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Sunday, July 7, 2019

Whole-genome comparative analysis of Salmonella enterica serovar Newport strains reveals lineage-specific divergence.

Salmonella enterica subsp. enterica serovar Newport has been associated with various foodborne outbreaks in humans and animals. Phylogenetically, serovar Newport is one of several Salmonella serovars that are polyphyletic. To understand more about the polyphyletic nature of this serovar, six food, environment, and human isolates from different Newport lineages were selected for genome comparison analyses. Whole genome comparisons demonstrated that heterogeneity mostly occurred in the prophage regions. Lineage-specific characteristics were also present in the Salmonella pathogenicity islands and fimbrial operons. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written…

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Sunday, July 7, 2019

Complete genome sequences of three Salmonella enterica subsp. enterica serovar Saintpaul isolates associated with a 2013 multistate outbreak in the United States.

In 2013, a multistate outbreak of Salmonella enterica subsp. enterica serovar Saintpaul from cucumber caused 84 cases of salmonellosis in the United States. In this announcement, we report the complete genome sequences of three clinical Salmonella Saintpaul isolates associated with the 2013 outbreak. Copyright © 2017 Yao et al.

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Sunday, July 7, 2019

Comparative sequence analysis of multidrug-resistant IncA/C plasmids from Salmonella enterica

Determinants of multidrug resistance (MDR) are often encoded on mobile elements, such as plasmids, transposons, and integrons, which have the potential to transfer among foodborne pathogens, as well as to other virulent pathogens, increasing the threats these traits pose to human and veterinary health. Our understanding of MDR among Salmonella has been limited by the lack of closed plasmid genomes for comparisons across resistance phenotypes, due to difficulties in effectively separating the DNA of these high-molecular weight, low-copy-number plasmids from chromosomal DNA. To resolve this problem, we demonstrate an efficient protocol for isolating, sequencing and closing IncA/C plasmids from Salmonella…

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Sunday, July 7, 2019

IS26-mediated formation of a virulence and resistance plasmid in Salmonella Enteritidis.

To characterize a novel virulence-resistance plasmid pSE380T carried by a Salmonella enterica serotype Enteritidis clinical strain SE380.The plasmid pSE380T was conjugated to Escherichia coli strain J53 and sequenced by PacBio RSII, followed by subsequent annotation and genetic analysis.Sequence analysis of this plasmid revealed that the entire Salmonella Enteritidis-specific virulence plasmid, pSEN, had been incorporated into an IncHI2 MDR plasmid, which comprises the cephalosporin and fosfomycin resistance determinants blaCTX-M-14 and fosA3. Based on BLAST analysis and scrutiny of insertion footprints, the insertion event was found to involve a replicative transposition process mediated by IS26, an IS element frequently detected in various…

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Sunday, July 7, 2019

Genome sequence of an Australian monophasic Salmonella enterica subsp. enterica Typhimurium isolate (TW-Stm6) carrying a large plasmid with multiple antimicrobial resistance genes.

We report the genome sequence of a monophasic Salmonella enterica subsp. enterica Typhimurium strain (TW-Stm6) isolated in Australia that is similar to epidemic multidrug-resistant strains from Europe and elsewhere. This strain carries additional antibiotic and heavy-metal resistance genes on a large (275-kb) IncHI2 plasmid. Copyright © 2017 Dyall-Smith et al.

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Sunday, July 7, 2019

Complete genome sequence of Salmonella enterica subsp. enterica serovar Paratyphi B sequence type 28 harboring mcr-1.

In 2015, plasmid-mediated colistin resistance was reported to be caused by a mobilized phosphoethanolamine transferase gene (mcr-1) in Enterobacteriaceae Here, we announce the complete genome sequence of the earliest d-tartrate-fermenting Salmonella enterica subsp. enterica serovar Paratyphi B isolate harboring mcr-1 from the collection of the German National Reference Laboratory for Salmonella. Copyright © 2017 Borowiak et al.

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Sunday, July 7, 2019

Distinct mechanisms of acquisition of mcr-1 -bearing plasmid by Salmonella strains recovered from animals and food samples.

Since the report of its discovery in E. coli in late 2015, the plasmid-mediated colistin resistance gene, mcr-1, has been detected in various bacterial species in clinical setting and various environmental niches. However, the transmission mechanisms of this gene in Salmonella is less defined. In this study, we conducted a comprehensive study to characterize the genetic features of mcr-1-positive Salmonella strains isolated from animals and foods. Our data revealed that Salmonella recovered from animals and food specimens exhibited highly different PFGE patterns, and acquired mcr-1-encoding plasmids via different mechanism. Plasmids harboring mcr-1 in Salmonella food isolates were all conjugative and…

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Sunday, July 7, 2019

Whole-genome sequencing identification of a multidrug-resistant Salmonella enterica serovar Typhimurium strain carrying blaNDM-5 from Guangdong, China.

A carbapenem-resistant Salmonella enterica serovar Typhimurium (sequence type 34 [ST34]) strain was isolated from a fecal specimen from a child with acute diarrhea. Whole-genome sequencing revealed that the 84.5-kb IncFII plasmid pST41-NDM carrying the NDM-5 carbapenemase gene possesses a structure identical to that of the IncFII-type plasmid backbone. However, the blaNDM-5 flanking sequence found in this plasmid is identical to the blaNDM-5-positive IncX3 plasmids carried by 10 strains of Enterobacteriaceae identified in the same hospital. Copyright © 2017 Elsevier B.V. All rights reserved.

