Cluster A (28), which was designated according to the NCBI Pathogen Detection Isolates Browser

Summary

Introduction

Salmonella enterica serovar Enteritidis (SE) is a long-standing public health concern in the US (1); salmonellosis can result in hospitalization or death of infants, the elderly, and those with compromised immune systems (2, 3). This pathogen has been strongly associated with poultry farms, eggs, and egg products (4, 5). Mice are important biological vehicles contributing to SE dissemination and amplification in chicken houses, especially among laying hens (8, 9). Understanding the evolutionary relationships among SE isolates from mice, poultry, environmental surfaces, and clinical cases is important both for outbreak investigations and for identifying strains with genetic markers for virulence or capacity for rapid host adaptation, such as mutations in the mismatch repair gene mutS that can contribute to rapid evolution in immunocompromised hosts (11)

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Conclusion