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. 2020 Mar 3;18(3):e06007.
doi: 10.2903/j.efsa.2020.6007. eCollection 2020 Mar.

The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018

European Food Safety Authority; European Centre for Disease Prevention and Control

The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018

European Food Safety Authority et al. EFSA J. .

Abstract

Data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs), jointly analysed by EFSA and ECDC and reported in a yearly EU Summary Report. The annual monitoring of AMR in animals and food within the EU is targeted at selected animal species corresponding to the reporting year. The 2017 monitoring specifically focussed on pigs and calves under 1 year of age, as well as their derived carcases/meat, while the monitoring performed in 2018 specifically focussed on poultry and their derived carcases/meat. Monitoring and reporting of AMR in 2017/2018 included data regarding Salmonella, Campylobacter and indicator Escherichia coli isolates, as well as data obtained from the specific monitoring of ESBL-/AmpC-/carbapenemase-producing E. coli isolates. Additionally, some MSs reported voluntary data on the occurrence of meticillin-resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility. This report provides, for the first time, an overview of the main findings of the 2017/2018 harmonised AMR monitoring in the main food-producing animal populations monitored, in related carcase/meat samples and in humans. Where available, data monitoring obtained from pigs, calves/cattle, broilers, laying hens and turkeys, as well as from carcase/meat samples and humans were combined and compared at the EU level, with particular emphasis on multiple drug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates exhibiting presumptive ESBL-/AmpC-/carbapenemase-producing phenotypes. The outcome indicators for AMR in food-producing animals, such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL-/AmpC-producing E. coli have been also specifically analysed over the period 2014-2018.

Keywords: ESBL; MRSA; antimicrobial resistance; indicator bacteria; zoonotic bacteria.

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Figures

Figure 1
Figure 1
Occurrence of resistance to selected antimicrobials in Salmonella spp. and selected serovars isolated from humans, 2018

  1. Horizontal line represents median, and blue diamond represents the resistance at the reporting‐MS level.

Figure 2
Figure 2
Spatial distribution of combined ‘microbiological’ resistance to ciprofloxacin and cefotaxime among (a) Salmonella spp., (b) S. Infantis and (c) S. Kentucky isolated from human cases, 2018

  1. Pink indicates less than 10 isolates tested.

Figure 3
Figure 3
Number of MDR isolates, isolates resistant to 1 and/or 2 antimicrobial classes and completely susceptible Salmonella isolates from humans in 2018
Figure 4
Figure 4
Occurrence of resistance to selected antimicrobials in Salmonella spp. from carcases of pigs, calves (< 1 year of age), broilers and fattening turkeys, reporting EU MSs, 2017/2018

  1. AMP: ampicillin, SMX: sulfamethoxazole, TET: tetracycline, CIP: ciprofloxacin, CTX: cefotaxime, CIP/CTX: combined ‘microbiological’ resistance to ciprofloxacin and cefotaxime, N: total number of Salmonella spp. reported by MSs. Blue diamond shows resistance at the reporting‐MS group level.

Figure 5
Figure 5
MDR and completely susceptible Salmonella spp. recovered from carcases of pigs (fatteners), calves (under 1 year of age), broilers and fattening turkeys, for all reporting countries (including 1 non‐MS in pig carcases and 2 non‐MSs in broiler carcases) in 2017/2018

  1. MDR and complete susceptibility levels are also expressed as a percentage; N: total number of Salmonella spp. reported by MSs and non‐MSs.

Figure 6
Figure 6
Spatial distributions of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from (a) fattening pig carcases and (b) calf carcases (less than 1 year of age), using harmonised ECOFFs, 2017
Figure 7
Figure 7
Spatial distributions of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from (a) broiler carcases and (b) fattening turkey carcases, using harmonised ECOFFs, 2018
Figure 8
Figure 8
Occurrence of resistance to selected antimicrobials in Salmonella spp. from fattening pigs, cattle, broilers, laying hens and fattening turkeys, reporting EU MSs, 2017/2018

  1. AMP: ampicillin, SMX: sulfamethoxazole, TET: tetracycline, CIP: ciprofloxacin, CTX: cefotaxime, CIP/CTX: combined ‘microbiological’ resistance to ciprofloxacin and cefotaxime, N: total number of Salmonella spp. reported by MSs. Blue diamond shows resistance at the reporting‐MS group level.

    Note: Member States reporting at least 10 isolates are shown in the graph; all isolates are included in the calculation of resistance at the reporting‐MS group level.

