Retailpork E. Coli

Retailpork – E. coli

A total of 92 E. coliwere isolated during the 12 month sampling period. The overall prevalenceofE. coliin retail pork was 18.1% and ranged duringmonthly sampling from 5.9% to 26.5%. The 92E. coliisolateswere tested forAMR. Thereduction in pork/E. coli isolates available for AMR testing correspondingly results in a minor decrease from 95% toapproximately 93.5% probability of detecting 1 AMR isolate in 92 if AMR prevalence nominallyoccurs at 3% prevalence (see FRSC communication note Appendix C).

Antimicrobial drug resistance:The prevalence of multiple drug resistance inE. coliis presented in Figure 9Figure. The distribution of MICs and resistance inE. coliis presented in Table 18. Resistance to one or more antimicrobials was observed in 80.4% of isolates. Resistance to tetracycline (44.5%), ampicillin (28.2%), streptomycin (17.4%), chloramphenicol (13%) and trimethoprim/sulfamethoxazole (13%)weremostoften observed. Resistance to florfenicol (8.7%), amoxicillin / clavulanic acid (3.3%), cefazolin (3.3%), kanamycin (3.3%) and gentamicin (1.1%) were also observed.

AMR patterns:A total of 24 AMR patterns were identified (Table 14). Resistance totetracycline alone was the most commonly observed AMR pattern (13%). Twenty-two percentof isolateswere resistant to3 ormore antimicrobials and comprised 14 of the 24 AMR patterns identified. Five of the 14 patterns were found in multiple isolates. The largest AMR patterns identified included resistanceto ampicillin-streptomycin-tetracycline- trimethoprim/ sulfamethoxazolein conjunction with combinations ofchloramphenicol, florfenicoland kanamycin resistance.

Pork-E.coli5

051015202530354045

Percentageofisolates

Figure 9. Multiple drug resistance inE. coli from retail pork samples (n=92)

Table 14.Multiple antimicrobial resistance phenotypes present in E. colifromretail pork.

Pattern / Resistancephenotype* / Percentage
0 / Nopattern / 42
1 / tet / 13
1 / amp / 4
1 / str / 2
1 / ffn / 1
2 / amptet / 8
2 / strtet / 3
2 / genstr / 1
2 / augfaz / 1
2 / tetsxt / 1
2 / chltet / 1
3 / ampchltet / 3
3 / augampfaz / 2
3 / ampstrtet / 2
3 / ampchlsxt / 1
3 / ampkantet / 1
4 / chlstrtetsxt / 2
4 / ampstrtetsxt / 1
4 / ampchlffntet / 1
4 / chlffntetsxt / 1
5 / chlffnstrtetsxt / 2
5 / ampchlffntetsxt / 1
6 / ampffnkanstrtetsxt / 1
6 / ampchlffnstrtetsxt / 1
6 / ampchlkanstrtetsxt / 1

*Amoxicillin/Clavulanicacid,aug;Ampicillin,amp;Cefazolin,faz;Cefotaxime,fot;Cefoxitin,fox;Ceftiofur,xnl;Ceftriaxone,axo;Chloramphenicol,Ciprofloxacin,cip;Florfenicol,ffn;Gentamicin,gen;Meropenem,mer;NalidixicAcid,nal;Streptomycin,str;Tetracycline,tet;Trimethoprim/Sulfamethoxazole,sxt.

Retailpork – Enterococcus

A total of 178Enterococcus were isolated during the 12 month sampling period. The overall prevalence ofEnterococcus in retail porkwas 86.0% and ranged during monthly sampling from 70.6% to 94.7%. Screening ofEnterococcusisolates by PCR determined that 83.1% of isolates wereE. faecalis. E. faeciumwas not identified using PCR. One hundredE. faecalisisolateswere randomly selected for AMR testing.

Antimicrobial drug resistance:The prevalence of multiple drug resistance in Enterococcus is presented in Figure 10. The distributionof MICs and resistance inEnterococcus is presented in Table 15.Resistance to one or more antimicrobials was observed in 22% ofisolates.Resistancetotetracycline(17%) was observedmost often. Isolateswith resistance to chloramphenicol, erythromycin,flavomycin, kanamycin, streptomycin and tigecycline were observed witha prevalence≤7%. Resistance to the clinicallysignificant antimicrobials gentamicin, linezolid and vancomycinwas not observed.

