AMR Complex Report Example

On-Farm AMR Report

1 September 2020

Poultry On-Farm Antimicrobial Resistance
Progress Report
Dr. Randall Singer, DVM, MPVM, PhD

Professor of Epidemiology
Department of Veterinary and Biomedical Sciences
University of Minnesota
205E Veterinary Sciences Building
1971 Commonwealth Ave., St. Paul, MN 55108
612-625-6271 (Office)
651-233-6542 (Cell)
[email protected]

Page 1 of 4

On-Farm AMR Report

1 September 2020

Introduction
Antimicrobial resistance (AMR) continues to be a pressing public health concern. The Food and
Drug Administration (FDA) began a program in cooperation with the U. S. Department of
Agriculture (USDA) to monitor the level of resistance to many of the medically-important
antimicrobial agents in bacteria such as Salmonella sp., E. coli and Campylobacter sp. that were
isolated from poultry in processing plants. The concern is that the isolates collected in the
processing plant might not reflect the diversity of resistance present on the farm and the
pressures, such as antibiotic use, that occur on the farm. Furthermore, the poultry industry is
undergoing dramatic changes with respect to antibiotic usage, in part due to FDA GFI #209,
#213 and the Veterinary Feed Directive, and in part due to consumer demand.
An important gap in our scientific understanding of AMR is whether antibiotic use, from
hatchery to slaughter, actually contributes to changes in the prevalence of antibiotic resistance.
Although the broiler industry has dramatically reduced its antibiotic use on-farm, antibiotic
resistance in some bacteria has persisted. By collecting on-farm antimicrobial use and resistance
data from the same farms, we can begin to close this information gap. Collecting on-farm data
that include antibiotic use and resistance from the same farms is a better way to assess the
relationship between the two, rather than trying to correlate national datasets.
Approach
The current goal of the On-farm Monitoring of Antimicrobial Use and Resistance in U.S. Broiler
Production study is to have a national representation of the U. S. broiler chicken industry by
enrolling companies that collectively account for at least 50% of annual production. The
proposed design is to enroll complexes within participating companies, with complexes selected
by company representatives. Each complex is then sampled quarterly, with approximately 4
(between 4 and 8, depending on complex enrollment) farms selected for sampling. One house on
each selected farm is sampled. No farm is sampled more than once per calendar year.
From each sampled house, we collect 2 composite litter samples and then culture for Salmonella,
E. coli, Campylobacter, and Enterococcus using standard methods. The samples are collected
between 21 days-of-age and slaughter; ideally, the samples are taken as closer to slaughter age as
possible.
Presumptive colonies of Salmonella, Campylobacter, and Enterococcus are confirmed by PCR.
Salmonella isolates are serotyped by an Intergenic Sequence Ribotyping (ISR) method
developed by Dr. Jean Guard at USDA:ARS. Campylobacter isolates are speciated into C. jejuni,
C. coli or Campylobacter sp. by a multiplex PCR approach. Enterococcus isolates are speciated
into E. faecium, E. faecalis or Enterococcus sp. by a multiplex PCR approach. Antibiotic
susceptibility testing is performed with the Sensititre system.

Page 2 of 4

On-Farm AMR Report

1 September 2020

Results (these are fictitious results for this mock report)
Complex Z1Z
The following table shows the sampling conducted in Complex Z1Z. Age is at time of sampling
is calculated as the number of days between Dates of Placement and Sampling.
Complex: A4H
Placement (Age)

Salmonella

Campylobacter

E. coli

Farm 1

1/30/2020 (41)

Farm 2

1/28/2020 (42)

Farm 3

2/4/2020 (32)

Farm 4

2/5/2020 (32)

+
-

+
+
+

+
+
+
+

+
+
+

+
+
+
+

+
+
+
+

Quarter 1 2020

Quarter 2 2020
Farm 1

5/12/2020 (31)

Farm 2

4/29/2020 (47)

Farm 3

4/26/2020 (52)

Farm 4

5/11/2020 (31)

Page 3 of 4

On-Farm AMR Report

1 September 2020

The specific antibiotic susceptibility patterns for the Salmonella and Campylobacter isolates are
shown in the figure below. In this heat map, green represents Susceptible, yellow represents
Intermediate and red represents Resistant for the respective antibiotic. The acronyms for the
different antibiotics are explained in the table below. For Salmonella, the serotype is provided (if
it has been completed). For Campylobacter, the species is provided.
Salmonella
Quarter
Q1
Q1
Q2
Q2
Q2
Q2
Q2
Q2

Farm
1
1
1
1
2
2
4
4

Campylobacter
Quarter
Q1
Q1
Q1
Q1
Q1
Q1
Q2
Q2
Q2
Q2
Q2
Q2
Q2
Q2

Farm
2
2
3
3
4
4
1
1
2
2
3
3
4
4

Serotype
Hadar
Hadar
Infantis
Infantis
Kentucky
Kentucky
Kentucky
Braenderup

Species
jejuni
jejuni
coli
coli
jejuni
jejuni
coli
coli
jejuni
jejuni
jejuni
jejuni
jejuni
jejuni

GEN STR AUG AXO FOX FIS

GEN CLI

SXT AZI MER AMP CHL CIP

AZI ERY MER FFN

CIP

NAL TET

NAL TET

Antibiotic acronyms used in the heat maps throughout this document.
Abbreviation
Antibiotic
Abbreviation
Antibiotic
GEN
Gentamicin
AZI
Azithromycin
STR
Streptomycin
MER
Meropenem
AUG
Amoxicillin / clav acid
AMP
Ampicillin
AXO
Ceftriaxone
CHL
Chloramphenicol
FOX
Cefoxitin
CIP
Ciprofloxacin
FIS
Sulfisoxazole
NAL
Nalidixic Acid
SXT
Trimeth / sulfamethox
TET
Tetracycline
CLI
Clindamycin
ERY
Erythromycin
FFN
Florfenicol

Page 4 of 4