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. 2018 Feb 27;16(2):e05182.
doi: 10.2903/j.efsa.2018.5182. eCollection 2018 Feb.

The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016

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 2016

European Food Safety Authority et al. EFSA J. .

Abstract

The data on antimicrobial resistance in zoonotic and indicator bacteria in 2016, submitted by 28 EU Member States (MSs), were jointly analysed by the EFSA and ECDC. Resistance in bacterial isolates of zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as in meticillin-resistant Staphylococcus aureus from animals and food were addressed. 'Microbiological' resistance was assessed using epidemiological cut-off (ECOFF) values; for some countries, qualitative data on isolates from humans were interpreted in a way that corresponds closely to ECOFF-defined 'microbiological' resistance. In Salmonella from humans, the occurrence of resistance to ampicillin, sulfonamides and tetracyclines was high, whereas resistance to third-generation cephalosporins was low. In Salmonella and E. coli isolates from broilers, fattening turkeys and their meat, resistance to ampicillin, (fluoro)quinolones, tetracyclines and sulfonamides was frequently high, whereas resistance to third-generation cephalosporins was rare. The occurrence of ESBL-/AmpC producers was low in Salmonella and E. coli from poultry and in Salmonella from humans. The prevalence of ESBL-/AmpC-producing E. coli, assessed in poultry and its meat for the first time, showed marked variations among MSs. Fourteen presumptive carbapenemase-producing E. coli were detected from broilers and its meat in two MSs. Resistance to colistin was observed at low levels in Salmonella and E. coli from poultry and meat thereof and in Salmonella from humans. In Campylobacter from humans, broilers and broiler meat, resistance to ciprofloxacin and tetracyclines was high to extremely high, whereas resistance to erythromycin was low to moderate. Combined resistance to critically important antimicrobials in isolates from both humans and animals was generally uncommon, but very high to extremely high multidrug resistance levels were observed in certain Salmonella serovars. Specific serovars of Salmonella (notably Kentucky) from both humans and animals exhibited high-level resistance to ciprofloxacin, in addition to findings of ESBL.

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

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Figures

Figure 1
Figure 1
Distribution of the occurrence of resistance to ciprofloxacin (CIP), erythromycin (ERY), gentamicin (GEN) and tetracyclines (TET) in C. jejuni from broilers, 24 EU MSs, 2016

  1. Dots represent reporting MSs.

Figure 2
Figure 2
Distribution of the occurrence of resistance to ciprofloxacin (CIP), erythromycin (ERY), gentamicin (GEN) and tetracyclines (TET) in C. jejuni from fattening turkeys, nine EU MSs, 2016

  1. Dots represent reporting MSs.

Figure 3
Figure 3
Distribution of the occurrence of resistance to ampicillin (AMP), ciprofloxacin (CIP), colistin (CST), cefotaxime (CTX) and tetracyclines (TET) in indicator commensal E. coli from broilers, 27 EU MSs, 2016

  1. Dots represent reporting MSs.

Figure 4
Figure 4
Distribution of the occurrence of resistance to ampicillin (AMP), ciprofloxacin (CIP), colistin (CST), cefotaxime (CTX) and tetracyclines (TET) in indicator commensal E. coli from fattening turkeys, 10 EU MSs, 2016

  1. Dots represent reporting MSs.

Figure 5
Figure 5
Inferred MRSA types in food‐producing animals – pigs, 2016 (232 MRSA isolates were reported, of which 176 were spa‐typed; some of these were MLST typed)
Figure 6
Figure 6
Percentage of MRSA types reported in 2016, inferred from spa‐typing data (198 MRSA isolates were spa‐typed) – from meat, food‐producing animals, solipeds, companion/wild/zoo animals (including clinical investigations)
Figure 7
Figure 7
Overview of MRSA types by animal species reported in 2016, including healthy animals and clinical investigations

  1. MLST types have for the most part been inferred from spa‐typing data, some isolates were MLST typed. Both spa‐types t1190 and t153 were not categorised as CA‐MRSA or HA‐MRSA as further typing data including PVL status were not reported. In total, 198 MRSA isolates were spa‐typed.

