Next Generation Sequencing – Chancen und Grenzen für die Krankenhaushygiene

Die Unterscheidung von Mikroorganismen ist für das Hygienemanagement im klinischen Alltag von entscheidender Wichtigkeit. Das sog. „Next Generation Sequencing“ (NGS) bietet hier zahlreiche neue Möglichkeiten – es weist aber auch noch einige Limitationen auf. Dieser Beitrag stellt die derzeit verfügbaren NGS-Plattformen vor, beschreibt ihre Vor- und Nachteile sowie ihre Anwendungsgebiete und Grenzen.

Schlüsselwörter

Next Generation Sequencing - Sequenzierplattformen - Ausbruchsuntersuchungen - Speziesbestimmung - Metagenomsequenzierungen

• Literatur

• 1 Jolley KA, Bliss CM, Bennett JS. et al. Ribosomal multi-locus sequence typing: universal characterisation of bacteria from domain to strain. Microbiology 2012; 158: 1005-1015
• 2 Harmsen D, Claus H, Witte W. et al. Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol 2003; 41: 5442-5448
• 3 Jolley KA, Brehony C, Maiden MCJ. Molecular typing of meningococci: recommendations for target choice and nomenclature. FEMS Microbiol Rev 2007; 31: 89-96
• 4 Maiden MC, Bygraves JA, Feil E. et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 1998; 95: 3140-3145
• 5 Sheppard SK, McCarthy ND, Falush D. et al. Convergence of Campylobacter species: implications for bacterial evolution. Science 2008; 320: 237-239
• 6 Bennett JS, Jolley KA, Sparling PF. et al. Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from multilocus sequence typing. BMC Biol 2007; 5: 35
• 7 Rang FJ, Kloosterman WP, de Ridder J. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biol 2018; 19: 90
• 8 Silva M, Machado MP, Silva DN. et al. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 2018;
• 9 Mellmann A, Andersen PS, Bletz S. et al. High interlaboratory reproducibility and accuracy of next-generation-sequencing-based bacterial genotyping in a ring trial. J Clin Microbiol 2017; 55: 908-913
• 10 Köser CU, Holden MTG, Ellington MJ. et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 2012; 366: 2267-2275
• 11 Harris SR, Cartwright EJ, Török ME. et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis 2013; 13: 130-136
• 12 Senn L, Clerc O, Zanetti G. et al. The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus. MBio 2016; 7: e02039-15
• 13 Price JR, Cole K, Bexley A. et al. Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing. Lancet Infect Dis 2017; 17: 207-214
• 14 Zhou K, Lokate M, Deurenberg RH. et al. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae. Sci Rep 2016; 6: 20840
• 15 Kommission für Krankenhaushygiene und Infektionsprävention (KRINKO). Hygienemaßnahmen bei Infektionen oder Besiedlung mit multiresistenten gramnegativen Stäbchen. Bundesgesundheitsbl 2012; 55: 1311-1354
• 16 Zhou X, Chlebowicz MA, Bathoorn E. et al. Elucidating vancomycin-resistant Enterococcus faecium outbreaks: the role of clonal spread and movement of mobile genetic elements. J Antimicrob Chemother 2018; 73: 3259-3267
• 17 Jackson BR, Tarr C, Strain E. et al. Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clin Infect Dis 2016; 63: 380-386
• 18 Wolfgang WJ, Passaretti TV, Jose R. et al. Neisseria oralis sp. nov., isolated from healthy gingival plaque and clinical samples. Int J Syst Evol Microbiol 2013; 63: 1323-1328
• 19 Bennett JS, Jolley KA, Maiden MCJ. Genome sequence analyses show that Neisseria oralis is the same species as ʼNeisseria mucosa var. heidelbergensisʼ. Int J Syst Evol Microbiol 2013; 63: 3920-3926
• 20 Alikhan N-F, Zhou Z, Sergeant MJ. et al. A genomic overview of the population structure of Salmonella. PLoS Genet 2018; 14: e1007261
• 21 Tong SYC, Schaumburg F, Ellington MJ. et al. Novel staphylococcal species that form part of a Staphylococcus aureus-related complex: the non-pigmented Staphylococcus argenteus sp. nov. and the non-human primate-associated Staphylococcus schweitzeri sp. nov. Int J Syst Evol Microbiol 2015; 65: 15-22
• 22 Moldovan MA, Gelfand MS. Pangenomic definition of prokaryotic species and the phylogenetic structure of Prochlorococcus spp. Front Microbiol 2018; 9: 428 doi:10.3389/fmicb.2018.00428
• 23 Kay GL, Sergeant MJ, Zhou Z. et al. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat Commun 2015; 6: 6717
• 24 Rasmussen S, Allentoft ME, Nielsen K. et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 2015; 163: 571-582
• 25 Couto N, Schuele L, Raangs EC. et al. Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens. Sci Rep 2018; 8: 13767 doi:10.1038/s41598-018-31873-w
• 26 Greninger AL, Zerr DM, Qin X. et al. Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections. J Clin Microbiol 2017; 55: 177-182
• 27 Ruppitsch W, Pietzka A, Prior K. et al. Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Listeria monocytogenes. J Clin Microbiol 2015; 53: 2869-2876
• 28 Ewels P, Magnusson M, Lundin S. et al. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32: 3047-3048
• 29 Forouzan E, Maleki MSM, Karkhane AA. et al. Evaluation of nine popular de novo assemblers in microbial genome assembly. J Microbiol Methods 2017; 143: 32-37
• 30 Gupta A, Jordan IK, Rishishwar L. stringMLST: a fast k-mer based tool for multilocus sequence typing. Bioinformatics 2017; 33: 119-121
• 31 Jia B, Raphenya AR, Alcock B. et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45: D566-D573
• 32 Antonopoulos DA, Assaf R, Aziz RK. et al. PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform 2017;