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 | |
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] |