Genome-Wide Screen for Salmonella Genes Required for Long-Term Systemic Infection of the Mouse
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{"title"=>"Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse", "type"=>"journal", "authors"=>[{"first_name"=>"Trevor D.", "last_name"=>"Lawley", "scopus_author_id"=>"7006033598"}, {"first_name"=>"Kaman", "last_name"=>"Chan", "scopus_author_id"=>"55477588300"}, {"first_name"=>"Lucinda J.", "last_name"=>"Thompson", "scopus_author_id"=>"7403729867"}, {"first_name"=>"Charles C.", "last_name"=>"Kim", "scopus_author_id"=>"35487505600"}, {"first_name"=>"Gregory R.", "last_name"=>"Govoni", "scopus_author_id"=>"6602259584"}, {"first_name"=>"Denise M.", "last_name"=>"Monack", "scopus_author_id"=>"6701752752"}], "year"=>2006, "source"=>"PLoS Pathogens", "identifiers"=>{"pmid"=>"16518469", "issn"=>"15537366", "sgr"=>"33645777008", "pui"=>"43555761", "scopus"=>"2-s2.0-33645777008", "isbn"=>"1553-7374 (Electronic)", "doi"=>"10.1371/journal.ppat.0020011"}, "id"=>"59d1f6df-7cba-3174-80a2-a12eb2b91a85", "abstract"=>"A microarray-based negative selection screen was performed to identify Salmonella enterica serovar Typhimurium (serovar Typhimurium) genes that contribute to long-term systemic infection in 129X1/SvJ (Nramp1r) mice. A high-complexity transposon-mutagenized library was used to infect mice intraperitoneally, and the selective disappearance of mutants was monitored after 7, 14, 21, and 28 d postinfection. One hundred and eighteen genes were identified to contribute to serovar Typhimurium infection of the spleens of mice by 28 d postinfection. The negatively selected mutants represent many known aspects of Salmonella physiology and pathogenesis, although the majority of the identified genes are of putative or unknown function. Approximately 30% of the negatively selected genes correspond to horizontally acquired regions such as those within Salmonella pathogenicity islands (SPI 1–5), prophages (Gifsy-1 and −2 and remnant), and the pSLT virulence plasmid. In addition, mutations in genes responsible for outer membrane structure and remodeling, such as LPS- and PhoP-regulated and fimbrial genes, were also selected against. Competitive index experiments demonstrated that the secreted SPI2 effectors SseK2 and SseJ as well as the SPI4 locus are attenuated relative to wild-type bacteria during systemic infection. Interestingly, several SPI1-encoded type III secretion system effectors/translocases are required by serovar Typhimurium to establish and, unexpectedly, to persist systemically, challenging the present description of Salmonella pathogenesis. Moreover, we observed a progressive selection against serovar Typhimurium mutants based upon the duration of the infection, suggesting that different classes of genes may be required at distinct stages of infection. Overall, these data indicate that Salmonella long-term systemic infection in the mouse requires a diverse repertoire of virulence factors. This diversity of genes presumably reflects the fact that bacteria sequentially encounter a variety of host environments and that Salmonella has evolved to respond to these selective forces in a way that permits both the bacteria and the host to survive.", "link"=>"http://www.mendeley.com/research/genomewide-screen-salmonella-genes-required-longterm-systemic-infection-mouse", "reader_count"=>137, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>6, "Student > Doctoral Student"=>7, "Researcher"=>36, "Student > Ph. D. Student"=>45, "Student > Postgraduate"=>6, "Student > Master"=>11, "Other"=>1, "Student > Bachelor"=>14, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>6, "Student > Doctoral Student"=>7, "Researcher"=>36, "Student > Ph. D. Student"=>45, "Student > Postgraduate"=>6, "Student > Master"=>11, "Other"=>1, "Student > Bachelor"=>14, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>17, "Agricultural and Biological Sciences"=>91, "Medicine and Dentistry"=>6, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Physics and Astronomy"=>1, "Immunology and Microbiology"=>13}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>13}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>91}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>17}, "Unspecified"=>{"Unspecified"=>5}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>3, "Luxembourg"=>1, "Sudan"=>1, "Italy"=>2, "Indonesia"=>1, "Spain"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/960478"], "description"=>"<p>Horizontal bars indicate the geometric means of CI values, and individual CI values are illustrated with open circles. The geometric means and standard errors for each mutant at day 3 in the MLN and spleen are: ΔSPI1, 0.20 ± 0.06 and 0.30 ± 0.03; <i>orgA</i>::Tc, 0.12 ± 0.06 and 0.17 ± 0.04; <i>sipB</i>::Cm, 0.19 ± 0.03 and 0.21 ± 0.05; <i>sipC</i>::Cm, 0.22 ± 0.03 and 0.18 ± 0.04; <i>sipD</i>::Cm, 0.20 ± 0.03 and 0.22 ± 0.05; <i>sseJ</i>::Kan, 0.32 ± 0.50 and 0.24 ± 0.07; and <i>avrA</i>::Cm, 1.01 ± 0.14 and 0.91 ± 0.32. Those values for day 30 are given in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0020011#ppat-0020011-t003\" target=\"_blank\">Table 3</a>. Geometric means in red indicate attenuated mutants whereas those in blue are not as assessed by the Mann-Whitney test.