AMR patterns:A total of 11 AMR patterns were identified (Table 16). Resistance to2 or more antimicrobials was observed in 11% of isolates. The largest AMR patterns observed wereresistance tochloramphenicol-erythromycin-kanamycin -streptomycin-tetracycline (5 antimicrobials;2 isolates; 2%) and erythromycin-flavomycin-kanamycin- streptomycin- tetracycline (5 antimicrobials; 1 isolate; 1%).

Pork-Enterococci

020406080100

Percentageofisolates

Figure 10.Multiple drug resistance inEnterococcus faecalisfrom retail pork samples (n=100)

Table 15.Distribution of MICs and resistance inEnterococcusfaecalisfrom retail poultry, beef, and pork.

AntimicrobialProductN=

Resistant

[95%CI]

Distribution(%)ofMICs

0.0150.030.060.120.250.5124816326412825651210242048>2048

AmpicillinPoultry1000.0[0.00–3.62] / 98.02.0
Beef1000.0[0.00–3.62] / 96.04.0
Pork1000.0[0.00–3.62] / 98.02.0
ChloramphenicolPoultry1001.0[0.03–5.45] / 6.01.074.018.0 / 1.0
Beef1003.0[0.62–8.52] / 9.015.066.07.0 / 3.0
Pork1002.0[0.24–7.04] / 4.04.086.04.0 / 1.0 / 1.0
DaptomycinPoultry1000.0[0.00–3.62] / 16.039.042.03.0
Beef1000.0[0.00–3.62] / 39.032.022.07.0
Pork1000.0[0.00–3.62] / 34.026.036.04.0
ErythromycinPoultry10048.0[37.90–58.22] / 45.07.0 / 2.03.0 / 43.0
Beef1006.0[2.23–12.60] / 85.07.02.0 / 1.0 / 5.0
Pork1007.0[2.86–13.89] / 84.08.01.0 / 7.0
FlavomycinPoultry1003.0[0.62–8.52] / 12.053.029.03.0 / 3.0
Beef1007.0[2.86–13.89] / 12.039.028.012.02.0 / 2.0 / 5.0
Pork1007.0[2.86–13.89] / 84.08.01.0 / 7.0
GentamicinPoultry1000.0[0.00–3.62] / 100.0
Beef1001.0[0.03–5.45] / 99.0 / 1.0
Pork1000.0[0.00–3.62] / 99.01.0
KanamycinPoultry1009.0[4.20–16.40] / 88.03.0 / 1.01.0 / 7.0
Beef1003.0[0.62–8.52] / 97.0 / 3.0
Pork1004.0[1.10–9.93] / 96.0 / 4.0
LinezolidPoultry1000.0[0.00–3.62] / 4.07.089.0
Beef1000.0[0.00–3.62] / 10.02.087.01.0
Pork1000.0[0.00–3.62] / 5.07.087.01.0
PenicillinPoultry1000.0[0.00–3.62] / 9.020.035.036.0
Beef1000.0[0.00–3.62] / 30.017.021.032.0
Pork1000.0[0.00–3.62] / 16.023.022.036.03.0
StreptomycinPoultry1005.0[1.64–11.28] / 95.0 / 1.0 / 4.0
Beef1003.0[0.62–8.52] / 97.0 / 2.0 / 1.0
Pork1005.0[1.64–11.28] / 95.0 / 2.0 / 3.0
TeicoplaninPoultry1000.0[0.00–3.62] / 99.01.0
Beef1000.0[0.00–3.62] / 100.0
Pork1000.0[0.00–3.62] / 99.01.0
TetracyclinePoultry10076.0[66.43–83.98] / 23.01.0 / 1.03.0 / 72.0
Beef10015.0[8.65–23.53] / 82.03.0 / 2.0 / 13.0
Pork10017.0[10.23–25.82] / 81.02.0 / 4.02.0 / 11.0
TigecyclinePoultry1006.0[2.23–12.60]3.05.012.034.040.0 / 6.0
Beef10010.0[4.90–17.62]2.09.022.040.017.0 / 10.0
Pork1003.0[0.62–8.52]2.04.07.022.034.028.0 / 3.0
Vancomycin1Poultry1000.0[0.00–3.62] / 4.010.060.026.0
Beef1000.0[0.00–3.62] / 3.036.040.021.0
Pork1000.0[0.00–3.62] / 1.026.045.028.0

Verticallinesindicatebreakpointsforresistance.

