EULabCap country profile

CZECH REPUBLICReport on 2016 data

Version 1, 19 December 2017

Executive summary for Czech Republic

What are the key questions of EULabCap survey? Does the EU/EEA public health microbiology system possess the critical capabilities and adequate level of core capacity to provide timely and reliable information on pathogen detection and characterisation for effective infectious disease prevention, alert and control at Member State and EU/EEA level and how does it progress over time?

How well was your country performing in 2016? Overall, Czech Republic provided data for 100% of the indicators. With an overall EULabCap index of 8.2/10 in 2016, as compared with 7.3 to 8.4 in 2013-15, data provided by the Czech Republic indicated a high and improving level of capability/capacity for their public health microbiology system.

On the positive side: Czech Republic showed a high overall performance, as compared with other EU/EEA countries, indicated by scores in the top quartile for the majority of the indicators. Top performance was achieved for implementation of EU standards for antimicrobial susceptibility testing and regulation of National Reference Laboratories. High performance was found for the regulation and guidance for diagnostic testing. For all key diseases surveyed, diagnostic testing guidelines were available at the national level and their clinical use was monitored except for antenatal screening of congenital infections and for diagnostic of Clostridium difficile infection. There was very good provision of reference diagnostic confirmation services, antimicrobial resistance monitoring and strong networking capacity for laboratory-based surveillance at national level and improving participation in EU disease networks. National Reference Laboratories participation to outbreak response also showed high performance.

For attention: Diagnostic testing utilisation rates decreased for some diseases in 2016. Laboratory preparedness for emerging resistance colistin-resistance appears limited.

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EULabCap country profile on 2016 data

Figure 1 shows the 2016 survey scores for Czech Republic (in red) and the EU/EEA interquartile range(IQR, in grey) for each of the 12 targets within the three EULabCap dimensions.

Figure 1.

Figure 2 shows the yearly EULabCap median index scores for Czech Republic and the interquartile rangeof EU/EEA scores by target, 2013-2016.

Figure 2.

Results

0

2

4

6

8

101.1 Regulation clin micro

1.2 Diag guidance

1.3 Diag test use

1.4 AST

2.1 Regulation NRL

2.2 Ref diag id

2.3 Molecular surveillance

2.4 AMR monitoring

3.1 Surveillance

3.2 EULabNetparticipation

3.3 Outbreak response

3.4 Preparednessresponse

Target scores

Dimensions

1. Primary diagnostic testing

2. NRL services

3. Surveillance/ epidemic response support

Czech Republic, 2016EU/EEA IQR, 2016

7.0 8.0 8.0

8.0

0

2

4

6

8

10

2013 2014 2015 2016

Inde

x sc

ore

Target 1.1

8.0 8.09.0 9.0

0

2

4

6

8

10

2013 2014 2015 2016

Inde

x sc

ore

Target 2.1

8.0

10.0 10.09.0

0

2

4

6

8

10

2013 2014 2015 2016

Inde

x sc

ore

Target 3.1

8.0 8.0 8.0 8.0

0

2

4

6

8

10

2013 2014 2015 2016

Target 1.2

9.0

8.0 8.0

9.0

0

2

4

6

8

10

2013 2014 2015 2016

Target 2.2

8.0

5.0

6.7

8.3

0

2

4

6

8

10

2013 2014 2015 2016

Target 3.2

5.0

8.0

9.0

7.0

0

2

4

6

8

10

2013 2014 2015 2016

Target 1.3

5.0

7.0 7.0

6.0

0

2

4

6

8

10

2013 2014 2015 2016

Target 2.3

6.0

9.0 9.0 9.0

0

2

4

6

8

10

2013 2014 2015 2016

Target 3.3

8.0

10.010.0 10.0

0

2

4

6

8

10

2013 2014 2015 2016

Target 1.4

9.0 9.0 9.08.0

0

2

4

6

8

10

2013 2014 2015 2016

Target 2.4

6.0 6.07.0 7.0

0

2

4

6

8

10

2013 2014 2015 2016

Target 3.4

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EULabCap country profile on 2016 dataFigure 3 shows: left, the EULabCap indicator scores (range from 0-2) for Czech Republic from 2013-2016,and right, the 2016 indicator score distribution for EU/EEA countries. Figure 3.

2013 2014 2015 20161.11 Test reimbursement 2 10.0 10.0 21.12 Laboratory licencing 1 5.0 5.0 11.13 Laboratory accreditation 1 5.0 5.0 11.14 Biosafety general 2 10.0 10.0 21.15 Biosafety tuberculosis 1 10.0 10.0 2

1.21 Antenatal screening 1 5.0 5.0 11.22 HIV testing 2 10.0 10.0 21.23 C. difficile testing 1 5.0 5.0 11.24 CPE screening 2 10.0 10.0 21.25 Tuberculosis drug susceptibility testing (DST) 2 10.0 10.0 2

1.31 Diagnostic tests migrants 2 10.0 10.0 21.32 Blood culture test rate 1 10.0 10.0 11.33 C. difficile test rate 0 10.0 10.0 21.34 Tuberculosis culture confirmation and DST 0 0.0 5.0 01.35 HIV late diagnosis 2 10.0 10.0 2

1.41 National Antimicrobial Susceptibility Committee 2 10.0 10.0 21.42 Clinical laboratories using EUCAST breakpoints 2 10.0 10.0 21.43 EARS-Net participants using EUCAST breakpoints 2 10.0 10.0 21.44 ERLTB-Net participation in EQA for DST 2 10.0 10.0 21.45 Gonorrhoea antimicrobial susceptibility testing 0 NA 10.0 2