</p>", "links"=>[], "tags"=>["time-course", "demonstrating", "spi1", "effectors", "sipd", "mln", "spleens"], "article_id"=>630472, "categories"=>["Microbiology", "Infectious Diseases"], "users"=>["Trevor D Lawley", "Kaman Chan", "Lucinda J Thompson", "Charles C Kim", "Gregory R Govoni", "Denise M Monack"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.0020011.g004", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CI_Time_Course_Demonstrating_the_Requirement_of_the_SPI1_Effectors_SipB_SipC_and_SipD_for_the_Establishment_and_Maintenance_of_Infection_in_the_MLN_and_Spleens_of_Nramp1_r_Mice_/630472", "title"=>"CI Time-Course Demonstrating the Requirement of the SPI1 Effectors SipB, SipC, and SipD for the Establishment and Maintenance of Infection in the MLN and Spleens of <i>Nramp1<sup>r</sup></i> Mice", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:50:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/960308"], "description"=>"<p>The dendogram was generated from a single dataset which included arrays from both mouse passages. For the first passage, spleen pooled arrays from 7, 14, 21, 28, and 49 d postinfection, as well as input arrays, were included and are indicated by the prefix “P1.” For the second 29-d passage, spleen and liver pooled arrays, input arrays, and individual mouse tissue arrays were included. Arrays corresponding to the same time point are grouped according to color boxes.</p>", "links"=>[], "tags"=>["dendogram", "illustrating", "points"], "article_id"=>630316, "categories"=>["Microbiology", "Infectious Diseases"], "users"=>["Trevor D Lawley", "Kaman Chan", "Lucinda J Thompson", "Charles C Kim", "Gregory R Govoni", "Denise M Monack"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.0020011.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microarray_Dendogram_Illustrating_the_Relationship_between_the_Different_Time_Points_and_Passages_/630316", "title"=>"Microarray Dendogram Illustrating the Relationship between the Different Time Points and Passages", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:49:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/960218"], "description"=>"<p>SAM two-class analysis was performed grouping various time points in order to identify the features that are most significantly different between time points. The data corresponding to these SGLs were manually assembled and verified to have the expected hybridization patterns, and then duplicate features were removed. The arrays were organized by time point and the features placed in genome order. Colored bars at the top indicate grouping of technical microarray replicates for the same time point, and the same color scheme was employed to delineate groups of features that exhibit the same time-dependent pattern (vertical bars on right of microarray data figure). Also indicated is the average splenic log10 CFU/ml bacterial load observed over the course of infection along with the predicted stages of the host immune response (S. Clare and G. Dougan, unpublished data). The orange circle on the <i>y</i>-axis indicates the initial inoculum of 1.6 × 10<sup>4</sup> CFUs. Bacterial loads were comparable between liver and spleen. The microarray data in this figure have been made available in a format that can be viewed in both Treeview and Excel (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0020011#ppat-0020011-sd001\" target=\"_blank\">Dataset S1</a>).</p>", "links"=>[], "tags"=>["serovar", "typhimurium"], "article_id"=>630226, "categories"=>["Microbiology", "Infectious Diseases"], "users"=>["Trevor D Lawley", "Kaman Chan", "Lucinda J Thompson", "Charles C Kim", "Gregory R Govoni", "Denise M Monack"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.0020011.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Time_Dependent_Negative_Selection_of_Serovar_Typhimurium_Mutants_/630226", "title"=>"Time-Dependent Negative Selection of Serovar Typhimurium Mutants", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:48:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/471749", "https://ndownloader.figshare.com/files/471761", "https://ndownloader.figshare.com/files/471807", "https://ndownloader.figshare.com/files/471824"], "description"=>"<div><p>A microarray-based negative selection screen was performed to identify Salmonella enterica serovar Typhimurium (serovar Typhimurium) genes that contribute to long-term systemic infection in 129X1/SvJ <em>(Nramp1<sup>r</sup>)</em> mice. A high-complexity transposon-mutagenized library was used to infect mice intraperitoneally, and the selective