دورية أكاديمية
أعرض في EDS

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

التفاصيل البيبلوغرافية
العنوان: Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58.
المؤلفون: Rutanga JP; College of Science and Technology, University of Rwanda, Kigali, Rwanda.; Institute of Tropical Medicine, Antwerp, Belgium.; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., de Block T; Institute of Tropical Medicine, Antwerp, Belgium., Cuypers WL; Institute of Tropical Medicine, Antwerp, Belgium.; Department of Computer Science, University of Antwerp, Antwerp, Belgium., Cafmeyer J; Institute of Tropical Medicine, Antwerp, Belgium., Peeters M; Institute of Tropical Medicine, Antwerp, Belgium., Umumararungu E; Rwanda Biomedical Centre, Kigali, Rwanda., Ngabonziza JCS; Rwanda Biomedical Centre, Kigali, Rwanda.; Department of Clinical Biology, University of Rwanda, Kigali, Rwanda., Rucogoza A; Rwanda Biomedical Centre, Kigali, Rwanda., Vandenberg O; Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Hôpital Erasme-Cliniques universitaires de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium., Martiny D; Department of Microbiology, Laboratoire des Hôpitaux Universitaires de Bruxelles - Universitaire Laboratorium Brussel (LHUB-ULB), Brussels, Belgium.; National Reference Centre for Campylobacter, CHU Saint-Pierre, Brussels, Belgium.; Faculté de Médecine et Pharmacie, Université de Mons (UMONS), Mons, Belgium., Dusabe A; Centre Hospitalier Universtaire de Kigali (CHUK), Kigali, Rwanda., Nkubana T; Centre Hospitalier Universtaire de Kigali (CHUK), Kigali, Rwanda., Dougan G; Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom., Muvunyi CM; College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda., Mwikarago IE; Rwanda Biomedical Centre, Kigali, Rwanda., Jacobs J; Institute of Tropical Medicine, Antwerp, Belgium.; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Deborggraeve S; Institute of Tropical Medicine, Antwerp, Belgium., Van Puyvelde S; Institute of Tropical Medicine, Antwerp, Belgium.; Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom.; Wellcome Trust Sanger Institute, Hinxton, United Kingdom.; Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
المصدر: PLoS neglected tropical diseases [PLoS Negl Trop Dis] 2023 Jun 16; Vol. 17 (6), pp. e0011285. Date of Electronic Publication: 2023 Jun 16 (Print Publication: 2023).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101291488 Publication Model: eCollection Cited Medium: Internet ISSN: 1935-2735 (Electronic) Linking ISSN: 19352727 NLM ISO Abbreviation: PLoS Negl Trop Dis Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science
مواضيع طبية MeSH: Salmonella typhi*/genetics , Typhoid Fever*/epidemiology, Humans ; Haplotypes ; Anti-Bacterial Agents/therapeutic use ; Rwanda ; Whole Genome Sequencing ; Microbial Sensitivity Tests
مستخلص: 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.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Rutanga et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
References: Lancet Glob Health. 2017 Mar;5(3):e310-e323. (PMID: 28193398)
J Med Microbiol. 1996 May;44(5):317-9. (PMID: 8636944)
Ann Soc Belg Med Trop. 1986;66(1):47-56. (PMID: 3718022)
PLoS Negl Trop Dis. 2012;6(11):e1921. (PMID: 23166855)
Nucleic Acids Res. 2016 Jul 8;44(W1):W16-21. (PMID: 27141966)
Nat Commun. 2018 Nov 30;9(1):5094. (PMID: 30504848)
Nat Genet. 2015 Jun;47(6):632-9. (PMID: 25961941)
