Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia



Darboe, Saffiatou ORCID: 0000-0002-4711-3307, Bradbury, Richard ORCID: 0000-0002-5524-506X, Phelan, Jody ORCID: 0000-0001-8323-7019, Kanteh, Abdoulie, Muhammad, Abdul-Khalie, Worwui, Archibald, Yang, Shangxin ORCID: 0000-0001-9991-1178, Nwakanma, Davis ORCID: 0000-0002-6706-6069, Perez-Sepulveda, Blanca ORCID: 0000-0002-2891-4010, Kariuki, Samuel
et al (show 2 more authors) (2020) Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia.

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Abstract

Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan African. Specific lineages of serovars S . Typhimurium and S . Enteritidis are implicated. We characterised the genomic diversity of 100 clinical Non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern and 2006 to 2018 in the western regions of The Gambia respectively. Phenotypic susceptibility applied Kirby Baur disk diffusion and whole genome sequencing utilized Illumina platforms. The predominant serovars were S. Typhimurium ST19 (31/100) and S. Enteritidis ST11 (18/100) restricted to invasive disease with the notable absence of S. Typhimurium ST313. Phylogenetic analysis performed in the context of 495 African strains from the European Nucleotide Archive confirmed the presence of the S . Enteritidis virulent epidemic invasive multidrug resistant West African clade. Multidrug resistance including chloramphenicol and azithromycin has emerged among the West African S. Enteritidis clade 7/9 (78%) with potential for spread, thus having important implications for patient management warranting systematic surveillance and epidemiologic investigations to inform control. <h4>Data summary</h4> Sequences are deposited in the NCBI sequence reads archive (SRA) under BioProject ID:PRJEB38968. The genomic assemblies are available for download from the European Nucleotide Archive (ENA): http://www.ebi.ac.uk/ena/data/view/ . Accession numbers SAMEA6991082 to SAME6991180

Item Type: Article
Depositing User: Symplectic Admin
Date Deposited: 06 Nov 2020 10:27
Last Modified: 12 Mar 2021 05:10
DOI: 10.1101/2020.10.30.316588
Open Access URL: https://doi.org/10.1101/2020.10.30.316588
URI: https://livrepository.liverpool.ac.uk/id/eprint/3106171