Thewhitefieldsdenoterangeofdilutionstestedforeachantimicrobial.ValuesabovetherangedenoteMICvaluesgreaterthanthehighestconcentrationintherange.MICsequaltoorlowerthanthelowestconcentrationtestedaregivenasthelowestconcentration.

1FivevancomycinresistantE.faecalisisolatesfromeachretailmeatsource(N=15)wererandomlychosenandtestedforthepresenceofvanAandvanBgenesusingPolymeraseChain

Amplification.All15vancomycinresistantE.faecalisisolateswerenegativeforbothvanAandvanB(BradburyandCollignon,pers.comm.).

Table 16.Multiple antimicrobial resistance phenotypes present in Enterococcus faecalisfrom retail pork.

Pattern / Resistancephenotype* / Percentage
0 / Nopattern / 78
1 / flv / 2
1 / tet / 6
1 / tgc / 2
1 / flv / 1
2 / flvtet / 1
2 / strtet / 2
2 / erytet / 3
3 / flvtettgc / 1
3 / erykantet / 1
5 / eryflvkanstrtet / 1
5 / chlerykanstrtet / 2

*Ampicillin,amp;Chloramphenicol,chl;Daptomycin,dap;Erythromycin,ery;Flavomycin,flv;Gentamicin,gen;Kanamycin,kan;Linezolid,lzd;Penicillin,pen;Streptomycin,str;Teicoplanin,tei;Tetracycline,tet;Tigecycline,tgc;Vancomycin,van.

Retail lettuce–E. coli

A total of sevenE. coliwere isolated during the 12 month sampling period. The overall prevalenceofE. coliin retail lettuce was 1.0% and ranged from during monthly sampling 0.0% to 2.5%. The sevenE. coliisolates weretested forAMR.

Antimicrobial drug resistance:The prevalence of multiple drug resistance inE. coliis presented in Figure 11. The distribution of MICs and resistance inE. coliis presented in Table 18. Resistance to one or more antimicrobials was observed in 5 of7 isolates (71%). Resistance toampicillin(57.1%) was observed most often. Resistanceto amoxicillin/clavulanic acid (28.6%), cefazolin(28.6%), streptomycin (14.3%), tetracycline (28.6%) and trimethoprim /sulfamethoxazole(14.3%) was also identified.

AMR patterns:A total of 4 AMR patterns were identified in 5 isolates (Table 17). Resistance toampicillin alone was identified in two isolates. The largest AMR patterns identified were resistancetoampicillin-streptomycin-tetracycline-trimethoprim /sulfamethoxazole(4 antimicrobials;1 isolate; 14.3%) and amoxicillin / clavulanicacid-ampicillin-cefazolin-tetracycline (4 antimicrobials; 1 isolate; 14.3%).

Lettuce-E.coli3

051015202530

Percentageofisolates

Figure 11. Multiple drug resistance inE. coli fromretail lettuce samples (n=7)

Table 17.Multiple antimicrobial resistance phenotypes present in E. colifromretail lettuce.

PatternResista / ncephenotype* / Percentage
0 / Nopattern / 29
1 / amp / 29
2 / augfaz / 14
4 / ampstrtetsxt / 14
4 / augampfaztet / 14

Table 18.Distribution of MICs and resistance inE. colifromretailpoultry, beef, pork and lettuce.

AntimicrobialProductN=% Resistant[95%CI]

