scholarly journals Genomic Comparison of Salmonella enterica Serovars and Salmonella bongori by Use of an S. enterica Serovar Typhimurium DNA Microarray

2003 ◽  
Vol 185 (2) ◽  
pp. 553-563 ◽  
Author(s):  
Kaman Chan ◽  
Stephen Baker ◽  
Charles C. Kim ◽  
Corrella S. Detweiler ◽  
Gordon Dougan ◽  
...  
Keyword(s):  
Host Range ◽  
Dna Microarray ◽  
Salmonella Enterica ◽  
Genetic Relatedness ◽  
Host Adaptation ◽  
Enzyme Electrophoresis ◽  
Genomic Changes ◽  
Serovar Typhimurium ◽  
Taxonomic Organization ◽  
Insight Into

ABSTRACT The genus Salmonella consists of over 2,200 serovars that differ in their host range and ability to cause disease despite their close genetic relatedness. The genetic factors that influence each serovar's level of host adaptation, how they evolved or were acquired, their influence on the evolution of each serovar, and the phylogenic relationships between the serovars are of great interest as they provide insight into the mechanisms behind these differences in host range and disease progression. We have used an Salmonella enterica serovar Typhimurium spotted DNA microarray to perform genomic hybridizations of various serovars and strains of both S. enterica (subspecies I and IIIa) and Salmonella bongori to gain insight into the genetic organization of the serovars. Our results are generally consistent with previously published DNA association and multilocus enzyme electrophoresis data. Our findings also reveal novel information. We observe a more distant relationship of serovar Arizona (subspecies IIIa) from the subspecies I serovars than previously measured. We also observe variability in the Arizona SPI-2 pathogenicity island, indicating that it has evolved in a manner distinct from the other serovars. In addition, we identify shared genetic features of S. enterica serovars Typhi, Paratyphi A, and Sendai that parallel their unique ability to cause enteric fever in humans. Therefore, whereas the taxonomic organization of Salmonella into serogroups provides a good first approximation of genetic relatedness, we show that it does not account for genomic changes that contribute to a serovar's degree of host adaptation.

scholarly journals In SituStructures of Polar and Lateral Flagella Revealed by Cryo-Electron Tomography

2019 ◽  
Vol 201 (13) ◽  
Author(s):  
Shiwei Zhu ◽  
Maren Schniederberend ◽  
Daniel Zhitnitsky ◽  
Ruchi Jain ◽  
Jorge E. Galán ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Electron Tomography ◽  
Additional Insight ◽  
Content Type ◽  
Bacterial Flagellum ◽  
Cryo Electron Tomography ◽  
Serovar Typhimurium ◽  
Flagellar Assembly ◽  
Insight Into

ABSTRACTThe bacterial flagellum is a sophisticated self-assembling nanomachine responsible for motility in many bacterial pathogens, includingPseudomonas aeruginosa,Vibriospp., andSalmonella enterica. The bacterial flagellum has been studied extensively in the model systemsEscherichia coliandSalmonella entericaserovar Typhimurium, yet the range of variation in flagellar structure and assembly remains incompletely understood. Here, we used cryo-electron tomography and subtomogram averaging to determinein situstructures of polar flagella inP. aeruginosaand peritrichous flagella inS. Typhimurium, revealing notable differences between these two flagellar systems. Furthermore, we observed flagellar outer membrane complexes as well as many incomplete flagellar subassemblies, which provide additional insight into mechanisms underlying flagellar assembly and loss in bothP. aeruginosaandS. Typhimurium.IMPORTANCEThe bacterial flagellum has evolved as one of the most sophisticated self-assembled molecular machines, which confers locomotion and is often associated with virulence of bacterial pathogens. Variation in species-specific features of the flagellum, as well as in flagellar number and placement, results in structurally distinct flagella that appear to be adapted to the specific environments that bacteria encounter. Here, we used cutting-edge imaging techniques to determine high-resolutionin situstructures of polar flagella inPseudomonas aeruginosaand peritrichous flagella inSalmonella entericaserovar Typhimurium, demonstrating substantial variation between flagella in these organisms. Importantly, we observed novel flagellar subassemblies and provided additional insight into the structural basis of flagellar assembly and loss in bothP. aeruginosaandS. Typhimurium.

scholarly journals Draft Genome Sequences of 12 Monophasic Salmonella enterica subsp. enterica Serotype Typhimurium 1,4,[5],12:i:− Strains Isolated from Wild Griffon Vultures in Eastern Spain

