Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.

Abstract:

:A highly invasive form of non-typhoidal Salmonella (iNTS) disease has recently been documented in many countries in sub-Saharan Africa. The most common Salmonella enterica serovar causing this disease is Typhimurium (Salmonella Typhimurium). We applied whole-genome sequence-based phylogenetic methods to define the population structure of sub-Saharan African invasive Salmonella Typhimurium isolates and compared these to global Salmonella Typhimurium populations. Notably, the vast majority of sub-Saharan invasive Salmonella Typhimurium isolates fell within two closely related, highly clustered phylogenetic lineages that we estimate emerged independently ∼52 and ∼35 years ago in close temporal association with the current HIV pandemic. Clonal replacement of isolates from lineage I by those from lineage II was potentially influenced by the use of chloramphenicol for the treatment of iNTS disease. Our analysis suggests that iNTS disease is in part an epidemic in sub-Saharan Africa caused by highly related Salmonella Typhimurium lineages that may have occupied new niches associated with a compromised human population and antibiotic treatment.

journal_name

Nat Genet

journal_title

Nature genetics

authors

Okoro CK,Kingsley RA,Connor TR,Harris SR,Parry CM,Al-Mashhadani MN,Kariuki S,Msefula CL,Gordon MA,de Pinna E,Wain J,Heyderman RS,Obaro S,Alonso PL,Mandomando I,MacLennan CA,Tapia MD,Levine MM,Tennant SM,Parkhill J,

doi

10.1038/ng.2423

subject

Has Abstract

pub_date

2012-11-01 00:00:00

pages

1215-21

issue

11

eissn

1061-4036

issn

1546-1718

pii

ng.2423

journal_volume

44

pub_type

杂志文章
  • Increased LIS1 expression affects human and mouse brain development.

    abstract::Deletions of the PAFAH1B1 gene (encoding LIS1) in 17p13.3 result in isolated lissencephaly sequence, and extended deletions including the YWHAE gene (encoding 14-3-3epsilon) cause Miller-Dieker syndrome. We identified seven unrelated individuals with submicroscopic duplication in 17p13.3 involving the PAFAH1B1 and/or ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.302

    authors: Bi W,Sapir T,Shchelochkov OA,Zhang F,Withers MA,Hunter JV,Levy T,Shinder V,Peiffer DA,Gunderson KL,Nezarati MM,Shotts VA,Amato SS,Savage SK,Harris DJ,Day-Salvatore DL,Horner M,Lu XY,Sahoo T,Yanagawa Y,Beaudet AL,

    更新日期:2009-02-01 00:00:00

  • Fras1 deficiency results in cryptophthalmos, renal agenesis and blebbed phenotype in mice.

    abstract::Loss of tight association between epidermis and dermis underlies several blistering disorders and is frequently caused by impaired function of extracellular matrix (ECM) proteins. Here we describe a new protein in mouse, Fras1, that is specifically detected in a linear fashion underlying the epidermis and the basal su...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1168

    authors: Vrontou S,Petrou P,Meyer BI,Galanopoulos VK,Imai K,Yanagi M,Chowdhury K,Scambler PJ,Chalepakis G

    更新日期:2003-06-01 00:00:00

  • Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration.

    abstract::Leber congenital amaurosis (LCA) is a blinding retinal disease that presents within the first year after birth. Using exome sequencing, we identified mutations in the nicotinamide adenine dinucleotide (NAD) synthase gene NMNAT1 encoding nicotinamide mononucleotide adenylyltransferase 1 in eight families with LCA, incl...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2356

    authors: Koenekoop RK,Wang H,Majewski J,Wang X,Lopez I,Ren H,Chen Y,Li Y,Fishman GA,Genead M,Schwartzentruber J,Solanki N,Traboulsi EI,Cheng J,Logan CV,McKibbin M,Hayward BE,Parry DA,Johnson CA,Nageeb M,Finding of Rare Dis

    更新日期:2012-09-01 00:00:00

  • Loss of Cdk4 expression causes insulin-deficient diabetes and Cdk4 activation results in beta-islet cell hyperplasia.