    VCCI: at veterinary clinic clinical investigation; NHCI: Natural habitat clinical investigations; OFCI: On‐farm clinical investigations; ARM: At retail monitoring; MLST: multilocus sequence typing; CA: community‐associated; HA: healthcare‐associated; LA: livestock‐associated; MRSA: meticillin‐resistant Staphylococcus aureus.

Figure 8
Figure 8
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.

Figure 9
Figure 9
Comparison of CBPs for non‐susceptibility (intermediate and resistant categories combined) and ECOFFs used to interpret MIC data reported for Salmonella spp. from humans, animals or food
Figure 10
Figure 10
Spatial distribution of combined ‘microbiological’ resistance to ciprofloxacin and cefotaxime among Salmonella spp. from human cases, EU/EEA MSs, 2016
Figure 11
Figure 11
Frequency distribution of Salmonella spp. isolates from humans completely susceptible or resistant to one to nine antimicrobial classes in 2016

  1. N: total number of isolates tested for susceptibility against the whole common set of antimicrobials for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one up to nine antimicrobial classes of the common set for Salmonella.

Figure 12
Figure 12
Spatial distribution of ciprofloxacin resistance among S. Enteritidis from human cases, EU/EEA MSs, 2016
Figure 13
Figure 13
Spatial distribution of cefotaxime resistance among S. Enteritidis from human cases, EU/EEA MSs, 2016
Figure 14
Figure 14
Trends in resistance to ampicillin, ciprofloxacin/pefloxacin/nalidixic acid, cefotaxime and tetracycline in Salmonella Enteritidis isolates from humans in 22 reporting countries, 2013–2016

  1. Statistically significant increasing trends over 3–4 years, as tested by logistic regression (p ≤ 0.05), were observed for ciprofloxacin in Finland and Germany, for ampicillin in Finland, Germany and Hungary, and for tetracyclines in Finland, Hungary and Norway. Statistically significant decreasing trends over 3–4 years were observed for ciprofloxacin in France, Hungary, Malta, Spain and the United Kingdom, for ampicillin in Italy, Latvia, Lithuania, Luxembourg, Malta, Romania, Slovenia and Spain, and for tetracyclines in Portugal. Only countries testing at least 10 isolates per year were included in the analysis.

Figure 15
Figure 15
Frequency distribution of Salmonella Enteritidis isolates from humans completely susceptible or resistant to one to nine antimicrobial classes in 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one up to nine antimicrobial classes of the common set for Salmonella.

Figure 16
Figure 16
Spatial distribution of fluoroquinolone resistance among S. Typhimurium from human cases, EU/EEA MSs, 2016
Figure 17
Figure 17
Spatial distribution of cefotaxime resistance among S. Typhimurium from human cases, EU/EEA MSs, 2016
Figure 18
Figure 18
Trends in resistance to ampicillin, ciprofloxacin/pefloxacin, cefotaxime and tetracycline in Salmonella Typhimurium from humans in 21 reporting countries, 2013–2016

  1. Statistically significant increasing trends over 3–4 years, as tested by logistic regression (p ≤ 0.05), were observed for ciprofloxacin in Estonia, Finland, Hungary, the Netherlands and Portugal, for ampicillin in Belgium, Lithuania, Slovakia and the United Kingdom, for tetracyclines in Belgium, Denmark and the United Kingdom, and for cefotaxime in Austria, Statistically significant decreasing trends over 3–4 years were observed for ciprofloxacin in Lithuania, for ampicillin in Finland, Hungary, Luxembourg, Norway and Spain, and for tetracyclines in Finland, Germany, Hungary, the Netherlands and Spain. Only countries testing at least 10 isolates per year were included in the analysis.

Figure 19
Figure 19
Frequency distribution of Salmonella Typhimurium isolates from humans completely susceptible or resistant to one to nine antimicrobial classes in 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one up to nine antimicrobial classes of the common set for Salmonella.

