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 |