Ontology type: schema:ScholarlyArticle Open Access: True
2019-12
AUTHORSJ. J. van Aartsen, C. E. Moore, C. M. Parry, P. Turner, N. Phot, S. Mao, K. Suy, T. Davies, A. Giess, A. E. Sheppard, T. E. A. Peto, N. P. J. Day, D. W. Crook, A. S. Walker, N. Stoesser
ABSTRACTBACKGROUND: Extended-spectrum cephalosporin resistance (ESC-R) in Escherichia coli and Klebsiella pneumoniae is a healthcare threat; high gastrointestinal carriage rates are reported from South-east Asia. Colonisation prevalence data in Cambodia are lacking. The aim of this study was to determine gastrointestinal colonisation prevalence of ESC-resistant E. coli (ESC-R-EC) and K. pneumoniae (ESC-R-KP) in Cambodian children/adolescents and associated socio-demographic risk factors; and to characterise relevant resistance genes, their genetic contexts, and the genetic relatedness of ESC-R strains using whole genome sequencing (WGS). RESULTS: Faeces and questionnaire data were obtained from individuals < 16 years in north-western Cambodia, 2012. WGS of cultured ESC-R-EC/KP was performed (Illumina). Maximum likelihood phylogenies were used to characterise relatedness of isolates; ESC-R-associated resistance genes and their genetic contexts were identified from de novo assemblies using BLASTn and automated/manual annotation. 82/148 (55%) of children/adolescents were ESC-R-EC/KP colonised; 12/148 (8%) were co-colonised with both species. Independent risk factors for colonisation were hospitalisation (OR: 3.12, 95% CI [1.52-6.38]) and intestinal parasites (OR: 3.11 [1.29-7.51]); school attendance conferred decreased risk (OR: 0.44 [0.21-0.92]. ESC-R strains were diverse; the commonest ESC-R mechanisms were blaCTX-M 1 and 9 sub-family variants. Structures flanking these genes were highly variable, and for blaCTX-M-15, - 55 and - 27 frequently involved IS26. Chromosomal blaCTX-M integration was common in E. coli. CONCLUSIONS: Gastrointestinal ESC-R-EC/KP colonisation is widespread in Cambodian children/adolescents; hospital admission and intestinal parasites are independent risk factors. The genetic contexts of blaCTX-M are highly mosaic, consistent with rapid horizontal exchange. Chromosomal integration of blaCTX-M may result in stable propagation in these community-associated pathogens. More... »
PAGES59
http://scigraph.springernature.com/pub.10.1186/s12866-019-1431-9
DOIhttp://dx.doi.org/10.1186/s12866-019-1431-9
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1112738991
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/30866820
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "University of Liverpool",
"id": "https://www.grid.ac/institutes/grid.10025.36",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK",
"Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, The Ronald Ross Building, 8 West Derby Street, L69 7BE, Liverpool, UK"
],
"type": "Organization"
},
"familyName": "van Aartsen",
"givenName": "J. J.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oxford",
"id": "https://www.grid.ac/institutes/grid.4991.5",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK"
],
"type": "Organization"
},
"familyName": "Moore",
"givenName": "C. E.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Liverpool School of Tropical Medicine",
"id": "https://www.grid.ac/institutes/grid.48004.38",
"name": [
"Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK"
],
"type": "Organization"
},
"familyName": "Parry",
"givenName": "C. M.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oxford",
"id": "https://www.grid.ac/institutes/grid.4991.5",
"name": [
"Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia",
"Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK"
],
"type": "Organization"
},
"familyName": "Turner",
"givenName": "P.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Angkor Hospital for Children",
"id": "https://www.grid.ac/institutes/grid.459332.a",
"name": [
"Angkor Hospital for Children, Siem Reap, Cambodia"
],
"type": "Organization"
},
"familyName": "Phot",
"givenName": "N.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Angkor Hospital for Children",
"id": "https://www.grid.ac/institutes/grid.459332.a",
"name": [
"Angkor Hospital for Children, Siem Reap, Cambodia"
],
"type": "Organization"
},
"familyName": "Mao",
"givenName": "S.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Angkor Hospital for Children",
"id": "https://www.grid.ac/institutes/grid.459332.a",
"name": [
"Angkor Hospital for Children, Siem Reap, Cambodia"
],
"type": "Organization"
},
"familyName": "Suy",
"givenName": "K.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oxford",
"id": "https://www.grid.ac/institutes/grid.4991.5",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK"
],
"type": "Organization"
},
"familyName": "Davies",
"givenName": "T.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oxford",
"id": "https://www.grid.ac/institutes/grid.4991.5",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK"
],
"type": "Organization"
},
"familyName": "Giess",
"givenName": "A.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oxford",
"id": "https://www.grid.ac/institutes/grid.4991.5",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK"
],
"type": "Organization"
},
"familyName": "Sheppard",
"givenName": "A. E.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oxford",
"id": "https://www.grid.ac/institutes/grid.4991.5",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK"
],
"type": "Organization"
},
"familyName": "Peto",
"givenName": "T. E. A.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Mahidol University",
"id": "https://www.grid.ac/institutes/grid.10223.32",
"name": [
"Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK",
"Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand"
],
"type": "Organization"
},
"familyName": "Day",
"givenName": "N. P. J.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oxford",
"id": "https://www.grid.ac/institutes/grid.4991.5",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK"
],
"type": "Organization"
},
"familyName": "Crook",
"givenName": "D. W.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oxford",
"id": "https://www.grid.ac/institutes/grid.4991.5",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK"
],
"type": "Organization"
},
"familyName": "Walker",
"givenName": "A. S.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "John Radcliffe Hospital",
"id": "https://www.grid.ac/institutes/grid.8348.7",
"name": [
"Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK",
"Department of Microbiology/Infectious Diseases, John Radcliffe Hospital, Headley Way, OX3 9DU, Headington, UK"
],
"type": "Organization"
},
"familyName": "Stoesser",
"givenName": "N.",
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1097/inf.0000000000001187",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001331743"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1097/inf.0000000000001187",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001331743"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1097/inf.0000000000001187",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001331743"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/cmr.00023-13",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004626633"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jac/dkv021",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005868252"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.ijantimicag.2010.03.005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007146830"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/jcm.00378-15",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008915759"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/tmi.12398",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009128838"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1080/20469047.2015.1109241",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011034927"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/tmi.12824",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011921290"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1179/2046905515y.0000000008",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012014153"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/j.1365-2958.2006.05172.x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012203977"