scholarly journals Corrected Genome Annotations Reveal Gene Loss and Antibiotic Resistance as Drivers in the Fitness Evolution of Salmonella enterica Serovar Typhimurium

2016 ◽  
Vol 198 (23) ◽  
pp. 3152-3161 ◽  
Author(s):  
Sandip Paul ◽  
Evgeni V. Sokurenko ◽  
Sujay Chattopadhyay
Keyword(s):  
Multidrug Resistance ◽  
Salmonella Enterica ◽  
Gene Loss ◽  
Bacterial Genome ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Content Type ◽  
Chromosomal Genes ◽  
Serovar Typhimurium ◽  
Genome Annotations

ABSTRACT Horizontal acquisition of novel chromosomal genes is considered to be a key process in the evolution of bacterial pathogens. However, the identification of gene presence or absence could be hindered by the inconsistencies in bacterial genome annotations. Here, we performed a cross-annotation of omnipresent core and mosaic accessory genes in the chromosome of Salmonella enterica serovar Typhimurium across a total of 20 fully assembled genomes deposited into GenBank. Cross-annotation resulted in a 32% increase in the number of core genes and a 3-fold decrease in the number of genes identified as mosaic genes (i.e., genes present in some strains only) by the original annotation. Of the remaining noncore genes, the vast majority were prophage genes, and 255 of the nonphage genes were actually of core origin but lost in some strains upon the emergence of the S . Typhimurium serovar, suggesting that the chromosomal portion of the S . Typhimurium genome acquired a very limited number of novel genes other than prophages. Only horizontally acquired nonphage genes related to bacterial fitness or virulence were found in four recently sequenced isolates, all located on three different genomic islands that harbor multidrug resistance determinants. Thus, the extensive use of antimicrobials could be the main selection force behind the new fitness gene acquisition and the emergence of novel Salmonella pathotypes. IMPORTANCE Significant discrepancies in the annotations of bacterial genomes could mislead the conclusions about evolutionary origin of chromosomal genes, as we demonstrate here via a cross-annotation-based analysis of Salmonella Typhimurium genomes from GenBank. We conclude that despite being able to infect a broad range of vertebrate hosts, the genomic diversity of S . Typhimurium strains is almost exclusively limited to gene loss and the transfer of prophage DNA. Only nonphage chromosomal genes acquired after the emergence of the serovar are linked to the genomic islands harboring multidrug resistance factors. Since the fitness factors could lead to increased virulence, this poses an important research question: could overuse or misuse of antimicrobials act as selection forces for the emergence of more pathogenic strains of Salmonella ?

scholarly journals Binding of the RamR Repressor to Wild-Type and Mutated Promoters of theramAGene Involved in Efflux-Mediated Multidrug Resistance in Salmonella enterica Serovar Typhimurium

2011 ◽  
Vol 56 (2) ◽  
pp. 942-948 ◽  
Author(s):  
Sylvie Baucheron ◽  
Franck Coste ◽  
Sylvie Canepa ◽  
Marie-Christine Maurel ◽  
Etienne Giraud ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Dna Binding ◽  
Binding Site ◽  
Salmonella Enterica ◽  
Transcriptional Start Site ◽  
Local Level ◽  
Wild Type ◽  
Binding Model ◽  
Content Type ◽  
Serovar Typhimurium

ABSTRACTThe transcriptional activator RamA is involved in multidrug resistance (MDR) by increasing expression of the AcrAB-TolC RND-type efflux system in several pathogenicEnterobacteriaceae. InSalmonella entericaserovar Typhimurium (S.Typhimurium),ramAexpression is negatively regulated at the local level by RamR, a transcriptional repressor of the TetR family. We here studied the DNA-binding activity of the RamR repressor with theramApromoter (PramA). As determined by high-resolution footprinting, the 28-bp-long RamR binding site covers essential features of PramA, including the −10 conserved region, the transcriptional start site oframA, and two 7-bp inverted repeats. Based on the RamR footprint and on electrophoretic mobility shift assays (EMSAs), we propose that RamR interacts with PramAas a dimer of dimers, in a fashion that is structurally similar to the QacR-DNA binding model. Surface plasmon resonance (SPR) measurements indicated that RamR has a 3-fold-lower affinity (KD[equilibrium dissociation constant] = 191 nM) for the 2-bp-deleted PramAof an MDRS.Typhimurium clinical isolate than for the wild-type PramA(KD= 66 nM). These results confirm the direct regulatory role of RamR in the repression oframAtranscription and precisely define how an alteration of its binding site can give rise to an MDR phenotype.

