NDLI: Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

Content Provider	Springer Nature : BioMed Central
Author	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 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.
Related Links	https://aricjournal.biomedcentral.com/counter/pdf/10.1186/s13756-018-0361-x.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
ISSN	20472994
DOI	10.1186/s13756-018-0361-x
Journal	Antimicrobial Resistance & Infection Control
Issue Number	1
Volume Number	7
Language	English
Publisher	BioMed Central
Publisher Date	2018-06-08
Access Restriction	Open
Subject Keyword	Medical Microbiology Drug Resistance Infectious Diseases E. coli Multi-locus sequence typing Serotyping And virulence Whole genome sequencing Tanzania
Content Type	Text
Resource Type	Article
Subject	Public Health, Environmental and Occupational Health Infectious Diseases Microbiology (medical) Pharmacology (medical)
Journal Impact Factor	4.8/2023
5-Year Journal Impact Factor	5.8/2023

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