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

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van Aartsen, J J, Moore, C E, Parry, Christopher, Turner, P, Phot, N, Mao, S, Suy, K, Davies, T, Giess, A, Sheppard, A E, Peto, T E A, Day, N P J, Crook, D W, Walker, A S and Stoesser, N (2019) 'Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia.'. BMC Microbiology, Vol 19, Issue 1, p. 59.

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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 bla 1 and 9 sub-family variants. Structures flanking these genes were highly variable, and for bla frequently involved IS26. Chromosomal bla 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 bla are highly mosaic, consistent with rapid horizontal exchange. Chromosomal integration of bla may result in stable propagation in these community-associated pathogens.

Item Type: Article
Subjects: QU Biochemistry > Genetics > QU 460 Genomics. Proteomics
QW Microbiology and Immunology > Bacteria > QW 138 Enterobacteriaceae
WA Public Health > Health Problems of Special Population Groups > WA 320 Child Welfare. Child Health Services.
WA Public Health > Health Problems of Special Population Groups > WA 395 Health in developing countries
WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 260 Enterobacteriaceae and other enteric infections
WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 290 Escherichia coli infections
WS Pediatrics > Diseases of Children and Adolescents > By System > WS 310 Digestive system
Faculty: Department: Clinical Sciences & International Health > Clinical Sciences Department
Digital Object Identifer (DOI): https://doi.org/10.1186/s12866-019-1431-9
Depositing User: Stacy Murtagh
Date Deposited: 18 Mar 2019 11:58
Last Modified: 18 Mar 2019 11:58
URI: http://archive.lstmed.ac.uk/id/eprint/10395

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