دورية أكاديمية
أعرض في EDS

Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing.

التفاصيل البيبلوغرافية
العنوان: Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing.
المؤلفون: Ferreira I; Ares Genetics GmbH, 1030 Vienna, Austria.; Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.; Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria., Lepuschitz S; Ares Genetics GmbH, 1030 Vienna, Austria., Beisken S; Ares Genetics GmbH, 1030 Vienna, Austria., Fiume G; Ares Genetics GmbH, 1030 Vienna, Austria., Mrazek K; Ares Genetics GmbH, 1030 Vienna, Austria., Frank BJH; Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Vienna-Speising, 1130 Vienna, Austria., Huber S; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria., Knoll MA; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria., von Haeseler A; Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.; Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria.; Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, 1090 Vienna, Austria., Materna A; Ares Genetics GmbH, 1030 Vienna, Austria., Hofstaetter JG; Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Vienna-Speising, 1130 Vienna, Austria., Posch AE; Ares Genetics GmbH, 1030 Vienna, Austria., Weinberger J; Ares Genetics GmbH, 1030 Vienna, Austria.
المصدر: Microorganisms [Microorganisms] 2021 Aug 05; Vol. 9 (8). Date of Electronic Publication: 2021 Aug 05.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI AG Country of Publication: Switzerland NLM ID: 101625893 Publication Model: Electronic Cited Medium: Print ISSN: 2076-2607 (Print) Linking ISSN: 20762607 NLM ISO Abbreviation: Microorganisms Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI AG, [2013]-
مستخلص: The increasing incidence of antimicrobial resistance (AMR) is a major global challenge. Routine techniques for molecular AMR marker detection are largely based on low-plex PCR and detect dozens to hundreds of AMR markers. To allow for comprehensive and sensitive profiling of AMR markers, we developed a capture-based next generation sequencing (NGS) workflow featuring a novel AMR marker panel based on the curated AMR database ARESdb. Our primary objective was to compare the sensitivity of target enrichment-based AMR marker detection to metagenomics sequencing. Therefore, we determined the limit of detection (LOD) in synovial fluid and urine samples across four key pathogens. We further demonstrated proof-of-concept for AMR marker profiling from septic samples using a selection of urine samples with confirmed monoinfection. The results showed that the capture-based workflow is more sensitive and requires lower sequencing depth compared with metagenomics sequencing, allowing for comprehensive AMR marker detection with an LOD of 1000 CFU/mL. Combining the ARESdb AMR panel with 16S rRNA gene sequencing allowed for the culture-free detection of bacterial taxa and AMR markers directly from septic patient samples at an average sensitivity of 99%. Summarizing, the newly developed ARESdb AMR panel may serve as a valuable tool for comprehensive and sensitive AMR marker detection.
References: Genome Med. 2015 Dec 01;7:113. (PMID: 26620704)
Sci Rep. 2018 Feb 21;8(1):3416. (PMID: 29467368)
Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404)
Clin Infect Dis. 2017 Jul 15;65(2):332-335. (PMID: 28379472)
Microbiology (Reading). 2002 Jan;148(Pt 1):257-266. (PMID: 11782518)
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. (PMID: 23193283)
Can J Infect Dis Med Microbiol. 2005 Nov;16(6):349-60. (PMID: 18159518)
Lancet. 2018 May 19;391(10134):1976-1978. (PMID: 29864011)
Microbiome. 2017 Aug 14;5(1):99. (PMID: 28807017)
Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278)
Bioinformatics. 2015 Jan 15;31(2):166-9. (PMID: 25260700)
Front Microbiol. 2020 Aug 05;11:1883. (PMID: 32849463)
Antimicrob Agents Chemother. 2019 Dec 20;64(1):. (PMID: 31611361)
PLoS One. 2012;7(12):e52249. (PMID: 23284954)
Genome Biol. 2018 Oct 4;19(1):153. (PMID: 30286803)
J Clin Microbiol. 2014 Jan;52(1):139-46. (PMID: 24172157)
Nucleic Acids Res. 2019 Aug 22;47(14):e83. (PMID: 31114866)
J Antimicrob Chemother. 2017 Jan;72(1):104-114. (PMID: 27667325)
Nat Methods. 2016 Jul;13(7):581-3. (PMID: 27214047)
J Clin Microbiol. 2017 Aug;55(8):2334-2347. (PMID: 28490492)
BMC Genomics. 2018 Sep 27;19(1):714. (PMID: 30261842)
Eur J Clin Microbiol Infect Dis. 2017 Jul;36(7):1325-1338. (PMID: 28285331)
Sci Rep. 2017 Oct 16;7(1):13202. (PMID: 29038571)
Nat Biotechnol. 2009 Feb;27(2):182-9. (PMID: 19182786)
J Clin Microbiol. 2020 Jun 24;58(7):. (PMID: 32295890)
Bioinformatics. 2016 Oct 1;32(19):3047-8. (PMID: 27312411)
Clin Infect Dis. 2018 Oct 15;67(9):1333-1338. (PMID: 29648630)
Biotechnol Prog. 2016 Jul 8;32(4):823-39. (PMID: 27160415)
J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712)
Clin Microbiol Infect. 2004 Nov;10 Suppl 4:1-9. (PMID: 15522034)
معلومات مُعتمدة: 24478239 Wirtschaftsagentur Wien; 871243 Österreichische Forschungsförderungsgesellschaft; 879570 Österreichische Forschungsförderungsgesellschaft
فهرسة مساهمة: Keywords: antimicrobial resistance; human pathogens; infectious disease surveillance; molecular detection; next generation sequencing; synovial fluid; target enrichment; urinary tract infection
تواريخ الأحداث: Date Created: 20210827 Latest Revision: 20210831
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC8398375
DOI: 10.3390/microorganisms9081672
PMID: 34442751
قاعدة البيانات: MEDLINE
الوصف
تدمد:2076-2607
DOI:10.3390/microorganisms9081672