Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

Frontiers in Microbiology
Walid MottaweaDele Ogunremi

Abstract

Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR) of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific s...Continue Reading

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Citations

Feb 6, 2020·Microbial Genomics·Siân V OwenJay C D Hinton
Jun 25, 2019·Frontiers in Cellular and Infection Microbiology·Leyla MinnullinaAyslu Mardanova
Sep 21, 2018·Frontiers in Microbiology·Louis-Charles Fortier
Jun 14, 2019·Frontiers in Microbiology·Junrong LiangXin Wang
Nov 24, 2019·Theoretical Population Biology·Amjad Khan, Lindi M Wahl

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Datasets Mentioned

BETA
MG1655

Methods Mentioned

BETA
electrophoresis

Software Mentioned

iTOL
Galaxy
PHAST
Multiple Alignment using Fast Fourier Transform ( MAFFT )
ANOSIM
BLASTX
Quantitative Insights Into Microbial Ecology ( QIIME )
Multiple Alignment using Fast Fourier Transform ( MAFFT
PHAge Search Tool Enhanced ( PHASTER
PHASTER

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