scholarly journals Multidrug Resistance Regulators MarA, SoxS, Rob, and RamA Repress Flagellar Gene Expression and Motility in Salmonella enterica Serovar Typhimurium

2019 ◽  
Vol 201 (23) ◽  
Author(s):  
Srinivas S. Thota ◽  
Lon M. Chubiz
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Multidrug Resistance ◽  
Related Species ◽  
Salmonella Enterica ◽  
Mrna Translation ◽  
Flagellar Gene ◽  
Content Type ◽  
E Coli ◽  
Serovar Typhimurium

ABSTRACT Production of flagella is costly and subject to global multilayered regulation, which is reflected in the hierarchical control of flagellar production in many bacterial species. For Salmonella enterica serovar Typhimurium and its relatives, global regulation of flagellar production primarily occurs through the control of flhDC transcription and mRNA translation. In this study, the roles of the homologous multidrug resistance regulators MarA, SoxS, Rob, and RamA (constituting the mar-sox-rob regulon in S. Typhimurium) in regulating flagellar gene expression were explored. Each of these regulators was found to inhibit flagellar gene expression, production of flagella, and motility. To different degrees, repression via these transcription factors occurred through direct interactions with the flhDC promoter, particularly for MarA and Rob. Additionally, SoxS repressed flagellar gene expression via a posttranscriptional pathway, reducing flhDC translation. The roles of these transcription factors in reducing motility in the presence of salicylic acid were also elucidated, adding a genetic regulatory element to the response of S. Typhimurium to this well-characterized chemorepellent. Integration of flagellar gene expression into the mar-sox-rob regulon in S. Typhimurium contrasts with findings for closely related species such as Escherichia coli, providing an example of plasticity in the mar-sox-rob regulon throughout the Enterobacteriaceae family. IMPORTANCE The mar-sox-rob regulon is a large and highly conserved stress response network in the Enterobacteriaceae family. Although it is well characterized in E. coli, the extent of this regulon in related species is unclear. Here, the control of costly flagellar gene expression is connected to the mar-sox-rob regulon of S. Typhimurium, contrasting with the E. coli regulon model. These findings demonstrate the flexibility of the mar-sox-rob regulon to accommodate novel regulatory targets, and they provide evidence for its broader regulatory role within this family of diverse bacteria.

scholarly journals Efficiency of Conditionally Attenuated Salmonella enterica Serovar Typhimurium in Bacterium-Mediated Tumor Therapy

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Michael Frahm ◽  
Sebastian Felgner ◽  
Dino Kocijancic ◽  
Manfred Rohde ◽  
Michael Hensel ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Tumor Targeting ◽  
Antitumor Effect ◽  
Treatment Options ◽  
Tumor Therapy ◽  
Therapeutic Benefit ◽  
Industrialized Countries ◽  
Content Type ◽  
Serovar Typhimurium ◽  
Therapeutic Molecules

ABSTRACTIncreasing numbers of cancer cases generate a great urge for new treatment options. Applying bacteria likeSalmonella entericaserovar Typhimurium for cancer therapy represents an intensively explored option. These bacteria have been shown not only to colonize solid tumors but also to exhibit an intrinsic antitumor effect. In addition, they could serve as tumor-targeting vectors for therapeutic molecules. However, the pathogenicS. Typhimurium strains used for tumor therapy need to be attenuated for safe application. Here, lipopolysaccharide (LPS) deletion mutants (ΔrfaL, ΔrfaG, ΔrfaH, ΔrfaD, ΔrfaP, and ΔmsbBmutants) ofSalmonellawere investigated for efficiency in tumor therapy. Of such variants, the ΔrfaDand ΔrfaGdeep rough mutants exhibited the best tumor specificity and lowest pathogenicity. However, the intrinsic antitumor effect was found to be weak. To overcome this limitation, conditional attenuation was tested by complementing the mutants with an inducible arabinose promoter. The chromosomal integration of the respective LPS biosynthesis genes into thearaBADlocus exhibited the best balance of attenuation and therapeutic benefit. Thus, the present study establishes a basis for the development of an applicably cancer therapeutic bacterium.IMPORTANCECancer has become the second most frequent cause of death in industrialized countries. This and the drawbacks of routine therapies generate an urgent need for novel treatment options. Applying appropriately modifiedS. Typhimurium for therapy represents the major challenge of bacterium-mediated tumor therapy. In the present study, we demonstrated thatSalmonellabacteria conditionally modified in their LPS phenotype exhibit a safe tumor-targeting phenotype. Moreover, they could represent a suitable vehicle to shuttle therapeutic compounds directly into cancerous tissue without harming the host.