Figure 9
Figure 9
MDR and completely susceptible Salmonella spp. recovered from fattening pigs, cattle, broilers, laying hens and fattening turkeys, all reporting countries, 2017/2018

  1. MDR and complete susceptibility are expressed as percentages; N: total number of Salmonella spp. reported by MSs and non‐MSs.

Figure 10
Figure 10
Spatial distributions of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from (a) fattening pigs and (b) cattle, using harmonised ECOFFs, 2017
Figure 11
Figure 11
Spatial distributions of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from (a) broilers, (b) laying hens and (c) fattening turkeys, using harmonised ECOFFs, 2018
Figure 12
Figure 12
Distribution of MIC levels among ciprofloxacin‐resistant Salmonella spp. from carcases of pigs, calves, broilers and turkeys, as well as fattening pigs, cattle, broilers, laying hens and fattening turkeys, for all reporting EU MSs, 2017/2018

  1. n: Total number of Salmonella spp. exhibiting CIP resistance (MSs only); N: total number of Salmonella spp. reported by MSs.

  2. 1In accordance with breakpoints stated in Decision 2013/652/EU.

  3. The proportion of isolates showing high‐level resistance is not included with those exhibiting ‘clinical’ or ‘microbiological’ resistance; similarly, the proportion of isolates showing ‘clinical’ resistance is not included with those displaying ‘microbiological’ resistance. The Figure above excludes one isolate reported from laying hens (by the Republic of North Macedonia), which was ‘microbiologically’ resistant to ciprofloxacin.

Figure 13
Figure 13
Breakdown of the number of tigecycline‐resistant isolates by serovar, where detected among the animal/carcase origins by reporting MSs in 2017/2018

  1. n: Total number of tigecycline‐resistant isolates reported by the MSs; predominant serovars are also expressed as a percentage.

  2. Note: No tigecycline‐resistant isolates were reported among Salmonella spp. from calf carcases (N = 82, 7 MSs).

Figure 14
Figure 14
Breakdown of the number of colistin‐resistant isolates by serovar, where detected among the animal/carcase origins by reporting MSs in 2017/2018

  1. n: Total number of colistin‐resistant isolates reported by the MSs; predominant serovars are expressed as a percentage.

Figure 15
Figure 15
Occurrence of resistance to selected antimicrobials in C. jejuni and C. coli isolates from humans, 2018

  1. Horizontal line represents median, and blue diamond represents the resistance at the reporting‐MS level.

Figure 16
Figure 16
Combined resistance to the critically important antimicrobials ciprofloxacin and erythromycin in (a) C. jejuni and (b) C. coli isolates from humans, 2018

  1. Note: For Finland, travel information was missing from the AMR data while from other sources, travel‐associated cases were known to account for 80% of Finnish Campylobacter infections in 2018.

Figure 17
Figure 17
Number of MDR isolates, isolates resistant to 1 and/or 2 antimicrobials and completely susceptible Campylobacter isolates from humans, 2018
Figure 18
Figure 18
Erythromycin MIC distribution in C. jejuni and C. coli isolates from humans, 2018

  1. MIC: minimum inhibitory concentration.

Figure 19
Figure 19
Occurrence of resistance to selected antimicrobials in C. jejuni/C. coli isolates from broilers, fattening turkeys and fattening pigs, reporting EU MSs, 2017/2018

  1. GEN: gentamicin, STR: streptomycin, TET: tetracycline CIP: ciprofloxacin, ERY: erythromycin, CIP/ERY: combined ‘microbiological’ resistance to ciprofloxacin and erythromycin. N: Total number of isolates reported by all Member States (MSs). Blue diamond: occurrence of resistance at the reporting‐MS group level.

Figure 20
Figure 20
Spatial distribution of combined resistance to ciprofloxacin and erythromycin in Campylobacter jejuni from (a) broilers (29 EU/EEA MSs, 2018), (b) fattening turkeys (11 EU/EEA MSs, 2018) and (c) calves (5 MSs, 2017)
Figure 21
Figure 21
Spatial distribution of combined resistance to ciprofloxacin and erythromycin in Campylobacter coli isolates from a) broilers, 6 EU/EEA MSs, 2018 and b) fattening pigs, 7 EU/EEA MSs, 2017
Figure 22
Figure 22
Proportions of isolates completely susceptible and MDR in C. jejuni and C. coli from fattening pigs, broilers and fattening turkeys, reporting EU/EEA MSs, 2017/2018

