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. 2021 Apr 12;19(4):e06490.
doi: 10.2903/j.efsa.2021.6490. eCollection 2021 Apr.

The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019

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 2018/2019

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 the EFSA and the 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 2018 monitoring specifically focussed on poultry and their derived carcases/meat, while the monitoring performed in 2019 specifically focused on pigs and calves under 1 year of age, as well as their derived carcases/meat. Monitoring and reporting of AMR in 2018/2019 included data regarding Salmonella, Campylobacter and indicator Escherichia coli isolates, as well as data obtained from the specific monitoring of presumptive 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 an overview of the main findings of the 2018/2019 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, 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 multidrug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates possessing ESBL-/AmpC-/carbapenemase 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 2015-2019.

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, 2019
Figure 2
Figure 2
Spatial distribution of combined ‘microbiological’ resistance to ciprofloxacin and cefotaxime among (a) Salmonella spp., (b) S. Typhimurium, (c) S. Infantis and (d) S. Kentucky isolated from human cases, 2019 (pink indicates fewer 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 2019


  1. The MDR analysis of human isolates included the following antimicrobials: ampicillin, cefotaxime/ceftazidime, chloramphenicol, ciprofloxacin/pefloxacin/nalidixic acid, gentamicin, meropenem, sulfonamides/sulfamethoxazole, tetracyclines and trimethoprim/trimethoprim‐sulfamethoxazole (co‐trimoxazole).

Figure 4
Figure 4
Occurrence of resistance to selected antimicrobials in Salmonella spp. recovered from (a) carcases of broilers, fattening turkeys and fattening pigs, and (b) broilers, laying hens, fattening turkeys and fattening pigs, reporting EU MSs, 2018/2019


  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: Only MSs reporting data for 10 or more isolates are shown in the graph; however, all isolates are included in the calculation of resistance at the reporting MS‐group level. As only two MSs reported data on 10 or more Salmonella isolates recovered from calves or their derived carcases, resistance levels for these origins are not presented in Figure 4 (a and b).

Figure 5
Figure 5
MDR and completely susceptible Salmonella spp. recovered from carcases of broilers, fattening turkeys, fattening pigs and calves (< 1 year of age), for all reporting countries (including two non‐MSs in broiler carcases and one non‐MS in pig carcases) in 2018/2019


  1. The MDR analysis of carcase isolates included the following antimicrobials: ampicillin, cefotaxime/ceftazidime, chloramphenicol, ciprofloxacin/nalidixic acid, gentamicin, meropenem, sulfamethoxazole, tetracycline, tigecycline and trimethoprim. 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) broiler carcases and (b) fattening turkey carcases, using harmonised ECOFFs, 2018
Figure 7
Figure 7
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, 2019
Figure 8
Figure 8
MDR and completely susceptible Salmonella spp. recovered from broilers, laying hens, fattening turkeys, fattening pigs and calves (< 1 year of age), for all reporting countries (including 1 non‐MS in broilers and laying hens), 2018/2019


  1. The MDR analysis of animal isolates included the following antimicrobials: ampicillin, cefotaxime/ceftazidime, chloramphenicol, ciprofloxacin/nalidixic acid, gentamicin, meropenem, sulfamethoxazole, tetracycline, tigecycline and trimethoprim. MDR and complete susceptibility are expressed as percentages; N: total number of Salmonella spp. reported by MSs and non‐MSs.

Figure 9
Figure 9
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 10
Figure 10
Distribution of MIC levels among ciprofloxacin‐resistant Salmonella spp. from carcases of broilers, turkeys, pigs and calves (< 1 year of age), as well as broilers, laying hens, fattening turkeys, fattening pigs and calves (< 1 year of age), for all reporting EU MSs, 2018/2019


  1. n: Total number of Salmonella spp. exhibiting CIP resistance (MSs only); N: total number of Salmonella spp. reported by MSs.
1In accordance with breakpoints stated in Decision 2013/652/EU.
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. Figure 10 excludes one isolate reported from laying hens (by the Republic of North Macedonia), which was ‘microbiologically’ resistant to ciprofloxacin; as well as one isolate reported from pigs (by Switzerland), which showed ‘clinical’ resistance to ciprofloxacin.

