Table 2.
Number of EU/EEA countries using WGS-based typing in the National Public Health Reference Laboratories and respective typing scheme, sampling frame, bioinformatic analysis, and raw data storage by disease group and pathogen, 2016.
| Foodborne pathogens | Antimicrobial-resistant pathogens | Vaccine-preventable pathogens | ||||||
|---|---|---|---|---|---|---|---|---|
| L. monocytogenes | S. enterica | Shiga toxin-producing E. coli (STEC) | carbapenemase-producing Enterobacteriaceae (CPE) | AR N. gonorrhoeae | multidrug-resistant (MDR) M. tuberculosis | Human Influenza virus | N. meningitidis | |
| Number of countries using WGS-based typing | 13 | 11 | 13 | 9 | 5 | 10 | 12 | 15 |
| Typing scheme | ||||||||
| First-line | 6 | 3 | 7 | 5 | 5 | 5 | 2 | 6 |
| Second-line | 7 | 8 | 6 | 4 | – | 5 | 10 | 9 |
| Sampling frame | ||||||||
| Continuous comprehensive | 8 | 1 | 6 | 2 | – | 8 | – | 9 |
| Sentinel/subset of samples | 4 | 10 | 7 | 7 | 5 | 2 | 12 | 6 |
| Bioinformatic analysisa | ||||||||
| Core genome multi-locus sequence typing | 10 | 8 | 5 | 5 | 4 | 4 | – | 11 |
| Single-nucleotide polymorphism | 7 | 8 | 8 | 4 | 3 | 8 | 4 | 4 |
| Resistome prediction | 3 | 6 | 7 | 8 | – | 9 | 10 | 4 |
| wgMLST | 2 | 2 | 4 | 3 | 3 | 1 | – | – |
| Virulome/mobilome prediction | 1 | 4 | 11 | 4 | 1 | – | – | – |
| MLST prediction | 3 | 1 | 2 | – | – | – | – | – |
| Serogroup prediction | 3 | 2 | 3 | – | – | – | – | – |
| NG-MAST | – | – | – | – | 4 | – | – | – |
| Speciation | – | – | – | – | – | 1 | – | – |
| Hemagglutinin and neuraminidase sequence prediction | – | – | – | – | – | – | 9 | – |
| Phylogenetic relationship | – | – | – | – | – | – | 10 | – |
| Identification of specific point mutations | – | – | – | – | – | – | 10 | – |
| rMLST | – | – | – | – | – | – | – | 5 |
| MLST + porA VR1 and VR2 + fetA | – | – | – | – | – | – | – | 13 |
| Vaccine antigens prediction | – | – | – | – | – | – | – | 3 |
| Other not specified | – | – | – | – | – | – | – | 2 |
| Raw sequence data storage | ||||||||
| Dedicated closed database(s) | 11 | 9 | 11 | 8 | 4 | 9 | 9 | 10 |
| Publicly available database(s) | 1 | 1 | – | – | – | – | 1 | 3 |
| Both dedicated closed database(s) and publicly available database(s) | 1 | 1 | 2 | 1 | 1 | 1 | 2 | 2 |
aNot mutually exclusive.