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0022-2836(05)80360-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013618994"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/trstmh/trt005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014377755"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0123719",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015389193"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/mbio.00762-15",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018097862"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/0471250953.bi1105s31",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018775132"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/j.1574-6976.2011.00268.x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018812640"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkj014",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021624519"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aac.01503-13",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029484409"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3201/eid1505.071299",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029553785"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0138179",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029769383"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btu153",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031501454"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aac.50.4.1257-1262.2006",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032185686"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/jcm.43.8.4178-4182.2005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033170488"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jac/dks065",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034505415"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/2047-2994-1-39",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034525156",
"https://doi.org/10.1186/2047-2994-1-39"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jac/dkr434",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1037122471"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aac.00025-11",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042655017"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jac/dkt180",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044677035"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/mbio.00444-16",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046116132"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btl446",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046470836"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s10096-015-2350-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047515154",
"https://doi.org/10.1007/s10096-015-2350-9"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s10096-015-2350-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047515154",
"https://doi.org/10.1007/s10096-015-2350-9"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s1473-3099(08)70041-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047909659"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/j.1469-0691.2005.01358.x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047961065"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jac/dks118",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048832235"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pntd.0002880",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050185508"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s1473-3099(16)30319-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051092654"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/mbio.02162-15",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052423446"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1086/604713",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1058809803"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3855/jidc.1502",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1071482129"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.7326/0003-4819-74-5-657",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1073728675"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/jcm.02316-16",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1084221987"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/jcm.02316-16",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1084221987"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.ijid.2017.10.025",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1092636842"
],
"type": "CreativeWork"
}
],
"datePublished": "2019-12",
"datePublishedReg": "2019-12-01",
"description": "BACKGROUND: Extended-spectrum cephalosporin resistance (ESC-R) in Escherichia coli and Klebsiella pneumoniae is a healthcare threat; high gastrointestinal carriage rates are reported from South-east Asia. Colonisation prevalence data in Cambodia are lacking. The aim of this study was to determine gastrointestinal colonisation prevalence of ESC-resistant E. coli (ESC-R-EC) and K. pneumoniae (ESC-R-KP) in Cambodian children/adolescents and associated socio-demographic risk factors; and to characterise relevant resistance genes, their genetic contexts, and the genetic relatedness of ESC-R strains using whole genome sequencing (WGS).\nRESULTS: Faeces and questionnaire data were obtained from individuals <\u200916\u2009years in north-western Cambodia, 2012. WGS of cultured ESC-R-EC/KP was performed (Illumina). Maximum likelihood phylogenies were used to characterise relatedness of isolates; ESC-R-associated resistance genes and their genetic contexts were identified from de novo assemblies using BLASTn and automated/manual annotation. 82/148 (55%) of children/adolescents were ESC-R-EC/KP colonised; 12/148 (8%) were co-colonised with both species. Independent risk factors for colonisation were hospitalisation (OR: 3.12, 95% CI [1.52-6.38]) and intestinal parasites (OR: 3.11 [1.29-7.51]); school attendance conferred decreased risk (OR: 0.44 [0.21-0.92]. ESC-R strains were diverse; the commonest ESC-R mechanisms were blaCTX-M 1 and 9 sub-family variants. Structures flanking these genes were highly variable, and for blaCTX-M-15, -\u200955 and\u2009-\u200927 frequently involved IS26. Chromosomal blaCTX-M integration was common in E. coli.\nCONCLUSIONS: Gastrointestinal ESC-R-EC/KP colonisation is widespread in Cambodian children/adolescents; hospital admission and intestinal parasites are independent risk factors. The genetic contexts of blaCTX-M are highly mosaic, consistent with rapid horizontal exchange. Chromosomal integration of blaCTX-M may result in stable propagation in these community-associated pathogens.",
"genre": "research_article",
"id": "sg:pub.10.1186/s12866-019-1431-9",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.3638139",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1024253",
"issn": [
"1471-2180"
],
"name": "BMC Microbiology",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "19"
}
],
"name": "Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia",
"pagination": "59",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"9ae3babbefc25cc318f3d35fa71042db8141e700d0093193fd6bfefdfa1cca8b"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"30866820"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"100966981"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/s12866-019-1431-9"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1112738991"
]
}
],
"sameAs": [
"https://doi.org/10.1186/s12866-019-1431-9",
"https://app.dimensions.ai/details/publication/pub.1112738991"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-11T13:19",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000368_0000000368/records_78953_00000001.jsonl",
"type": "ScholarlyArticle",
"url": "https://link.springer.com/10.1186%2Fs12866-019-1431-9"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s12866-019-1431-9'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s12866-019-1431-9'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12866-019-1431-9'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12866-019-1431-9'
This table displays all metadata directly associated to this object as RDF triples.
301 TRIPLES
21 PREDICATES
71 URIs
21 LITERALS
9 BLANK NODES