Figure 20
Figure 20
Spatial distribution of ciprofloxacin resistance among S. Infantis from human cases, EU/EEA MSs, 2016
Figure 21
Figure 21
Spatial distribution of cefotaxime resistance among S. Infantis from human cases, EU/EEA MSs, 2016
Figure 22
Figure 22
Trends in resistance to ampicillin, ciprofloxacin/pefloxacin/nalidixic acid, cefotaxime and tetracycline in Salmonella Infantis from humans in 10 reporting countries, 2013–2016

  1. Statistically significant increasing trends over 3–4 years, as tested by logistic regression (p ≤ 0.05), were observed for ciprofloxacin in Germany, for ampicillin in Germany and for tetracyclines in the Netherlands. Statistically significant decreasing trends over 3–4 years were observed for ampicillin in Slovakia and for cefotaxime in Belgium. Only countries testing at least 10 isolates per year were included in the analysis.

Figure 23
Figure 23
Frequency distribution of Salmonella Infantis isolates from humans completely susceptible or resistant to one to nine antimicrobial classes in 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one up to nine antimicrobial classes of the common set for Salmonella.

Figure 24
Figure 24
Spatial distribution of ciprofloxacin resistance among S. Kentucky from human cases, EU/EEA MSs, 2016
Figure 25
Figure 25
Spatial distribution of cefotaxime resistance among S. Kentucky from human cases, EU/EEA MSs, 2016
Figure 26
Figure 26
Trends in resistance to ampicillin, ciprofloxacin/pefloxacin, cefotaxime and tetracycline in Salmonella Kentucky from humans in six reporting countries, 2013–2016

  1. Statistically significant increasing trends over 3–4 years, as tested by logistic regression (p ≤ 0.05), were observed for ciprofloxacin in Germany and Malta and for ampicillin in Malta. Only countries testing at least 10 isolates per year were included in the analysis.

Figure 27
Figure 27
Frequency distribution of Salmonella Kentucky isolates from humans completely susceptible or resistant to one to nine antimicrobial classes in 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one up to nine antimicrobial classes of the common set for Salmonella.

Figure 28
Figure 28
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobial classes in Salmonella spp. from broiler meat, EU MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one antimicrobial classes/resistance to nine antimicrobial classes of the common set for Salmonella.

Figure 29
Figure 29
Spatial distribution of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from broiler meat, using harmonised ECOFFs, 20 EU/EEA MSs, 2016
Figure 30
Figure 30
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobial classes in Salmonella spp. from turkey meat, EU MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res5: resistance to one antimicrobial classes/resistance to five antimicrobial classes of the common set for Salmonella.

Figure 31
Figure 31
Spatial distribution of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from turkey meat, using harmonised ECOFFs, 8 EU MSs, 2016
Figure 32
Figure 32
Spatial distribution of cefotaxime (a) and ciprofloxacin (b) resistance among Salmonella spp. from broiler flocks, using harmonised ECOFFs, 24 EU/EEA MSs, 2016
Figure 33
Figure 33
Spatial distribution of combined resistance to cefotaxime and ciprofloxacin in Salmonella spp. from broiler flocks, using harmonised ECOFFs, 24 EU/EEA MSs, 2016
Figure 34
Figure 34
Trends in ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP), nalidixic acid (NAL) and tetracyclines (TET) resistance in Salmonella spp. from broiler flocks, using harmonised ECOFFs, EU MSs, 2008–2016

  1. Statistical significance of trends over 4‐5 or more years was tested by a logistic regression model (p ≤ 0.05). Statistically significant increasing trends were observed for ampicillin in the Czech Republic, Italy and Spain, for ciprofloxacin and nalidixic acid in Austria, Italy, Poland, Romania and Slovenia, for cefotaxime in Italy and Romania, as well as for tetracycline in Austria, Denmark, Italy, Poland, Romania, Slovenia and Spain.

