Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia
<p><strong>Background</strong> 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...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Journal article |
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BioMed Central
2019
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| _version_ | 1797087609270304768 |
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| author | Van Aartsen, J Moore, C Parry, C Turner, P Phot, N Mao, S Suy, K Davies, T Geiss, A Sheppard, A Peto, T Day, N Crook, D Walker, A Stoesser, N |
| author_facet | Van Aartsen, J Moore, C Parry, C Turner, P Phot, N Mao, S Suy, K Davies, T Geiss, A Sheppard, A Peto, T Day, N Crook, D Walker, A Stoesser, N |
| author_sort | Van Aartsen, J |
| collection | OXFORD |
| description | <p><strong>Background</strong> 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).</p><br/> <p><strong>Results</strong> 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.</p><br/> <p><strong>Conclusions</strong> 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.</p> |
| first_indexed | 2024-03-07T02:38:05Z |
| format | Journal article |
| id | oxford-uuid:a979fc6d-5db0-435c-9d92-97973c69a6c3 |
| institution | University of Oxford |
| last_indexed | 2024-03-07T02:38:05Z |
| publishDate | 2019 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:a979fc6d-5db0-435c-9d92-97973c69a6c32022-03-27T03:08:47ZEpidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west CambodiaJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:a979fc6d-5db0-435c-9d92-97973c69a6c3Symplectic Elements at OxfordBioMed Central2019Van Aartsen, JMoore, CParry, CTurner, PPhot, NMao, SSuy, KDavies, TGeiss, ASheppard, APeto, TDay, NCrook, DWalker, AStoesser, N<p><strong>Background</strong> 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).</p><br/> <p><strong>Results</strong> 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.</p><br/> <p><strong>Conclusions</strong> 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.</p> |
| spellingShingle | Van Aartsen, J Moore, C Parry, C Turner, P Phot, N Mao, S Suy, K Davies, T Geiss, A Sheppard, A Peto, T Day, N Crook, D Walker, A Stoesser, N Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west 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 |
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