Complete Genome Sequences of Salmonella enterica Serovar Heidelberg Strains Associated with a Multistate Food-Borne Illness Investigation

Evans, Peter; Luo, Yan; Muruvanda, Tim; Ayers, Sherry; Hiatt, Brian; Hoffman, M. L.; Zhao, Shaohua; Allard, Marc W.; Brown, Eric W.

doi:10.1128/genomea.01154-13

Cited by 11 publications

(9 citation statements)

References 3 publications

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“…Heidelberg, and S . Cubana, which we analyzed previously [ 11 , 20 – 22 ]. In total, we observed 18 motifs among the nine Salmonella serovars, 16 m6A motifs, one m4C motif, m4 CCWWG G , and one Type I MTase which encodes both m6A and m4C activities, G m6 ATGN 5 G 4m G C ( Fig 1 ; an underscore represents the base which is methylated in the opposite DNA strand; W = A or T).…”

Section: Resultsmentioning

confidence: 99%

“…Here, we sequenced and closed the genomes of six Salmonella enterica isolates from five serovars. We then analysed their methylomes, along with the methylomes of four additional serovars that we sequenced previously [ 11 , 20 – 22 ], and employed a bioinformatics approach to identify methyltransferases and match them to observed methylated motifs in the genomes. We also examined how methylation patterns varied between Salmonella serovars.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars

et al. 2015

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The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. Salmonella is an important foodborne pathogen, and methylation in Salmonella is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven Salmonella enterica isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N6-methyladenine (m6A) methylated motifs, one N4-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases) associated with 13 of the motifs. Some motifs are conserved across all Salmonella serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems), indicating the high diversity of methylation patterns present in Salmonella.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars

et al. 2015

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“…In 2012 alone, Salmonella was implicated in 25% of the 423 outbreaks associated with an infectious agent [ 2 ]. S. enterica serotype Heidelberg ( S. Heidelberg) consistently ranks in the top ten serotypes detected from laboratory-confirmed Salmonella infections [ 2 , 5 – 7 ]. Additionally, S .…”

Section: Introductionmentioning

confidence: 99%

Phenotypic and Genotypic Characterization of Animal-Source Salmonella Heidelberg Isolates

Clothier

Byrne

2016

Journal of Veterinary Medicine

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Salmonella enterica serotype Heidelberg (S. Heidelberg) is frequently implicated in human foodborne Salmonella infections and often produces more severe clinical disease than other serotypes. Livestock and poultry products represent a potential risk for transmission to humans. The purpose of this study was to evaluate 49 S. Heidelberg veterinary isolates for exponential growth rate (EGR), PFGE pattern, and antimicrobial resistance to evaluate these parameters as mechanisms by which S. Heidelberg emerged as a virulent foodborne pathogen. Isolates were categorized by species of origin; clinical or environmental sources; and time frame of recovery. Growth rates were determined in nutrient media using serial dilutions and colony counts; PFGE was performed according to the CDC PulseNet protocol. Minimum inhibitory concentration and susceptibility determinations were performed against antimicrobials important in human medicine. Eighteen unique PFGE patterns were detected in the isolates tested. Antimicrobial resistance was significantly greater (P < 0.05) for ten of 15 drugs in clinical over environmental isolates; for four drugs between the time frames; and for ten drugs between species of origin. The large genetic diversity present in isolates of this serotype may convey competitive advantages to this organism, while the presence of antimicrobial resistance represents a potential zoonotic risk via animal-source food products.

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“…For highly clonal bacteria, such as Salmonella enterica serovar Enteritidis, WGS approaches have been shown to be advantageous since current typing methods (e.g. PFGE) sometimes lack the resolution required for detection of outbreaks, traceback and determination of transmission routes [ 5 – 7 ]. For such organisms, WGS approaches for molecular typing enhance outbreak detection by correctly associating epidemiologically linked isolates to outbreaks, while excluding genetically similar strains that are not associated with the cluster [ 5 , 6 ].…”

Section: Discussionmentioning

confidence: 99%

GeneSippr: A Rapid Whole-Genome Approach for the Identification and Characterization of Foodborne Pathogens such as Priority Shiga Toxigenic Escherichia coli

et al. 2015

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The timely identification and characterization of foodborne bacteria for risk assessment purposes is a key operation in outbreak investigations. Current methods require several days and/or provide low-resolution characterization. Here we describe a whole-genome-sequencing (WGS) approach (GeneSippr) enabling same-day identification of colony isolates recovered from investigative food samples. The identification of colonies of priority Shiga-toxigenic Escherichia coli (STEC) (i.e., serogroups O26, O45, O103, O111, O121, O145 and O157) served as a proof of concept. Genomic DNA was isolated from single colonies and sequencing was conducted on the Illumina MiSeq instrument with raw data sampling from the instrument following 4.5 hrs of sequencing. Modeling experiments indicated that datasets comprised of 21-nt reads representing approximately 4-fold coverage of the genome were sufficient to avoid significant gaps in sequence data. A novel bioinformatic pipeline was used to identify the presence of specific marker genes based on mapping of the short reads to reference sequence libraries, along with the detection of dispersed conserved genomic markers as a quality control metric to assure the validity of the analysis. STEC virulence markers were correctly identified in all isolates tested, and single colonies were identified within 9 hrs. This method has the potential to produce high-resolution characterization of STEC isolates, and whole-genome sequence data generated following the GeneSippr analysis could be used for isolate identification in place of lengthy biochemical characterization and typing methodologies. Significant advantages of this procedure include ease of adaptation to the detection of any gene marker of interest, as well as to the identification of other foodborne pathogens for which genomic markers have been defined.

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Complete Genome Sequences of Salmonella enterica Serovar Heidelberg Strains Associated with a Multistate Food-Borne Illness Investigation

Cited by 11 publications

References 3 publications

Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars

Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars

Phenotypic and Genotypic Characterization of Animal-Source Salmonella Heidelberg Isolates

GeneSippr: A Rapid Whole-Genome Approach for the Identification and Characterization of Foodborne Pathogens such as Priority Shiga Toxigenic Escherichia coli

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