Is the Evolution of Salmonella enterica subsp.<i>enterica</i>Linked to Restriction-Modification Systems?

Roer, Louise; Hendriksen, René S.; Leekitcharoenphon, Pimlapas; Lukjancenko, Oksana; Kaas, Rolf Sommer; Hasman, Henrik; Aarestrup, Frank Møller

doi:10.1128/msystems.00009-16

Cited by 102 publications

(97 citation statements)

References 63 publications

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“…It was previously found that for many bacteria, including some of the studied species, the pangenome is not closed, meaning that with the sequencing of additional strains new pangenes will be added to the pangenome (Rasko et al, 2008 ; Gordienko et al, 2013 ; Holt et al, 2015 ; Rouli et al, 2015 ; Maiden and Harrison, 2016 ; Roer et al, 2016 ). Thus, despite the high number of strains analyzed in each species, it is still possible that we do not capture the whole diversity of the “rare” pangenome in these species and underestimate the amount of shared “rare” pangenes.…”

Section: Resultsmentioning

confidence: 99%

Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species

Bolotin

Hershberg

2017

Front. Microbiol.

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Horizontal gene transfer (HGT) serves as an important source of innovation for bacterial species. We used a pangenome-based approach to identify genes that were horizontally acquired by four closely related bacterial species, belonging to the Enterobacteriaceae family. This enabled us to examine the extent to which such closely related species tend to share horizontally acquired genes. We find that a high percent of horizontally acquired genes are shared among these closely related species. Furthermore, we demonstrate that the extent of sharing of horizontally acquired genes among these four closely related species is predictive of the extent to which these genes will be found in additional bacterial species. Finally, we show that acquired genes shared by more species tend to be better optimized for expression within the genomes of their new hosts. Combined, our results demonstrate the existence of a large pool of frequently horizontally acquired genes that have distinct characteristics from horizontally acquired genes that are less frequently shared between species.

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Section: Resultsmentioning

confidence: 99%

Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species

Bolotin

Hershberg

2017

Front. Microbiol.

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“…The virulence analysis identified 14 Salmonella Pathogenicity Islands. The identified SPIs were typical for S. Gallinarum and few in numbers (1-14 SPI, [29]).…”

Section: Discussionmentioning

confidence: 96%

Complete genome and plasmid sequences of a multidrug-resistant Salmonella enterica subsp. enterica serovar Panama isolate from a German cattle farm

2020

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We describe a rare isolate of Salmonella enterica subsp. enterica serovar Panama with an extended-spectrum β-lactamase (ESBL) profile from a German cattle-fattening farm. Applying two next-generation sequencing methods we generated sequences of the genome as well as the plasmids; assembled the draft genome sequence of Salmonella enterica subsp. enterica serovar Panama isolate 18PM0209. Antimicrobial resistance genes, virulence-associated genes and plasmids were analyzed using bioinformatics. Occurrence of multidrug-resistant Salmonella serovars at cattle-fattening farms indicate the need of enhanced surveillance to prevent further spread of these organisms.

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“…Antibiotic resistance (ABR) determinants in genomes were predicted using ResFinder (90% threshold for identity and 60% for minimum length) ( Zankari et al, 2012 ) to identify acquired ABR genes and PointFinder (90% threshold for identity and 60% for minimum length) ( Zankari et al, 2017 ) to identify point mutations conferring ABR. The representative subset of the isolates ( n = 31) was also examined for virulence factors using VirulenceFinder ( Joensen et al, 2014 ) and VFDB VFanalyzer ( Liu et al, 2018 ) and Salmonella Pathogenicity Islands (SPIs) using SPIFinder (v1.0; 95% threshold for identity and 60% for minimum length) ( Roer et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Genomic characterization and phylogenetic analysis ofSalmonella entericaserovar Javiana

Hudson

Constantine-Renna

Thomas

et al. 2020

PeerJ

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Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.

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Is the Evolution of Salmonella enterica subsp.entericaLinked to Restriction-Modification Systems?

Cited by 102 publications

References 63 publications

Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species

Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species

Complete genome and plasmid sequences of a multidrug-resistant Salmonella enterica subsp. enterica serovar Panama isolate from a German cattle farm

Genomic characterization and phylogenetic analysis ofSalmonella entericaserovar Javiana

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