Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia
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 dete...
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| Format: | Article |
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BMC
2019-03-01
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| Series: | BMC Microbiology |
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| Online Access: | http://link.springer.com/article/10.1186/s12866-019-1431-9 |
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| author | 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 |
| author_facet | 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 |
| author_sort | J. J. van Aartsen |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T11:47:45Z |
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| id | doaj.art-c4addd6b031b4a85892c3c26e6d226ec |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-13T11:47:45Z |
| publishDate | 2019-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-c4addd6b031b4a85892c3c26e6d226ec2022-12-21T23:47:28ZengBMCBMC Microbiology1471-21802019-03-0119111410.1186/s12866-019-1431-9Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west CambodiaJ. J. van Aartsen0C. E. Moore1C. M. Parry2P. Turner3N. Phot4S. Mao5K. Suy6T. Davies7A. Giess8A. E. Sheppard9T. E. A. Peto10N. P. J. Day11D. W. Crook12A. S. Walker13N. Stoesser14Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordNuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordClinical Sciences, Liverpool School of Tropical MedicineCambodia-Oxford Medical Research Unit, Angkor Hospital for ChildrenAngkor Hospital for ChildrenAngkor Hospital for ChildrenAngkor Hospital for ChildrenNuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordNuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordNuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordNuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordCentre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordNuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordNuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordNuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of OxfordAbstract 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.http://link.springer.com/article/10.1186/s12866-019-1431-9PaediatricESBLCarriageCambodia |
| spellingShingle | 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 Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia BMC Microbiology Paediatric ESBL Carriage Cambodia |
| title | Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia |
| title_full | Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia |
| title_fullStr | Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia |
| title_full_unstemmed | Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia |
| title_short | Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia |
| title_sort | epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin resistant escherichia coli and klebsiella pneumoniae isolates in north west cambodia |
| topic | Paediatric ESBL Carriage Cambodia |
| url | http://link.springer.com/article/10.1186/s12866-019-1431-9 |
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