BMC Microbiology (Mar 2019)

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

  • 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

DOI
https://doi.org/10.1186/s12866-019-1431-9
Journal volume & issue
Vol. 19, no. 1
pp. 1 – 14

Abstract

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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 CTX-M 1 and 9 sub-family variants. Structures flanking these genes were highly variable, and for bla CTX-M-15, − 55 and − 27 frequently involved IS26. Chromosomal bla CTX-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 bla CTX-M are highly mosaic, consistent with rapid horizontal exchange. Chromosomal integration of bla CTX-M may result in stable propagation in these community-associated pathogens.

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