    Statistically significant decreasing trends were observed for ampicillin in Austria and France, for ciprofloxacin and nalidixic acid in Spain, for cefotaxime in the Czech Republic, Portugal and Spain, for nalidixic acid in Portugal, as well as for tetracycline in the Czech Republic and France.

Figure 35
Figure 35
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella spp. from broiler flocks, EU MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one antimicrobial classes/resistance to nine antimicrobial classes of the common set for Salmonella.

Figure 36
Figure 36
Spatial distribution of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from broiler flocks, using harmonised ECOFFs, 24 EU/EEA MSs, 2016
Figure 37
Figure 37
Breakdown of Salmonella serovars in broiler flocks, EU MSs, 2016 (N = 1,707)
Figure 38
Figure 38
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella Infantis from broilers, EU MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one antimicrobial classes/resistance to nine antimicrobial classes of the common set for Salmonella.

Figure 39
Figure 39
Spatial distribution of cefotaxime (a) and ciprofloxacin (b) resistance among Salmonella Infantis from broiler flocks, using harmonised ECOFFs, 19 EU/EEA MSs, 2016
Figure 40
Figure 40
Spatial distribution of combined resistance to cefotaxime and ciprofloxacin in Salmonella Infantis from broiler flocks, using harmonised ECOFFs, 19 EU/EEA MSs, 2016
Figure 41
Figure 41
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella Enteritidis from broilers in MSs in 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res8: resistance to one antimicrobial classes/resistance to eight antimicrobial classes of the common set for Salmonella.

Figure 42
Figure 42
Spatial distribution of ciprofloxacin resistance among Salmonella Enteritidis from broiler flocks, using harmonised ECOFFs, 12 EU MSs, 2016
Figure 43
Figure 43
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella Kentucky from broilers in MSs in 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res7: resistance to one antimicrobial classes/resistance to seven antimicrobial classes of the common set for Salmonella.

Figure 44
Figure 44
Spatial distribution of ciprofloxacin resistance among Salmonella Kentucky from broilers, using harmonised ECOFFs, 8 EU MSs, 2016
Figure 45
Figure 45
Spatial distribution of cefotaxime (a) and ciprofloxacin (b) resistance in Salmonella spp. from laying hen flocks, 23 EU/EEA MSs, 2016
Figure 46
Figure 46
Spatial distribution of co‐resistance to cefotaxime and ciprofloxacin resistance in Salmonella spp. from laying hen flocks, 23 EU/EEA MSs, 2016
Figure 47
Figure 47
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella spp. from laying hen flocks, EU MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one antimicrobial classes/resistance to nine antimicrobial classes of the common set for Salmonella.

Figure 48
Figure 48
Spatial distribution of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from laying hen flocks, using harmonised ECOFFs, 23 EU/EEA MSs, 2016
Figure 49
Figure 49
Trends in ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP), nalidixic acid (NAL) and tetracycline (TET) resistance in tested Salmonella spp. from laying hens, EU MSs, 2008–2016

  1. Statistical significance of trends over 4‐5 or more years was tested by a logistic regression model (p ≤ 0.05). Statistically significant increasing trends were observed for ampicillin in Romania, for ciprofloxacin in the United Kingdom, for ciprofloxacin and nalidixic acid in Italy and Romania, as well as for tetracycline in Austria.

    Statistically significant decreasing trends were observed for ampicillin in France, Greece, Italy, Poland and Spain, for ciprofloxacin and nalidixic acid in France, Greece, Poland and Spain, for cefotaxime in Italy and Spain, for nalidixic acid in Portugal, as well as for tetracycline in France, Greece, Italy, Portugal and Romania.

Figure 50
Figure 50
Breakdown of serovars among Salmonella isolates from laying hen flocks tested for susceptibility, EU MSs, 2016. (N = 1,194)
Figure 51
Figure 51
Spatial distribution of ciprofloxacin resistance among Salmonella Enteritidis from laying hen flocks, 18 EU MSs, 2016
Figure 52
Figure 52
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella Enteritidis from laying hen flocks, 18 EU MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; CZ: the Czech Republic; UK: the United Kingdom; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one antimicrobial classes/resistance to nine antimicrobial classes of the common set for Salmonella.