  1. N: Total number of isolates reported by the EU MSs.

Figure 23
Figure 23
Trends in ciprofloxacin (CIP), erythromycin (ERY), streptomycin (STR) and tetracycline (TET) resistance in C. jejuni from broilers, 2009–2018
Figure 24
Figure 24
Trends in ciprofloxacin (CIP), erythromycin (ERY), streptomycin (STR), and tetracycline (TET) resistance in C. jejuni from turkeys, reporting EU MSs, 2014–2018
Figure 25
Figure 25
MICs of Campylobacter jejuni isolates exhibiting erythromycin resistance in broilers and turkeys, reporting EU MSs and non‐EU MSs, 2017/2018

  1. N: Total number of C. jejuni or C. coli isolates exhibiting erythromycin resistance.

  2. *: Includes data on erythromycin‐resistant isolates reported by non‐EU MSs.

Figure 26
Figure 26
MICs of Campylobacter spp. isolates exhibiting erythromycin resistance in pigs, broilers and turkeys, reporting EU MSs and non‐EU MSs in 2017/2018

  1. N: Total number of C. jejuni or C. coli isolates exhibiting erythromycin resistance; ERY: erythromycin.

Figure 27
Figure 27
Comparison of clinical breakpoints (CBPs) and epidemiological cut‐off values (ECOFFs) used to interpret MIC data reported for Campylobacter spp. from humans, animals or food
Figure 28
Figure 28
Distribution of occurrence of resistance to selected antimicrobials in indicator E. coli isolates recovered from fattening pigs and calves under 1 year of age, 2017 and from broilers and fattening turkeys, 2018, EU MSs and non‐MSs, 2017/2018

  1. AMP: ampicillin, SMX: sulfamethoxazole, TET: tetracycline, CIP: ciprofloxacin, CTX: cefotaxime, CIP/CTX: combined ‘microbiological’ resistance to ciprofloxacin and cefotaxime, N: total number of E. coli reported by MSs. Blue diamond shows resistance at the reporting‐MS group level.

    Note: Member States reporting at least 10 isolates are shown in the graph; all isolates are included in the calculation of resistance at the reporting‐MS group level.

Figure 29
Figure 29
Spatial distribution of combined ‘microbiological’ resistance to cefotaxime and ciprofloxacin in indicator Escherichia coli. (a) fattening pigs, 28 MSs and 3 non‐MSs 2017, (b) calves under 1 year of age, 10 MSs and 2 non‐MSs 2017, (c) broilers, 27 MSs and 3 non‐MSs 2018, (d) fattening turkeys, 11 MSs and 1 non‐MSs 2018
Figure 30
Figure 30
Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracyclines (TET) in indicator E. coli from pigs, reporting countries, 2009–2017
Figure 31
Figure 31
Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracyclines (TET) in indicator E. coli from calves under 1 year of age, 2009–2017
Figure 32
Figure 32
Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracyclines (TET) in indicator E. coli from broilers, 2009–2018
Figure 33
Figure 33
Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracycline (TET) in indicator E. coli from fattening turkeys, 2014–2018
Figure 34
Figure 34
Spatial distribution of complete susceptibility to the antimicrobials tested in indicator E. coli. (a) fattening pigs, 28 MSs, 3 non‐MSs, 2017; (b) calves < 1 year of age, 10 MSs, 2 non‐MSs, 2017; (c) broilers, 28 MSs, 4 non‐MSs, 2018; (d) fattening turkeys, 11 MSs, 1 non‐MSs, 2018, EU MSs and non‐MSs
Figure 35
Figure 35
Changes in the occurrence of complete susceptibility to the panel of antimicrobials tested in indicator E. coli isolates from (a) fattening pigs and (b) calves < 1 year of age, between 2015 and 2017

  1. (↓)/(↑): indicates statistically significant trends between 2015 and 2017.

    The upper bounds of the 95% confidence interval of the occurrence of complete susceptibility and the rate of change (in %) are also indicated.

Figure 36
Figure 36
Changes in the occurrence of complete susceptibility to the panel of antimicrobials tested in indicator E. coli isolates from (a) broilers and (b) fattening turkeys, 2014–2018

  1. (↓)/(↑): indicates statistically significant trends over the 2014–2018 period. The upper bounds of the 95% confidence interval of the occurrence of complete susceptibility and the rate of change (in %) are also indicated.