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Clara Marin ◽  
Giuseppe D’Auria ◽  
Llúcia Martínez-Priego ◽  
Francisco Marco-Jiménez
Keyword(s):  
Salmonella Enterica ◽  
Draft Genome ◽  
Wild Animals ◽  
Genome Sequences ◽  
Host Pathogen Interactions ◽  
Content Type ◽  
Zoonotic Pathogens ◽  
Host Pathogen ◽  
Serovar Typhimurium ◽  
Insight Into

Monophasic Salmonella enterica subsp. enterica serovar Typhimurium is one of the most common zoonotic pathogens. Salmonella species reside in a wide variety of hosts, including wild animals. Thus, we report here the genome sequences of 12 monophasic S. Typhimurium strains isolated from healthy wild vultures to gain better insight into their epidemiology and host-pathogen interactions.

scholarly journals Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

2017 ◽  
Author(s):  
Nicole E. Wheeler ◽  
Paul P. Gardner ◽  
Lars Barquist
Keyword(s):  
Random Forest ◽  
Host Range ◽  
Salmonella Enterica ◽  
Bacterial Pathogen ◽  
Host Adaptation ◽  
Random Forest Classifier ◽  
Sub Saharan Africa ◽  
Broad Host Range ◽  
Invasive Infection ◽  
Emerging Pathogens

AbstractEmerging pathogens are a major threat to public health, however understanding how pathogens adapt to new niches remains a challenge. New methods are urgently required to provide functional insights into pathogens from the massive genomic data sets now being generated from routine pathogen surveillance for epidemiological purposes. Here, we measure the burden of atypical mutations in protein coding genes across independently evolved Salmonella enterica lineages, and use these as input to train a random forest classifier to identify strains associated with extraintestinal disease. Members of the species fall along a continuum, from pathovars which cause gastrointestinal infection and low mortality, associated with a broad host-range, to those that cause invasive infection and high mortality, associated with a narrowed host range. Our random forest classifier learned to perfectly discriminate long-established gastrointestinal and invasive serovars of Salmonella. Additionally, it was able to discriminate recently emerged Salmonella Enteritidis and Typhimurium lineages associated with invasive disease in immunocompromised populations in sub-Saharan Africa, and within-host adaptation to invasive infection. We dissect the architecture of the model to identify the genes that were most informative of phenotype, revealing a common theme of degradation of metabolic pathways in extraintestinal lineages. This approach accurately identifies patterns of gene degradation and diversifying selection specific to invasive serovars that have been captured by more labour-intensive investigations, but can be readily scaled to larger analyses.

scholarly journals Salmonella enterica Serovar Typhi Possesses a Unique Repertoire of Fimbrial Gene Sequences

2001 ◽  
Vol 69 (5) ◽  
pp. 2894-2901 ◽  
Author(s):  
Stacy M. Townsend ◽  
Naomi E. Kramer ◽  
Robert Edwards ◽  
Stephen Baker ◽  
Nancy Hamlin ◽  
...  
Keyword(s):  
Host Range ◽  
Salmonella Enterica ◽  
Host Adaptation ◽  
Unique Combination ◽  
Gene Sequences ◽  
Simple Correlation ◽  
Salmonella Enterica Serovar Typhi ◽  
Type Iv ◽  
Reference Collection ◽  
First Time

ABSTRACT Salmonella enterica serotype Typhi differs from nontyphoidal Salmonella serotypes by its strict host adaptation to humans and higher primates. Since fimbriae have been implicated in host adaptation, we investigated whether the serotype Typhi genome contains fimbrial operons which are unique to this pathogen or restricted to typhoidal Salmonella serotypes. This study established for the first time the total number of fimbrial operons present in an individual Salmonella serotype. The serotype Typhi CT18 genome, which has been sequenced by the Typhi Sequencing Group at the Sanger Centre, contained a type IV fimbrial operon, an orthologue of the agf operon, and 12 putative fimbrial operons of the chaperone-usher assembly class. In addition tosef, fim, saf, and tcf, which had been described previously in serotype Typhi, we identified eight new putative chaperone-usher-dependent fimbrial operons, which were termedbcf, sta, stb, ste, std, stc, stg, and sth. Hybridization analysis performed with 16 strains ofSalmonella reference collection C and 22 strains ofSalmonella reference collection B showed that all eight putative fimbrial operons of serotype Typhi were also present in a number of nontyphoidal Salmonella serotypes. Thus, a simple correlation between host range and the presence of a single fimbrial operon seems at present unlikely. However, the serotype Typhi genome differed from that of all other Salmonella serotypes investigated in that it contained a unique combination of putative fimbrial operons.

scholarly journals Host Restriction of Salmonella enterica Serotype Typhimurium Pigeon Isolates Does Not Correlate with Loss of Discrete Genes