Figure 11
Figure 11
Breakdown of the number of tigecycline‐resistant isolates by serovar, where detected among the animal/carcase origins by reporting MSs in 2018/2019


  1. n: Total number of tigecycline‐resistant isolates reported by the MSs; predominant serovars are also expressed as a percentage; * monophasic S. Typhimurium includes antigenic formulas; salmonellas in the legend are listed according to their predominance within all the animal/carcase origins.

Figure 12
Figure 12
Breakdown of the number of colistin‐resistant isolates by serovar, where detected among the animal/carcase origins by reporting MSs in 2018/2019


  1. n: Total number of colistin‐resistant isolates reported by the MSs; predominant serovars are expressed as a percentage;
* monophasic S. Typhimurium includes antigenic formulas; salmonellas in the legend are listed according to their predominance within all the animal/carcase origins.

Figure 13
Figure 13
Occurrence of resistance to selected antimicrobials in C. jejuni and C. coli isolates from humans, 2019
Figure 14
Figure 14
Combined resistance to the critically‐important antimicrobials ciprofloxacin and erythromycin in (a) C. jejuni and (b) C. coli isolates from humans


  1. Note: For Finland, travel information was missing from the AMR data while from the case surveillance data, travel‐associated cases were known to account for 78% of Finnish Campylobacter infections in 2019.

Figure 15
Figure 15
Number of MDR isolates, isolates resistant to 1 and/or 2 antimicrobials and completely susceptible Campylobacter isolates from humans in 2019


  1. N: Total number of isolates reported.

Figure 16
Figure 16
Erythromycin MIC distribution in C. jejuni and C. coli isolates from humans, 2019
Figure 17
Figure 17
Occurrence of resistance to selected antimicrobials in (a) C. jejuni isolates from calves, broilers and fattening turkeys and (b) C. coli from fattening pigs, calves, broilers and fattening turkeys in reporting EU MSs, 2018/2019


  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: EU level.

Figure 18
Figure 18
Spatial distribution of combined resistance to ciprofloxacin and erythromycin in Campylobacter jejuni isolates from (a) broilers (29 EU/EEA MSs, 2018); (b) fattening turkeys (11 EU/EEA MSs, 2018)
Figure 19
Figure 19
Spatial distribution of combined resistance to ciprofloxacin and erythromycin in Campylobacter coli isolates from (a) broilers (6 EU/EEA MSs, 2018); (b) fattening pigs (11 EU/EEA MSs, 2019)
Figure 20
Figure 20
Proportions of isolates completely susceptible and MDR in C. jejuni and/or C. coli from broilers, fattening turkeys, fattening pigs and calves, in reporting EU MSs, 2018/2019


  1. N: Total number of isolates reported by the EU MSs.
Complete susceptibility is defined as susceptibility to ciprofloxacin/nalidixic acid, erythromycin, gentamicin and tetracycline. MDR is defined as resistance to at least three antimicrobial substances (panel of antimicrobial tested: ciprofloxacin, nalidixic acid, erythromycin, gentamicin, tetracycline).

Figure 21
Figure 21
Trends in ciprofloxacin (CIP), erythromycin (ERY), streptomycin (STR) and tetracycline (TET) resistance in C. jejuni from broilers, 2008–2019


  1. CIP: ciprofloxacin; ERY: erythromycin; STR: streptomycin; TET: tetracycline. Arrows indicate significant increasing (up) or decreasing (down) significant trend over the entire period. Please note that between‐year fluctuation in the occurrence resistance (%) may not be captured in the overall evaluation of the trend for the entire period (2009–2019).

