Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia View Full Text


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Article Info

DATE

2019-12

AUTHORS

J. 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

ABSTRACT

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). 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... »

PAGES

59

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12866-019-1431-9

DOI

http://dx.doi.org/10.1186/s12866-019-1431-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112738991

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30866820


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

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'


 

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281 Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
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283 https://www.grid.ac/institutes/grid.10223.32 schema:alternateName Mahidol University
284 schema:name Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
285 Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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287 https://www.grid.ac/institutes/grid.459332.a schema:alternateName Angkor Hospital for Children
288 schema:name Angkor Hospital for Children, Siem Reap, Cambodia
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290 https://www.grid.ac/institutes/grid.48004.38 schema:alternateName Liverpool School of Tropical Medicine
291 schema:name Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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293 https://www.grid.ac/institutes/grid.4991.5 schema:alternateName University of Oxford
294 schema:name Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
295 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
296 Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
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298 https://www.grid.ac/institutes/grid.8348.7 schema:alternateName John Radcliffe Hospital
299 schema:name Department of Microbiology/Infectious Diseases, John Radcliffe Hospital, Headley Way, OX3 9DU, Headington, UK
300 Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
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