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Sunday, July 7, 2019

Comparative whole genome analysis of three consecutive Salmonella diarizonae isolates.

Infections of very young children or immunocompromised people with Salmonella of higher subspecies are a well-known phenomenon often associated with contact to cold-blooded animals. We describe the molecular characterization of three S. enterica subsp. diarizonae strains, isolated consecutively over a period of several months from a hospital patient suffering from diarrhea and sepsis with fatal outcome. With the initial isolate the first complete genome sequence of a member of subsp. diarizonae is provided and based on this reference we revealed the genomic differences between the three isolates by use of next-generation sequencing and confirmed by phenotypical tests. Genome comparisons revealed…

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Sunday, July 7, 2019

Complete genetic analysis of a Salmonella enterica serovar Indiana isolate accompanying four plasmids carrying mcr-1, ESBL and other resistance genes in China

One mcr-1-carrying Salmonella enterica serovar Indiana strain D90, was identified from 1320 Salmonella enterica isolates from poultry slaughterhouse in 2012 in China. The objective of this study was to verify the transferability of the mcr-1 gene and also completely characterize the sequence of the strain at the whole-genome level. Broth matting assays were carried out to detect the transferability and whole-genome sequencing (WGS) of S. enterica serovar Indiana D90 was performed using the PacBio RS II system. Open reading frames were assigned using Rapid Annotation using Subsystem Technology (RAST) and analysed by BLASTn and BLASTp. Salmonella Pathogenisity Islands (SPIs) were…

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Sunday, July 7, 2019

A novel hybrid plasmid carrying multiple antimicrobial resistance and virulence genes in Salmonella enterica serovar Dublin.

Virulence plasmids and antibiotic resistance plasmids are usually maintained separately in Salmonella spp.; however, we report an instance of a hybrid plasmid (pN13-01125) in Salmonella enterica serovar Dublin. Review of the complete sequence of the 172,265-bp plasmid suggests that pN13-01125 is comprised of the previously described pSDVr and pSH696_135 plasmids and that the mechanism of hybridization likely involves IS6 (IS26) insertion sequence elements. The plasmid has a low conjugation frequency, confers resistance to six classes of antimicrobials, and contains a complete spv virulence operon.© Crown copyright 2017.

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Sunday, July 7, 2019

Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa.

The ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified.We analysed the whole genome sequences of S. Typhimurium isolates from UK patients that were generated following the introduction of routine whole-genome sequencing (WGS) of Salmonella enterica by Public Health England in 2014.We found that 2.7% (84/3147) of S. Typhimurium from patients in England and Wales were ST313 and were associated with gastrointestinal infection. Phylogenetic analysis revealed novel diversity of ST313 that distinguished UK-linked gastrointestinal isolates from African-associated extra-intestinal isolates. The…

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Sunday, July 7, 2019

Complete genomic sequences of two Salmonella enterica subsp. enterica serogroup C2 (O:6,8) strains from Central California.

Salmonella enterica subsp. enterica strains RM11060, serotype 6,8:d:-, and RM11065, serotype 6,8:-:e,n,z15, were isolated from environmental samples collected in central California in 2009. We report the complete genome sequences of these two strains. These genomic sequences are distinct and will provide additional data to our understanding of S. enterica genomics.

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Sunday, July 7, 2019

Complete genome sequence of Salmonella enterica subsp. enterica serovar Minnesota strain

Mango has been implicated as food vehicle in several Salmonella-causing foodborne outbreaks. Here, Salmonella enterica subsp. enterica serovar Minnesota was isolated from fresh mango fruit imported from Mexico in 2014. The complete genome sequence of S. Minnesota CFSAN017963 was sequenced using single-molecule real-time DNA sequencing. Distinct prophage regions, Salmonella pathogenicity islands, and fimbrial gene clusters were observed in comparative genomic analysis on S. Minnesota CFSAN017963 with other phylogenetically closely related Salmonella serovars. Core genome multilocus sequencing typing analysis of all the S. Minnesota isolates in the Genbank and Enterobase also revealed a high genomic diversity among the genomes analyzed.

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Sunday, July 7, 2019

Phenotypic and genotypic features of a Salmonella Heidelberg strain isolated in broilers in Brazil and their possible association to antibiotics and short-chain organic acids resistance and susceptibility.

Salmonella enterica serovar Heidelberg is a human pathogen also found in broilers. A strain (UFPR1) has been associated with field reports of resistance to short-chain organic acids (SCOA) in broilers in the South of Brazil, but was susceptible to aBacillus subtilis-based probiotic added in feed in a related study. This work aimed to (i) report clinical symptoms caused by SH UFPR1 in broilers, (ii) study its susceptibility to some antibioticsin vitro, and (iii) SCOAin vivo; and (iv) relate these phenotypic observations with its genome characteristics. Twoin vivotrials used 1-day-old chicks housed for 21?days in 8 sterilized isolated negative pressure rooms…

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