The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2019-2020

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 2020 monitoring specifically focussed on poultry and their derived carcases/meat, while the monitoring performed in 2019 specifically focused on fattening pigs and calves under 1 year of age, as well as their derived carcases/meat. Monitoring and reporting of AMR in 2019-2020 included data regarding Salmonella, Campylobacter and indicator E. 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 methicillin-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 2019-2020 harmonised AMR monitoring in the main food-producing animal populations monitored, in carcase/meat samples and in humans. Where available, monitoring data 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 key 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 specifically analysed over the period 2014-2020.

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

Figure 1

Occurrence of resistance to selected antimicrobials in Salmonella spp. and selected serovars isolated from humans, 2020

Figure 2

Spatial distribution of combined ‘microbiological’ resistance to ciprofloxacin and cefotaxime among (a) Salmonella spp., (b) S. Infantis and (c) monophasic S. Typhimurium isolated from human cases, 2020 (pink indicates fewer than 10 isolates tested)

Figure 3

Number of MDR isolates, isolates resistant to 1 and/or 2 antimicrobial classes and completely susceptible Salmonella isolates from humans in 2020

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

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, 2019–2020

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 4a,b.

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 2019–2020

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

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, 2020

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

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 one non‐MS in broilers and laying hens), 2019–2020

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

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, 2020

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, 2019–2020

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

   (1): In 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

Breakdown of the number of tigecycline‐resistant isolates by serovar, where detected among the animal/carcase origins by reporting MSs in 2019–2020

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;

   †: serovar unspecified;

   Salmonellas in the legend are listed according to their predominance within all the animal/carcase origins.

Figure 12

Breakdown of the number of colistin‐resistant isolates by serovar, where detected among the animal/carcase origins by reporting MSs in 2019–2020

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.

   †: Serovar unspecified; salmonellas in the legend are listed according to their predominance within all the animal/carcase origins.

Figure 13

Occurrence of resistance to selected antimicrobials in C. jejuni and C. coli isolates from humans, 2020

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 49% of Finnish Campylobacter infections in 2020.

Figure 15

Number of MDR isolates, isolates resistant to 1 and/or 2 antimicrobials and completely susceptible Campylobacter isolates from humans in 2020

1. N: Total number of isolates reported.

Figure 16

Erythromycin MIC distribution in C. jejuni and C. coli isolates from humans, 2020

1. Note: Not visible in the graph due to a very small proportion are three isolates of C. jejuni at MIC 32, 128 and ≥ 256 mg/L.

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, 2019–2020

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); Horizontal line represents median; Blue diamond: resistance at reporting MS group level (including UK); Green diamond: resistance at reporting MS group level (excluding UK, 2020).

Figure 18

Spatial distribution of combined resistance to ciprofloxacin and erythromycin in Campylobacter jejuni isolates from (a) broilers (27 EU MS and 3 non‐MS, 2020); (b) fattening turkeys (nine EU MSs and two non‐MS, 2020)

Figure 19

Spatial distribution of combined resistance to ciprofloxacin and erythromycin in Campylobacter coli isolates from (a) broilers (7 EU MS and 1 non MS, 2020); (b) fattening pigs 8 EU MS and 3 non MS, 2019)

Figure 20

Proportions of isolates completely susceptible, resistant to one or two antimicrobial classes and MDR in C. jejuni and/or C. coli from broilers, fattening turkeys, fattening pigs and calves, in reporting EU MSs, 2019–2020

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 classes (panel of antimicrobial tested: ciprofloxacin, nalidixic acid, erythromycin, gentamicin, tetracycline).

Figure 21

Trends in ciprofloxacin (CIP), erythromycin (ERY), streptomycin (STR) and tetracycline (TET) resistance in C. jejuni from broilers, 2009–2020

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 (2009–2020).