    abstract::To ascertain the role of cyclin-dependent kinase 4 (Cdk4) in vivo, we have targeted the mouse Cdk4 locus by homologous recombination to generate two strains of mice, one that lacks Cdk4 expression and one that expresses a Cdk4 molecule with an activating mutation. Embryonic fibroblasts proliferate normally in the abse...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/8751

    authors: Rane SG,Dubus P,Mettus RV,Galbreath EJ,Boden G,Reddy EP,Barbacid M

    更新日期:1999-05-01 00:00:00

  • Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia.

    abstract::Differences in three-dimensional (3D) chromatin architecture can influence the integrity of topologically associating domains (TADs) and rewire specific enhancer-promoter interactions, impacting gene expression and leading to human disease. Here we investigate the 3D chromatin architecture in T cell acute lymphoblasti...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-020-0602-9

    authors: Kloetgen A,Thandapani P,Ntziachristos P,Ghebrechristos Y,Nomikou S,Lazaris C,Chen X,Hu H,Bakogianni S,Wang J,Fu Y,Boccalatte F,Zhong H,Paietta E,Trimarchi T,Zhu Y,Van Vlierberghe P,Inghirami GG,Lionnet T,Aifantis I

    更新日期:2020-04-01 00:00:00

  • Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.

    abstract::Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to ~1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency ≤ 0.01) variant BP associations (P < 5 × 10-8), of which 32...

    journal_title:Nature genetics

    pub_type: 杂志文章,meta分析

    doi:10.1038/s41588-020-00713-x

    authors: Surendran P,Feofanova EV,Lahrouchi N,Ntalla I,Karthikeyan S,Cook J,Chen L,Mifsud B,Yao C,Kraja AT,Cartwright JH,Hellwege JN,Giri A,Tragante V,Thorleifsson G,Liu DJ,Prins BP,Stewart ID,Cabrera CP,Eales JM,Akbarov A

    更新日期:2020-12-01 00:00:00

  • Biological and biomedical implications of the co-evolution of pathogens and their hosts.

    abstract::Co-evolution between host and pathogen is, in principle, a powerful determinant of the biology and genetics of infection and disease. Yet co-evolution has proven difficult to demonstrate rigorously in practice, and co-evolutionary thinking is only just beginning to inform medical or veterinary research in any meaningf...

    journal_title:Nature genetics

    pub_type: 杂志文章,评审

    doi:10.1038/ng1202-569

    authors: Woolhouse ME,Webster JP,Domingo E,Charlesworth B,Levin BR

    更新日期:2002-12-01 00:00:00

  • Genome-wide meta-analyses identify multiple loci associated with smoking behavior.

    abstract::Consistent but indirect evidence has implicated genetic factors in smoking behavior. We report meta-analyses of several smoking phenotypes within cohorts of the Tobacco and Genetics Consortium (n = 74,053). We also partnered with the European Network of Genetic and Genomic Epidemiology (ENGAGE) and Oxford-GlaxoSmithKl...

    journal_title:Nature genetics

    pub_type: 杂志文章,meta分析

    doi:10.1038/ng.571

    authors: Tobacco and Genetics Consortium.

    更新日期:2010-05-01 00:00:00

  • Effect of the myotonic dystrophy (DM) mutation on mRNA levels of the DM gene.

    abstract::Myotonic dystrophy (DM) results from the amplification of an unstable CTG repeat in the 3' untranslated region of a transcript encoding a putative serine/threonine kinase. We have analysed the amplification of the repeat and the steady state levels of the DM kinase (DMK) mRNA in tissues and cell lines from normal and ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0793-233

    authors: Sabouri LA,Mahadevan MS,Narang M,Lee DS,Surh LC,Korneluk RG

    更新日期:1993-07-01 00:00:00

  • Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity.

    abstract::Cells respond to stimuli by changes in various processes, including signaling pathways and gene expression. Efforts to identify components of these responses increasingly depend on mRNA profiling and genetic library screens. By comparing the results of these two assays across various stimuli, we found that genetic scr...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.337

    authors: Yeger-Lotem E,Riva L,Su LJ,Gitler AD,Cashikar AG,King OD,Auluck PK,Geddie ML,Valastyan JS,Karger DR,Lindquist S,Fraenkel E

    更新日期:2009-03-01 00:00:00

  • CACP, encoding a secreted proteoglycan, is mutated in camptodactyly-arthropathy-coxa vara-pericarditis syndrome.