2.11 NRL funding 1 5.0 5.0 12.12 NRL nomination 2 10.0 10.0 22.13 NRL core functions 2 10.0 10.0 22.14 NRL accreditation 2 10.0 10.0 22.15 NRL BSL3 1 5.0 10.0 2

2.21 Diagnostic identification 53 EU notifiable diseases 1 10.0 10.0 22.22 Legionella culture confirmed 2 10.0 10.0 22.23 Pertussis laboratory confirmed 2 5.0 5.0 12.24 Serogroup STEC 2 5.0 5.0 22.25 SARI viral testing 2 10.0 10.0 2

2.31 WGS-based surveillance 0 5.0 5.0 12.32 Salmonella genotyped * 0.0 0.0 02.33 MDR-TB MIRU-VNTR genotyped * 10.0 10.0 22.34 N. meningitidis genotyped 2 10.0 10.0 22.35 HIV ARV genotyped 1 10.0 10.0 1

2.41 MRSA characterisation resistance 2 10.0 10.0 22.42 Carbapenemase identification 2 10.0 10.0 22.43 ESBL identification using EUCAST guidance 2 10.0 10.0 22.44 Influenza AST to neuraminidase inhibitors 1 5.0 5.0 22.45 Cross-sector monitoring of AMR * 2 10.0 10.0 0

3.11 Laboratory surveillance networks 2 10.0 10.0 23.12 Laboratory data reporting 1 10.0 10.0 23.13 Laboratory-based outbreak detection 2 10.0 10.0 23.14 Sentinel network for ARI 2 10.0 10.0 13.15 Chlamydia trachomatis surveillance system 1 10.0 10.0 2

3.21 ELDS-Net participation 2 10.0 10.0 NA3.22 EVD-LabNet participation 2 5.0 NA 23.23 IBD-LabNet participation 2 NA NA NA3.24 ERLTB-Net participation 2 5.0 5.0 23.25 Euro-GASP participation 0 0.0 5.0 1

3.31 NRL role preparedness 1 10.0 10.0 23.32 NRL role outbreak investigation 2 10.0 10.0 23.33 NRL 24/7 response duty 1 10.0 10.0 23.34 Listeria monocytogenes genotyped 0 5.0 5.0 13.35 Hepatitis A virus genotyped 2 10.0 10.0 2

3.41 Diagnostic capability MERS-CoV 2 10.0 10.0 23.42 Diagnostic capability Influenza A(H5/7Nx) 2 10.0 10.0 23.43 Diagnostic capability Ebola virus 0 0.0 0.0 13.44 Diagnostic capability for detection 5 rare agents 2 10.0 10.0 23.45 Colistin susceptibility testing * 0 0.0 5.0 0

Indicator score: NA 0 1 2

EU/EEA indicator score distribution

* Indicator replaced in 2016 (score not comparable with previous years).

1

1

11

14

2

234

18

1

1

2

30

301

4

23

1

13

17

3

55

83

1

11213

175

33

2

2

12

1

27

2

11514

103

15

13

132

4

2

3

11

7

1

13

4

520

133

1410

1213

10

15

112

21

5

4

129

214

8

1811

412

125

15

67

98

6

110

82110

4

9

96

109

8

57

222

11

2922

910

24

1115

914

19

281313

1113

2526

2329

1719

2815

22

3012

161514

157

1218

14

2323

2017

11

2817

199

14

24

2917

1824

1918

12

2423

725

14

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EULabCap country profile on 2016 data

What is the purpose of the EULabCap monitoring system? To monitor key public health microbiologycapabilities and capacity for surveillance and epidemic preparedness. ECDC in close collaboration withthe National Microbiology Focal Points (NMFP) and the Advisory Forum, has developed the EULabCap system.The EULabCap EU/EEA and the EULabCap country profile reports (provided to NMFP for national dissemination) aim to help policymakers identifying possible areas for action.

What is this EULabCap country profile report about? It compares the 2016 indicator scores of yourcountry with those in previous surveys in comparison to all EU/EEA countries. The main areas with low 2016scores, or score changes over the years, are identified to inform national authorities about areas requiringattention, and/or on the possible impact of capacity strengthening actions and health system reforms.

EULabCap survey tool methodology. This monitoring tool combines 60 technical indicators groupedinto 12 targets, distributed across the following three public health microbiology system dimensions: primarydiagnostic testing, national microbiology reference laboratory (NRL) services and laboratory-based surveillance and epidemic response support (Figure 4).Figure 4.

Data collection. A mixed method was used for data collection and scoring: (a) information for 20 indicatorswas retrieved by ECDC from data sets accessible in The European Surveillance System (TESSy) and EUdisease network reports; (b) NMFP used a questionnaire to collect information from their country for theremaining 40 indicators. Data underwent a round of validation by the NMFP.

Scoring system. Each indicator was scored at three levels: low (0, “No or limited capability/capacity”),intermediate (1, “Partial capability/ capacity", e.g. below the EU target, or partial compliance) and high(2, “Complete capability/ capacity", e.g. EU target reached, or high compliance). Indicators were notscored for which data were not available or not applicable (NA) to the country.

Data analysis and interpretation. Aggregated EULabCap indices were calculated for each target anddimension as the mean of component indicator scores, converting index values on a scale of 0–10. Overall EULabCap system indices per country were graded qualitatively at three performance levels:low (0-5.9), intermediate (6.0-7.9) and high (8.0-10). Data completeness was calculated as a percentage of missing data (NA) for each indicator per country. As NA values were not included in the calculation of the target index, the performance estimates for these targets can be biased towards either under-, or over-estimation of performance. Trends over time should be carefully interpreted for indicators that have been revised over time (indicated with * in Figure 3).

For more information:Visit our website https://ecdc.europa.eu/en/microbiology/laboratory-capacity-and-capability or contactus at: EU.LabCap@ecdc.europa.eu.

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