Figure 22

Trends in ciprofloxacin (CIP), erythromycin (ERY), streptomycin (STR) and tetracycline (TET) resistance in C. coli from broilers, 2009–2020

Figure 23

Trends in streptomycin (STR), ciprofloxacin (CIP), erythromycin (ERY), and tetracycline (TET) resistance in C. jejuni from fattening turkeys, 2014–2020

Figure 24

MICs of Campylobacter jejuni isolates exhibiting erythromycin resistance in (a) broilers and fattening turkeys, and C. coli in (b) broilers and fattening turkeys and (c) fattening pigs and calves, in reporting EU MSs and non‐EU MSs, 2020 and 2019

Figure 25

MICs of Campylobacter spp. isolates exhibiting erythromycin resistance in broilers, fattening turkeys, pigs and calves in reporting EU MSs and non‐EU MSs, 2019–2020

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

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

Distribution of occurrence of resistance to selected antimicrobials in indicator E. coli isolates recovered from fattening pigs (pigs) and bovines under 1 year of age (calves) in 2019 and from broilers and fattening turkeys (turkeys) in 2020. 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

Spatial distribution of combined ‘microbiological’ resistance to cefotaxime and ciprofloxacin in indicator Escherichia coli. (a) fattening pigs (pigs) 2019, (b) bovines under 1 year of age (calves) 2019, (c) broilers 2020 and (d) fattening turkeys (turkeys) 2020

Figure 29

Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracyclines (TET) in indicator E. coli from fattening pigs (pigs), MSs and non‐MSs

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

Figure 30

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

1. (↓)(↑): indicates statistically significant trends over the period 2014–2019

Figure 31

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

1. (↓)(↑): indicates statistically significant trends over the period 2014–2019.

Figure 32

Trends in resistance to ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP) and tetracyclines (TET) in indicator E. coli from broilers, MSs and non‐MSs 2009–2020

1. (↓)(↑): indicates statistically significant trends over the period 2015–2020.

Figure 33

Spatial distribution of complete susceptibility to the antimicrobials tested in indicator E. coli. (a) fattening pigs (pigs) 2019; (b) bovines under 1 year of age (calves) 2019; (c) broilers 2020; (d) fattening turkeys (turkeys) 2020

Figure 34

Changes in the occurrence of complete susceptibility to the panel of antimicrobials tested in indicator E. coli isolates from (a) fattening pigs (pigs) and (b) bovines under 1 year of age (calves) 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

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 (turkeys) in the years 2014, 2016, 2018 and 2020

1. (↓)(↑): indicates statistically significant trends over the period 2014–2020. The upper bounds of the 95% CI are also shown.

Figure 36

Changes in weighted key outcome indicator of complete susceptibility (KOICS) in 25 EU MSs and four non‐MSs

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

Figure 37

Temporal trends in resistance to colistin in indicator E. coli from fattening turkeys (turkeys), 2014–2020 (10 MSs, two non‐MS). Statistically significant increase (↑) or decrease (↓) indicated (p ≤ 0.05)

Figure 38

Prevalence of presumptive ESBL‐producing (a) and AmpC‐producing (b) E. coli from the specific monitoring of ESBL/AmpC‐producing E. coli, 2019–2020

Figure 39

Spatial distribution of the prevalence of presumptive ESBL and/or AmpC‐producing E. coli from (a) meat from broilers in 2020, (b) meat from pigs in 2019 and c) meat from bovines in 2019, EU MSs and non‐MSs, 2019–2020

Figure 40

Spatial distribution of the prevalence of presumptive ESBL and/or AmpC‐producing E. coli from (a) broilers in 2020, (b) fattening turkeys in 2020, (c) fattening pigs in 2019 and (d) bovines under 1 year of age in 2019, EU MSs and non‐MSs, 2019–2020

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, 2020

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

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

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 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 2015–2020, 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%).

Figure 45

Trends on the prevalence of presumptive ESBL and/or AmpC‐producing E. coli in (a) broilers, (b) fattening turkeys, (c) fattening pigs and (d) bovines under 1 year of age, over the period 2015–2020, 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.

Figure 46

Changes in Outcome Indicator of ESBL‐ and/or AmpC producing E. coli (OI_ESC), 27 EU MSs and four non‐MSs, 2015–2020

1. (↓)(↑): indicates statistically significant decreasing/increasing trends over the 2015–2020 period.

   Rates of change are shown for the statistically significant decreasing/increasing trends observed.