Figure 22
Figure 22
Trends in streptomycin (STR), ciprofloxacin (CIP), erythromycin (ERY) and tetracycline (TET) resistance in C. jejuni from turkeys, reporting EU MSs, 2014–2018
Figure 23
Figure 23
Trends in ciprofloxacin (CIP), erythromycin (ERY), streptomycin (STR) and tetracycline (TET) resistance in C. coli from pigs, reporting EU MSs, 2009–2019
Figure 24
Figure 24
MICs of Campylobacter jejuni isolates exhibiting erythromycin resistance in, broilers and turkeys (a), and C. coli in fattening pigs and calves (b) in reporting EU MSs and non‐EU MSs, 2018/2019
Figure 25
Figure 25
MICs of Campylobacter spp. isolates exhibiting erythromycin resistance in broilers, turkeys, pigs and calves in reporting EU MSs and non‐EU MSs, 2018/2019


  1. N: Total number of C. jejuni or C. coli isolates exhibiting erythromycin resistance. ERY: erythromycin.
ERY resistance in C. jejuni isolates: 4 mg/L < MIC < 128 mg/L. ERY resistance in C. coli isolates: 8 mg/L < MIC < 128 mg/L.

Figure 26
Figure 26
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 27
Figure 27
Distribution of occurrence of resistance to selected antimicrobials in indicator E. coli isolates recovered from fattening pigs and calves under 1 year of age in 2019 and from broilers and fattening turkeys in 2018. MSs and non‐MSs


  1. N: Total number of isolates reported by Member States (MSs) and non‐Member States (non‐MSs); AMP: ampicillin, SMX: sulfamethoxazole, TET: tetracycline, CIP: ciprofloxacin, CTX: cefotaxime, CIP/CTX: combined ‘microbiological’ resistance to ciprofloxacin and cefotaxime; blue diamond: EU level of resistance; horizontal line in the box plot: the median.

Figure 28
Figure 28
Spatial distribution of combined ‘microbiological’ resistance to cefotaxime and ciprofloxacin in indicator Escherichia coli. (a) fattening pigs, 28 MSs and 4 non‐MSs 2019, (b) calves under 1 year of age, 9 MSs and 3 non‐MSs 2019, (c) broilers, 27 MSs and 4 non‐MSs 2018, (d) fattening turkeys, 11 MSs and 1 non‐MSs 2018
Figure 29
Figure 29
Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracyclines (TET) in indicator E. coli from pigs, 27 EU MSs and 3 non‐MSs, 2009–2019


  1. (↑)/(↓): indicates statistically significant trends over the period 2015–2019.

Figure 30
Figure 30
Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracyclines (TET) in indicator E. coli from calves under 1 year of age, 9 EU MSs and 2 non‐EU MSs, 2009–2019

  1. (↑)/(↓): indicates statistically significant trends over the period 2015–2019.
Data from Croatia was not included in the calculation of the Total (MSs) as data for calves (<1 year) was not reported for the year 2015.

Figure 31
Figure 31
Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracyclines (TET) in indicator E. coli from broilers, 27 EU MSs and 2 non‐MSs, 2009–2019


  1. (↑)/(↓): indicates statistically significant trends over the period 2015–2019.

Figure 32
Figure 32
Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracycline (TET) in indicator E. coli from fattening turkeys, 11 EU MSs, 2014–2018


  1. (↑)/(↓): indicates statistically significant trends over the period 2015–2019.

Figure 33
Figure 33
Spatial distribution of complete susceptibility to the antimicrobials tested in indicator E. coli. (a) fattening pigs, 28 MSs, 4 non‐MSs, 2019; (b) calves < 1 year of age, 9 MSs, 3 non‐MSs, 2019; (c) broilers, 28 MSs, 4 non‐MSs, 2018; (d) fattening turkeys, 11 MSs, 1 non‐MSs, 2018
Figure 34
Figure 34
Changes in the occurrence of complete susceptibility to the panel of antimicrobials tested in indicator E. coli isolates from (a) fattening pigs (27 MSs; 2 non‐MSs) and (b) calves < 1 year of age (9 MSs; 2 non‐MSs) in the years 2015, 2017 and 2019


  1. (↑)/(↓): indicates statistically significant trends over the period 2015–2019. The upper bounds of the 95% confidence interval of the occurrence of complete susceptibility are also indicated.

Figure 35
Figure 35
Changes in the occurrence of complete susceptibility to the panel of antimicrobials tested in indicator E. coli isolates from (a) broilers (27 MSs; 3 non‐MSs) and (b) fattening turkeys (11 MSs; 1 non‐MS) in the years 2014, 2016 and 2018


  1. (↑)/(↓): indicates statistically significant trends over the period 2014–2018. The upper bounds of the 95% CI are also shown.