disappearance of mutants was monitored after 7, 14, 21, and 28 d postinfection. One hundred and eighteen genes were identified to contribute to serovar Typhimurium infection of the spleens of mice by 28 d postinfection. The negatively selected mutants represent many known aspects of <em>Salmonella</em> physiology and pathogenesis, although the majority of the identified genes are of putative or unknown function. Approximately 30% of the negatively selected genes correspond to horizontally acquired regions such as those within <em>Salmonella</em> pathogenicity islands (SPI 1–5), prophages (Gifsy-1 and −2 and remnant), and the pSLT virulence plasmid. In addition, mutations in genes responsible for outer membrane structure and remodeling, such as LPS- and PhoP-regulated and fimbrial genes, were also selected against. Competitive index experiments demonstrated that the secreted SPI2 effectors SseK2 and SseJ as well as the SPI4 locus are attenuated relative to wild-type bacteria during systemic infection. Interestingly, several SPI1-encoded type III secretion system effectors/translocases are required by serovar Typhimurium to establish and, unexpectedly, to persist systemically, challenging the present description of <em>Salmonella</em> pathogenesis. Moreover, we observed a progressive selection against serovar Typhimurium mutants based upon the duration of the infection, suggesting that different classes of genes may be required at distinct stages of infection. Overall, these data indicate that <em>Salmonella</em> long-term systemic infection in the mouse requires a diverse repertoire of virulence factors. This diversity of genes presumably reflects the fact that bacteria sequentially encounter a variety of host environments and that <em>Salmonella</em> has evolved to respond to these selective forces in a way that permits both the bacteria and the host to survive.</p></div>", "links"=>[], "tags"=>["genome-wide", "genes", "systemic"], "article_id"=>153012, "categories"=>["Cancer", "Microbiology"], "users"=>["Trevor D Lawley", "Kaman Chan", "Lucinda J Thompson", "Charles C Kim", "Gregory R Govoni", "Denise M Monack"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.0020011.sd001", "https://dx.doi.org/10.1371/journal.ppat.0020011.sg001", "https://dx.doi.org/10.1371/journal.ppat.0020011.st001", "https://dx.doi.org/10.1371/journal.ppat.0020011.st002"], "stats"=>{"downloads"=>16, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Screen_for_Salmonella_Genes_Required_for_Long_Term_Systemic_Infection_of_the_Mouse/153012", "title"=>"Genome-Wide Screen for <em>Salmonella</em> Genes Required for Long-Term Systemic Infection of the Mouse", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2006-02-24 00:50:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/960384"], "description"=>"<div><p>(A) The features corresponding to genes in the SPI1 were extracted from each of the passage 1 and passage 2 datasets. Each row represents a feature presented in genome order. Each column corresponds to an array, and columns are grouped by color bars to indicate either technical replicates or samples from the same type of organ. Passage 1 arrays include spleen pooled arrays and input arrays whereas passage 2 arrays include input, spleen, and liver pooled, and individual mouse tissue arrays (indicated by numbers) and are labeled at the top of each panel. Asterisks along the left of each panel correspond to features that were identified by SAM analysis as being significant. Black bars along the right group together the features that correspond to the same gene. Grey indicates features that have missing data, blue or black indicate mutants that are still present in the sample relative to the library reference, and yellow indicates mutants that are absent in the sample relative to the library reference.</p><p>(B) Genetic map of SPI1 illustrating genes identified as contributing to systemic disease for 28 d postchallenge. Vertical arrows below ORF indicate specific genes identified in the screen, with black arrows showing those identified in both passages and grey arrows showing those genes identified in one passage. ORF are colored to represent function: blue represents T3SS; green, regulartory/chaperone; and red, secreted effectors.</p></div>", "links"=>[], "tags"=>["genes", "negatively"], "article_id"=>630391, "categories"=>["Microbiology", "Infectious Diseases"], "users"=>["Trevor D Lawley", "Kaman Chan", "Lucinda J Thompson", "Charles C Kim", "Gregory R Govoni", "Denise M Monack"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.0020011.g003", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SPI1_Genes_That_Were_Negatively_Selected_/630391", "title"=>"SPI1 Genes That Were Negatively Selected", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:49:44"}

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Relative Metric

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