. 2014 Jun 11;3(2):437–458. doi: 10.3390/pathogens3020437

Table 2.

Methodologies and analysis execution techniques of recently published bacterial outbreak investigations.

Species	Focus ^a	Type(s) of Methods	Tools ^b	Ref.
Clostridium difficile/Escherichia coli	Transmission	Mapping, variant calling, phylogeny	Independent and/or custom	[15]
	MLST	de novo assembly, sequence search	Independent and/or custom
	Antibiotic resistance genes	de novo assembly, sequence search	Independent and/or custom
E. coli	Diversity/Resolution	Mapping, variant calling, phylogeny	Independent and/or custom	[33]
	Relationship to historical isolates	de novo assembly, multiple sequence alignment	Independent and/or custom
	Gene content comparison	de novo assembly, annotation	Independent and/or custom
E. coli	Differentiation	Mapping, variant calling	CLC Genomics Workbench	[34]
	MLST	de novo assembly, sequence search	CLC Genomics Workbench
	Antibiotic resistance genes	de novo assembly, sequence search	CLC Genomics Workbench/custom
	Relationship to historical isolates	Mapping, variant calling, network/de novo assembly	CLC Genomics Workbench/custom
Klebsiella pneumoniae	Transmission	Mapping, variant calling, minimum spanning tree	Independent and/or custom	[17]
Legionella pneumophilia	Differentiation	Mapping, variant calling, phylogeny	Independent and/or custom	[35]
Mycobacterium tuberculosis	Diversity/Resolution	Mapping, variant calling, phylogeny	Independent and/or custom	[36]
Neisseria meningitidis	Diversity/Resolution	de novo assembly, sequence search	Independent/BIGSdb	[16]
Neisseria meningitidis	MLST, other typing	de novo assembly, sequence search	Independent/BIGSdb	[16]
Shigella sonnei	Differentiation	Mapping, variant calling, phylogeny	Independent and/or custom	[37]
Staphylococcus aureus	Differentiation	Mapping, variant calling, multiple sequence alignment (references), phylogeny	Independent and/or custom	[13]
S. aureus	Differentiation	Mapping, variant calling, phylogeny	Independent and/or custom	[14]
	MLST	Mapping, read depth analysis, variant calling	Independent and/or custom
	Toxin genes	Mapping, read depth analysis, variant calling	Independent and/or custom
	Antibiotic resistance genes	Mapping, read depth analysis, variant calling	Independent and/or custom

^a Differentiation—the aim was to differentiate outbreak from non-outbreak strains; Diversity/resolution—the aim was to assess the diversity and/or resolve the phylogenetic relationships among outbreak strains; Transmission—the aim of the study was to resolve the relationships between strains specifically to enable transmission tracing;

^b Independent and/or custom—refers to the use of independent bioinformatics tools for different analysis stages (e.g., separate open source tools for mapping and variant calling) and/or custom analyses/scripts.