scholarly journals Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium Strain UPM 260, Isolated from a Broiler Chicken in Perak, Malaysia

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Najwa Syahirah Roslan ◽  
Shagufta Jabeen ◽  
Nurulfiza Mat Isa ◽  
Abdul Rahman Omar ◽  
Mohd Hair Bejo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Salmonella Enterica ◽  
Broiler Chicken ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Typhimurium Strain ◽  
Serovar Typhimurium

ABSTRACT Salmonella enterica subsp. enterica serovar Typhimurium is one of several well-categorized Salmonella serotypes recognized globally. Here, we report the whole-genome sequence of S. Typhimurium strain UPM 260, isolated from a broiler chicken.

scholarly journals Association of a Protective Monoclonal IgA with the O Antigen of Salmonella enterica Serovar Typhimurium Impacts Type 3 Secretion and Outer Membrane Integrity

2012 ◽  
Vol 80 (7) ◽  
pp. 2454-2463 ◽  
Author(s):  
Stephen J. Forbes ◽  
Daniel Martinelli ◽  
Chyongere Hsieh ◽  
Jeffrey G. Ault ◽  
Michael Marko ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Epithelial Cells ◽  
Outer Membrane ◽  
Salmonella Enterica ◽  
Membrane Integrity ◽  
Effector Proteins ◽  
Content Type ◽  
O Antigen ◽  
Serovar Typhimurium ◽  
Type 3

ABSTRACTInvasion of intestinal epithelial cells bySalmonella entericaserovar Typhimurium is an energetically demanding process, involving the transfer of effector proteins from invading bacteria into host cells via a specialized organelle known as theSalmonellapathogenicity island 1 (SPI-1) type 3 secretion system (T3SS). By a mechanism that remains poorly understood, entry ofS. Typhimurium into epithelial cells is inhibited by Sal4, a monoclonal, polymeric IgA antibody that binds an immunodominant epitope within the O-antigen (O-Ag) component of lipopolysaccharide. In this study, we investigated how the binding of Sal4 to the surface ofS. Typhimurium influences T3SS activity, bacterial energetics, and outer membrane integrity. We found that Sal4 treatment impaired T3SS-mediated translocon formation and attenuated the delivery of tagged effector proteins into epithelial cells. Sal4 treatment coincided with a partial reduction in membrane energetics and intracellular ATP levels, possibly explaining the impairment in T3SS activity. Sal4's effects on bacterial secretion and energetics occurred concurrently with an increase in O-Ag levels in culture supernatants, alterations in outer membrane permeability, and changes in surface ultrastructure, as revealed by transmission electron microscopy and cryo-electron microscopy. We propose that Sal4, by virtue of its ability to bind and cross-link the O-Ag, induces a form of outer membrane stress that compromises the integrity of theS. Typhimurium cell envelope and temporarily renders the bacterium avirulent.

scholarly journals Draft Genome Sequence of Lactobacillus fermentum Lf2, an Exopolysaccharide-Producing Strain Isolated from Argentine Cheese

2018 ◽  
Vol 7 (18) ◽  
Author(s):  
Hugh M. B. Harris ◽  
Elisa C. Ale ◽  
Jorge A. Reinheimer ◽  
Ana G. Binetti ◽  
Paul W. O’Toole
Keyword(s):  
Genome Sequence ◽  
Salmonella Enterica ◽  
Draft Genome ◽  
Protective Role ◽  
Lactobacillus Fermentum ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Serovar Typhimurium ◽  
High Concentrations

Lactobacillus fermentum Lf2, an Argentine cheese isolate, can produce high concentrations of exopolysaccharides (EPS). These EPS were shown to improve the texture and rheology of yogurt, as well as to play a protective role in mice exposed to Salmonella enterica serovar Typhimurium.

scholarly journals Highly Resistant Salmonella enterica Serovar Typhi with a NovelgyrAMutation Raises Questions about the Long-Term Efficacy of Older Fluoroquinolones for Treating Typhoid Fever

2012 ◽  
Vol 56 (5) ◽  
pp. 2761-2762 ◽  
Author(s):  
Kanika Deshpande Koirala ◽  
Duy Pham Thanh ◽  
Sudeep Dhoj Thapa ◽  
Amit Arjyal ◽  
Abhilasha Karkey ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Typhoid Fever ◽  
Treatment Failure ◽  
Salmonella Enterica ◽  
Systemic Infection ◽  
Resistant Isolate ◽  
Content Type ◽  
Salmonella Enterica Serovar Typhi ◽  
Term Efficacy