    abstract::Altered growth and function of synoviocytes, the intimal cells which line joint cavities and tendon sheaths, occur in a number of skeletal diseases. Hyperplasia of synoviocytes is found in both rheumatoid arthritis and osteoarthritis, despite differences in the underlying aetiologies of the two disorders. We have stud...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/15496

    authors: Marcelino J,Carpten JD,Suwairi WM,Gutierrez OM,Schwartz S,Robbins C,Sood R,Makalowska I,Baxevanis A,Johnstone B,Laxer RM,Zemel L,Kim CA,Herd JK,Ihle J,Williams C,Johnson M,Raman V,Alonso LG,Brunoni D,Gerstein A,

    更新日期:1999-11-01 00:00:00

  • A single-nucleotide polymorphism tagging set for human drug metabolism and transport.

    abstract::Interindividual variability in drug response, ranging from no therapeutic benefit to life-threatening adverse reactions, is influenced by variation in genes that control the absorption, distribution, metabolism and excretion of drugs. We genotyped 904 single-nucleotide polymorphisms (SNPs) from 55 such genes in two po...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1488

    authors: Ahmadi KR,Weale ME,Xue ZY,Soranzo N,Yarnall DP,Briley JD,Maruyama Y,Kobayashi M,Wood NW,Spurr NK,Burns DK,Roses AD,Saunders AM,Goldstein DB

    更新日期:2005-01-01 00:00:00

  • Mitochondrial aspartyl-tRNA synthetase deficiency causes leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation.

    abstract::Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation (LBSL) has recently been defined based on a highly characteristic constellation of abnormalities observed by magnetic resonance imaging and spectroscopy. LBSL is an autosomal recessive disease, most often manifesting in early childho...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng2013

    authors: Scheper GC,van der Klok T,van Andel RJ,van Berkel CG,Sissler M,Smet J,Muravina TI,Serkov SV,Uziel G,Bugiani M,Schiffmann R,Krägeloh-Mann I,Smeitink JA,Florentz C,Van Coster R,Pronk JC,van der Knaap MS

    更新日期:2007-04-01 00:00:00

  • Loss-of-function mutations in TYROBP (DAP12) result in a presenile dementia with bone cysts.

    abstract::Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL; MIM 221770), also known as Nasu-Hakola disease, is a recessively inherited disease characterized by a combination of psychotic symptoms rapidly progressing to presenile dementia and bone cysts restricted to wrists and ankles. PLOSL ha...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/77153

    authors: Paloneva J,Kestilä M,Wu J,Salminen A,Böhling T,Ruotsalainen V,Hakola P,Bakker AB,Phillips JH,Pekkarinen P,Lanier LL,Timonen T,Peltonen L

    更新日期:2000-07-01 00:00:00

  • Cretinism with combined hormone deficiency caused by a mutation in the PIT1 gene.

    abstract::Cretinism is marked by irreversible mental and growth retardation. We describe here an entirely new case of cretinism showing combined pituitary hormone deficiencies of thyrotropin, growth hormone and prolactin that appears to be caused by homozygosity for a nonsense mutation in the gene for the pituitary specific tra...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0492-56

    authors: Tatsumi K,Miyai K,Notomi T,Kaibe K,Amino N,Mizuno Y,Kohno H

    更新日期:1992-04-01 00:00:00

  • LMNA, encoding lamin A/C, is mutated in partial lipodystrophy.

    abstract::The lipodystrophies are a group of disorders characterized by the absence or reduction of subcutaneous adipose tissue. Partial lipodystrophy (PLD; MIM 151660) is an inherited condition in which a regional (trunk and limbs) loss of fat occurs during the peri-pubertal phase. Additionally, variable degrees of resistance ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/72807

    authors: Shackleton S,Lloyd DJ,Jackson SN,Evans R,Niermeijer MF,Singh BM,Schmidt H,Brabant G,Kumar S,Durrington PN,Gregory S,O'Rahilly S,Trembath RC

    更新日期:2000-02-01 00:00:00

  • Contribution of the FMR1 gene mutation to human intellectual dysfunction.