Figure 36
Figure 36
Changes in weighted key outcome indicator of complete susceptibility (KOICS) in 28 EU MSs and 3 non‐MSs
Figure 37
Figure 37
Temporal trends in resistance to colistin in indicator E. coli from fattening turkeys, 2014–2018 (11 MSs). Statistically significant increase (↑) or decrease (↓) indicated (p ≤ 0.05)
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, 2018/2019


  1. Blue diamonds show the assessed prevalence at the MS‐group level.

Figure 39
Figure 39
Spatial distribution of the prevalence of presumptive ESBL and/or AmpC‐producing E. coli from (a) meat from broilers in 2018, (b) meat from pigs in 2019 and (c) meat from bovines in 2019, EU MSs and non‐ MSs, 2018/2019
Figure 40
Figure 40
Spatial distribution of the prevalence of presumptive ESBL and/or AmpC‐producing E. coli from (a) broilers in 2018, (b) fattening turkeys in 2018, (c) fattening pigs in 2019 and (d) bovines under 1 year of age in 2019, EU MSs and non‐ MSs, 2018/2019
Figure 41
Figure 41
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 42
Figure 42
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, 2019


  1. The upper bounds of the 95% confidence interval of the prevalence of ESBL‐ and/or AmpC‐producing E. coli are also indicated. Please note the different scales used for the x‐axis in the sub‐figures to improve the visibility of the variations among countries.

Figure 43
Figure 43
Prevalence of presumptive ESBL‐producing vs. AmpC‐producing E. coli from (a) bovine meat and (b) bovines under 1 year of age, EU MSs and non‐EU MSs, 2019


  1. The upper bounds of the 95% confidence interval of the prevalence of ESBL‐ and/or AmpC‐producing E. coli are also indicated. Please note the different scales used for the x‐axis in the sub‐figures to improve the visibility of the variations among countries.

Figure 44
Figure 44
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 2015–2019, 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 are also indicated. Please note the different scales used for the x‐axis in the sub‐figures to improve the visibility of the variations among countries (a, 0–100%; b‐c, 0–30%). (↑)/(↓): indicates statistically significant decreasing/increasing trends over the 2015–2019 period.
Rates of change are shown only for the statistically significant decreasing/increasing trends observed.

Figure 45
Figure 45
Trends on the prevalence of presumptive ESBL and/or AmpC‐producing E. coli in (a) broilers, (b) fattening turkeys, (c) bovines under 1 year of age and (d) fattening pigs, over the period 2015–2019, 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 are also indicated.
(↑)/(↓): indicates statistically significant decreasing/increasing trends over the 2015–2019 period.
Rates of change are shown only for the statistically significant decreasing/increasing trends observed.

Figure 46
Figure 46
Changes in Outcome Indicator of ESBL‐ and/or AmpC producing E. coli (OIESC), 28 EU MSs and 3 non‐MSs, 2015–2019
Figure 47
Figure 47
MRSA occurrence in food, 2018/2019 (only food origins where positive isolates were obtained are presented)


  1. N: Total number of sample units tested; AT: Austria; CH: Switzerland; DE: Germany; NL: the Netherlands.
* spa‐types not reported.
1: spa‐types: t008 ST8 (1 isolate), t011 (2), t127 ST1 (2), t2346 (1). The t008 isolate was PVL‐positive; the two t127 isolates were PVL‐negative.
2: spa‐types were not reported; however, both isolates were confirmed to belong to CC398 using the sau1‐hsdS1 CC398 PCR reaction (Stegger et al., 2011).
3: spa‐types: t002 ST5 (1 isolate), t003 ST3944 (1), t008 ST8 (1), t011 (22), t011 ST398 (1), t034 (12), t127 ST1 (2), t321 ST5050 (1), t843 ST130 (1), t899 (5), t1451 (2), t1456 (1). The t002 and t008 isolates were PVL‐positive. The two t127 isolates, as well as the single t003 and t321 isolates were PVL‐negative. The t843 isolate was reported to carry the mecC gene.
4: spa‐type was not reported; however, the isolate was confirmed to belong to CC398 using the sau1‐hsdS1 CC398 PCR reaction (Stegger et al., 2011).
5: spa‐types: t011 (2 isolates), t034 (1).
6: spa‐types: t034 CC398 (1 isolate), t1430 (1), t571 CC398 (1), t13177 (1).
7: spa‐type : t011 (1 isolate).

