Assessment of animal diseases caused by bacteria resistant to antimicrobials: Swine

Abstract

In this opinion, the antimicrobial-resistant bacteria responsible for transmissible diseases that constitute a threat to the health of pigs have been assessed. The assessment has been performed following a methodology based on information collected by an extensive literature review and expert judgement. Details of the methodology used for this assessment are explained in a separate opinion. A global state of play of antimicrobial resistant Escherichia coli, Streptococcus suis, Actinobacillus pleuropneumoniae, Pasteurella multocida, Glaeserella parasuis, Bordetella bronchiseptica, Staphylococcus aureus, Staphylococcus hyicus, Brachyspira hyodysenteriae, Trueperella pyogenes, Erysipelothrix rhusiopathiae, Streptococcus dysgalactiae, Mycoplasma hyosynoviae, Mycoplasma hyorhinis, Mycoplasma hyopneumoniae and Brachyspira pilosicoli has been provided. Among those bacteria, EFSA identified E. coli and B. hyodysenteriae with > 66% certainty as being the most relevant antimicrobial resistant bacteria in the EU based on the available evidence. The animal health impact of these most relevant bacteria, as well as their eligibility for being listed and categorised within the animal health law framework will be assessed in separate scientific opinions.

Keywords: animal health law; antimicrobial resistance; extensive literature review; pig; swine.

Figure 1

Year of publication of the 77 studies included in the extensive literature review

Figure 2

Geographical distribution of the 77 studies included

Figure 3

Distribution of E. coli isolates per site of infection

Figure 4

Escherichia coli resistance data for each included study sorted by continent


1. Each circle represents one study, and the size of each circle reflects how many isolates were included in the study. The colour of the circle illustrates resistance only (red circle) or resistance merged with intermediate (blue circle). The dashed lines indicate, for each antibiotic, the weighted arithmetic mean of %R (red dashed line) or %R+I (blue dashed line). The exact percentages these lines represent are listed in Appendix E. Numbers written to the left of the antibiotic names reflect the number of studies for a certain drug/continent combination.

Figure 5

Proportion (%) of clinical swine E. coli isolates retrieved from pig enteritis cases resistant to eight antimicrobials of interest reported by the FINRES‐Vet monitoring programme

Figure 6

Proportion (%) of clinical swine ETEC E. coli isolates retrieved mostly from pig enteritis and oedema disease cases resistant to seven antimicrobials of interest reported by the DANMAP monitoring programme. Vertical dotted line separates the years in which only information from O149 isolates were included (2015–2017) from those in which all haemolytic isolates were typed (2018–2019)

Figure 7

Proportion (%) of clinical swine E. coli isolates resistant to 10 antimicrobials of interest reported by the RESAPATH monitoring programme (Amoxiclav: amoxicillin + clavulanic acid)

Figure 8

Proportion (%) of clinical swine E. coli isolates resistant to eight antimicrobials of interest reported by the SWEDRES‐Svarm monitoring programme

Figure 9

Proportion (%) of clinical swine E. coli isolates resistant to nine antimicrobials of interest reported by the UK‐VARSS monitoring programme

Figure 10

Proportion (%) of clinical swine E. coli isolates resistant to five antimicrobials of interest reported by the GERM‐Vet monitoring programme (Amoxiclav: amoxicillin + clavulanic acid)

Figure 11

Distribution of S. suis isolates per site of infection

Figure 12

Streptococcus suis resistance data for each included study sorted by continent


1. Each circle represents one study, and the size of each circle reflects how many isolates were included in the study. The colour of a circle illustrates resistance only (red circle) or resistance merged with intermediate (blue circle). The dashed lines indicate, for each antibiotic, the weighted arithmetic mean of %R (red dashed line) or %R + I (blue dashed line). The exact percentages these lines represent are listed in Appendix E. Numbers written to the left of the antibiotic names reflect the number of studies for a certain drug/continent combination.