2004 ◽  
Vol 186 (9) ◽  
pp. 2619-2628 ◽  
Author(s):  
Helene L. Andrews-Polymenis ◽  
Wolfgang Rabsch ◽  
Steffen Porwollik ◽  
Michael McClelland ◽  
Carlos Rosetti ◽  
...  
Keyword(s):  
Host Range ◽  
Dna Microarray ◽  
Salmonella Enterica ◽  
Broad Host Range ◽  
Fluid Accumulation ◽  
Host Restriction ◽  
Phage Types ◽  
Chromosomal Genes ◽  
Large Groups ◽  
Intestinal Persistence

ABSTRACT The definitive phage types (DT) 2 and 99 of Salmonella enterica serotype Typhimurium are epidemiologically correlated with a host range restricted to pigeons, in contrast to phage types with broader host ranges such as epidemic cattle isolates (DT104 and DT204). To determine whether phage types with broad host range possess genetic islands absent from host-restricted phage types, we compared the genomes of four pigeon isolates to serotype Typhimurium strain LT2 using a DNA microarray. Three of the four isolates tested caused fluid accumulation in bovine ligated ileal loops, but they had reduced colonization of liver and spleen in susceptible BALB/c mice and were defective for intestinal persistence in Salmonella-resistant CBA mice. The genomes of the DT99 and DT2 isolates were extremely similar to the LT2 genome, with few notable differences on the level of complete individual genes. Two large groups of genes representing the Fels-1 and Fels-2 prophages were missing from the DT2 and DT99 phage types we analyzed. One of the DT99 isolates examined was lacking a third cluster of five chromosomal genes (STM1555 to -1559). Results of the microarray analysis were extended using Southern analysis to a collection of 75 serotype Typhimurium clinical isolates of 24 different phage types. This analysis revealed no correlation between the presence of Fels-1, Fels-2, or STM1555 to -1559 and the association of phage types with different host reservoirs. We conclude that serotype Typhimurium phage types with broad host range do not possess genetic islands influencing host restriction, which are absent from the host-restricted pigeon isolates.

scholarly journals Salmonella enterica serovar Typhimurium from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type

2021 ◽  
Author(s):  
Yezhi Fu ◽  
Nkuchia M. M'ikanatha ◽  
Jeffrey M. Lorch ◽  
David S. Blehert ◽  
Brenda Berlowski-Zier ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Genetic Relatedness ◽  
Virulence Gene ◽  
The United States ◽  
Domestic Animal ◽  
Wild Birds ◽  
Passerine Birds ◽  
Source Attribution ◽  
Serovar Typhimurium ◽  
Water Birds

Salmonella enterica serovar Typhimurium is typically considered a host generalist, however certain strains are associated with specific hosts and show genetic features of host adaptation. Here, we sequenced 131 S. Typhimurium strains from wild birds collected in 30 U.S. states during 1978-2019. We found that isolates from broad taxonomic host groups including passerine birds, water birds (Aequornithes), and larids (gulls and terns) represented three distinct lineages and certain S. Typhimurium CRISPR types presented in individual lineages. We also showed that lineages formed by wild bird isolates differed from most strains originating from domestic animal sources, and genomes from these lineages substantially improved source attribution of Typhimurium genomes to wild birds by a machine learning classifier. Furthermore, virulence gene signatures that differentiated S. Typhimurium from passerines, water birds, and larids were detected. Passerine isolates tended to lack S. Typhimurium-specific virulence plasmids. Isolates from the passerine, water bird, and larid lineages had close genetic relatedness with human clinical isolates, including those from a 2021 U.S. outbreak linked to passerine birds. These observations indicate that S. Typhimurium from wild birds in the U.S. are likely host-adapted, and the representative genomic dataset examined in this study can improve source prediction and facilitate outbreak investigation.

scholarly journals Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar

mBio ◽  
2013 ◽  
Vol 4 (5) ◽  
Author(s):  
Robert A. Kingsley ◽  
Sally Kay ◽  
Thomas Connor ◽  
Lars Barquist ◽  
Leanne Sait ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Salmonella Enterica ◽  
Host Adaptation ◽  
Whole Genome ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Content Type ◽  
Serovar Typhimurium ◽  
Genetic Signatures

ABSTRACTSalmonella entericaserovar Typhimurium definitive type 2 (DT2) is host restricted toColumba livia(rock or feral pigeon) but is also closely related toS. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster withinS. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 andS. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely relatedS. Typhimurium strains. We report a novelin silicoapproach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartatein vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility.IMPORTANCEWhereasSalmonella entericaserovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within aSalmonellaserovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2)S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.

