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Table 3 Examples of infectious disease outbreaks for which next-generation sequencing has been used

From: Clinical detection and characterization of bacterial pathogens in the genomics era

Causative agent Date of outbreaka Country Setting NGS platform Impact on disease control and/or findings Reference
Multi-drug resistant Acinetobacter baumannii 2009 UK Hospital Roche GS-FLX Proof of patient-to-patient transmission [114]
Bordetella pertussis 2012 USA Community PacBio RS Identification of several concomitant clones [131]
Clostridium difficile 2007-2011 UK Hospital and community Illumina Only one-third of cases were acquired from symptomatic patients [132]
Carbapenem-resistant Enterobacter cloacae 2008-2009 UK Hospital Illumina MiSeq Retrospective identification of two distinct strains [133]
Vancomycin-resistant Enterococcus faecium NA UK Hospital Illumina MiSeq Retrospective identification of the clonality of the causative strain [133]
Escherichia coli O104:H4 2011 Germany Community Ion Torrent PGM, PacBio RS Identification of the source of infection [134],[135]
Francisella tularensis holarctica 2010 Sweden Community Ion Torrent PGM, PacBio RS Retrospective identification of several clones [136]
Carbapenemase-producing Klebsiella pneumoniae 2012 Nepal Hospital PacBio RS, Illumina HiSeq Identification of a clone responsible for three distinct outbreaks [137]
Legionella pneumophila 2012 Canada Community Illumina MiSeq Identification of the source of infection [138]
Listeria monocytogenes 2008 Canada Community Roche GS-FLX Retrospective identification of three clones responsible for a nationwide outbreak [139]
Mycobacterium abscessus 2007-2011 UK Cystic fibrosis center Illumina HiSeq Proof of patient-to- patient transmission [140]
Mycobacterium tuberculosis 2006-2008 Canada Hospital Illumina Genome Analyzer II Retrospective identification of two concomitant outbreaks [141]
Mycobacterium tuberculosis 2010 UK Community Illumina MiSeq Identification and treatment of contact patients [119]
Neisseria meningitidis 1997 UK Hospital Illumina Genome Analyzer II Retrospective identification of the causative clone [142]
Salmonella Newport 2011 Europe Community Illumina HiSeq Confirmation of watermelons as source of international spread of a Salmonella newport clone [143]
Salmonella Enteritidis 2010-2012 USA Hospital IonTorrent PGM Retrospective and prospective identification of a single clone responsible for the outbreak [144]
Methicillin-resistant Staphylococcus aureus 2009 USA Pediatric hospital Illumina MiSeq Retrospective identification of the causative clone and its resistome [61]
Methicillin-resistant Staphylococcus aureus 2011 UK Hospital Illumina HiSeq Identification of carriage by a staff member [145]
Staphylococcus aureus 2011 USA Hospital Illumina HiSeq Proof of absence of patient-to-patient transmission [146]
Vibrio cholerae 2010 Haiti Community PacBio RS Identification of the source of the causative clone [59]
Vibrio cholerae 2012 Guinea Community Illumina MiSeq Identification of the source of the causative clone [147]
  1. aAbbreviations: NA, data not available.