AVIA - CIPARS Farm Surveillance Poultry (broilers, turkeys...

CIPARS Farm Surveillance Poultry (broilers, turkeys, layers)

2016 ANNUAL REPORT OVERVIEW

January 16, 2018 2:00-4:00 PM (EST)

Teleconference Information Dial: 1-877-413-4782 (Canada) ID: 987 492 4Should you have any technical difficulties please call Louise Bellai at 519-826-2348 (email: [email protected])

Before we get started…• Please MUTE your phone during the presentation please.• Avoid putting your phone on HOLD as some systems play music while

on HOLD which disrupts the meeting.• To download meeting materials go to the CAHSS website:

– https://www.cahss.ca/groups/cipars-national-meeting/– PowerPoint file (EN, FR)– Industry Reports – Broilers, Turkeys (EN, FR)

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Meeting Objectives• KTE!• AMU updates• Present poultry-specific highlights from the 2016 farm sample and data

collection year– Farm based data integrated with CIPARS Retail and Abattoir AMR data– Present antimicrobial use findings

• Present ongoing refinements to quantitative AMU metrics– Broiler chickens, turkeys and some layer flock results

• Opportunity for industry to provide context/potential explanations for trends/questions emerging from the surveillance findings

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Outline

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• Review of materials and methods• AMU metrics review• Highlights

– Broiler chickens– Turkeys– Layers (AMR only)

• Animal health – use of farm-level operational risk factor data• Summary & conclusions• Discussions

Outline: antimicrobial use• Broiler chicken

– Trends in AMU metrics• Mg/PCU• nDDDvetCA/1,000 broiler chicken-days at risk• NEW! nDDDvetCA/PCU

– Trends in coccidiostat use• Turkeys

– Review of the 2013-2015 data (British Columbia only); not reported elsewhere and full article will be submitted to a peer-reviewed journal. Trends in AMU metrics:

• Mg/PCU• nDDDvetCA/1,000 turkey-days at risk• NEW! nDDDvetCA/PCU

– 2016 data• Presenting Farm-Level data for the first time in this report from BC, Ontario and

Québec

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Outline: Antimicrobial Resistance

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• We will cover selected figures and tables from the report:– Recovery by

• Organism– Generic E. coli, Salmonella, Campylobacter

• Region– Prevalence

• Organism• Region

– Data integration – farm data combined with the abattoir and retail data• Temporal trends across the different surveillance components.• Representativeness – validity of farm sample (similar trends across components).

• Data from broiler chickens, turkeys and layers (limited layer data from FoodNet Canada sentinel sites).– Only the pre-harvest data are presented; please refer to the industry report for

the broiler chick placement results.

Review of design and methods

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• Surveillance design– No change.

• Sampling methods– No change in 2016-2017; chick placement sampling conducted in a subset

of flocks but ongoing sampling is dependent on overall PHAC funding and if required (chick placement stage will not be sampled in 2018).

– Number of turkey flocks to be adjusted in certain provinces.• Bacterial isolation and AMR testing

– No change; resistance to meropenem, a carbapenem antimicrobial is reported for the first time in the 2016 CIPARS Annual Report.

• Antimicrobial use– No change– nDDDvetCA/PCU is reported for the first time in the 2016 CIPARS annual

report and publications.– Ionophores and chemical coccidiostats are reported in a separate

subsection. Overall quantity (mg/PCU) will be reported in the Integrated Chapter.

No. of positive fecal samples

% Recovery (E. coli, Salmonella, Campylobacter)

Resistant isolates (for each antimicrobial tested and for each organism)

% Resistant (for each antimicrobial tested and %

multiclass resistant for each organism)

/ Total samples

/ Positive samples

1) RBroilerPCUx PCUBroilers

AMRIndicator

Index(AMRIx)

2) RTurkeyPCU

3) RLayerPCU

No. of flock reporting use

Inclusion rate via feed (g/tonne), water (g/liter), in ovo/subcutaneous

(mg/egg or chick/poult)

Milligrams (by antimicrobial active ingredient,

antimicrobial class and total)

/ flocks surveyed

% of flocks using specific antimicrobial

Biomass at risk of

being treated

(kg)Number of Canadian defined daily doses for animals (nDDDvetCA)

/DDDvetCA standard (mgdrug/kganimal)

/1,000 x days at risk

Mg/PCU

Total biomass at risk of

being treated (poultry

only)

nDDDvetCA/1,000 animal-days at risk

nDDDvetCA/PCU

x PCUTurkeys

x PCULayers

INTEGRATION

Minimum Inhibitory Concentration

Farm visit (1 flock/farm x 4 samples each

farm)

x total feed and water consumed (integral calculus) and total mg injected

1+2+3

Please refer to the Appendix section of the industry reports for the formulae and the 2015 CIPARS annual report for detailed methods.