    abstract::The degree to which genetic factors influence human intelligence remains a matter of some controversy. However, there is little doubt that single gene mutations can significantly alter brain development and function. For example, mutations affecting the FMR1 gene cause the fragile X syndrome, the most prevalent known ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1195-331

    authors: Reiss AL,Freund LS,Baumgardner TL,Abrams MT,Denckla MB

    更新日期:1995-11-01 00:00:00

  • Identification of a novel X-linked gene responsible for Emery-Dreifuss muscular dystrophy.

    abstract::Emery-Dreifuss muscular dystrophy (EDMD) is an X-linked recessive disorder characterized by slowly progressing contractures, wasting of skeletal muscle and cardiomyopathy. Heart block is a frequent cause of death. The disease gene has been mapped to distal Xq28. Among many genes in this region, we selected eight trans...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1294-323

    authors: Bione S,Maestrini E,Rivella S,Mancini M,Regis S,Romeo G,Toniolo D

    更新日期:1994-12-01 00:00:00

  • A human homologue of the Drosophila eyes absent gene underlies branchio-oto-renal (BOR) syndrome and identifies a novel gene family.

    abstract::A candidate gene for Branchio-Oto-Renal (BOR) syndrome was identified at chromosome 8q13.3 by positional cloning and shown to underlie the disease. This gene is a human homologue of the Drosophila eyes absent gene (eya), and was therefore called EYA1. A highly conserved 271-amino acid C-terminal region was also found ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0297-157

    authors: Abdelhak S,Kalatzis V,Heilig R,Compain S,Samson D,Vincent C,Weil D,Cruaud C,Sahly I,Leibovici M,Bitner-Glindzicz M,Francis M,Lacombe D,Vigneron J,Charachon R,Boven K,Bedbeder P,Van Regemorter N,Weissenbach J,Petit C

    更新日期:1997-02-01 00:00:00

  • A mutant PTH/PTHrP type I receptor in enchondromatosis.

    abstract::Enchondromas are common benign cartilage tumors of bone. They can occur as solitary lesions or as multiple lesions in enchondromatosis (Ollier and Maffucci diseases). Clinical problems caused by enchondromas include skeletal deformity and the potential for malignant change to chondrosarcoma. The extent of skeletal inv...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng844

    authors: Hopyan S,Gokgoz N,Poon R,Gensure RC,Yu C,Cole WG,Bell RS,Jüppner H,Andrulis IL,Wunder JS,Alman BA

    更新日期:2002-03-01 00:00:00

  • Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells.

    abstract::The conversion of lineage-committed cells to induced pluripotent stem cells (iPSCs) by reprogramming is accompanied by a global remodeling of the epigenome, resulting in altered patterns of gene expression. Here we characterize the transcriptional reorganization of large intergenic non-coding RNAs (lincRNAs) that occu...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.710

    authors: Loewer S,Cabili MN,Guttman M,Loh YH,Thomas K,Park IH,Garber M,Curran M,Onder T,Agarwal S,Manos PD,Datta S,Lander ES,Schlaeger TM,Daley GQ,Rinn JL

    更新日期:2010-12-01 00:00:00

  • Identification of DOK genes as lung tumor suppressors.

    abstract::Genome-wide analyses of human lung adenocarcinoma have identified regions of consistent copy-number gain or loss, but in many cases the oncogenes and tumor suppressors presumed to reside in these loci remain to be determined. Here we identify the downstream of tyrosine kinase (Dok) family members Dok1, Dok2 and Dok3 a...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.527

    authors: Berger AH,Niki M,Morotti A,Taylor BS,Socci ND,Viale A,Brennan C,Szoke J,Motoi N,Rothman PB,Teruya-Feldstein J,Gerald WL,Ladanyi M,Pandolfi PP

    更新日期:2010-03-01 00:00:00

  • The fecal metabolome as a functional readout of the gut microbiome.

    abstract::The human gut microbiome plays a key role in human health 1 , but 16S characterization lacks quantitative functional annotation 2 . The fecal metabolome provides a functional readout of microbial activity and can be used as an intermediate phenotype mediating host-microbiome interactions 3 . In this comprehensive desc...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-018-0135-7

    authors: Zierer J,Jackson MA,Kastenmüller G,Mangino M,Long T,Telenti A,Mohney RP,Small KS,Bell JT,Steves CJ,Valdes AM,Spector TD,Menni C

    更新日期:2018-06-01 00:00:00

  • Association of host genome with intestinal microbial composition in a large healthy cohort.