Figure 53
Figure 53
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella Infantis from laying hens, 18 EU MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; CZ: the Czech Republic; UK: the United Kingdom; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one antimicrobial classes/resistance to nine antimicrobial classes of the common set for Salmonella.

Figure 54
Figure 54
Spatial distribution of ciprofloxacin resistance among Salmonella Infantis from laying hen flocks, 18 EU MSs, 2016
Figure 55
Figure 55
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella Kentucky from laying hens, 9 EU MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; UK: the United Kingdom; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res7: resistance to one antimicrobial classes/resistance to seven antimicrobial classes of the common set for Salmonella.

Figure 56
Figure 56
Spatial distribution of ciprofloxacin resistance among Salmonella Kentucky from laying hen flocks, 9 EU MSs, 2016
Figure 57
Figure 57
Trends in ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP), nalidixic acid (NAL) and tetracycline (TET) resistance in tested Salmonella spp. from Gallus gallus, EU MSs, 2008–2016

  1. Statistical significance of trends over 4‐5 or more years was tested by a logistic regression model (p ≤ 0.05). Statistically significant increasing trends were observed for ampicillin in the Czech Republic, Germany, Italy, Latvia, Portugal, Romania, Slovakia and Spain, for ciprofloxacin in Spain, for ciprofloxacin and nalidixic acid in Austria, Germany, Italy, Romania, Slovakia and Slovenia, for cefotaxime in Italy, Romania and Slovakia, for nalidixic acid in Hungary, as well as for tetracycline in Austria, Denmark, Germany, Hungary, Italy, Slovenia, Slovakia and Spain.

    Statistically significant decreasing trends were observed for ampicillin in Austria, Belgium, Croatia, Greece, Hungary, the Netherlands, Poland, Slovenia and the United Kingdom, for ciprofloxacin and nalidixic acid in Belgium, Greece, the Netherlands, Poland and the United Kingdom, for cefotaxime in Belgium, Croatia, Germany, Greece, Hungary, the Netherlands, Slovenia, Spain and the United Kingdom, for nalidixic acid in Portugal and Spain, as well as for tetracycline in the Czech Republic, France, Greece, the Netherlands, Portugal, Romania and the United Kingdom.

Figure 58
Figure 58
Spatial distribution of cefotaxime (a) and ciprofloxacin (b) resistance among Salmonella spp. from fattening turkeys, using harmonised ECOFFs, 15 EU MSs, 2016
Figure 59
Figure 59
Frequency distribution of completely susceptible isolates and resistant isolates to one to nine antimicrobials classes in Salmonella spp. from fattening turkeys in 2016

  1. N: total number of isolates tested for susceptibility against the whole common antimicrobial set for Salmonella; CZ: the Czech Republic, UK: the United Kingdom; sus: susceptible to all antimicrobial classes of the common set for Salmonella; res1–res9: resistance to one antimicrobial classes/resistance to nine antimicrobial classes of the common set for Salmonella.

Figure 60
Figure 60
Spatial distribution of complete susceptibility to the panel of antimicrobials tested among Salmonella spp. from fattening turkey flocks, using harmonised ECOFFs, 15 EU MSs, 2016
Figure 61
Figure 61
Trends in ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP), nalidixic acid (NAL) and tetracycline (TET) resistance in tested Salmonella spp. isolates from turkeys, EU MSs, 2008–2016

  1. Statistical significance of trends over 4‐5 or more years was tested by a logistic regression model (p ≤ 0.05).

    Statistically significant increasing trends were observed for ampicillin in Spain, for ciprofloxacin and nalidixic acid in the Czech Republic, France, Hungary and Italy, for nalidixic acid in Austria, Spain and the United Kingdom, as well as for tetracycline in Hungary, Italy, Spain and the United Kingdom.