ABSTRACTAs a consequence of multidrug resistance, clinicians are highly dependent on fluoroquinolones for treating the serious systemic infection typhoid fever. While reduced susceptibility to fluoroquinolones, which lessens clinical efficacy, is becoming ubiquitous, comprehensive resistance is exceptional. Here we report ofloxacin treatment failure in typhoidal patient infected with a novel, highly fluoroquinolone-resistant isolate ofSalmonella entericaserovar Typhi. The isolation of this organism has serious implications for the long-term efficacy of ciprofloxacin and ofloxacin for typhoid treatment.

scholarly journals Regulation of RamA by RamR in Salmonella enterica Serovar Typhimurium: Isolation of a RamR Superrepressor

2012 ◽  
Vol 56 (11) ◽  
pp. 6037-6040 ◽  
Author(s):  
Vito Ricci ◽  
Stephen J. W. Busby ◽  
Laura J. V. Piddock
Keyword(s):  
Transcription Factor ◽  
Salmonella Enterica ◽  
Fluorescent Protein ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Promoter Sequence ◽  
Palindromic Sequence ◽  
Content Type ◽  
Gfp Reporter ◽  
Serovar Typhimurium ◽  
Green Fluorescent

ABSTRACTRamA is a transcription factor involved in regulating multidrug resistance inSalmonella entericaserovar Typhimurium SL1344. Green fluorescent protein (GFP) reporter fusions were exploited to investigate the regulation of RamA expression by RamR. We show that RamR represses theramApromoter by binding to a palindromic sequence and describe a superrepressor RamR mutant that binds to theramApromoter sequence more efficiently, thus exhibiting aramAinactivated phenotype.

scholarly journals Curcumin Reduces the Motility of Salmonella enterica Serovar Typhimurium by Binding to the Flagella, Thereby Leading to Flagellar Fragility and Shedding

2016 ◽  
Vol 198 (13) ◽  
pp. 1798-1811 ◽  
Author(s):  
Sandhya Amol Marathe ◽  
Arjun Balakrishnan ◽  
Vidya Devi Negi ◽  
Deepika Sakorey ◽  
Nagasuma Chandra ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Binding Assay ◽  
Protein A ◽  
Intestinal Barrier ◽  
Site Directed Mutagenesis ◽  
Content Type ◽  
Serovar Typhimurium ◽  
Flagellar Filament ◽  
Fluorescence Binding ◽  
Fluorescence Binding Assay

ABSTRACTOne of the important virulence properties of the pathogen is its ability to travel to a favorable environment, cross the viscous mucus barrier (intestinal barrier for enteric pathogens), and reach the epithelia to initiate pathogenesis with the help of an appendage, like flagella. Nonetheless, flagella can act as an “Achilles heel,” revealing the pathogen's presence to the host through the stimulation of innate and adaptive immune responses. We assessed whether curcumin, a dietary polyphenol, could alter the motility ofSalmonella, a foodborne pathogen. It reduced the motility ofSalmonella entericaserovar Typhimurium by shortening the length of the flagellar filament (from ∼8 μm to ∼5 μm) and decreasing its density (4 or 5 flagella/bacterium instead of 8 or 9 flagella/bacterium). Upon curcumin treatment, the percentage of flagellated bacteria declined from ∼84% to 59%. However, no change was detected in the expression of the flagellin gene and protein. A fluorescence binding assay demonstrated binding of curcumin to the flagellar filament. This might make the filament fragile, breaking it into smaller fragments. Computational analysis predicted the binding of curcumin, its analogues, and its degraded products to a flagellin molecule at an interface between domains D1 and D2. Site-directed mutagenesis and a fluorescence binding assay confirmed the binding of curcumin to flagellin at residues ASN120, ASP123, ASN163, SER164, ASN173, and GLN175.IMPORTANCEThis work, to our knowledge the first report of its kind, examines how curcumin targets flagellar density and affects the pathogenesis of bacteria. We found that curcumin does not affect any of the flagellar synthesis genes. Instead, it binds to the flagellum and makes it fragile. It increases the torsional stress on the flagellar filament that then breaks, leaving fewer flagella around the bacteria. Flagella, which are crucial ligands for Toll-like receptor 5, are some of the most important appendages ofSalmonella. Curcumin is an important component of turmeric, which is a major spice used in Asian cooking. The loss of flagella can, in turn, change the pathogenesis of bacteria, making them more robust and fit in the host.

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