J Infect Dis. 2021 Dec 20;224(12 Suppl 2):S883-S889. (PMID: 34550365)
Elife. 2016 Mar 11;5:e14003. (PMID: 26974227)
Antimicrob Agents Chemother. 2013 Jul;57(7):3348-57. (PMID: 23650175)
Nat Commun. 2021 May 17;12(1):2879. (PMID: 34001879)
PLoS One. 2014 Feb 04;9(2):e87991. (PMID: 24505344)
Lancet. 2021 Aug 21;398(10301):675-684. (PMID: 34384540)
Front Microbiol. 2018 Mar 27;9:592. (PMID: 29636749)
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5. (PMID: 27095192)
Infect Drug Resist. 2015 May 11;8:99-106. (PMID: 25999745)
Lancet. 2018 Nov 10;392(10159):1684-1735. (PMID: 30496102)
Clin Infect Dis. 2012 Oct;55(8):1107-13. (PMID: 22752519)
J Infect Dev Ctries. 2010 Jun 30;4(6):393-6. (PMID: 20601792)
J Clin Microbiol. 2004 Apr;42(4):1477-82. (PMID: 15070992)
Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404)
Bioinformatics. 2014 May 1;30(9):1312-3. (PMID: 24451623)
J Clin Microbiol. 2010 Jun;48(6):2171-6. (PMID: 20392916)
Microb Genom. 2016 Apr 29;2(4):e000056. (PMID: 28348851)
Lancet Infect Dis. 2022 Apr;22(4):529-540. (PMID: 34942090)
Front Med (Lausanne). 2019 Jun 18;6:131. (PMID: 31275940)
Front Public Health. 2019 Nov 21;7:317. (PMID: 31824904)
J Infect Dev Ctries. 2020 Feb 29;14(2):169-176. (PMID: 32146451)
Indian J Med Microbiol. 2007 Oct;25(4):436-7. (PMID: 18087113)
BMC Microbiol. 2018 Nov 14;18(1):187. (PMID: 30428828)
PLoS Negl Trop Dis. 2019 Sep 12;13(9):e0007620. (PMID: 31513580)
Lancet. 2018 Nov 10;392(10159):1789-1858. (PMID: 30496104)
Ann Soc Belg Med Trop. 1985 Sep;65(3):281-92. (PMID: 3907525)
Curr Opin Infect Dis. 2003 Oct;16(5):467-72. (PMID: 14502000)
Annu Rev Microbiol. 2014;68:317-36. (PMID: 25208300)
Genome Biol. 2014 Mar 03;15(3):R46. (PMID: 24580807)
PLoS One. 2016 Jan 22;11(1):e0147101. (PMID: 26800248)
Antimicrob Agents Chemother. 2014 Nov;58(11):6501-7. (PMID: 25136011)
Antimicrob Agents Chemother. 1973 Dec;4(6):597-601. (PMID: 4602828)
Ann Soc Belg Med Trop. 1982 Dec;62(4):353-9. (PMID: 7168588)
J Comput Biol. 2012 May;19(5):455-77. (PMID: 22506599)
Clin Infect Dis. 2017 Oct 1;65(7):1229-1231. (PMID: 29136410)
PLoS Negl Trop Dis. 2011 Jul;5(7):e1245. (PMID: 21811646)
Bioinformatics. 2013 Apr 15;29(8):1072-5. (PMID: 23422339)
J Pak Med Assoc. 2016 Aug;66(8):1035-6. (PMID: 27524545)
N Engl J Med. 2021 Sep 16;385(12):1104-1115. (PMID: 34525285)
Emerg Infect Dis. 2011 Oct;17(10):1879-82. (PMID: 22000360)
Clin Infect Dis. 1997 Jan;24 Suppl 1:S106-9. (PMID: 8994789)
PLoS Negl Trop Dis. 2015 Apr 24;9(4):e0003748. (PMID: 25909750)
Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
Nat Commun. 2016 Oct 05;7:12827. (PMID: 27703135)
Med Mal Infect. 2007 May;37(5):266-9. (PMID: 17459634)
Bioinformatics. 2018 Sep 15;34(18):3094-3100. (PMID: 29750242)
Microb Genom. 2017 Sep 4;3(10):e000131. (PMID: 29177089)
Microb Genom. 2016 Nov 30;2(11):e000093. (PMID: 28348833)
Bioinformatics. 2014 Jul 15;30(14):2068-9. (PMID: 24642063)
Clin Microbiol Rev. 2015 Oct;28(4):901-37. (PMID: 26180063)
Clin Infect Dis. 2020 Jul 29;71(Suppl 2):S91-S95. (PMID: 32725234)
Foodborne Pathog Dis. 2019 Jul;16(7):504-512. (PMID: 31246502)
المشرفين على المادة: 0 (Anti-Bacterial Agents)
تواريخ الأحداث: Date Created: 20230616 Date Completed: 20230703 Latest Revision: 20231116
رمز التحديث: 20240829
مُعرف محوري في PubMed: PMC10310045
DOI: 10.1371/journal.pntd.0011285
PMID: 37327220
قاعدة البيانات: MEDLINE
الوصف
تدمد:1935-2735
DOI:10.1371/journal.pntd.0011285