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Title: Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. In this paper, we used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315 S. Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ~1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ~1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ~1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission ofmore » the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonella from pig herds in Denmark from 1996 to 2000. Finally, the results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections.« less
Authors:
 [1] ;  [2] ;  [3] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [9] ;  [2]
  1. Technical Univ. of Denmark, Lyngby (Denmark). National Food Inst.. Research Group for Genomic Epidemiology; Technical Univ. of Denmark, Lyngby (Denmark). Dept. of System Biology. Center for Biological Sequence Analysis
  2. Technical Univ. of Denmark, Lyngby (Denmark). National Food Inst.. Research Group for Genomic Epidemiology
  3. Inst. Pasteur, Paris (France). Centre National de Reference des Salmonella. Unite des Bacteries Pathogenes Enteriques
  4. Technical Univ. of Denmark, Soborg (Denmark). National Food Inst.
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Comparative Genomics Group
  6. Technical Univ. of Denmark, Lyngby (Denmark). Dept. of System Biology. Center for Biological Sequence Analysis; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Comparative Genomics Group
  7. Technical Univ. of Denmark, Lyngby (Denmark). Dept. of System Biology. Center for Biological Sequence Analysis
  8. Univ. of Oxford (United Kingdom). John Radcliffe Hospital. Nuffield Dept. of Medicine
  9. Univ. of Oxford (United Kingdom). John Radcliffe Hospital. Nuffield Dept. of Medicine; Univ. of Oxford (United Kingdom). Wellcome Trust Centre for Human Genetics
Publication Date:
OSTI Identifier:
1185725
Grant/Contract Number:
09-067103/DSF; 101237/Z/13/Z
Type:
Accepted Manuscript
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 82; Journal Issue: 8; Journal ID: ISSN 0099-2240
Publisher:
American Society for Microbiology
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
Center for Genomic Epidemiology (CGE) (Denmark); Wellcome Trust (United Kingdom); The Royal Society (United Kingdom)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES Whole genome sequence typing; SNPs; Salmonella; DT104; evolution