Figure 37
Figure 37
Changes in outcome indicator of complete susceptibility (OICS), 26 MSs and 3 non‐MSs, 2014–2018

  1. (↓)/(↑): indicates statistically significant decreasing/increasing trends over the 2018–2014 period. The upper bounds of the 95% confidence interval of the OICS and the rate of change (in %) are also indicated.

Figure 38
Figure 38
Prevalence of presumptive ESBL‐producing (a) and AmpC‐producing (b) E. coli from the specific monitoring of ESBL/AmpC‐producing E. coli, 2017/2018
Figure 39
Figure 39
Spatial distribution of the prevalence of presumptive ESBL‐producing E. coli from (a) meat from broilers in 2018, (b) meat from pigs in 2017 and (c) bovine meat in 2017, EU MSs and non‐MSs, 2017/2018
Figure 40
Figure 40
Spatial distribution of the prevalence of presumptive ESBL‐producing E. coli from (a) broilers in 2018, (b) fattening turkeys in 2018, (c) fattening pigs in 2017 and (d) calves under 1 year of age in 2017, EU MSs and non‐MSs, 2017/2018
Figure 41
Figure 41
Spatial distribution of prevalence of presumptive AmpC‐producing E. coli from (a) meat from broilers in 2018, (b) meat from pigs in 2017, and (c) bovine meat in 2017, EU MSs and non‐MSs, 2017/2018
Figure 42
Figure 42
Spatial distribution of prevalence of presumptive AmpC‐producing E. coli from (a) broilers in 2018, (b) fattening turkeys in 2018, (c) fattening pigs in 2017, and (d) calves under 1 year of age in 2017, EU MSs and non‐MSs, 2017/2018
Figure 43
Figure 43
Prevalence of presumptive ESBL‐producing vs. AmpC‐producing E. coli from (a) meat from broilers, (b) broilers and (c) fattening turkeys, EU MSs and non‐EU MSs, 2018

  1. The upper bounds of the 95% confidence interval of the prevalence of ESBL‐ and/or AmpC‐producing E. coli are also indicated.

Figure 44
Figure 44
Prevalence of presumptive ESBL‐producing vs. AmpC‐producing E. coli from (a) meat from pigs and (b) fattening pigs, EU MSs and non‐EU MSs, 2017

  1. The upper bounds of the 95% confidence interval of the prevalence of ESBL‐ and/or AmpC‐producing E. coli are also indicated.

Figure 45
Figure 45
Prevalence of presumptive ESBL‐producing vs. AmpC‐producing E. coli from (a) bovine meat and (b) calves under 1 year of age, EU MSs and non‐EU MSs, 2017

  1. The upper bounds of the 95% confidence interval of the prevalence of ESBL‐ and/or AmpC‐producing E. coli are also indicated.

Figure 46
Figure 46
Trends on the prevalence of presumptive ESBL and/or AmpC‐producing E. coli in (a) meat from broilers, (b) meat from pigs, and (c) bovine meat over the period 2015–2017, EU MSs and non‐MSs

  1. To improve the visibility of the differences, different scales were used for the y‐axis for the different sub‐figures (a, 0–100%; b–c, 0–30%). The upper bounds of the 95% confidence interval of the prevalence of ESBL‐ and/or AmpC‐producing E. coli are also indicated.

Figure 47
Figure 47
Trends on the prevalence of presumptive ESBL and/or AmpC‐producing E. coli in (a) broilers, (b) fattening turkeys, (c) fattening pigs and (d) calves under 1 year of age, over the period 2015–2017, EU MSs and non‐MSs

  1. The upper bounds of the 95% confidence interval of the prevalence of ESBL‐ and/or AmpC‐producing E. coli and the rate of change (in %) are also indicated.

Figure 48
Figure 48
Changes in Outcome Indicator of ESBL‐ and/or AmpC producing E. coli (OIESC), 28 EU MSs and 3 non‐MSs, 2015–2018

  1. (↓)/(↑): indicates statistically significant decreasing/increasing trends over the 2015–2018 period. The upper bounds of the 95% confidence interval of the OICS and the rate of change (in %) are also indicated. Note: ‘Total’ values from 26 MSs do not include Italy and Malta.

Figure 49
Figure 49
MRSA prevalence in food, 2017/2018 (only food origins where positive isolates were obtained are presented)

  1. N: Total number of sample units tested; DE: Germany; NL: the Netherlands; FI: Finland; ES: Spain; CH: Switzerland; AT: Austria.