Figure 48
Figure 48
MRSA types reported from food in (a) 2018 and (b) 2019, inferred from molecular typing data


  1. Inferred MRSA types in (a) were recovered from broiler meat (7 isolates) and turkey meat (1 isolate); inferred MRSA types in (b) were recovered from cattle meat (8 isolates) and pig meat (51 isolates).

Figure 49
Figure 49
MRSA occurrence in food‐producing animals (including horses), 2018/2019 (only origins where positive isolates were obtained are presented)


  1. N: Total number of sample units tested; BE: Belgium; CH: Switzerland; DE: Germany; DK: Denmark; NL: the Netherlands; NO: Norway; PT: Portugal. CHC: controlled housing conditions.
* spa‐types not reported.
† These comprised multiplier herds.
1: spa‐types were not reported; however, all 11 isolates were confirmed to belong to CC398 using the sau1‐hsdS1 CC398 PCR reaction (Stegger et al., 2011).
2: spa‐types: t011 CC398 (1 isolate), t034 CC398 (8), t779 CC398 (1), t1580 CC398 (1).
3: spa‐types: t011 CC398 (65 isolates), t034 CC398 (8), t1451 CC398 (1), t1580 CC398 (2), t3423 CC398 (1), t3479 CC398 (1), t9433 CC398 (1).
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 confirmed to belong to ST22, harbour the tst gene and IEC genes (chp, sak and scn) from WGS data.
5: spa‐types: t127 CC1 (1 isolate), t843 CC130 (1). The t127 isolate was PVL‐negative, as well as negative for the human IEC gene scn. spa‐type t843 was confirmed to carry the mecC gene.
6: spa‐types: t034 (7 isolates), t267 CC97 (1).
7: 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.
8: spa‐types: t011 CC398 (3), unspecified (168).
9: spa‐type: t034 CC398 (1 isolate).
10: spa‐types were not reported; however, 159/160 isolates were confirmed to belong to CC398 using the sau1‐hsdS1 CC398 PCR reaction (Stegger et al., 2011). The remaining isolate did not survive cryo‐conservation; therefore, typing could not be performed.
11: spa‐types: t011 CC398 (67 isolates), t034 CC398 (11), t1451 CC398 (2), t1457 CC398 (1), t2346 CC398 (1), t2370 CC398 (2), t2383 CC398 (1), t3041 CC398 (1), t3119 CC398 (1), unspecified (18).
12: 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).
13: spa‐types: t011 CC398 (4 isolates), t034 CC398 (15), t588 CC398 (1), t1456 CC398 (1).
14: spa‐types: t011 CC398 (57 isolates), t034 CC398 (18), t108 CC398 (2), t779 CC398 (1), t2346 CC398 (1), t2582 CC398 (1), t2922 CC398 (1), t3119 CC398 (2).
15: spa‐types: t011 CC398 (10 isolates), t034 CC398 (57), t1928 CC398 (1), t4652 CC398 (1).
16: spa‐types: t011 CC398 (6 isolates), t034 CC398 (24), t1250 CC398 (2), t1793 CC398 (1), t3171 CC398 (1).
17: spa‐types: t011 CC398 (4 isolates), t034 CC398 (6), t1451 CC398 (1), t843 CC130 (1), t3256 CC130 (1). spa‐types t843 and t3256 were confirmed to carry the mecC gene.
18: spa‐types: t011 CC398 (3 isolates), t034 CC398 (6), t843 CC130 (1). spa‐type t843 was confirmed to carry the mecC gene.
19: spa‐types: t011 CC398 (2 isolates), t034 CC398 (2).
20: spa‐types: t011 CC398 (6 isolates), t034 CC398 (19), t571 CC398 (1), t588 CC398 (1), t1456 CC398 (1), t1457 CC398 (2), t13790 CC1 (1).