Distribution(%)ofMICs

0.1250.250.51248163264128

Amoxicillin/ClavulanicacidaPoultry1001.0[0.03–5.45] / 3.016.057.022.01.0 / 1.0
Beef1003.0[0.62–8.52] / 3.020.063.09.02.0 / 2.0 / 1.0
Pork923.3[0.68–9.23] / 4.17.655.426.16.5 / 2.2 / 1.1
Lettuce714.3[0.36–57.87] / 14.342.928.6 / 14.3
AmpicillinPoultry10038.0[29.09–47.80] / 35.024.01.02.0 / 1.03.0 / 34.0
Beef10011.0[5.62–18.83] / 46.035.03.05.0 / 2.02.0 / 7.0
Pork9228.2[19.36–38.61] / 26.140.23.32.2 / 4.3 / 23.9
Lettuce757.2[18.41–90.10] / 28.614.3 / 14.3 / 42.9
CefazolinPoultry1002.0[0.24–7.04] / 96.02.0 / 2.0
Beef1003.0[0.62–8.52] / 90.07.0 / 3.0
Pork923.3[0.68–9.23] / 90.26.5 / 3.3
Lettuce728.6[3.67–70.96] / 71.4 / 28.6
CefotaximePoultry1000.0[0.00–3.62] / 100.0
Beef1000.0[0.00–3.62] / 98.02.0
Pork920.0[0.00–3.93] / 100.0
Lettuce70.0[0.00–40.96] / 71.428.6
CefoxitinPoultry1000.0[0.00–3.62] / 25.055.017.03.0
Beef1000.0[0.00–3.62] / 21.055.022.02.0
Pork920.0[0.00–3.93] / 8.757.629.34.3
Lettuce70.0[0.00–40.96] / 42.914.342.9
CeftiofurPoultry1000.0[0.00–3.62] / 99.01.0
Beef1000.0[0.00–3.62] / 98.01.01.0
Pork920.0[0.00–3.93] / 100.0
Lettuce70.0[0.00–40.96] / 100.0
CeftriaxonePoultry1000.0[0.00–3.62] / 98.02.0
Beef1000.0[0.00–3.62] / 97.01.02.0
Pork920.0[0.00–3.93] / 97.82.2
Lettuce70.0[0.00–40.96] / 100.0
ChloramphenicolPoultry1001.0[0.03–5.45] / 37.059.03.0 / 1.0
Beef1000.0[0.00–3.62] / 6.026.067.01.0
Pork9213.0[6.93–21.68] / 2.218.558.77.6 / 8.74.3
Lettuce70.0[0.00–40.96] / 28.657.114.3
CiprofloxacinPoultry1000.0[0.00–3.62]98.02.0
Beef1000.0[0.00–3.62]99.01.0
Pork920.0[0.00–3.93]97.81.11.1
Lettuce70.0[0.00–40.96]85.714.3
FlorfenicolPoultry1002.0[0.24–7.04] / 8.062.028.0 / 2.0
Beef1000.0[0.00–3.62] / 7.040.053.0
Pork928.7[3.83–16.42] / 3.341.346.7 / 8.7
Lettuce70.0[0.00–40.96] / 42.942.914.3
GentamicinPoultry1004.0[1.10–9.93] / 83.013.0 / 4.0
Beef1000.0[0.00–3.62] / 93.07.0
Pork921.1[0.03–5.91] / 87.010.91.1 / 1.1
Lettuce70.0[0.00–40.96] / 100.0
KanamycinPoultry1008.0[3.52–15.16] / 84.08.0 / 8.0

AntimicrobialProductN=% Resistant[95%CI]

Distribution(%)ofMICs

0.1250.250.51248163264128

Beef1002.0[0.24–7.04] / 94.04.0 / 2.0
Pork923.3[0.68–9.23] / 83.712.01.1 / 1.1 / 2.2
Lettuce70.0[0.00–40.96] / 85.714.3
MeropenemPoultry1000.0[0.00–3.62] / 99.01.0
Beef1000.0[0.00–3.62] / 100.0
Pork920.0[0.00–3.93] / 100.0
Lettuce70.0[0.00–40.96] / 100.0
NalidixicAcidPoultry1000.0[0.00–3.62] / 52.047.01.0
Beef1000.0[0.00–3.62] / 44.054.02.0
Pork920.0[0.00–3.93] / 29.366.34.3
Lettuce70.0[0.00–40.96] / 85.714.3
StreptomycinPoultry10019.0[11.84–28.07] / 81.0 / 4.0 / 15.0
Beef1007.0[2.86–13.89] / 93.0 / 4.0 / 3.0
Pork9217.4[10.28–26.70] / 82.6 / 8.7 / 8.7
Lettuce714.3[0.36–57.87] / 85.7 / 14.3
TetracyclinePoultry10047.0[36.94–57.24] / 53.0 / 5.08.0 / 34.0
Beef1007.0[2.86–13.89] / 91.02.0 / 7.0
Pork9244.5[34.19–55.30] / 54.31.1 / 1.14.3 / 39.1
Lettuce728.6[3.67–70.96] / 71.4 / 14.3 / 14.3
Trimethoprim/SulfamethoxazolePoultry10022.0[14.33–31.39]65.09.03.01.0 / 22.0
Beef1005.0[1.64–11.28]90.02.02.01.0 / 3.0 / 2.0
Pork9213.0[6.93–21.68]67.416.33.3 / 4.3 / 8.7
Lettuce714.3[0.36–57.87]85.7 / 14.3

Verticallinesindicatebreakpointsforresistance

aConcentrationofamoxicillingiven,testedwithclavulanicacidinconcentration2:1