    Statistically significant decreasing trends were observed for ampicillin in the Czech Republic, Germany, Hungary, Italy, Poland and the United Kingdom, for ciprofloxacin in Austria, Spain and the United Kingdom, for cefotaxime in Hungary and Spain, for nalidixic acid in Germany and Poland, as well as for tetracycline in the Czech Republic and France.

Figure 62
Figure 62
Breakdown of Salmonella serovars in fattening turkey flocks, EU MSs, 2016 (N = 656)
Figure 63
Figure 63
Tigecycline resistance in Salmonella spp. from broilers, laying hens, fattening turkeys
Figure 64
Figure 64
Colistin resistance in Salmonella spp. from (a) broilers, fattening turkeys and (b) meat from these animals
Figure 65
Figure 65
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 66
Figure 66
Spatial distribution of ciprofloxacin resistance among Campylobacter jejuni from human cases in reporting countries in 2016
Figure 67
Figure 67
Spatial distribution of erythromycin resistance among Campylobacter jejuni from human cases in reporting countries in 2016
Figure 68
Figure 68
Trends in ciprofloxacin, erythromycin and tetracycline resistance in Campylobacter jejuni from humans in reporting countries, 2013–2016

  1. Statistically significant increasing trends over 3–4 years, as tested by logistic regression (p ≤ 0.05), were observed for ciprofloxacin in Austria, Estonia, France, Italy and Norway, for erythromycin in Lithuania, Norway and the United Kingdom and for tetracycline in Austria, Estonia, Italy, Lithuania and Slovenia. Statistically significant decreasing trends over 3–4 years were observed for ciprofloxacin in Malta and Spain, for erythromycin in Luxembourg and Malta. Only countries testing at least 10 isolates per year were included in the analysis.

Figure 69
Figure 69
Erythromycin MIC distribution in C. jejuni from humans, 2016 (n = 3,198)
Figure 70
Figure 70
Frequency distribution of Campylobacter jejuni isolates from humans completely susceptible or resistant to one to four antimicrobial classes in 2016
Figure 71
Figure 71
Spatial distribution of ciprofloxacin resistance among Campylobacter coli from human cases in reporting countries in 2016
Figure 72
Figure 72
Spatial distribution of erythromycin resistance among Campylobacter coli from human cases in reporting countries in 2016
Figure 73
Figure 73
Trends in ciprofloxacin, erythromycin and tetracycline resistance in Campylobacter coli from humans in reporting countries, 2013–2016

  1. Statistically significant increasing trends over 3–4 years, as tested by logistic regression (p ≤ 0.05), were observed for ciprofloxacin in Lithuania and Luxembourg and for tetracycline in Austria, France, Lithuania, Malta, the Netherlands and the United Kingdom. Statistically significant decreasing trends over 3–4 years were observed for erythromycin in France. Only countries testing at least 10 isolates per year were included in the analysis.

Figure 74
Figure 74
Erythromycin MIC distribution in C. coli from humans, 2016 (n = 337)
Figure 75
Figure 75
Frequency distribution of Campylobacter coli isolates from humans completely susceptible or resistant to one to four antimicrobial classes in 2016
Figure 76
Figure 76
Spatial distribution of ciprofloxacin (a) and erythromycin (b) resistance in Campylobacter jejuni from broilers of Gallus gallus, EU/EEA MSs, 2016
Figure 77
Figure 77
Spatial distribution of combined resistance to ciprofloxacin and erythromycin in Campylobacter jejuni from broilers of Gallus gallus, EU/EEA MSs, 2016
Figure 78
Figure 78
Trends in ciprofloxacin (CIP), erythromycin (ERY) nalidixic acid (NAL), streptomycin (STR) and tetracycline (TET) resistance in Campylobacter jejuni from broilers in reporting MSs, 2008–2016

  1. Statistical significance of trends over 4‐5 or more years was tested by a logistic regression model (p ≤ 0.05).

    Statistically significant increasing trends were observed for ciprofloxacin (and nalidixic acid) in Austria, the Czech Republic, Denmark, Finland, France, Germany, Hungary, the Netherlands, Spain and Switzerland, for erythromycin in the Netherlands, for gentamicin in the Netherlands and Switzerland, for streptomycin in Austria, the Czech Republic, the Netherlands and Switzerland, as well as for tetracycline in Austria, the Czech Republic, Finland, France, Germany, Hungary, Spain, Sweden and Switzerland.

