دورية أكاديمية
أعرض في EDS

Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity.

التفاصيل البيبلوغرافية
العنوان: Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity.
المؤلفون: Tanmoy AM; Child Health Research Foundation, Dhaka, Bangladesh.; Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands., Hooda Y; Child Health Research Foundation, Dhaka, Bangladesh.; MRC-Laboratory Molecular Biology, Cambridge, UK., Sajib MSI; Child Health Research Foundation, Dhaka, Bangladesh.; Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK., da Silva KE; Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA., Iqbal J; Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan., Qamar FN; Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan., Luby SP; Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA., Dougan G; Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK., Dyson ZA; Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK.; Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia., Baker S; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK., Garrett DO; Applied Epidemiology Team, Sabin Vaccine Institute, Washington, DC, USA., Andrews JR; Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA., Saha SK; Child Health Research Foundation, Dhaka, Bangladesh.; Department of Microbiology, Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh., Saha S; Child Health Research Foundation, Dhaka, Bangladesh. senjutisaha@chrfbd.org.
المصدر: Nature communications [Nat Commun] 2022 Dec 23; Vol. 13 (1), pp. 7912. Date of Electronic Publication: 2022 Dec 23.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Paratyphoid Fever* , Anti-Infective Agents*, Humans ; Salmonella paratyphi A/genetics ; Genotype ; Genomics
مستخلص: Salmonella Paratyphi A, the primary etiology of paratyphoid, is estimated to cause 3.4 million infections annually, worldwide. With rising antimicrobial resistance and no licensed vaccines, genomic surveillance is key to track and monitor transmission, but there is currently no reliable genotyping framework for this pathogen. Here, we sequence 817 isolates from South Asia and add 562 publicly available genomes to build a global database representing 37 countries, covering 1917-2019. We develop a single nucleotide polymorphism-based genotyping scheme, Paratype, that segregates Salmonella Paratyphi A population into three primary and nine secondary clades, and 18 genotypes. Each genotype is assigned a unique allele definition located on an essential gene. Using Paratype, we identify spatiotemporal genomic variation and antimicrobial resistance markers. We release Paratype as an open-access tool that can use raw read files from both Illumina and Nanopore platforms, and thus can assist surveillance studies tracking Salmonella Paratyphi A across the globe.
(© 2022. The Author(s).)
References: Am J Trop Med Hyg. 2017 Dec;97(6):1706-1709. (PMID: 29016327)
J Infect Dis. 2018 Nov 10;218(suppl_4):S188-S194. (PMID: 30304505)
Bioinformatics. 2015 Nov 15;31(22):3691-3. (PMID: 26198102)
Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):478-483. (PMID: 30598444)
PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. (PMID: 28594827)
BMC Genomics. 2009 Jan 21;10:36. (PMID: 19159446)
Nat Methods. 2012 Mar 04;9(4):357-9. (PMID: 22388286)
Expert Rev Vaccines. 2013 Sep;12(9):1021-31. (PMID: 24053396)
Emerg Infect Dis. 2017 May;23(5):833-836. (PMID: 28418315)
J Infect Dis. 2018 Nov 10;218(suppl_4):S227-S231. (PMID: 30060199)
Bioinformatics. 2014 Jul 15;30(14):2068-9. (PMID: 24642063)
Clin Infect Dis. 2010 Jan 15;50(2):241-6. (PMID: 20014951)
Virus Evol. 2018 Jun 08;4(1):vey016. (PMID: 29942656)
PeerJ. 2016 Apr 05;4:e1752. (PMID: 27069781)
J Antimicrob Chemother. 2020 Feb 1;75(2):337-341. (PMID: 31665304)
Pediatr Infect Dis J. 2001 May;20(5):521-4. (PMID: 11368111)
Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404)
Bioinformatics. 2014 May 1;30(9):1312-3. (PMID: 24451623)
Clin Infect Dis. 2019 Mar 7;68(Suppl 2):S117-S123. (PMID: 30845325)
Methods Mol Biol. 2020;2075:285-294. (PMID: 31584170)
BMC Evol Biol. 2007 Nov 08;7:214. (PMID: 17996036)
Nucleic Acids Res. 2019 Jun 20;47(11):5539-5549. (PMID: 31076776)
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259. (PMID: 30931475)
mBio. 2019 Aug 27;10(4):. (PMID: 31455646)
PLoS Negl Trop Dis. 2018 Apr 23;12(4):e0006408. (PMID: 29684021)
Antibiotics (Basel). 2021 Jan 20;10(2):. (PMID: 33498344)
J Antimicrob Chemother. 2020 Dec 1;75(12):3491-3500. (PMID: 32780112)
PLoS One. 2020 Jan 30;15(1):e0228250. (PMID: 32000262)
PLoS Negl Trop Dis. 2015 Jul 17;9(7):e0003859. (PMID: 26186586)
mBio. 2021 Feb 16;12(1):. (PMID: 33593966)
PLoS Negl Trop Dis. 2017 Oct 26;11(10):e0005999. (PMID: 29073137)
Lancet Infect Dis. 2019 Apr;19(4):369-381. (PMID: 30792131)
J Antimicrob Chemother. 2018 Feb 1;73(2):365-372. (PMID: 29216342)
Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12199-204. (PMID: 25092320)
Nat Genet. 2015 Jun;47(6):632-9. (PMID: 25961941)
PLoS Negl Trop Dis. 2019 Nov 15;13(11):e0007868. (PMID: 31730615)
Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
Nat Commun. 2016 Oct 05;7:12827. (PMID: 27703135)
Microb Genom. 2016 Nov 30;2(11):e000092. (PMID: 28348832)
Nat Genet. 2004 Dec;36(12):1268-74. (PMID: 15531882)
Nucleic Acids Res. 2015 Feb 18;43(3):e15. (PMID: 25414349)
معلومات مُعتمدة: INV-023821 United States GATES Bill & Melinda Gates Foundation
المشرفين على المادة: 0 (Anti-Infective Agents)
تواريخ الأحداث: Date Created: 20221223 Date Completed: 20221227 Latest Revision: 20240923
رمز التحديث: 20240923
مُعرف محوري في PubMed: PMC9782287
DOI: 10.1038/s41467-022-35587-6
PMID: 36564386
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-022-35587-6