Genome sequence of a clinical Salmonella Enteritidis sequence type 11 strain from South Africa

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dc.contributor.author Rule, Roxanne
dc.contributor.author Said, H.M. (Halima Mohammed)
dc.contributor.author Mbelle, Nontombi Marylucy
dc.contributor.author Osei Sekyere, John
dc.date.accessioned 2020-03-18T05:45:26Z
dc.date.issued 2019-12
dc.description.abstract OBJECTIVES : The underlying resistance mechanism and phylogenetic relationship of a colistin-resistant Salmonella enterica serovar Enteritidis strain EC20120916 that resulted in fatal meningitis in an immunocompromised patient was investigated by whole-genome sequencing (WGS) analysis. METHODS : WGS of strain EC20120916 was performed on an Illumina MiSeq platform and annotation of the sequence was performed using the Prokaryotic Genome Annotation Pipeline (PGAP). Antimicrobial resistance genes, plasmid replicons and pathogenicity islands were identified. A phylogenetic tree was constructed using Parsnp and was edited with FigTree. RESULTS : The genome size of strain EC20120916 is 4 699 318 bp with a GC content of 55.2% and 4471 protein-coding genes. The aac(6ʹ)-laa gene, encoding resistance to aminoglycosides, was identified although this was not expressed phenotypically in the isolate. No colistin resistance-conferring mutations or plasmid-mediated mechanisms were identified to explain the colistin resistance. The strain was phylogenetically related to three international strains, although it was not close enough to suggest importation from outside of South Africa. CONCLUSION : This is the first report of a colistin-resistant Salmonella Enteritidis isolate causing meningitis in an immunocompromised patient in South Africa. The absence of colistin resistance-conferring mutations or plasmid-mediated resistance mechanisms suggest that a novel mechanism is responsible for the colistin resistance in this isolate. The isolate was acquired locally. en_ZA
dc.description.department Medical Microbiology en_ZA
dc.description.embargo 2020-12-01
dc.description.librarian hj2020 en_ZA
dc.description.sponsorship The National Health Laboratory Services (Grant No.: 94445) and the University of Pretoria (Grant No.: A0702). en_ZA
dc.description.uri http://www.elsevier.com/locate/jgar en_ZA
dc.identifier.citation Rule, R., Said, M., Mbelle, N. & Osei Sekyere, J. 2019, 'Genome sequence of a clinical Salmonella Enteritidis sequence type 11 strain from South Africa', Journal of Global Antimicrobial Resistance, vol. 19, pp. 164-166. en_ZA
dc.identifier.issn 2213-7165
dc.identifier.other 10.1016/j.jgar.2019.09.014
dc.identifier.uri http://hdl.handle.net/2263/73787
dc.language.iso en en_ZA
dc.publisher Elsevier en_ZA
dc.rights © 2019 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved. Notice : this is the author’s version of a work that was accepted for publication in Journal of Global Antimicrobial Resistance. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. A definitive version was subsequently published in Journal of Global Antimicrobial Resistance, vol. 19, pp. 164-166, 2019. doi : 10.1016/j.jgar.2019.09.014. en_ZA
dc.subject Salmonella enterica en_ZA
dc.subject Whole-genome sequencing (WGS) en_ZA
dc.subject Meningitis en_ZA
dc.subject Colistin resistance en_ZA
dc.subject South Africa (SA) en_ZA
dc.title Genome sequence of a clinical Salmonella Enteritidis sequence type 11 strain from South Africa en_ZA
dc.type Postprint Article en_ZA


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