Figure 50
Figure 50
MRSA types reported from food‐producing animals (including horses) in (a) 2018 and (b) 2019, inferred from molecular typing data


  1. Inferred MRSA types in (a) 2018 were recovered from pigs (171 isolates), cattle (109 isolates), laying hens (4 isolates), mink (31 isolates) and horses (10 isolates) at the herd/flock/farm/stable level; inferred MRSA types in (b) 2019 were recovered from pigs (243 isolates), cattle (13 isolates) and horses (13 isolates) at the herd/slaughter batch/stable level, as well as individual fattening pigs (159 isolates) and calves at slaughter (11 isolates).

Figure 51
Figure 51
Temporal trends of MRSA prevalence in various types of meat, 2011–2019


  1. CH: Switzerland; DE: Germany; NL: the Netherlands.
The 2‐S method of isolation was used by CH and DE from 2011–2018; while the 1‐S method was used by the NL from 2018–2019, as well as CH in 2019.
* spa‐types not reported.
1: In 2019, spa‐types were not reported; however, both isolates were confirmed to belong to CC398 using the sau1‐hsdS1 CC398 PCR reaction (Stegger et al., 2011).
2: In 2017, spa‐type: t011 (1 isolate), t002 (1). PVL status of the t002 isolate was not reported.
In 2019, spa‐type was not reported; however, the isolate was confirmed to belong to CC398 using the sau1‐hsdS1 CC398 PCR reaction (Stegger et al., 2011).
3: 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).

Figure 52
Figure 52
Temporal trends of MRSA prevalence in cattle, 2012–2019


  1. BE: Belgium; CH: Switzerland; DK: Denmark.
The 2‐S method of isolation was used by BE and CH from 2012–2018; while the 1‐S method was used by DK from 2018–2019, as well as CH in 2019.
* 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.
In 2019, spa‐types were not reported; however, all 11 isolates were confirmed to belong to CC398 using the sau1‐hsdS1 CC398 PCR reaction (Stegger et al., 2011).
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 2018, spa‐types: t034 (7 isolates), t267 CC97 (1).
In 2019, spa‐types: t127 CC1 (1 isolate), t843 CC130 (1). The t127 isolate was PVL‐negative, as well as negative for the human IEC gene scn. spa‐type t843 was confirmed to carry the mecC gene.
5: 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, harbour the tst gene and IEC genes (chp, sak and scn) from WGS data.

Figure 53
Figure 53
Temporal trends of MRSA prevalence in pigs, 2010–2019


  1. BE: Belgium; CH: Switzerland; DE: Germany; DK: Denmark; NO: Norway.
The 2‐S method of isolation was used by BE and DE from 2016–2019, as well as DK in 2016, CH from 2010–2017 and NO from 2014–2017. The 1‐S method was used by CH in 2019 and DK in 2018, as well as NO from 2018–2019.
* spa‐types not reported.
† Prevalence data for fattening pig herds (not raised under controlled housing conditions) from 2018 are not included.
1: 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).
In 2019, spa‐types were not reported; however, 159/160 isolates were confirmed to belong to CC398 using the sau1‐hsdS1 CC398 PCR reaction (Stegger et al., 2011). The remaining isolate did not survive cryo‐conservation, therefore typing could not be performed.
2: In 2016, spa‐types: t011 CC398 (71 isolates), t1451 (1), t1456 (1), t1456 CC398 (1), t1580 (5), t1985 (8), t1985 CC398 (3), t034 (7), t034 CC398 (2), t037 (1), t898 (1), unspecified (11).
In 2019, spa‐types: t011 CC398 (67 isolates), t034 CC398 (11), t1451 CC398 (2), t1457 CC398 (1), t2346 CC398 (1), t2370 CC398 (2), t2383 CC398 (1), t3041 CC398 (1), t3119 CC398 (1), unspecified (18).
3: 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).
4: In 2016, spa‐types: t011 CC398 (55 isolates), t1451 (2), t1456 (1), t1456 CC398 (3), t1580 (1), t1985 (5), t1985 CC398 (1), t034 (1), t034 CC398 (4), t4659 CC398 (1), unspecified (17).
In 2019, spa‐types: t011 CC398 (57 isolates), t034 CC398 (18), t108 CC398 (2), t779 CC398 (1), t2346 CC398 (1), t2582 CC398 (1), t2922 CC398 (1), t3119 CC398 (2).
5: 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).
6: In 2014, spa‐type: t011 CC398 (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 2019, spa‐type: t034 CC398 (1).