Figure 47

MRSA occurrence in food, 2019–2020

1. Only food origins where positive isolates were obtained are presented.

   N: Total number of sample units tested; AT: Austria; DE: Germany; NL: the Netherlands; SK: Slovakia; CH: Switzerland.

   [1] Broiler meat (AT, 2020): spa‐types: t011 (four isolates) t034 (4).

   [2] Bovine meat (AT, 2019): spa‐types: t008 ST8 (one isolate), t011 (2), t127 ST1 (2), t2346 (1). The t008 isolate was PVL‐positive; the two t127 isolates were PVL‐negative.

   [3] Bovine meat (CH) : 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).

   [4] Pig meat (AT, 2019) : 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.

   [5] Pig meat (CH, 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).

   [6] Sheep meat (DE, 2020) spa‐type: t011 (2 isolates), t034 (1), t1451 (1), t2576 (1), t19979 ST 398 (1), t223 (2), t267 (1), t1154, ST5 (1) t15010 ST97 (1).

   *: spa‐types not reported.

Figure 48

MRSA occurrence in food‐producing animals (including horses), 2019–2020

1. Only animal origins where positive isolates were obtained are presented.

   N: Total number of sample units tested; BE: Belgium; CH: Switzerland; DE: Germany; DK: Denmark; NL: the Netherlands; NO: Norway; PT: Portugal.

   [1] Broiler flocks, BE 2020: spa‐types: t011 CC398 (2 isolates).

   [2] Fattening turkey flocks, BE 2020: spa‐types: t011 CC398 (2 isolates).

   [3] Veal calf herds, DK 2019: spa‐types : t011 CC398 (1 isolate), t034 CC398 (8), t779 CC398 (1), t1580 CC398 (1).

   [4] Calves < 1 year, CH2019: 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).

   [5] Dairy cow herds, DK 2019 : spa‐types : t127 CC1 (one 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] Fattening pig herds (BE 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).

   [7] Fattening pigs, slaughter batches (PT 2019) : spa‐types : t011 CC398 (3), unspecified (168).

   [8] Fattening pigs, (CH 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.

   [9] Pig herds (NO 2019) : spa‐type : t034 CC398 (1 isolate).

   [10] Breeding pig herds (BE 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).

   [11] Breeding pig herds (DK 2019) : spa‐types: t011 CC398 (10 isolates), t034 CC398 (57), t1928 CC398 (1), t4652 CC398 (1). † These comprised multiplier herds.

   [12] Horse premises (DK 2019) : 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.

   *: spa‐types not reported.

Figure 49

MRSA types reported from food and animals in 2019 and 2020, inferred from molecular typing data. Spa‐type 899 was assigned to CC398

1. N = number of reported isolates with typing data, mecC: MRSA harbouring the mecC gene, HA‐MRSA: hospital acquired MRSA, CA‐MRSA: community acquired MRSA, LA‐MRSA: livestock associated MRSA, CC: clonal complex.

   Inferred MRSA types in 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). Isolates from animals in 2020 were derived from broiler flocks (2 isolates) and fattening turkey flocks (2 isolates).

   Inferred MRSA types in food in 2019 were recovered from cattle meat (8 isolates) and pig meat (55 isolates). Isolates from food in 2020 were recovered from broiler meat (8 isolates) and meat from sheep (11).

Figure 50

Temporal trends of MRSA prevalence in various types of meat, 2011–2020

1. AT: Austria; CH: Switzerland; DE: Germany; NL: the Netherlands.

   The 2‐S method of isolation was used by CH and DE from 2011 to 2018; while the 1‐S method was used by the NL from 2018 to 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 2018, spa‐types: t011 (2 isolates), t034 (1 isolate). In 2020, spa‐types: t011 (4 isolates), t034 (4 isolates)

   [4] 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 51

Temporal trends of MRSA prevalence in poultry, 2011–2020

1. BE: Belgium; DE: Germany.

   [1] Broiler flocks in 2014: spa‐types t011 CC398 (one isolate), t1985 CC398 (1)

   Broiler flocks in 2017 and 2020: spa‐type t011 (two isolates each)