1) AMUBroilerPCU

2) AMUTurkeyPCU

1+2+3

AMUIndicator

Index(AMUIx)

2) AMUlayersPCUNo data

Design and methods schematics

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AMU update1. Joint Programming Initiative on Antimicrobial Resistance (JPIAMR)

– Network on quantification of veterinary Antimicrobial usage at herd level and Analysis, CommunicaTion and benchmarkING to improve responsible usage (http://www.aacting.org/)

– Quantification, Benchmarking and Stewardship of Veterinary Antimicrobial Usage: First International Conference; 27 - 28 February 2018 Ghent

2. OIE Annual report on antimicrobial agents intended for use in animals (http://www.oie.int/fileadmin/Home/eng/Our_scientific_expertise/docs/pdf/AMR/Annual_Report_AMR_2.pdf )

– Biomass denominator!3. FDA 2016 Summary Report on Antimicrobials Sold or Distributed for use in Food-Producing Animals - no denominator…it is coming!

– (https://www.fda.gov/downloads/ForIndustry/UserFees/AnimalDrugUserFeeActADUFA/UCM588085.pdf)

– 9% of the domestic sales and distribution of medically important antimicrobials was intended for use in in turkeys and 6% intended for use in chickens

– It is estimated that 63% of domestic sales and distribution of penicillins was intended for use in turkeys

4. Codex ad hoc Intergovernmental Task Force on AMR: (http://www.fao.org/fao-who-codexalimentarius/meetings-reports/detail/en/?meeting=TFAMR&session=5)

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International comparison

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• Europe – 2015 data; Canada 2016 data• Ionophores and chemical coccidiostats

excluded.• No Own use importation/Active

pharmaceutical ingredients• Not specific to poultry

BROILER CHICKEN SECTION2013-2016

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Design & Method, farm program

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30130

4405

305

Nationally:138 flocks

15 Vets

AB Ag Lab, Edmonton AB

PHAC-NML Lab, Guelph ON

PHAC-NML Lab, St. Hyacinthe QC

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•Flocks were allocated per province, at implementation (minimum of 30 flocks in FoodNet Canada sites)

Trends in AMU metric (p21, p23, p24 EN; p25, p27, p28 FR)

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↓ overallTop 3: Bacitracins>Trimet.-sulfa>streptogramins

(blue) (purple) (aqua)

mg/PCU

↑ overallTop 3: Bacitracins>streptogramins>orthosomycins

(blue) (aqua) (pale blue)

These 2 metrics show similar trend; appear to correlate better

nDDDvetCA/PCU nDDDvetCA/1,000 CD

Antimicrobial use metrics (p19 EN, p23 FR)

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Mean (kg) Mean (days) (mg) (kg)b Total % change Total % change Total % changeBritish Columbia 2013 26 1.9 33 54,261,569 522,525 104 482 16

2014 30 1.9 33 67,501,580 650,756 104 0 379 -21 12 -222015 25 2.0 33 54,447,865 592,652 92 -11 402 6 13 92016 32 2.0 33 73,759,200 765,987 96 5 492 22 16 21

Prairies 2013 15 1.7 33 58,408,347 453,936 129 481 162014 37 1.9 34 153,398,813 910,594 168 31 447 -7 15 -62015 38 1.9 34 95,772,902 746,106 128 -24 424 -5 14 -62016 38 1.9 34 137,911,267 857,215 161 25 607 43 20 42

Ontario 2013 30 2.4 38 132,209,361 740,183 179 687 262014 42 2.2 36 172,264,675 999,661 172 -4 629 -8 22 -142015 49 2.4 38 227,842,085 1,204,851 189 10 678 8 25 132016 40 2.2 36 112,172,080 884,702 127 -33 604 -11 21 -15

Québec 2013 28 1.9 33 80,394,607 581,995 138 633 212014 34 2.0 33 109,661,081 739,406 148 7 592 -7 20 -62015 24 1.8 33 68,033,382 491,834 138 -7 468 -21 15 -222016 26 1.9 33 72,716,755 544,595 134 -3 598 28 19 27

National 2013 99 2.0 34 325,273,884 2,298,639 142 590 202014 143 2.0 34 502,826,150 3,300,417 152 8 523 -11 18 -132015 136 2.1 35 446,096,233 3,035,442 147 -4 534 2 18 52016 136 2.0 34 396,559,302 3,052,498 130 -12 576 8 19 5

nDDDvetCA/PCUmg/PCUActive ingredient Province/

Region

Preharvest weight

Age sampledYear

nDDDvetCA/1,000 broiler chicken-days at risk

Broiler weights Number of

flocks

• Regional and temporal variations in AMU quantity.• Generally decreased in mg/PCU but increased in dose-based metrics due to the shift in the

use of some antimicrobials (drugs with lower average daily dose and DDDvetCA standards, e.g., avilamycin and virginiamycin).