    Statistically significant decreasing trends were observed for ciprofloxacin in Slovenia, for erythromycin in Hungary and Spain, for gentamicin in Hungary and Spain, for streptomycin in Italy and Spain, as well as for tetracycline in the Netherlands.

Figure 79
Figure 79
Frequency distribution of Campylobacter jejuni isolates completely susceptible and resistant to one to four antimicrobials, in broilers, EU/EEA MSs, 2016
Figure 80
Figure 80
Frequency distribution of Campylobacter coli isolates completely susceptible and resistant to one to four antimicrobials, in broilers, EU/EEA MSs, 2016

  1. N: total number of isolates tested for susceptibility against the whole harmonised set of antimicrobials for Campylobacter; sus: susceptible to all antimicrobial classes of the harmonised set for Campylobacter; res1–res4: resistance to one up to four antimicrobial classes of the harmonised set for Campylobacter.

Figure 81
Figure 81
Spatial distribution of ciprofloxacin (a) and erythromycin (b) resistance among Campylobacter jejuni from fattening turkeys, nine EU MSs, 2016
Figure 82
Figure 82
Spatial distribution of combined resistance to ciprofloxacin and erythromycin in Campylobacter jejuni from fattening turkeys, nine EU MSs, 2016
Figure 83
Figure 83
Occurrence of resistance in ciprofloxacin (CIP), erythromycin (ERY) nalidixic acid (NAL), streptomycin (STR) and tetracycline (TET) resistance in Campylobacter jejuni from fattening turkeys in reporting MSs in 2014 and 2016

  1. Stars indicate statistically significant changes in occurrence of resistance between 2014 and 2016. CIP: ciprofloxacin; ERY: erythromycin; GEN: gentamicin; NAL: nalidixic acid; STR: streptomycin; TET: tetracycline.

Figure 84
Figure 84
Frequency distribution of Campylobacter jejuni isolates completely susceptible and resistant to one to four antimicrobials, from fattening turkeys, nine EU MSs, 2016
Figure 85
Figure 85
MIC distribution to erythromycin in Campylobacter jejuni from broilers and fattening turkeys, 2016
Figure 86
Figure 86
Spatial distribution of resistance to cefotaxime (a) and ciprofloxacin (b) in indicator Escherichia coli from broilers, using harmonised ECOFFs, 30 EU/EEA Member States, 2016
Figure 87
Figure 87
Spatial distribution of combined resistance to cefotaxime and ciprofloxacin in indicator Escherichia coli from broilers, using harmonised ECOFFs, 30 EU/EEA Member States, in 2016
Figure 88
Figure 88
Trends in ampicillin (AMP), cefotaxime (CTX), ciprofloxacin (CIP), nalidixic acid (NAL) and tetracyclines (TET) resistance in indicator commensal Escherichia coli from broilers in reporting countries, 2008–2016

  1. Statistical significance of trends over 4‐5 or more years was tested by a logistic regression model (p ≤ 0.05). Statistically significant increasing trends were observed for ampicillin in Belgium, Denmark, France and Poland, for ciprofloxacin in Finland, France, Hungary, Poland and Switzerland, for cefotaxime in France, as well as for tetracycline in Poland.

    Statistically significant decreasing trends were observed for ampicillin in Austria, Germany, Hungary, the Netherlands, Norway and Spain, for ciprofloxacin in Austria, Croatia, the Netherlands, Norway and Spain, for cefotaxime in Belgium, Croatia, Germany, the Netherlands, Poland and Spain, for nalidixic acid in Belgium and the Netherlands, as well as for tetracycline in Austria, Belgium, Croatia, France, Germany, the Netherlands, Spain and Switzerland.

