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 Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 854 ◽  
Author(s):  
Fong ◽  
Tremblay ◽  
Delaquis ◽  
Goodridge ◽  
Levesque ◽  
...  
Keyword(s):  
Host Range ◽  
Salmonella Enterica ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Broad Host Range ◽  
Natural Environments ◽  
Host Interactions ◽  
Knowledge Framework ◽  
Isolation And Characterization ◽  
Opportunistic Human Pathogen

Phages infecting members of the opportunistic human pathogen, Salmonella enterica, are widespread in natural environments and offer a potential source of agents that could be used for controlling populations of this bacterium; yet, relatively little is known about these phages. Here we describe the isolation and characterization of 45 phages of Salmonella enterica from disparate geographic locations within British Columbia, Canada. Host-range profiling revealed host-specific patterns of susceptibility and resistance, with several phages identified that have a broad-host range (i.e., able to lyse >40% of bacterial hosts tested). One phage in particular, SE13, is able to lyse 51 out of the 61 Salmonella strains tested. Comparative genomic analyses also revealed an abundance of sequence diversity in the sequenced phages. Alignment of the genomes grouped the phages into 12 clusters with three singletons. Phages within certain clusters exhibited extraordinarily high genome homology (>98% nucleotide identity), yet between clusters, genomes exhibited a span of diversity (<50% nucleotide identity). Alignment of the major capsid protein also supported the clustering pattern observed with alignment of the whole genomes. We further observed associations between genomic relatedness and the site of isolation, as well as genetic elements related to DNA metabolism and host virulence. Our data support the knowledge framework for phage diversity and phage–host interactions that are required for developing phage-based applications for various sectors, including biocontrol, detection and typing.

scholarly journals Emergence and Spread of Different ESBL-Producing Salmonella enterica Serovars in Hospitalized Horses Sharing a Highly Transferable IncM2 CTX-M-3-Encoding Plasmid

2020 ◽  
Vol 11 ◽  
Author(s):  
Ziv Dor ◽  
Anat Shnaiderman-Torban ◽  
Kira Kondratyeva ◽  
Maya Davidovich-Cohen ◽  
Assaf Rokney ◽  
...  
Keyword(s):  
Host Range ◽  
Salmonella Enterica ◽  
Meta Analysis ◽  
Health Hazard ◽  
Companion Animals ◽  
Antibiotic Resistance Genes ◽  
Complete Sequence ◽  
Control Measures ◽  
Health Concern ◽  
Broad Host Range

Salmonella enterica is a major causative pathogen of human and animal gastroenteritis. Antibiotic resistant strains have emerged due to the production of extended-spectrum β-lactamases (ESBLs) posing a major health concern. With the increasing reports on ESBL-producing Enterobacterales that colonize companion animals, we aimed to investigate ESBL dissemination among ESBL-producing Salmonella enterica (ESBL-S) in hospitalized horses. We prospectively collected ESBL-S isolates from hospitalized horses in a Veterinary-Teaching Hospital during Dec 2015–Dec 2017. Selection criteria for ESBL-S were white colonies on CHROMagarESBL plates and an ESBL phenotypic confirmation. Salmonella enterica serovars were determined using the Kaufmann-White-Le-Minor serological scheme. ESBL-encoding plasmids were purified, transformed and compared using restriction fragment length polymorphism (RFLP). Whole genome sequencing (Illumina and MinION platforms) were performed for detailed phylogenetic and plasmid analyses. Twelve ESBL-S were included in this study. Molecular investigation and Sequence Read Archive (SRA) meta-analysis revealed the presence of three unique Salmonella enterica serovars, Cerro, Havana and Liverpool, all reported for the first time in horses. PFGE revealed the clonal spread of S. Cerro between seven horses. All twelve isolates carried blaCTX–M–3 and showed an identical multidrug resistance profile with co-resistance to trimethoprim/sulfamethoxazole and to aminoglycosides. Plasmid RFLP proved the inter-serovar horizontal spread of a single blaCTX–M–3-encoding plasmid. Complete sequence of a representative plasmid (S. Havana strain 373.3.1), designated pSEIL-3 was a -86.4 Kb IncM2 plasmid, that encoded nine antibiotic resistance genes. pSEIL-3 was virtually identical to pCTX-M3 from Citrobacter freundii, and showed high identity (&gt;95%) to six other blaCTX–M–3 or blaNDM–1 IncM2 broad host range plasmids from various Enterobacterales of human origin. Using a specific six gene-based multiplex PCR, we detected pSEIL-3 in various Enterobacterales species that co-colonized the horses’ gut. Together, our findings show the alarming emergence of ESBL-S in hospitalized horses associated with gut shedding and foal morbidity and mortality. We demonstrated the dissemination of CTX-M-3 ESBL among different Salmonella enterica serovars due to transmission of a broad host range plasmid. This report highlights horses as a zoonotic reservoir for ESBL-S, including highly transmissible plasmids that may represent a ‘One-Health’ hazard. This risk calls for the implementation of infection control measures to monitor and control the spread of ESBL-S in hospitalized horses.