Trends in coccidiostats used in feed, 2013-2016 (p40 EN, p44 FR)

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Chemical coccidiostats: Nicarbazin was the most frequently used

Ionophores:Narasin-nicarbazin > Salinomycin > Monensin

Recovery rates, 2013-2016 (p55 EN, p59 FR)

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Salmonella recovery rates decreased nationally and in all provinces/regions.Campylobacter recovery decreased nationally and in most provinces/regions.

13%

5%

Salmonella serovar distribution in 2016 (p48 EN, p52 FR)

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Red fonts – implicated in human outbreaks over the last 2 years

Resistance of Salmonella from broiler chickens (p52 EN, p56 FR)

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Ceftriaxone resistance (mostly S. Kentucky, 1 S. Heidelberg and 1 S Infantis)

CRO-R ↓

CRO-R ↓ CRO-R ↓ CRO-R stable

Data integration: resistance of Salmonella to ceftriaxone from chickens and humans and farm-level antimicrobial use data

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AMU- p35 EN, p39 FR

Data integration: resistance of Salmonella to gentamicin from chickens and humans and farm-level antimicrobial use

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AMU- p35 EN, p39 FR

Resistance of Escherichia coli from broiler chickens (p54 EN, p59 FR)

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CRO-R ↓& GEN-R ↓

CRO-R ↓& GEN-R ↑

CRO-R↓ & GEN-R ↑

CRO-R↓ & GEN-R stable

Data integration: Resistance of E. coli to ceftriaxone from chickens and farm-level antimicrobial use

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AMU- p35 EN, p39 FR

Data integration: resistance of E. coli to gentamicin from chickens and farm-level antimicrobial use data

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AMU- p35 EN, p39 FR

Lincomycin-spectinomycin use co-selecting for gentamicin resistance

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Resistance of Campylobacter from broiler chickens (p54 EN, p58 FR)

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CIP-R: Stable but highest compared to other regions

CIP-R ↑CIP-R ↓

No CIP-R detected

Data integration: resistance of Campylobacter to ciprofloxacin from chickens

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• Slight decrease in CIP-R resistance from farm and abattoir chicken isolates between 2015 and 2016.

• Between 2013 to 2016: CIP-R ranged from 13% to 16%

2013 national CFIA microbiological baseline study

Other surveillance results – Canadian chickens• Ousmane et al, 2017. What affects antimicrobial resistance in

Campylobacter along the broiler chicken supply chain? Abstract book of the 19th International Workshop on Campylobacter, Helicobacter and related organisms. Sept. 10-14, 2017. Nantes, France. p184. https://www.researchgate.net/publication/320034131_19th_International_workshop_CHRO_2017_on_Campylobacter_Helicobacter_and_Related_Organisms

– 1,460 isolates tested (2013).– No marked difference in AMR was observed between the data from this study

and CIPARS.

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Summary and conclusions – broiler chickens• Antimicrobial use decreased in terms of mg/PCU but

increased in the dose-based metrics: – nDDDvetCA/1,000 broiler chicken-days at risk. – nDDDvetCA/PCU.

• Resistance to ceftriaxone decreased;– Multiple surveillance components and across

provinces/regions.– No reported use of ceftiofur.

• Resistance to gentamicin increased; – Multiple surveillance components and across

provinces/regions.– Reported use of gentamicin and lincomycin-

spectinomycin across the provinces/regions sampled.• Persistency of ciprofloxacin resistance among

Campylobacter spp.; – resistant isolates were largely from British Columbia (9/13

of the CIP-R isolates).

