Please use this identifier to cite or link to this item:
Title: Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory.
Austin Authors: Sherry, Norelle L ;Porter, Jessica L;Seemann, Torsten;Watkins, Andrew;Stinear, Timothy P;Howden, Benjamin P 
Affiliation: Department of Microbiology, Austin Health, Melbourne, Australia
Issue Date: 13-Feb-2013
Publication information: Journal of Clinical Microbiology 2013; 51(5): 1396-401
Abstract: Next-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.
Gov't Doc #: 23408689
DOI: 10.1128/JCM.03332-12
Type: Journal Article
Subjects: Australia
Bacterial Typing Techniques
Base Sequence
DNA, Bacterial.analysis
Disease Outbreaks
Drug Resistance, Multiple, Bacterial.genetics
Escherichia coli.classification.drug effects.genetics
Escherichia coli Infections.diagnosis.drug therapy
Genome, Bacterial.genetics
High-Throughput Nucleotide Sequencing
Infant, Newborn
Intensive Care Units, Neonatal
Meningitis, Bacterial.complications
Multilocus Sequence Typing
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Urinary Tract Infections.complications
beta-Lactam Resistance.genetics
Appears in Collections:Journal articles

Show full item record

Page view(s)

checked on Dec 2, 2022

Google ScholarTM


Items in AHRO are protected by copyright, with all rights reserved, unless otherwise indicated.