scholarly journals Loss of Multicellular Behavior in Epidemic African Nontyphoidal Salmonella enterica Serovar Typhimurium ST313 Strain D23580

mBio ◽  
2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Larissa A. Singletary ◽  
Joyce E. Karlinsey ◽  
Stephen J. Libby ◽  
Jason P. Mooney ◽  
Kristen L. Lokken ◽  
...  
Keyword(s):  
Stress Resistance ◽  
Salmonella Enterica ◽  
Genomic Analysis ◽  
Bloodstream Infections ◽  
Host Adaptation ◽  
Sub Saharan Africa ◽  
Loss Of Function ◽  
Serovar Typhimurium ◽  
Mode Of Transmission ◽  
Sub Saharan

ABSTRACT Nontyphoidal Salmonella enterica serovar Typhimurium is a frequent cause of bloodstream infections in children and HIV-infected adults in sub-Saharan Africa. Most isolates from African patients with bacteremia belong to a single sequence type, ST313, which is genetically distinct from gastroenteritis-associated ST19 strains, such as 14028s and SL1344. Some studies suggest that the rapid spread of ST313 across sub-Saharan Africa has been facilitated by anthroponotic (person-to-person) transmission, eliminating the need for Salmonella survival outside the host. While these studies have not ruled out zoonotic or other means of transmission, the anthroponotic hypothesis is supported by evidence of extensive genomic decay, a hallmark of host adaptation, in the sequenced ST313 strain D23580. We have identified and demonstrated 2 loss-of-function mutations in D23580, not present in the ST19 strain 14028s, that impair multicellular stress resistance associated with survival outside the host. These mutations result in inactivation of the KatE stationary-phase catalase that protects high-density bacterial communities from oxidative stress and the BcsG cellulose biosynthetic enzyme required for the RDAR (red, dry, and rough) colonial phenotype. However, we found that like 14028s, D23580 is able to elicit an acute inflammatory response and cause enteritis in mice and rhesus macaque monkeys. Collectively, these observations suggest that African S . Typhimurium ST313 strain D23580 is becoming adapted to an anthroponotic mode of transmission while retaining the ability to infect and cause enteritis in multiple host species. IMPORTANCE The last 3 decades have witnessed an epidemic of invasive nontyphoidal Salmonella infections in sub-Saharan Africa. Genomic analysis and clinical observations suggest that the Salmonella strains responsible for these infections are evolving to become more typhoid-like with regard to patterns of transmission and virulence. This study shows that a prototypical African nontyphoidal Salmonella strain has lost traits required for environmental stress resistance, consistent with an adaptation to a human-to-human mode of transmission. However, in contrast to predictions, the strain remains capable of causing acute inflammation in the mammalian intestine. This suggests that the systemic clinical presentation of invasive nontyphoidal Salmonella infections in Africa reflects the immune status of infected hosts rather than intrinsic differences in the virulence of African Salmonella strains. Our study provides important new insights into the evolution of host adaptation in bacterial pathogens.

scholarly journals Long-Term Dissemination of CTX-M-5-Producing Hypermutable Salmonella enterica Serovar Typhimurium Sequence Type 328 Strains in Russia, Belarus, and Kazakhstan

2014 ◽  
Vol 58 (9) ◽  
pp. 5202-5210 ◽  
Author(s):  
Varvara K. Kozyreva ◽  
Elena N. Ilina ◽  
Maja V. Malakhova ◽  
Alessandra Carattoli ◽  
Ilya S. Azizov ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Genetic Relatedness ◽  
Single Point ◽  
Point Mutations ◽  
Sequence Type ◽  
Quinolone Resistance ◽  
Resistance Mutations ◽  
Content Type ◽  
Serovar Typhimurium

ABSTRACTIn this paper, we present evidence of long-term circulation of cefotaxime-resistant clonally relatedSalmonella entericaserovar Typhimurium strains over a broad geographic area. The genetic relatedness of 88 isolates collected from multiple outbreaks and sporadic cases of nosocomial salmonellosis in various parts of Russia, Belarus, and Kazakhstan from 1996 to 2009 was established by multilocus tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST). The isolates belong to sequence type 328 (ST328) and produce CTX-M-5 β-lactamase, whose gene is carried by highly related non-self-conjugative but mobilizable plasmids. Resistance to nalidixic acid and low-level resistance to ciprofloxacin is present in 37 (42%) of the isolates and in all cases is determined by various single point mutations in thegyrAgene quinolone resistance-determining region (QRDR). Isolates of the described clonal group exhibit a hypermutable phenotype that probably facilitates independent acquisition of quinolone resistance mutations.

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