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TURKEYS2013-2015 (British Columbia) and 2016 (3 provinces)

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Design and Method (2013-2015)

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303



PHAC-NML Lab, St. Hyacinth QC

•Flocks were allocated per province, at implementation (minimum of 30 flocks in FoodNet Canada [FNC] sites)

Historical data (2013-2015) in turkeys compared to available data (2013-2015) chickens

• Orientation, next slide:

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BROILER CHICKENS

TURKEYS

Total flocks 78 88

Total birds 1,765,933 791,907.00

Biomass(Population Correction Unit)

1,765,933 5,147,396

Days at risk (average age at day of sampling)

35 90

a. Kilograms

c. nDDDvetCA/1,000 animal-days at risk d. nDDDvetCA/PCU

b. Milligrams/population correction unit

Review of antimicrobial use data (2013-2015) in British Columbia; broilers added as reference (published in the 2015 CIPARS report)

Stable; AMU options changed

Stable; AMU options changed

Turkey data: not in the CIPARS report - full article to be submitted 32

Review of Salmonella serovar and AMR data (2013-2015) in British Columbia

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GEN-R ↑

CRO-R ↓

CIP-R ↑

Not in the CIPARS report - full article to be submitted

Fig. 1 Salmonella serovars (combined 3 years data) Fig. 2 Salmonella

Fig. 3 E. coli Fig. 4 Campylobacter

Design and Method, 2016

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304

305





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Please note: in 2018, 30 flocks will be sampled in Québec and 10 flocks will be sampled in Alberta

Overall antimicrobials used in turkey flocks, 2016

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Total antimicrobial use quantityper kg turkey (Mg/PCU)

• These figures will appear in the integrated chapter of the 2016 CIPARS report

• Overall: 60 mg/PCU • Broiler chickens: 130 mg/PCU

Antimicrobial use metrics summary, 2016 (p15 EN, p18 FR)

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In 2016, there were approximately 558,396 turkeys from the 72 flocks included in the sampling frame. Biomass (PCU) used in various AMU metrics:558,396 X 6.5 (ESVAC average weight at treatment for turkeys) =3, 629,571.

Mean (kg) Mean (days) (mg) (kg)British Columbia 2016 30 9 88 96,093,296 1,973,663 49 88 8Ontario 2016 30 10 91 102,433,244 1,170,514 88 143 12Québec 2016 12 12 96 20,915,816 485,394 43 73 6National 2016 72 10 90 219,442,355 3,629,571 60 104 9

nDDDvetCA/1,000 turkey-days at risk

nDDDvetCA/PCUProvince/

region

Preharvest weight

Age sampled

Active ingredient

Turkey weights mg/PCUNumber of

flocksYear

Frequency of antimicrobials used by route of administration, 2016 (p16,p21,p25 EN; p20,p24,p28 FR)

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Key findings:• Gentamicin – used in 81% of flocks (58/72

flocks)• Relatively few producers reported use in

water 11% (8/72 flocks)• TOP antimicrobials used via feed:

Virginiamycin > Bacitracin > Penicillin, Tylosin

• Spectrum of antimicrobials reportedly used in turkeys was largely similar to broilers (except avilamycin)

Fig 3. Feed

Fig. 2 WaterFig. 1 Injections

Recovery rates (2015 FNC Short Report, p37 en, p40 FR)

38BC (2013-2015) data was in the 2015 FNC Short Report

Salmonella serovar distribution in 2016 (p32 EN, p35 FR)

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Resistance of Salmonella from turkeys (p34 EN, p37 FR)

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CRO-R• Overall: 3% (ON

isolates only), S. Indiana and S. Bredeney

GEN-R• Overall: 33%• BC: 22%, ON:45%, QC:

14%• Serovar-driven (e.g.,

Indiana, Bredeney in Ontario)

Resistance of E. coli from turkeys, 2016 (p35 EN, p38 FR)

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GEN-R • Overall: 20% • BC: 25%, ON: 19%

and QC: 12%

Resistance of Campylobacter from turkeys, 2016 (p37 EN, p39 FR)

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CIP-R• Overall: 22%• BC: 44%, ON:5%, QC: 0%• 37 of the 40 CIP-R isolates

originated from BC

TET-R• Overall: 43%• BC: 19%, ON: 71%, QC:

45%

Summary and conclusions-turkeys• Spectrum of drugs reportedly used in turkeys was

largely similar to broiler chickens.• Historical (2013-2015) and current AMU in turkeys

were generally lower regardless of the metrics used.• Pathogen prevalence: relatively higher Campylobacter

isolation in turkeys compared to broiler chickens.• Serovars detected in turkeys differed from broiler

chickens.• Historical (2013-2015) and current resistance to

gentamicin were observed– Gentamicin use was reportedly used (2013-2015, 2016)

• Ciprofloxacin resistance was detected historically; data in 2016 confirmed the regional distribution of resistant Campylobacter.