    abstract::Intestinal microbiota is known to be important in health and disease. Its composition is influenced by both environmental and host factors. Few large-scale studies have evaluated the association between host genetic variation and the composition of microbiota. We recruited a cohort of 1,561 healthy individuals, of who...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3693

    authors: Turpin W,Espin-Garcia O,Xu W,Silverberg MS,Kevans D,Smith MI,Guttman DS,Griffiths A,Panaccione R,Otley A,Xu L,Shestopaloff K,Moreno-Hagelsieb G,GEM Project Research Consortium.,Paterson AD,Croitoru K

    更新日期:2016-11-01 00:00:00

  • A reference genome for pea provides insight into legume genome evolution.

    abstract::We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes,...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-019-0480-1

    authors: Kreplak J,Madoui MA,Cápal P,Novák P,Labadie K,Aubert G,Bayer PE,Gali KK,Syme RA,Main D,Klein A,Bérard A,Vrbová I,Fournier C,d'Agata L,Belser C,Berrabah W,Toegelová H,Milec Z,Vrána J,Lee H,Kougbeadjo A,Térézol

    更新日期:2019-09-01 00:00:00

  • Chaperone suppression of aggregation and altered subcellular proteasome localization imply protein misfolding in SCA1.

    abstract::Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder caused by expansion of a polyglutamine tract in ataxin-1. In affected neurons of SCA1 patients and transgenic mice, mutant ataxin-1 accumulates in a single, ubiquitin-positive nuclear inclusion. In this study, we show that these i...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/502

    authors: Cummings CJ,Mancini MA,Antalffy B,DeFranco DB,Orr HT,Zoghbi HY

    更新日期:1998-06-01 00:00:00

  • Activating germline mutations in STAT3 cause early-onset multi-organ autoimmune disease.

    abstract::Monogenic causes of autoimmunity provide key insights into the complex regulation of the immune system. We report a new monogenic cause of autoimmunity resulting from de novo germline activating STAT3 mutations in five individuals with a spectrum of early-onset autoimmune disease, including type 1 diabetes. These find...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3040

    authors: Flanagan SE,Haapaniemi E,Russell MA,Caswell R,Allen HL,De Franco E,McDonald TJ,Rajala H,Ramelius A,Barton J,Heiskanen K,Heiskanen-Kosma T,Kajosaari M,Murphy NP,Milenkovic T,Seppänen M,Lernmark Å,Mustjoki S,Otonkoski T

    更新日期:2014-08-01 00:00:00

  • Transferrin receptor is necessary for development of erythrocytes and the nervous system.

    abstract::Plasma iron circulates bound to transferrin (Trf), which solubilizes the ferric ion and attenuates its reactivity. Diferric Trf interacts with cell-surface Trf receptor (Trfr) to undergo receptor-mediated endocytosis into specialized endosomes. Endosomal acidification leads to iron release, and iron is transported out...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/7727

    authors: Levy JE,Jin O,Fujiwara Y,Kuo F,Andrews NC

    更新日期:1999-04-01 00:00:00

  • DNA repair mediated by endonuclease-independent LINE-1 retrotransposition.

    abstract::Long interspersed elements (LINE-1s) are abundant retrotransposons in mammalian genomes that probably retrotranspose by target site-primed reverse transcription (TPRT). During TPRT, the LINE-1 endonuclease cleaves genomic DNA, freeing a 3' hydroxyl that serves as a primer for reverse transcription of LINE-1 RNA by LIN...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng898

    authors: Morrish TA,Gilbert N,Myers JS,Vincent BJ,Stamato TD,Taccioli GE,Batzer MA,Moran JV

    更新日期:2002-06-01 00:00:00

  • Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis.

    abstract::The eighth annual Human Genome Variation Meeting was held in September 2006 in the Hong Kong Special Administrative Region, China. The meeting highlighted recent advances in characterization of genetic variation, including genome-wide association studies and structural variation. ...

    journal_title:Nature genetics

    pub_type:

    doi:10.1038/ng0207-153

    authors: Abecasis G,Tam PK,Bustamante CD,Ostrander EA,Scherer SW,Chanock SJ,Kwok PY,Brookes AJ

    更新日期:2007-02-01 00:00:00