scholarly journals Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

2019 ◽  
Author(s):  
Matt Bawn ◽  
Gaetan Thilliez ◽  
Mark Kirkwood ◽  
Nicole Wheeler ◽  
Liljana Petrovska ◽  
...  
Keyword(s):  
Host Range ◽  
Salmonella Enterica ◽  
Genotypic Variation ◽  
Avian Species ◽  
Whole Genome Sequence ◽  
Broad Host Range ◽  
Niche Adaptation ◽  
Disseminated Disease ◽  
Distinct Distribution ◽  
Anthropogenic Selection

AbstractSalmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and disseminated disease worldwide. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. A robust fully parsimonious phylogenetic tree constructed from recombination purged variation in the whole genome sequence of 131 diverse strains of S. Typhimurium revealed population structure composed of two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β predominantly contained subclades associated with wild avian species, with the notable exception of a subclade containing the DT204/49 complex. The contrasting epidemiology of α and β strains was reflected in a distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification associated with invasiveness of host adapted serotypes. Gene flux was predominantly driven by acquisition, loss or recombination of prophage. The acquisition of large genetic islands (SGI-1 and 4) was limited to two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) in clade α. Together, our data are consistent with the view that a broad host range common ancestor of S. Typhimurium diversified with clade α lineages remained largely associated with multiple domesticated animal species, while clade β spawned multiple lineages that underwent diversifying selection associated with adaptation to various niches, predominantly in wild avian species.

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 The role of flagella and chemotaxis genes in host pathogen interaction of the host adapted Salmonella enterica serovar Dublin compared to the broad host range serovar S. Typhimurium

2013 ◽  
Vol 13 (1) ◽  
pp. 67 ◽  
Author(s):  
John Elmerdahl Olsen ◽  
Kirsten Hobolt Hoegh-Andersen ◽  
Josep Casadesús ◽  
Jesper Rosenkranzt ◽  
Mark Simon Chadfield ◽  
...  
Keyword(s):  
Host Range ◽  
Salmonella Enterica ◽  
Broad Host Range ◽  
Host Pathogen Interaction ◽  
Host Pathogen ◽  
Salmonella Enterica Serovar Dublin

scholarly journals Cooperation of Adhesin Alleles in Salmonella-Host Tropism

mSphere ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Leon De Masi ◽  
Min Yue ◽  
Changmin Hu ◽  
Alexey V. Rakov ◽  
Shelley C. Rankin ◽  
...  
Keyword(s):  
Host Range ◽  
Salmonella Enterica ◽  
Bacterial Pathogen ◽  
The United States ◽  
Host Adaptation ◽  
Broad Host Range ◽  
Intestinal Epithelial ◽  
Content Type ◽  
Contaminated Food ◽  
Colonization Factors

