Please use this identifier to cite or link to this item: https://ahro.austin.org.au/austinjspui/handle/1/11675
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dc.contributor.authorSherry, Norelle L-
dc.contributor.authorPorter, Jessica L-
dc.contributor.authorSeemann, Torsten-
dc.contributor.authorWatkins, Andrew-
dc.contributor.authorStinear, Timothy P-
dc.contributor.authorHowden, Benjamin P-
dc.date.accessioned2015-05-16T01:17:34Z
dc.date.available2015-05-16T01:17:34Z
dc.date.issued2013-02-13-
dc.identifier.citationJournal of Clinical Microbiology 2013; 51(5): 1396-401en_US
dc.identifier.otherPUBMEDen
dc.identifier.urihttps://ahro.austin.org.au/austinjspui/handle/1/11675en
dc.description.abstractNext-generation sequencing (NGS) of bacterial genomes has recently become more accessible and is now available to the routine diagnostic microbiology laboratory. However, questions remain regarding its feasibility, particularly with respect to data analysis in nonspecialist centers. To test the applicability of NGS to outbreak investigations, Ion Torrent sequencing was used to investigate a putative multidrug-resistant Escherichia coli outbreak in the neonatal unit of the Mercy Hospital for Women, Melbourne, Australia. Four suspected outbreak strains and a comparator strain were sequenced. Genome-wide single nucleotide polymorphism (SNP) analysis demonstrated that the four neonatal intensive care unit (NICU) strains were identical and easily differentiated from the comparator strain. Genome sequence data also determined that the NICU strains belonged to multilocus sequence type 131 and carried the bla(CTX-M-15) extended-spectrum beta-lactamase. Comparison of the outbreak strains to all publicly available complete E. coli genome sequences showed that they clustered with neonatal meningitis and uropathogenic isolates. The turnaround time from a positive culture to the completion of sequencing (prior to data analysis) was 5 days, and the cost was approximately $300 per strain (for the reagents only). The main obstacles to a mainstream adoption of NGS technologies in diagnostic microbiology laboratories are currently cost (although this is decreasing), a paucity of user-friendly and clinically focused bioinformatics platforms, and a lack of genomics expertise outside the research environment. Despite these hurdles, NGS technologies provide unparalleled high-resolution genotyping in a short time frame and are likely to be widely implemented in the field of diagnostic microbiology in the next few years, particularly for epidemiological investigations (replacing current typing methods) and the characterization of resistance determinants. Clinical microbiologists need to familiarize themselves with these technologies and their applications.en_US
dc.language.isoenen
dc.subject.otherAustraliaen
dc.subject.otherBacterial Typing Techniquesen
dc.subject.otherBase Sequenceen
dc.subject.otherDNA, Bacterial.analysisen
dc.subject.otherDisease Outbreaksen
dc.subject.otherDrug Resistance, Multiple, Bacterial.geneticsen
dc.subject.otherEscherichia coli.classification.drug effects.geneticsen
dc.subject.otherEscherichia coli Infections.diagnosis.drug therapyen
dc.subject.otherGenome, Bacterial.geneticsen
dc.subject.otherGenotypeen
dc.subject.otherHigh-Throughput Nucleotide Sequencingen
dc.subject.otherHumansen
dc.subject.otherInfant, Newbornen
dc.subject.otherIntensive Care Units, Neonatalen
dc.subject.otherMaleen
dc.subject.otherMeningitis, Bacterial.complicationsen
dc.subject.otherMultilocus Sequence Typingen
dc.subject.otherPolymorphism, Single Nucleotideen
dc.subject.otherSequence Analysis, DNAen
dc.subject.otherUrinary Tract Infections.complicationsen
dc.subject.otherbeta-Lactam Resistance.geneticsen
dc.subject.otherbeta-Lactamases.geneticsen
dc.titleOutbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory.en_US
dc.typeJournal Articleen_US
dc.identifier.journaltitleJournal of Clinical Microbiologyen_US
dc.identifier.affiliationMicrobiologyen_US
dc.identifier.doi10.1128/JCM.03332-12en_US
dc.description.pages1396-401en
dc.relation.urlhttps://pubmed.ncbi.nlm.nih.gov/23408689en
dc.type.contentTexten_US
dc.type.austinJournal Articleen
local.name.researcherHowden, Benjamin P
item.languageiso639-1en-
item.fulltextNo Fulltext-
item.grantfulltextnone-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.cerifentitytypePublications-
item.openairetypeJournal Article-
crisitem.author.deptInfectious Diseases-
crisitem.author.deptInfectious Diseases-
crisitem.author.deptMicrobiology-
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