Journal article
Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania
Kilimanjaro Clinical Research Institute1
Copenhagen University Hospital Herlev and Gentofte2
National Food Institute, Technical University of Denmark3
Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark4
Kilimanjaro Christian Medical University College5
Department of Biotechnology and Biomedicine, Technical University of Denmark6
Center for Biological sequence analysis, Technical University of Denmark7
Department of Bio and Health Informatics, Technical University of Denmark8
Genomic Epidemiology, Department of Bio and Health Informatics, Technical University of Denmark9
Background: Limited information regarding the clonality of circulating E. coli strains in tertiary care hospitals in low and middle-income countries is available. The purpose of this study was to determine the serotypes, antimicrobial resistance and virulence genes. Further, we carried out a phylogenetic tree reconstruction to determine relatedness of E. coli isolated from patients in a tertiary care hospital in Tanzania.
Methods: E. coli isolates from inpatients admitted at Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced at KCMC hospital. Sequence analysis was done for identification of resistance genes, Multi-Locus Sequence Typing, serotyping, and virulence genes.
Phylogeny reconstruction using CSI Phylogeny was done to ascertain E. coli relatedness. Stata 13 (College Station, Texas 77,845 USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and whole genome sequence predicted antimicrobial resistance. Results: Out of 38 E. coli isolates, 21 different sequence types (ST) were observed.
Eight (21.1%) isolates belonged to ST131; of which 7 (87.5.%) were serotype O25:H4. Ten (18.4%) isolates belonged to ST10 clonal complex; of these, four (40.0%) were ST617 with serotype O89:H10. Twenty-eight (73.7%) isolates carried genes encoding beta-lactam resistance enzymes. On average, agreement across all drugs tested was 83.9%.
Trimethoprim/sulphamethoxazole (co-trimoxazole) showed moderate agreement: 45.8%, kappa = 15% and p = 0.08. Amoxicillin-clavulanate showed strongest agreement: 87.5%, kappa = 74% and p = 0.0001. Twenty-two (57.9%) isolates carried virulence factors for host cells adherence and 25 (65.7%) for factors that promote E. coli immune evasion by increasing survival in serum.
The phylogeny analysis showed that ST131 clustering close together whereas ST10 clonal complex had a very clear segregation of the ST617 and a mix of the rest STs. Conclusion: There is a high diversity of E. coli isolated from patients admitted to a tertiary care hospital in Tanzania. This underscores the necessity to routinely screen all bacterial isolates of clinical importance in tertiary health care facilities.
WGS use for laboratory-based surveillance can be an effective early warning system for emerging pathogens and resistance mechanisms in LMICs.
| Language: | English |
|---|---|
| Publisher: | BioMed Central |
| Year: | 2018 |
| Pages: | 72 |
| ISSN: | 20472994 |
| Types: | Journal article |
| DOI: | 10.1186/s13756-018-0361-x |
| ORCIDs: | 0000-0002-3835-3333 , Aarestrup, Frank Møller and Lund, Ole |
And virulence E. coli Multi-locus sequence typing Serotyping Tanzania Whole genome sequencing
Amoxicillin-Potassium Clavulanate Combination Anti-Bacterial Agents Cross-Sectional Studies Drug Resistance, Multiple, Bacterial Escherichia coli Escherichia coli Infections Genome, Bacterial Hospitals Humans Infectious and parasitic diseases Microbial Sensitivity Tests Multilocus Sequence Typing Phylogeny RC109-216 Tertiary Care Centers Trimethoprim, Sulfamethoxazole Drug Combination Virulence Factors Whole Genome Sequencing beta-Lactam Resistance beta-Lactamases
