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In our study, both stool sample groups showed S. ohio and S. typhimurium as the predominant serovars; nevertheless, many other serovars were present in both groups of samples in a considerable proportion (Table 1), which suggest that Salmonella diversity is more in comparison to E. coli, for which ETEC was considerably predominant (Table 1).
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Although the ultimate goal is to recover a fine-scaled, accurate phylogeny of global Salmonella serovar diversity, our efforts are focused on serovar diversity within S. enterica subsp. enterica, a pathogenic lineage that accounts for most of the clinical isolates from human and domestic animals.
By comparison, our knowledge of Salmonella phage genomic diversity has remained rather limited; in big part due to under-sampling.
For Salmonella serotype Newport, diversity of implicated food commodities might be related to intraserotype genetic variation because several distinct clades have been identified (22 ).
While the genomic diversity of Salmonella is increasingly well studied, our knowledge of Salmonella phage genomic diversity is still rather limited, despite the contributions of both lysogenic and lytic phages to Salmonella virulence, diversity and ecology (e.g., through horizontal gene transfer and Salmonella lysis).
While the comparative genomics analyses of these phages provide a number of new insights in the evolution and diversity of Salmonella phages, they only represent a first glimpse into the diversity of Salmonella phages that is likely to be discovered when phages from different environments are characterized.
Regardless of the previously available phage genome sequences, the diversity of Salmonella phages is still severely under-sampled and our knowledge of the genomic diversity of Salmonella phages associated with different environments is very limited.
Comparative genomic approaches provide abundant information to reveal the diversity among Salmonella serogroups.
The bacterium Salmonella enterica includes a diversity of serotypes that cause disease in humans and different animal species.
We thus elected to use phage isolates from dairy farm environments as a model to explore the genomic diversity of Salmonella phages associated with a specific environment.
In order to explore the evolutionary genetic diversity of Salmonella Montevideo, NGS analysis was performed on 47 strains of this serovar (Table 1).
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