Figure 54
Figure 54
Occurrence of resistance (%) to selected antimicrobials in MRSA isolates from food, 2018/2019


  1. N: Number of MRSA isolates reported/tested; AT: Austria; CH: Switzerland. *Susceptibility data are also included for four isolates recovered from additional ad hoc sampling.
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 55
Figure 55
Occurrence of resistance (%) to selected antimicrobials in MRSA isolates from cattle, 2018/2019


  1. N: Number of MRSA isolates reported/tested; SHM: slaughterhouse monitoring; 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 56
Figure 56
Occurrence of resistance (%) to selected antimicrobials in MRSA isolates from pigs, 2019


  1. N: Number of MRSA isolates reported/tested; SHB: slaughterhouse batch; SHM: slaughterhouse monitoring; BE: Belgium; CH: Switzerland; PT: Portugal. *Susceptibility data for a further 52 isolates recovered from batches of fattening pigs at slaughter were not reported. †Susceptibility data for one isolate recovered from a fattening pig was not available; the isolate did not survive cryo‐conservation.
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; LZD: linezolid; 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.

Figure A.1
Figure A.1
Resistance levels among MDR S. Kentucky isolates exhibiting high‐level ciprofloxacin resistance from poultry, reported by MSs in 2018


  1. n: Total number of MDR S. Kentucky isolates exhibiting high‐level ciprofloxacin resistance.
NB: The single S. Kentucky isolate recovered from a pig carcase in 2019, which also displayed high‐level ciprofloxacin resistance, additionally showed resistance to AMP‐GEN‐NAL‐SMX‐TET.

Figure A.2
Figure A.2
Spatial distribution of ciprofloxacin resistance among S. Kentucky from human cases 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; * serovar unspecified; salmonellas in the legend are listed according to their predominance within all the animal/carcase origins; in addition, a single S. Kentucky isolate displaying high‐level ciprofloxacin resistance was recovered from a pig carcase in 2019.

Figure C.1
Figure C.1
The six most commonly reported serovars from carcases of broilers, fattening turkeys, fattening pigs and calves (< 1 year of age), for all reporting countries (including 2 non‐MSs in broiler carcases and 1 non‐MS in pig carcases) in 2018/2019


  1. * Monophasic S. Typhimurium includes antigenic formulas; serovars in the legend are listed according to their predominance within all the carcase origins. From calf carcases, S. Dublin and S. London were joint fourth 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 fattening pigs, calves (< 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 2018/2019


  1. N: Total number of Salmonella spp. or total number of particular serovars recovered from the carcase monitoring; * monophasic S. Typhimurium includes antigenic formulas.

Figure C.3
Figure C.3
The six most commonly reported serovars recovered from broilers, laying hens, fattening turkeys, fattening pigs and calves (< 1 year of age), for all reporting countries (including 1 non‐MS in broilers and laying hens), 2018/2019


  1. * Monophasic S. Typhimurium includes antigenic formulas; serovars in the legend are listed according to their predominance within all the animal origins. From calves, S. Anatum and S. Meleagridis were the joint third most frequently reported; S. Enteritidis and S. Mbandaka were the joint fourth 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, calves (< 1 year of age), broilers, laying hens and fattening turkeys, for all reporting countries, 2018/2019


  1. * monophasic S. Typhimurium includes antigenic formulas.
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 (including 1 non‐MS in pig carcases, broilers and laying hens, and 2 non‐MSs in broiler carcases) in 2018/2019


  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; * monophasic S. Typhimurium includes antigenic formulas.