Figure 13

Proportion (%) of clinical swine S. suis isolates resistant to six antimicrobials of interest reported by the DANMAP monitoring programme

Figure 14

Proportion (%) of clinical swine S. suis isolates resistant to five antimicrobials of interest reported by the RESAPATH monitoring programme

Figure 15

Proportion (%) of clinical swine S. suis isolates resistant to six antimicrobials of interest reported by the UK‐VARSS monitoring programme

Figure 16

Proportion (%) of clinical swine S. suis isolates resistant to four antimicrobials of interest reported by the GERM‐Vet monitoring programme

Figure 17

Distribution of A. pleuropneumoniae isolates per site of infection

Figure 18

Actinobacillus pleuropneumoniae resistance data for each included study sorted by continent

1. Each circle represents one study, and the size of each circle reflects how many isolates were included in the study. The colour of a circle illustrates resistance only (red circle) or resistance merged with intermediate (blue circle). The dashed lines indicate, for each antibiotic, the weighted arithmetic mean of %R (red dashed line) or %R + I (blue dashed line). The exact percentages these lines represent are listed in Appendix E. Numbers written to the left of the antibiotic names reflect the number of studies for a certain drug/continent combination.

Figure 19

Proportion (%) of clinical swine A. pleuropneumoniae isolates resistant to six antimicrobials of interest reported by the DANMAP monitoring programme

Figure 20

Proportion (%) of clinical swine A. pleuropneumoniae isolates resistant to eight antimicrobials of interest reported by the RESAPATH monitoring programme

Figure 21

Proportion (%) of clinical swine A. pleuropneumoniae isolates resistant to four antimicrobials of interest reported by the UK‐VARSS monitoring programme

Figure 22

Distribution of P. multocida isolates per site of infection

Figure 23

Pasteurella multocida resistance data for each included study sorted by continent. Each circle represents one study, and the size of each circle reflects how many isolates were included in the study. The colour of a circle illustrates resistance only (red circle) or resistance merged with intermediate (blue circle). The dashed lines indicate, for each antibiotic, the weighted arithmetic mean of % R (red dashed line) or % R + I (blue dashed line). The exact percentages these lines represent are listed in Annex V. Numbers written to the left of antibiotic names reflect the number of studies for a certain drug/continent combination

1. Each circle represents one study, and the size of each circle reflects how many isolates were included in the study. The colour of a circle illustrates resistance only (red circle) or resistance merged with intermediate (blue circle). The dashed lines indicate, for each antibiotic, the weighted arithmetic mean of %R (red dashed line) or %R + I (blue dashed line). The exact percentages these lines represent are listed in Appendix E. Numbers written to the left of the antibiotic names reflect the number of studies for a certain drug/continent combination.

Figure 24

Proportion (%) of clinical swine P. multocida isolates resistant to eight antimicrobials of interest reported by the RESAPATH monitoring programme

Figure 25

Proportion (%) of clinical swine P. multocida isolates resistant to four antimicrobials of interest reported by the UK‐VARSS monitoring programme

Figure 26

Distribution of G. parasuis isolates per site of infection

Figure 27

Glaesserella parasuis resistance data for each included study sorted by country


1. Each circle represents one study, and the size of each circle reflects how many isolates were included in the study. The colour of a circle illustrates resistance only (red circle) or resistance merged with intermediate (blue circle). The dashed lines indicate, for each antibiotic, the weighted arithmetic mean of %R (red dashed line) or %R + I (blue dashed line). The exact percentages these lines represent are listed in Appendix E. Numbers written to the left of the antibiotic names reflect the number of studies for a certain drug/country combination.

Figure 28

Distribution of B. bronchiseptica isolates per site of infection

Figure 29

Bordetella bronchiseptica resistance data for each included study sorted by country


1. Each circle represents one study, and the size of each circle reflects how many isolates were included in the study. The colour of a circle illustrates resistance only (red circle) or resistance merged with intermediate (blue circle). The dashed lines indicate, for each antibiotic, the weighted arithmetic mean of %R (red dashed line) or %R + I (blue dashed line). The exact percentages these lines represent are listed in Annex V. Numbers written to the left of the antibiotic names reflect the number of studies for a certain drug/country combination.

Figure 30

Distribution of Staphylococcus isolates per site of infection

Figure 31

Staphylococcus spp. resistance data for each included study sorted by country


1. Each circle represents one study, and the size of each circle reflects how many isolates were included in the study. The colour of a circle illustrates resistance only (red circle) or resistance merged with intermediate (blue circle). The red dashed lines indicate, for each antibiotic, the weighted arithmetic mean of %R. The exact percentages these lines represent are listed in Appendix E. Numbers written to the left of the antibiotic names reflect the number of studies for a certain drug/country combination.

Figure 32

Distribution of B. hyodysenteriae isolates per site of infection

Figure 33

Brachyspira hyodysenteriae resistance data for each included study sorted by country

Figure 34

Level of certainty for the inclusion of the selected antimicrobial resistant pathogens of swine among the most relevant in the EU