ABSTRACT Salmonella enterica remains a leading foodborne bacterial pathogen in the United States; infected livestock serve often as the source of contaminated food products. A study estimated that over a billion Salmonella gastroenteritis cases and up to 33 million typhoid cases occur annually worldwide, with 3.5 million deaths. Although many Salmonella strains with a broad host range present preferential associations with certain host species, it is not clear what determines the various levels of host adaptation. Here, causal properties of host associations were determined with allelic variants of three colonization factors of S. enterica serovar Newport, a most frequent zoonotic serovar. This is the first study that related not only individual but also a small group of host-associated gene variants with functional properties that cooperate to determine the level of host-adapted virulence. The detected associations should help to identify sources of Salmonella infections in both humans and animals. Allelic combinations and host specificities for three fimbrial adhesins, FimH, BcfD, and StfH, were compared for 262 strains of Salmonella enterica serovar Newport, a frequent human and livestock pathogen. Like FimH, BcfD had two major alleles (designated A and B), whereas StfH had two allelic groups, each with two alleles (subgroup A1 and A2 and subgroup B1 and B2). The most prevalent combinations of FimH/BcfD/StfH alleles in S. Newport were A/A/A1 and B/B/B1. The former set was most frequently found in bovine and porcine strains, whereas the latter combination was most frequently found in environmental and human isolates. Bacteria genetically engineered to express Fim, Bcf, or Stf fimbriae on their surface were tested with the different alleles for binding to human, porcine, and bovine intestinal epithelial cells. The major allelic combinations with bovine and porcine strains (A/A/A1) or with human isolates (B/B/B1) provided at least two alleles capable of binding significantly better than the other alleles to an intestinal epithelial cell line from the respective host(s). However, each combination of alleles kept at least one allele mediating binding to an intestinal epithelial cell from another host. These findings indicated that allelic variation in multiple adhesins of S. Newport contributes to bacterial adaptation to certain preferential hosts without losing the capacity to maintain a broad host range. IMPORTANCE Salmonella enterica remains a leading foodborne bacterial pathogen in the United States; infected livestock serve often as the source of contaminated food products. A study estimated that over a billion Salmonella gastroenteritis cases and up to 33 million typhoid cases occur annually worldwide, with 3.5 million deaths. Although many Salmonella strains with a broad host range present preferential associations with certain host species, it is not clear what determines the various levels of host adaptation. Here, causal properties of host associations were determined with allelic variants of three colonization factors of S. enterica serovar Newport, a most frequent zoonotic serovar. This is the first study that related not only individual but also a small group of host-associated gene variants with functional properties that cooperate to determine the level of host-adapted virulence. The detected associations should help to identify sources of Salmonella infections in both humans and animals.

scholarly journals Host Restriction of Salmonella enterica Serotype Typhi Is Not Caused by Functional Alteration of SipA, SopB, or SopD

2005 ◽  
Vol 73 (12) ◽  
pp. 7817-7826 ◽  
Author(s):  
Manuela Raffatellu ◽  
Yao-Hui Sun ◽  
R. Paul Wilson ◽  
Quynh T. Tran ◽  
Daniela Chessa ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Fluid Secretion ◽  
Human Colon ◽  
Effector Proteins ◽  
Host Cells ◽  
Broad Host Range ◽  
Fluid Accumulation ◽  
T84 Cells ◽  
Sterile Culture ◽  
Functional Alteration

ABSTRACT Salmonella enterica serotype Typhi is a strictly human adapted pathogen that does not cause disease in nonprimate vertebrate hosts, while Salmonella enterica serotype Typhimurium is a broad-host-range pathogen. Serotype Typhi lacks some of the proteins (effectors) exported by the invasion-associated type III secretion system that are required by serotype Typhimurium for eliciting fluid secretion and inflammation in bovine ligated ileal loops. We investigated whether the remaining serotype Typhi effectors implicated in enteropathogenicity (SipA, SopB, and SopD) are functionally exchangeable with their serotype Typhimurium homologues. Serotype Typhi elicited fluid accumulation in bovine ligated ileal loops at levels similar to those elicited by a noninvasive serotype Typhimurium strain (the sipA sopABDE2 mutant) or by sterile culture medium. However, introduction of the cloned serotype Typhi sipA, sopB, and sopD genes complemented the ability of a serotype Typhimurium sipA sopABDE2 mutant to elicit fluid secretion in bovine ligated ileal loops. Introduction of the cloned serotype Typhi sipA, sopB, and sopD genes increased the invasiveness of a serotype Typhimurium sipA sopABDE2 mutant for human colon carcinoma epithelial (HT-29 and T84) cells and bovine kidney (MDBK) cells. Translational fusions between the mature TEM-1 β-lactamase reporter and SipA or SopD demonstrated that serotype Typhi translocates these effectors into host cells. We conclude that the inability of serotype Typhi to cause fluid accumulation in bovine ligated ileal loops is not caused by a functional alteration of its SipA, SopB, and SopD effector proteins with respect to their serotype Typhimurium homologues.

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.

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