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, 2019 ‐ 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. Infantis from humans, poultry and poultry carcases, reported by MSs in 2018


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

Figure D.3
Figure D.3
Occurrence of resistance to selected antimicrobials in S. Enteritidis from humans, poultry and broiler carcases, reported by MSs in 2018


  1. N: Total number of isolates reported by MSs.
NB. S. Enteritidis was not reported from turkey carcases.

Figure D.4
Figure D.4
Occurrence of resistance to selected antimicrobials in S. Kentucky from humans, poultry and poultry carcases, reported by MSs in 2018


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

Figure D.5
Figure D.5
Occurrence of resistance to selected antimicrobials in S. Typhimurium from humans, pig and calf carcases, fattening pigs and calves, reported by MSs in 2019


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

Figure D.6
Figure D.6
Occurrence of resistance to selected antimicrobials in monophasic S. Typhimurium from humans, pig and calf carcases, fattening pigs and calves, reported by MSs in 2019


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

Figure D.7
Figure D.7
Occurrence of resistance to selected antimicrobials in S. Derby from humans, pig and calf carcases, fattening pigs and calves, reported by MSs in 2019


  1. N: Total number of isolates reported by MSs.
NB: The S. Derby isolate reported from calves was completely susceptible to all of the 14 antimicrobials tested in the harmonised panel.

Figure E.1
Figure E.1
Temporal trends in resistance to colistin in indicator E. coli from calves under 1 year of age, 2014–2019 (9 MSs, 2 non‐MSs)


  1. Statistically significant increase (↑) or decrease (↓) indicated (p ≤ 0.05).
Data from Croatia was not included in the calculation of the Total (MSs) as data for calves (<1 year) was not reported for the year 2015.

Figure E.2
Figure E.2
Temporal trends in resistance to colistin in indicator E. coli from fattening pigs, 2014–2019 (27 MSs, 4 non‐MSs)


  1. Statistically significant increase (↑) or decrease (↓) indicated (p ≤ 0.05).

Figure E.3
Figure E.3
Temporal trends in resistance to colistin in indicator E. coli from broilers, 2014‐2019 (25 MSs, 3 non‐MSs)


  1. Statistically significant increase (↑) or decrease (↓) indicated (p ≤ 0.05).

Figure G.1
Figure G.1
Overview of MRSA types by species reported in 2018 and 2019, from food and healthy animals


  1. Note: this graph includes four isolates recovered from additional ad hoc sampling carried out by Austria in 2019.

See this image and copyright information in PMC

References

    1. Agersø Y, Torpdahl M, Zachariasen C, Seyfarth A, Hammerum AM and Nielsen EM, 2012. Tentative colistin epidemiological cut‐off value for Salmonella spp. Foodborne Pathogens and Disease, 9, 367–369. 10.1089/fpd.2011.1015 - DOI - PubMed
    1. Alba P, Feltrin F, Cordaro G, Porrero MC, Kraushaar B, Argudín MA, Nykäsenoja S, Monaco M, Stegger M, Aarestrup FM, Butaye P, Franco A and Battisti A, 2015. Livestock‐associated methicillin resistant and methicillin susceptible Staphylococcus aureus sequence type (CC)1 in European farmed animals: high genetic relatedness of isolates from Italian cattle herds and humans. PLoS ONE, 10, e0137143. 10.1371/journal.pone.0137143 - DOI - PMC - PubMed
    1. Angen Ø, Stegger M, Larsen J, Lilje B, Kaya H, Pedersen KS, Jakobsen A, Petersen A and Larsen AR, 2017. Report of mecC‐carrying MRSA in domestic swine. Journal of Antimicrobial Chemotherapy, 72, 60–63. 10.1093/jac/dkw389 - DOI - PMC - PubMed
    1. Aviv G, Tsyba K, Steck N, Salmon‐Divon M, Cornelius A, Rahav G, Grassl GA and Gal‐Mor O, 2014. A unique megaplasmid contributes to stress tolerance and pathogenicity of an emergent Salmonella enterica serovar Infantis strain. Environmental Microbiology, 16, 977–994. 10.1111/1462-2920.12351 - DOI - PubMed
    1. Bai L, Du P, Du Y, Sun H, Zhang P, Wan Y, Lin Q, Fanning S, Cui S and Wu Y, 2019. Detection of plasmid‐mediated tigecycline‐resistant gene tet(X4) in Escherichia coli from pork, Sichuan and Shandong Provinces, China, February 2019. Euro Surveillance, 24, 4. 10.2807/1560-7917.es.2019.24.25.1900340 - DOI - PMC - PubMed

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