    1. spa‐types: t034 (11 isolates), t011 (1), t2741 (1).

    2. spa‐types: t011 (1 isolate), t002 (1). PVL status of the t002 isolate was not reported.

    3. spa‐types: t011 (2 isolates), t034 (1).

    4. spa‐types: t034 CC398 (1 isolate), t1430 (1), t571 CC398 (1), t13177 (1).

    5. spa‐types : t011 (1).

    *: spa‐types not reported.

Figure 50
Figure 50
MRSA prevalence in food‐producing animals (excluding clinical investigations), 2017/2018 (only origins where positive isolates were obtained are presented)

  1. N: Total number of sample units tested; DE: Germany; CH: Switzerland; BE: Belgium; DK: Denmark; FI: Finland; NL: the Netherlands; NO: Norway; ES: Spain; CHC: controlled housing conditions.

    1: spa‐types: t011 (14 isolates), t034 (7), t127 (1), t17339 (2). PVL status of the t127 isolate was not reported.

    2: spa‐types: t011 CC398 (65 isolates), t034 CC398 (8), t1451 CC398 (1), t1580 CC398 (2), t3423 CC398 (1), t3479 CC398 (1), t9433 CC398 (1).

    3: spa‐types: t011 CC398 (8 isolates), t034 CC398 (1), t223 (3), t1257 (1). The t223 isolates were PVL negative; TSST status was not determined. The PVL status of the t1257 isolate was not reported.

    4: spa‐types: t011 CC398 (5 isolates), t1451 CC398 (1), t223 (2), t223 ST22 (1). All three t223 isolates were PVL negative. One t223 isolate was subjected to WGS and confirmed to belong to ST22 and harbour the tst gene.

    5. spa‐types: t034 (7 isolates), t267 CC97 (1).

    6. spa‐types: t011 CC398 (2 isolates).

    7. spa‐types: t011 CC398 (2 isolates), t037 ST239 (1). WGS of the t037 isolate confirmed it to belong to ST239 and carry sak and scn genes.

    8. spa‐types: t011 CC398 (2 isolates), t034 CC398 (2).

    9. spa‐types: t011 CC398 (6 isolates), t034 CC398 (19), t571 CC398 (1), t588 CC398 (1), t1456 CC398 (1), t1457 CC398 (2), t13790 CC1 (1).

    10. spa‐types: t034 (32 isolates), t2741 (25), t011 (9), t108 (6), t1250 (1), t1255 (1), t17061 (1). NB. All MRSA isolates were subject to spa‐typing; from one slaughter batch, up to three different spa‐types were detected. Therefore, the total number of individual spa‐types exceeds the number of positive batches.

    11. spa‐types: t091 CC7 (1 isolate), t843 CC130 (1), t6292 CC425 (1). The t091 isolate was PVL negative, spa‐types t843 and t6292 were confirmed to carry the mecC gene.

    12. spa‐types: t011 (203 isolates), t034 (32), t108 (14), t109 (1), t899 (2), t1197 (11), t1255 (2), t1451 (13), t1606 (1), t2011 (5), t2346 (1), t2748 (1), t3041 (2), t4208 (2), t17304 (1), t17627 (1).

    13. spa‐types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1).

    14. spa‐types: t011 CC398 (6 isolates), t034 CC398 (24), t1250 CC398 (2), t1793 CC398 (1), t3171 CC398 (1).

    15. spa‐types: t011 CC398 (4 isolates), t034 CC398 (15), t588 CC398 (1), t1456 CC398 (1).

    16. spa‐types: t011 CC398 (22 isolates), t034 CC398 (85), t571 CC398 (3), t898 CC398 (1), t2383 CC398 (1), t2974 CC398 (1), t3423 CC398 (1), t4652 CC398 (1), t9266 CC398 (1).

    17. spa‐types: t011 CC398 (3 isolates), t034 CC398 (6), t843 CC130 (1). spa‐type t843 was confirmed to carry the mecC gene.

    *: spa‐types not reported.

Figure 51
Figure 51
MRSA types reported from food‐producing animals in (a) 2017 and (b) 2018, inferred from spa‐typing data

  1. Inferred MRSA types in (a) 2017 were recovered from calves, pigs and broiler/laying hen flocks; inferred MRSA types in (b) 2018 were recovered from pigs, cattle, laying hens, mink and horses at the herd/flock/farm/stable level.

