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Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58

Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. Typhi haplotype in endemic areas of Asia and...

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Autores principales: Rutanga, Jean Pierre, de Block, Tessa, Cuypers, Wim L., Cafmeyer, Josephine, Peeters, Marjan, Umumararungu, Esperance, Ngabonziza, Jean Claude S., Rucogoza, Aniceth, Vandenberg, Olivier, Martiny, Delphine, Dusabe, Angélique, Nkubana, Théoneste, Dougan, Gordon, Muvunyi, Claude Mambo, Mwikarago, Ivan Emil, Jacobs, Jan, Deborggraeve, Stijn, Van Puyvelde, Sandra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10310045/
https://www.ncbi.nlm.nih.gov/pubmed/37327220
http://dx.doi.org/10.1371/journal.pntd.0011285
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author Rutanga, Jean Pierre
de Block, Tessa
Cuypers, Wim L.
Cafmeyer, Josephine
Peeters, Marjan
Umumararungu, Esperance
Ngabonziza, Jean Claude S.
Rucogoza, Aniceth
Vandenberg, Olivier
Martiny, Delphine
Dusabe, Angélique
Nkubana, Théoneste
Dougan, Gordon
Muvunyi, Claude Mambo
Mwikarago, Ivan Emil
Jacobs, Jan
Deborggraeve, Stijn
Van Puyvelde, Sandra
author_facet Rutanga, Jean Pierre
de Block, Tessa
Cuypers, Wim L.
Cafmeyer, Josephine
Peeters, Marjan
Umumararungu, Esperance
Ngabonziza, Jean Claude S.
Rucogoza, Aniceth
Vandenberg, Olivier
Martiny, Delphine
Dusabe, Angélique
Nkubana, Théoneste
Dougan, Gordon
Muvunyi, Claude Mambo
Mwikarago, Ivan Emil
Jacobs, Jan
Deborggraeve, Stijn
Van Puyvelde, Sandra
author_sort Rutanga, Jean Pierre
collection PubMed
description Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. Typhi haplotype in endemic areas of Asia and East sub-Saharan Africa. The situation in Rwanda is currently unknown and therefore to reveal the genetic diversity and AMR of S. Typhi in Rwanda, 25 historical (1984-1985) and 26 recent (2010-2018) isolates from Rwanda were analysed using whole genome sequencing (WGS). WGS was locally implemented using Illumina MiniSeq and web-based analysis tools, thereafter complemented with bioinformatic approaches for more in-depth analyses. Whereas historical S. Typhi isolates were found to be fully susceptible to antimicrobials and show a diversity of genotypes, i.e 2.2.2, 2.5, 3.3.1 and 4.1; the recent isolates showed high AMR rates and were predominantly associated with genotype 4.3.1.2 (H58, 22/26; 84,6%), possibly resulting from a single introduction in Rwanda from South Asia before 2010. We identified practical challenges for the use of WGS in endemic regions, including a high cost for shipment of molecular reagents and lack of high-end computational infrastructure for the analyses, but also identified WGS to be feasible in the studied setting and giving opportunity for synergy with other programs.
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spelling pubmed-103100452023-06-30 Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58 Rutanga, Jean Pierre de Block, Tessa Cuypers, Wim L. Cafmeyer, Josephine Peeters, Marjan Umumararungu, Esperance Ngabonziza, Jean Claude S. Rucogoza, Aniceth Vandenberg, Olivier Martiny, Delphine Dusabe, Angélique Nkubana, Théoneste Dougan, Gordon Muvunyi, Claude Mambo Mwikarago, Ivan Emil Jacobs, Jan Deborggraeve, Stijn Van Puyvelde, Sandra PLoS Negl Trop Dis Research Article Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. Typhi haplotype in endemic areas of Asia and East sub-Saharan Africa. The situation in Rwanda is currently unknown and therefore to reveal the genetic diversity and AMR of S. Typhi in Rwanda, 25 historical (1984-1985) and 26 recent (2010-2018) isolates from Rwanda were analysed using whole genome sequencing (WGS). WGS was locally implemented using Illumina MiniSeq and web-based analysis tools, thereafter complemented with bioinformatic approaches for more in-depth analyses. Whereas historical S. Typhi isolates were found to be fully susceptible to antimicrobials and show a diversity of genotypes, i.e 2.2.2, 2.5, 3.3.1 and 4.1; the recent isolates showed high AMR rates and were predominantly associated with genotype 4.3.1.2 (H58, 22/26; 84,6%), possibly resulting from a single introduction in Rwanda from South Asia before 2010. We identified practical challenges for the use of WGS in endemic regions, including a high cost for shipment of molecular reagents and lack of high-end computational infrastructure for the analyses, but also identified WGS to be feasible in the studied setting and giving opportunity for synergy with other programs. Public Library of Science 2023-06-16 /pmc/articles/PMC10310045/ /pubmed/37327220 http://dx.doi.org/10.1371/journal.pntd.0011285 Text en © 2023 Rutanga et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Rutanga, Jean Pierre
de Block, Tessa
Cuypers, Wim L.
Cafmeyer, Josephine
Peeters, Marjan
Umumararungu, Esperance
Ngabonziza, Jean Claude S.
Rucogoza, Aniceth
Vandenberg, Olivier
Martiny, Delphine
Dusabe, Angélique
Nkubana, Théoneste
Dougan, Gordon
Muvunyi, Claude Mambo
Mwikarago, Ivan Emil
Jacobs, Jan
Deborggraeve, Stijn
Van Puyvelde, Sandra
Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58
title Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58
title_full Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58
title_fullStr Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58
title_full_unstemmed Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58
title_short Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58
title_sort salmonella typhi whole genome sequencing in rwanda shows a diverse historical population with recent introduction of haplotype h58
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10310045/
https://www.ncbi.nlm.nih.gov/pubmed/37327220
http://dx.doi.org/10.1371/journal.pntd.0011285
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