Figure 89
Figure 89
Distribution of MICs of tigecycline in indicator Escherichia coli from broilers (5,013 isolates from 29 EU Member States) and fattening turkeys (1,714 isolates from 11 EU Member States), 2016
Figure 90
Figure 90
Frequency distribution of Escherichia coli isolates completely susceptible and resistant to 1–11 antimicrobials in broilers, 30 EU/EEA Member States, 2016

  1. N: total number of isolates tested for susceptibility against the whole harmonised set of antimicrobials for Escherichia coli; sus: susceptible to all antimicrobial classes of the harmonised set for E. coli; res1–res9: resistance to 1 up to 11 antimicrobial classes of the harmonised set for E. coli.

Figure 91
Figure 91
Spatial distribution of complete susceptibility to the panel of antimicrobials tested among indicator Escherichia coli from broilers, using harmonised ECOFFs, 30 EU/EEA Member States, 2016
Figure 92
Figure 92
Spatial distribution of resistance to cefotaxime (a) and ciprofloxacin (b) in indicator Escherichia coli from fattening turkeys, 12 EU/EEA MSs, in 2016
Figure 93
Figure 93
Spatial distribution of combined resistance to cefotaxime and ciprofloxacin in indicator Escherichia coli from fattening turkeys, 12 EU/EEA Member States, in 2016
Figure 94
Figure 94
Occurrence of resistance to ampicillin (AMP), tetracycline (TET), ciprofloxacin (CIP), nalidixic acid (NAL) and cefotaxime (CTX) in indicator E. coli from fattening turkeys, in reporting MSs, 2014 and 2016

  1. Asterisks indicate statistically significant changes in occurrence of resistance between 2014 and 2016.

Figure 95
Figure 95
Frequency distribution of Escherichia coli isolates completely susceptible and resistant to 1–11 antimicrobials in fattening turkeys, 12 EU/EEA Member States, 2016

  1. N: total number of isolates tested for susceptibility against the whole harmonised set of antimicrobials for Escherichia coli; sus: susceptible to all antimicrobial classes of the harmonised set for Escherichia coli; res1–res9: resistance to one up to 11 antimicrobial classes of the harmonised set for Escherichia coli.

Figure 96
Figure 96
Spatial distribution of complete susceptibility to the panel of antimicrobials tested among indicator Escherichia coli from fattening turkeys, using harmonised ECOFFs, 12 EU/EEA Member States, 2016
Figure 97
Figure 97
Distribution of MICs of colistin in indicator E. coli from broilers (5,013 isolates from 29 EU Member States) and fattening turkeys (1,714 isolates from 11 EU Member States), 2016
Figure 98
Figure 98
Overview of MRSA types by species reported in 2016, including healthy animals and clinical investigations

  1. MLST types have for the most part been inferred from spa‐typing data, some isolates were MLST typed.

    Both spa‐types t1190 and t153 were not categorised as CA‐MRSA or HA‐MRSA as further typing data including PVL status were not reported. In total, 198 MRSA isolates were spa‐typed.

    VCCI: At‐veterinary‐clinic clinical investigation; NHCI: Natural habitat clinical investigations; OFCI: On‐farm clinical investigations; ARM: At‐retail monitoring.

Figure 99
Figure 99
Prevalence of presumptive ESBL‐producing (a) and AmpC‐producing (b) E. coli isolates from broiler meat collected within the specific ESBL‐/AmpC‐/carbapenemase‐producing monitoring and subjected to supplementary testing in 2016
Figure 100
Figure 100
Prevalence of presumptive ESBL‐producing (a) and AmpC‐producing (b) E. coli isolates from broilers collected within the specific ESBL‐/AmpC‐/carbapenemase‐producing monitoring and subjected to supplementary testing in 2016
Figure 101
Figure 101
Prevalence of presumptive ESBL‐producing (a) and AmpC‐producing (b) E. coli isolates from fattening turkeys collected within the specific ESBL‐/AmpC‐/carbapenemase‐producing monitoring and subjected to supplementary testing in 2016
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