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- Title
Whole genome sequencing reveals high clonal diversity of <italic>Escherichia coli</italic> isolated from patients in a tertiary care hospital in Moshi, Tanzania.
- Authors
Sonda, Tolbert; Kumburu, Happiness; van Zwetselaar, Marco; Alifrangis, Michael; Mmbaga, Blandina T.; Aarestrup, Frank M.; Kibiki, Gibson; Lund, Ole
- Abstract
Background: Limited information regarding the clonality of circulating <italic>E. coli</italic> 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 <italic>E. coli</italic> isolated from patients in a tertiary care hospital in Tanzania. Methods: <italic>E. coli</italic> 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 <italic>E. coli</italic> 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 <italic>E. coli</italic> 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<italic>.</italic> On average, agreement across all drugs tested was 83.9%. Trimethoprim/sulphamethoxazole (co-trimoxazole) showed moderate agreement: 45.8%, kappa =15% and <italic>p</italic> = 0.08. Amoxicillin-clavulanate showed strongest agreement: 87.5%, kappa = 74% and <italic>p</italic> = 0.0001. Twenty-two (57.9%) isolates carried virulence factors for host cells adherence and 25 (65.7%) for factors that promote <italic>E. coli</italic> 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 <italic>E. coli</italic> 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.
- Subjects
TANZANIA; DIAGNOSIS of escherichia coli diseases; HOSPITALS; CLONE cells
- Publication
Antimicrobial Resistance & Infection Control, 2018, Vol 7, Issue 1, pN.PAG
- ISSN
2047-2994
- Publication type
Article
- DOI
10.1186/s13756-018-0361-x