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LAYERSBC data (2013-2014), Ontario data (2016-2017)

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Design and Method (2013-2015)

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26(2013-2014)





15(2016-2017)

Recovery rates, layersProvince and type of samples

Year Escherichia coli Salmonella Campylobacter

British Columbia (sponge swabs)

2013 82% (19/23) 4% (1/23)Mbandaka

0/23

2014 100% (31/31) 10% (3/31) InfantisLiverpoolLivingstone

0/31

Ontario (fecal samples)

2016-2017

98% (59/60) 3% (5/60)Kentucky (1)Livingstone (4)

53% (32/60)

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There were limited samples collected but the fecal samples appear to be the most appropriate sample matrix to use for the simultaneous detection of enteric pathogens from farm.Data not included in the CIPARS/FoodNet reports (for peer-reviewed publication).No AMU data collected (minimum data: population, age sampled).

Data source: FNC/CIPARS

Resistance of E. coli from layers in British Columbia (2013-2014)

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Overall, prevalence of resistance was generally low


Resistance patterns in E. coli from layers in British Columbia (2013-2014)

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Abbreviations found in the industry report


Resistance of E. coli from layers in Ontario(2016-2017)

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Overall, moderate to high resistance prevalence was detected


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Resistance patterns in E. coli from layers in Ontario (2016-2017)


Abbreviations found in the industry report

Resistance of Campylobacter from layers in Ontario (2016-2017)

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CIP-R3 C. jejuni isolatesTET-R80% (24/32 isolates)

Summary and conclusions - layers• Fecal samples yielded better recovery rates.

– Preferred for CIPARS/FoodNet Canada monitoring.

• Low to moderate prevalence of resistance was detected in E. coli isolates– Diverse multi-drug resistant isolates.– Public health implications – unknown (food

handling?).• Low resistance to Veterinary Drugs

Directorate’s Category I antimicrobials was detected.

• Antimicrobial use (low usage?) is a knowledge gap.

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ANIMAL HEALTH

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Flock / Herd size

Region / Location

Source of Birds/

Animals

Antimicrobial Use

Disease Status

Vaccination

Biosecurity / Infection Control

Production Type

Season

Farm contextual data collected

Antimicrobial Resistance54

Further analysis with contextual data

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Broiler Mortality per 1000 chicken days at

risk

Region

Clean & Disinfect

Medium & Medium & Large sized

Flock vs small

Spring, Summer & Fall

vs Winter

Coccidiosis (Confirmed &

Likely positive)

Vaccination

Infectious Bursal Disease

Vaccination

Injectable use of

AntimicrobialsCoccidiosis: Continuous treatment

vs Vaccination

Coccidiosis:

Vaccination

Coccidiosis: Shuttle

treatment vs Vaccination

Negative Binomial Regression Model: Preliminary Results

No Significant Effect

Large MediumSmall

Flock size

Summary-AMU and AMR in poultry in Canada• AMU – appear to be decreasing in broiler chickens and turkeys but in

broiler chickens, the number of doses per kg chicken or per bird may have increased (using the dose-based metrics).– Need to look at things more than one way

• AMU in turkeys, historically and in 2016, was generally lower regardless of the metrics used.

• A change in use policy in poultry appears to be having the desired goal of reducing use of antimicrobials of very high importance– However, this may be associated with changes in use and leading to increases

in resistance to other categories of antimicrobials? – What does the future hold?

• Research projects will fill some data gaps– Broiler breeders (2018-2019 sampling); CPRC funded.– Clostridium perfringens: resistance in Gram positive bacteria to bacitracin,

virginiamycin, penicillin, tylosin, avilamycin and selected ionophores.

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ACKNOWLEDGEMENTS• We would like to thank all those who contribute to CIPARS:

» Human (AMR)• Provincial Public Health Laboratories

» Farm (AMR and AMU):• The veterinarians, producers and commodity groups who participate in the farm

program, and Alberta Agriculture, Saskatchewan Agriculture, Ontario Ministry of Agriculture, Food and Rural Affairs and Canadian Poultry Research Council

» Abattoir:• The CFIA, abattoir operators, samplers and personnel

» Retail:• All the participating health units and institutions, particularly the University of

Prince Edward Island» Clinical Animal Isolates:

• Provincial Animal Health Laboratories» Antimicrobial Use - distribution in animals:

• Canadian Animal Health Institute, Impact Vet» Antimicrobial Use - distribution in humans:

• Centre for Communicable Diseases and Infection Control» Antimicrobials Sold as Pesticides for use in Crops:

• Health Canada

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Questions?

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