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Table 1 Characteristics of included studies (Jan 2015 to Sep 2018: n = 275)

From: Status and potential of bacterial genomics for public health practice: a scoping review

Study characteristic No. of studies (Jan 2015 to Sep 2018)
Outbreak investigations (n = 164) Control-oriented surveillance (n = 41) Strategy-oriented surveillance (n = 70)
Country¥,*
 USA and Canada 42 7 16
 UK and Ireland 33 13 15
 Australia and New Zealand 19 3 7
 Germany 14 2 4
 Denmark 9 4 0
 France 5 2 2
Setting¥
 Community 94 23 47
 Institutional (hospital, school, nursery, etc.) 73 21 25
Time orientation of NGS analyses¥
 Retrospective 97 18 59
 Quasi-real time 58 0 0
 Prospective 11 25 11
Level of implementation of NGS analyses¥
 Proof-of-concept 57 27 8
 Used to address a specific public health problem 100 10 61
 Implemented into routine public health 14 6 2
Sampling fraction of NGS analyses
 All available samples 57 25 21
 Subset of available samples (complementary) 107 16 48
Pathogens¥
Staphylococcus aureus 15 10 13
 Multidrug-resistant Gram-negative bacteria 27 4 12
 Vancomycin-resistant Enterococci (VRE) 5 6 0
Clostridium difficile 5 1 2
Streptococcus spp. 8 0 6
Listeria monocytogenes 13 4 1
Shigella spp. 1 2 2
Salmonella spp. 33 5 8
 Shiga toxin-producing Escherichia coli (STEC) 10 4 1
Campylobacter jejuni 5 0 0
Legionella spp. 10 0 1
Mycobacterium spp. 14 6 5
Neisseria spp. 6 0 14
 Others 13 1 6
  1. ¥One study can be assigned to multiple categories
  2. *Non-exhaustive list