    NB. All MRSA isolates recovered from Finnish fattening pigs in 2017 were subject to spa‐typing; from a slaughter batch of pigs, up to three different spa‐types were detected.

Figure 52
Figure 52
Temporal trends of MRSA prevalence in various types of meat, 2011–2018

  1. DE: Germany; ES: Spain; FI: Finland; CH: Switzerland.

    Where comparable longitudinal data were available, all reporting countries (4/4) used the 2‐S method of isolation (2011–2018).

    *: spa‐types not reported.

    1: In 2011, spa‐type: t011 (1 isolate).

    In 2012, 2013, 2014 and 2017, spa‐types not reported.

    2: In 2015, spa‐types: t034 (6 isolates), t2741 (3).

    In 2017, spa‐types: t034 (11 isolates), t011 (1), t2741 (1).

    3: In 2014, spa‐types: t011 (3 isolates), t032 (3), t034 (14), t571 (1) t899 (1).

    In 2016, spa‐types: t034 (3 isolates), t153 (1), t1430 (3), t2123 (2). PVL status of the t153 isolate was not reported.

    In 2018, spa‐types: t034 CC398 (1 isolate), t1430 (1), t571 CC398 (1), t13177 (1).

    4: In 2015 and 2017, spa‐types not reported.

    In 2016, spa‐types: t011 (3 isolates), t1190 (1). PVL status of the t1190 isolate was not reported.

Figure 53
Figure 53
Temporal trends of MRSA prevalence in cattle, 2012–2018

  1. BE: Belgium; CH: Switzerland; DE: Germany. Where comparable longitudinal data were available, all reporting countries (3/3) used the 2‐S method of isolation (2009–2018).

    *: spa‐types not reported.

    1: In 2012, spa‐types: t011 (40 isolates), t1451 (3), t1456 (1), t1985 (3), t3423 (1), untypable (1).

    In 2015, spa‐types: t011 (64 isolates), t034 (15), t037 (8), t044 (3), t1451 (3), t1580 (7), t1985 (8), t2287 (2), t3423 (5), untypable (1).. The t044 isolates were PVL negative.

    In 2018, spa‐types: t011 CC398 (65 isolates), t034 CC398 (8), t1451 CC398 (1), t1580 CC398 (2), t3423 CC398 (1), t3479 CC398 (1), t9433 CC398 (1).

    2: In 2015, spa‐types: t011 (11 isolates), t034 (6) and t008 (2). The t008 isolates were PVL positive.

    In 2017, spa‐types: t011 (14 isolates), t034 (7), t127 (1), t17339 (2). PVL status of the t127 isolate was not reported.

    3: In 2012, spa‐types: t011 (8 isolates), t037 (1), t388 (1), t1456 (1), t6228 (2), untypable (1).

    In 2015, t011 (4 isolates), t034 (1), t1580 (1), t1985 (2), t2383 (1), untypable (1).

    In 2018, spa‐types: t011 CC398 (8 isolates), t034 CC398 (1), t223 (3), t1257 (1). The t223 isolates were PVL negative; TSST status was not determined. The PVL status of the t1257 isolate was not reported.

    4: In 2012, spa‐types: t011 (16 isolates), t121 (1), t1456 (1), t1985 (1).

    In 2015, spa‐types: t011 (9 isolates), t034 (2), t1451 (1), t1580 (2), t2287 (1), t3423 (1).

    In 2018, spa‐types: t011 CC398 (5 isolates), t1451 CC398 (1), t223 (2), t223 ST22 (1). All three t223 isolates were PVL negative. One t223 isolate was confirmed to belong to ST22 and harbour the tst gene from WGS data.

Figure 54
Figure 54
Temporal trends of MRSA prevalence in pigs, 2009–2018

  1. CH: Switzerland; ES: Spain; FI: Finland; DE: Germany; DK: Denmark; NO: Norway; CHC: controlled housing conditions. 4/6 reporting countries used the 2‐S method of isolation (2009–2018). NO and DK used the 1‐S method of isolation in 2018.

    *: spa‐types not reported.

    †: Prevalence data for 2016 is from conventional fattening pig herds.

    1: In 2009, spa‐types not reported.

    In 2010, spa‐types: t034 ST398 (17 isolates), t011 ST398 (1), t208 ST49 (5).

    In 2011, spa‐types: t034 ST398 (19 isolates), t011 ST398 (1), t208 ST49 (1), t2279 ST1 (1).

    In 2012, spa‐types: t034 CC398 (61 isolates), t011 CC398 (9), t208 ST49 (2).

