Table 1.

Use of whole genome sequencing in outbreak investigation

Time period	Location, Country	Pathogens	Application ofWGS	WGS isolates	Sequencer	Source of the outbreak	Comments	Ref.
2011	Germany	E.coli O104:H4	Real time	1	Illumina	contaminated imported seeds	The outbreak strain belonged to enteroaggregative E. coli lineage and had acquired Shiga toxin 2 and antibiotic resistance genes.	[1]
2011	Germany	E.coli O104:H4	Real time	12	PacBio RS	contaminated imported seeds	The outbreak strain was different from other O104:H4 clone in containing prophage encoding Shiga toxin 2, additional virulence and antibiotic resistance factors.	[2]
2011	Germany	E. coli O104:H4	Real time	15	Illumina	contaminated imported seeds	The outbreak strains from Germany and France were clonally related to E coli O104:H4 from African countries.	[3*]
2009	Surrey, UK	E. coli O517:H7	Real time	16	454 pyrosequencing and Illumina	animal in a farm	WGS showed gross contamination of the outbreak strain across a farm that had been epidemiologically linked to human cases.	[4**]
2010	Artibonite, Haiti	Vibrio cholerae	Real time	5	PacBio RS		The outbreak strain is closely related to pandemic El Tor O1 strain.	[5]
2009	Cambridge, UK	Staphylococcus aureus	Retrospective	14	Illumina	nosocomial transmission	WGS showed a clear distinction between isolates in the outbreak and non-outbreak group.	[6**]
2011	Cambridge, UK	Staphylococcus aureus	Real time	15	Illumina	nosocomial transmission	WGS identified the transmission of bacteria among patients, which could not be confirmed with conventional method.	[7**]
1982-2003 2006-2007	ST239 worldwide	Staphylococcus aureus	Retrospective	46	Illumina		WGS data was used to estimate the time frame for the emergence of a bacterial pathogen clone and its evolution during epidemic spread.	[8]
2006-2008	Canada	Mycobacterium tuberculosis				transmission	WGS allowed for differentiation of the outbreak isolates into two distinct genetic lineages of M. tuberculosis that	[9]
1994-2011	Birmingham, Leicester, UK	Mycobacterium tuberculosis	Retrospective	390	Illumina	person-to-person tramission	WGS revealed no more than 5 SNPs separating epidemiologically-linked isolates.	[10**]
1997-2010	Hamburg, Germany	Mycobacterium tuberculosis	Retrospective	86	454 pyrosequencing	person-to-person transmission	WGS provides a measure of M. tuberculosis genome evolution over time in its natural host context.	[11]
2007-2011	Cambridge, UK	Mycobacterium abscessus	Retrospective	168	Illumina	person-to-person transmission	WGS showed person-person transmission of drug- resistant M. abscessus between cystic fibrosis patients.	[12**]
2011-2012	NewYork, US	Klebsiella pneumonia	Retrospective	18	454 pyrosequencing	nosocomial transmission	Three independent transmission events from isolates colonizing the different body sites of the index patient to the other cases were revealed by WGS.	[13**]
2011	Missouri, US	Apophysomyces trapeziformis	Real time	18	Illumina	environmental molds	WGS identified 4 different types of Apophysomyces trapeziformis that caused the mycormycosis outbreak.	[14**]