   [2] Laying hens in 2014: spa‐types t011 CC398 (one isolate), t037 (5)

   Laying hens in 2017: spa‐types t011 (two isolates), t037 ST239 (1)

   *: No spa‐types reported

Figure 52

Temporal trends of MRSA prevalence in pigs, 2010–2020

1. BE: Belgium; CH: Switzerland; DE: Germany; DK: Denmark; NO: Norway.

   Note: The 2‐S method of isolation was used by Belgium and Germany from 2016 to 2019, as well as by Denmark in 2016, in Switzerland from 2010 to 2017 and in Norway from 2014 to 2017. The 1‐S method was used by Switzerland since 2019 and by Denmark and Norway since 2018.

   *: 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). In 2019, spa‐types t011 CC398 (10), t034 CC398 (57), t1928 CC398 (1), t4652 CC398 (1) were identified in isolates from multiplier pig herds.

   [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 53

Antimicrobial resistance in MRSA from animals, in 2019

1. BE: Belgium; CH: Switzerland; PT: Portugal. N: number of tested isolates. All isolates were resistant to Penicillin and Cefoxitin.

   Portugal: susceptibility data for a further 52 isolates recovered from batches of fattening pigs at slaughter were not reported. Switzerland: susceptibility data for one isolate recovered from a fattening pig was not available; the isolate did not survive cryo‐conservation.

Figure 54

Antimicrobial resistance in MRSA from food in 2019 and 2020

1. AT: Austria; DE: Germany. N: number of tested isolates. All isolates were resistant to Penicillin and Cefoxitin.Austria: susceptibility data are also included for four isolates recovered from additional ad hoc sampling.Only food matrices with 10 or more reported isolates per country.

Figure A.1

Resistance levels among MDR S. Kentucky isolates exhibiting high‐level ciprofloxacin resistance from poultry, reported by MSs in 2020

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. None of the S. Kentucky isolates reported exhibited either azithromycin or colistin resistance.

Figure A.2

Number of isolates displaying high‐level ciprofloxacin resistance by serovar, reported from the different poultry origins by MSs in 2020

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

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 two non‐MSs in broiler carcases and one non‐MS in pig carcases) in 2019–2020

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

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 one non‐MS in pig carcases and two non‐MSs in broiler carcases) in 2019–2020

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

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 one non‐MS in broilers and laying hens), 2019–2020

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

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, 2019–2020

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

   *: Monophasic S. Typhimurium includes antigenic formulas.

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 2019–2020

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; serovars in the legend are listed according to their predominance within all the animal/carcase origins.

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. ? Only R category included.

Figure D.2

Occurrence of resistance to selected antimicrobials in S. Infantis from humans, poultry and poultry carcases, reported by MSs in 2020

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

Figure D.3

Occurrence of resistance to selected antimicrobials in S. Enteritidis from humans, poultry and broiler carcases, reported by MSs in 2020

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

   NB. S. Enteritidis was not reported from turkey carcases.

Figure D.4

Occurrence of resistance to selected antimicrobials in S. Kentucky from humans, poultry and poultry carcases, reported by MSs in 2020

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

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

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

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

Temporal trends in resistance to colistin in indicator E. coli from calves under 1 year of age, 2014–2019 (nine MSs, two non‐MSs). Statistically significant increase (↑) or decrease (↓) indicated (p ≤ 0.05)

Figure E.2

Temporal trends in resistance to colistin in indicator E. coli from fattening pigs, 2014–2019 (27 MSs, four non‐MSs). Statistically significant increase (↑) or decrease (↓) indicated (p ≤ 0.05)

Figure E.3

Temporal trends in resistance to colistin in indicator E. coli from broilers, 2014–2020 (25 MSs, four non‐MSs). Statistically significant increase (↑) or decrease (↓) indicated (p ≤ 0.05)

Figure F.1

Phenotypes inferred based on the resistance to the β‐lactams included in Panel 2

1. Presumptive ESBL‐producers include isolates exhibiting Phenotype 1 or 3.

   Presumptive AmpC producers include isolates exhibiting Phenotype 2 or 3.