    In 2013, spa‐types: t034 (63 isolates), t011 (10).

    In 2014, spa‐types: t034 (57 isolates), t011 (19), t208 (1), t899 (1), t2741 (1).

    In 2015, spa‐types: t034 (48 isolates), t011 (23), t032 (1), t571 (1), t899 (1), t1145 (1), t1250 (1), t4475 (1).

    In 2017, spa‐types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1).

    2: In 2011, spa‐types: t011 (97 isolates), t034 (8), t108 (3), t1197 (7), t1451 (3), t2346 (3), unspecified (68).

    In 2015, spa‐types not reported.

    In 2017, spa‐types: t011 (203 isolates), t034 (32), t108 (14), t109 (1), t899 (2), t1197 (11), t1255 (2), t1451 (13), t1606 (1), t2011 (5), t2346 (1), t2748 (1), t3041 (2), t4208 (2), t17304 (1), t17627 (1).

    3: In 2010, spa‐types: t108 (6 isolates) and t127 (5) were the most commonly detected.

    In 2017, spa‐types: t034 (32 isolates), t2741 (25), t011 (9), t108 (6), t1250 (1), t1255 (1), t17061 (1). NB. All MRSA isolates were subject to spa‐typing; from one slaughter batch, up to three different spa‐types were detected.

    4: In 2016, spa‐types not reported.

    In 2018, spa‐types: t011 CC398 (22 isolates), t034 CC398 (85), t571 CC398 (3), t898 CC398 (1), t2383 CC398 (1), t2974 CC398 (1), t3423 CC398 (1), t4652 CC398 (1), t9266 CC398 (1).

    5: In 2016, spa‐types not reported.

    In 2018, spa‐types: t011 CC398 (4 isolates), t034 CC398 (15), t588 CC398 (1), t1456 CC398 (1).

    6: In 2016, spa‐types not reported.

    In 2018, spa‐types: t011 CC398 (6 isolates), t034 CC398 (24), t1250 CC398 (2), t1793 CC398 (1), t3171 CC398 (1).

    7: In 2014, spa‐type: t011 (1).

    In 2015, spa‐type: t034 CC398 (2), t177 CC1 (2).

    In 2016, spa‐type: t034 CC398 (1).

    In 2017, spa‐types: t091 CC7 (1 isolate), t843 CC130 (1), t6292 CC425 (1). The t091 isolate was PVL negative, spa‐types t843 and t6292 were confirmed to carry the mecC gene.

    In 2018, no herds tested positive for MRSA.

Figure 55
Figure 55
Occurrence of resistance (%) to selected antimicrobials in MRSA isolates from food, 2017/2018

  1. N: Number of MRSA isolates reported/tested; FI: Finland; CH: Switzerland; AT: Austria.

    All isolates were tested against GEN: gentamicin; KAN: kanamycin; STR: streptomycin; CHL: chloramphenicol; RIF: rifampicin; CIP: ciprofloxacin; ERY: erythromycin; CLI: clindamycin; Q/D: quinupristin/dalfopristin; TIA: tiamulin; MUP: mupirocin; FUS: fusidic acid; SMX: sulfamethoxazole; TMP: trimethoprim; TET: tetracycline. All MRSA isolates were resistant to penicillin and cefoxitin, as expected. All isolates were susceptible to vancomycin and linezolid.

Figure 56
Figure 56
Occurrence of resistance (%) to selected antimicrobials in MRSA isolates from food‐producing animals, 2017/2018

  1. N: Number of MRSA isolates reported/tested; BE: Belgium; CH: Switzerland.

    All isolates were tested against GEN: gentamicin; KAN: kanamycin; STR: streptomycin; CHL: chloramphenicol; RIF: rifampicin; CIP: ciprofloxacin; ERY: erythromycin; CLI: clindamycin; Q/D: quinupristin/dalfopristin; TIA: tiamulin; MUP: mupirocin; FUS: fusidic acid; SMX: sulfamethoxazole; TMP: trimethoprim; TET: tetracycline. All MRSA isolates were resistant to penicillin and cefoxitin, as expected. All isolates were susceptible to vancomycin and linezolid.

Figure 57
Figure 57
Occurrence of resistance (%) to selected antimicrobials in MRSA isolates obtained from clinical investigations by Sweden in 2017

  1. N: Number of MRSA isolates reported/tested. All isolates were tested against GEN: gentamicin; CHL: chloramphenicol; CIP: ciprofloxacin; ERY: erythromycin; CLI: clindamycin; FUS: fusidic acid; TMP: trimethoprim; T+S: trimethoprim + sulfonamide; TET: tetracycline. All MRSA isolates were resistant to penicillin and cefoxitin, as expected, and susceptible to linezolid; vancomycin susceptibility was not reported.

Figure 58
Figure 58
Overview of MRSA types by species reported in 2017 and 2018, including isolates recovered from food, healthy animals, and following clinical investigations
Figure A.1
Figure A.1
Resistance levels to other selected antimicrobials in S. Kentucky isolates exhibiting high‐level ciprofloxacin resistance from poultry, reported by MSs in 2018

  1. n: Total number of S. Kentucky isolates exhibiting high‐level ciprofloxacin resistance.

Figure A.2
Figure A.2
Spatial distribution of ciprofloxacin resistance among S. Kentucky from human cases in reporting countries in 2018
Figure A.3
Figure A.3
Number of isolates displaying high‐level ciprofloxacin resistance by serovar, reported from the different poultry origins by MSs in 2018

  1. n: Total number of Salmonella isolates exhibiting high‐level ciprofloxacin resistance; ns: number of isolates by serovar exhibiting high‐level ciprofloxacin resistance.

Figure C.1
Figure C.1
Commonly reported serovars from carcases of pigs (fatteners), calves (under 1 year of age), broilers and fattening turkeys in 2017/2018

  1. From calf carcases, S. Livingstone, S. Montevideo and S. Typhimurium were joint sixth most frequently reported.

Figure C.2
Figure C.2
Proportions of isolates completely susceptible and MDR in Salmonella spp. and particular Salmonella serovars from carcases of pigs (fatteners), calves (under 1 year of age), broilers and fattening turkeys, for all reporting countries in 2017/2018

  1. N: Total number of Salmonella spp. or total number of particular serovars recovered from the carcase monitoring.

Figure C.3
Figure C.3
Commonly reported serovars recovered from fattening pigs, cattle, broilers, laying hens and fattening turkeys in 2017/2018

  1. From cattle, S. Derby and S. Mbandaka were the joint fifth most frequently reported.

Figure C.4
Figure C.4
Proportions of isolates completely susceptible and MDR in Salmonella spp. and certain serovars recovered from fattening pigs, cattle, broilers, laying hens and fattening turkeys, for all reporting countries in 2017/2018

  1. N: Total number of Salmonella spp. or total number of particular serovars recovered from the monitoring of animals.

Figure C.5
Figure C.5
Proportions of certain serovars exhibiting multiresistance to overall MDR levels in Salmonella spp. recovered from each of the food‐producing animal populations and derived carcases, for all reporting countries in 2017/2018

  1. n: Total number of Salmonella isolates exhibiting MDR; serovars contributing the highest levels of MDR to overall MDR levels in Salmonella spp. are illustrated with a percentage.

Figure D.1
Figure D.1
Comparison of CBPs and ECOFFs used to interpret MIC data reported for Salmonella spp. from humans, animals or food

  1. *: EUCAST has changed the definitions of SIR from 2019 (EUCAST, 2019b ‐ http://www.eucast.org/newsiandr/). For I, the new definition ‘susceptible, increased exposure’ is used when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.

Figure D.2
Figure D.2
Occurrence of resistance to selected antimicrobials in S. Typhimurium from humans, carcases of pigs and calves, fattening pigs and cattle, reported by MSs in 2017
Figure D.3
Figure D.3
Occurrence of resistance to selected antimicrobials in monophasic S. Typhimurium from humans, carcases of pigs and calves, fattening pigs and cattle, reported by MSs in 2017
Figure D.4
Figure D.4
Occurrence of resistance to selected antimicrobials in S. Derby from humans, carcases of pigs and calves, fattening pigs and cattle, reported by MSs in 2017
Figure D.5
Figure D.5
Occurrence of resistance to selected antimicrobials in S. Infantis from humans, poultry and poultry carcases, reported by MSs in 2018
Figure D.6
Figure D.6
Occurrence of resistance to selected antimicrobials in S. Enteritidis from humans, poultry and broiler carcases, reported by MSs in 2018

  1. Note: S. Enteritidis was not reported from turkey carcases.

Figure D.7
Figure D.7
Occurrence of resistance to selected antimicrobials in S. Kentucky from humans, poultry and poultry carcases, reported by MSs in 2018
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