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Looking for Foodborne Germs and Their Resistance to Antibiotics: Poultry

Updated August 21, 2019
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Russ Daly

Professor, SDSU Extension Veterinarian, State Public Health Veterinarian

Written collaboratively by Russ Daly, Alan Erickson, Laura Ruesch, Zachary Lau, and Deb Murray.

Are foodborne disease-causing germs becoming more resistant to antibiotics? Finding the answer to that question is the mission of the National Antimicrobial Resistance Monitoring System (NARMS). Since 1996, this multi-agency program has examined certain food-associated germs that can cause intestinal illness in people. Germ isolates from sick people (monitored by the Centers for Disease Control and Prevention), animals (monitored by the US Department of Agriculture), and retail meat products (monitored by the Food and Drug Administration) are part of the annual surveillance program.

South Dakota State University is in its third year of participation in NARMS, with their Food Safety Microbiology (SD-FSM) lab (part of the Animal Disease Research and Diagnostic Laboratory in Brookings) working with the FDA in the retail meat portion of the program. The SD-FSM tests these meat products, purchased in grocery stores in North and South Dakota, for the presence of these germs. The germs identified are then further tested for resistance to common antibiotics that might be used in treating human illness.

The NARMS program looks for 4 different germs. Two of these (Salmonella and Campylobacter) are significant causes of foodborne illness in the US, while the other 2 (generic E. coli and Enterococcus, both found more routinely in meat products) are examined as indicator organisms for antibiotic resistance.

The SD-FSM has recently compiled NARMS results for the period from June 2018 through May 2019. This report analyzes the results for the poultry products. Results from ground beef and pork products will be provided in separate reports.

A. Fresh Chicken

Prevalence of bacteria in chicken from North and South Dakota grocery stores

Overall, investigators identified Salmonella in 4.4% (21/480) of the fresh chicken samples, and Campylobacter in 3.0% (6/201 – Table 1). Salmonella was found more frequently in South Dakota samples (6.0%) than in those from North Dakota (2.8%), while Campylobacter was found more frequently in samples from North Dakota (4.7% vs. 1.7%). Levels of E. coli and Enterococcus were higher in North Dakota samples. Overall between the 2 states, higher rates of Salmonella and lower rates of the other 3 bacteria were observed, compared with the previous year.

Since national statistics for the same time period aren’t yet available, it’s not possible to directly compare data from the Dakotas with national data. However, information from 2015 – the most recent year available – showed that 2018-19 levels in the Dakotas were lower than the 2015 national averages for all 4 bacteria studied (Table 1).

Table 1. Prevalence of bacteria in chicken from North and South Dakota grocery stores, June 2018-May 2019.
 
North Dakota
South Dakota
Dakotas Total
 
Bacteria
No. Tested
Pos.
%
No. Tested
Pos.
%
No. Tested
Pos.
%
2017-18 rate
2015 National % Pos.
Salmonella
248
7
2.8%
232
14
6.0%
480
21
4.4%
0.8%
6.2%
Campylobacter
85
4
4.7%
116
2
1.7%
201
6
3.0%
8.3%
24.0%
E. coli
31
6
19.4%
29
3
10.3%
60
9
15.0%
21.7%
63.4%
Enterococcus
31
5
16.1%
29
3
10.3%
60
8
13.3%
23.3%
74.6%

Antimicrobial resistance in bacteria from chicken from stores in North and South Dakota

Isolates (individual growths) of the 4 germ species were submitted to the FDA for antimicrobial resistance testing. Data isn’t available yet for the June 2018-May 2019 time period; however, the resistance of germs found from February 2017 through December 2017, is summarized below (Table 2).

The FDA analyzes the action of 14 different relevant antimicrobial drugs on Salmonella isolates, and 9 drugs on Campylobacter isolates. A germ is classified as “Multi-Drug Resistant” (MDR) if it is resistant to 3 or more different classes of antimicrobials. During this time period, only 4 samples tested positive for Salmonella, all from chicken, with 1 classified as MDR. During the same period, 19 Campylobacter isolates were obtained from fresh chicken, only 1 of which was MDR.

For the indicator organisms E. coli and Enterococcus, the action of 14 and 16 antibiotics respectively, is measured. During the February-December 2017 time period, 25 E. coli isolates were obtained from chicken, with 9 of them being MDR. Antibiotic resistance of these E. coli isolates was most commonly toward the drugs streptomycin, tetracycline, and sulfasoxazole (36% each). Fifteen Enterococcus isolates were obtained from chicken during the same time period, with 7 of them MDR isolates. Antibiotic resistance of these gram-positive isolates was most commonly toward lincomycin (80% of isolates), and tetracyclines (53%).

Whole genome sequencing (WGS) methods employed at FDA during this project enables the detection of certain antibiotic resistance genes in bacterial isolates. All Salmonella and Campylobacter, and half the E. coli isolates are analyzed. All 4 Salmonella isolates contained resistance genes; the number of resistance genes detected correlated well with the laboratory-demonstrated resistance patterns. Eleven of 19 Campylobacter isolates contained resistance genes. These detections were somewhat less well-correlated with laboratory resistance patterns. Eight of 13 E. coli isolates contained antibiotic resistance genes.

Table 2. Antibiotic resistance in bacterial isolates from chicken from North and South Dakota grocery stores, February-December.
   
# of antibiotics that isolates were resistant to
 
Bacteria
Total
0
1
2
3
4
5
6
7
8
# of MDR
isolates
Salmonella
4
-
-
3
-
-
1
-
-
-
1/4
Campylobacter
19
12
4
2
-
1
-
-
-
-
1/19
E. coli
25
9
4
3
3
5
-
-
-
1
9/25
Enterococcus
15
-
2
6
1
2
-
2
2
-
7/15

B. Ground Turkey

Prevalence of bacteria in ground turkey from North and South Dakota grocery stores

Salmonella rates in ground turkey were similar to those in chicken samples, with an overall prevalence of 5.0% (12/240 – Table 3). No Campylobacter was found in ground turkey during this period. Levels of the indicator bacteria E. coli and Enterococcus in ground turkey were much higher than those found in chicken, with an overall incidence of 83.3% and 72.9%, respectively.

In comparing this data from the Dakotas with 2015 national statistics, Salmonella recovery from ground turkey was similar (5.0% vs. 6.1%), while Campylobacter levels were very low in the Dakotas and nationally.

E. coli levels in ground turkey were slightly higher in the Dakotas than nationally, while Enterococcus levels were lower. Once again, it is not possible to make direct comparisons since current national data is not yet available.

Table 3. Prevalence of bacteria in ground turkey from North and South Dakota grocery stores, June 2018-May 2019.
 
North Dakota
South Dakota
Dakotas Total
 
Bacteria
No. Tested
Pos.
%
No. Tested
Pos.
%
No. Tested
Pos.
%
2017-18 rate
2015 National % Pos.
Salmonella
124
9
7.3%
116
3
1.4%
240
12
5.0%
1.7%
6.1%
Campylobacter
124
0
0
116
0
0
240
0
0
0.4%
0.2%
E. coli
24
21
87.5%
24
18
79.2%
48
40
83.3%
81.3%
76.7%
Enterococcus
24
18
75.0%
24
17
70.8%
48
35
72.9%
72.9%
89.0%

Antimicrobial resistance in bacteria from ground turkey from stores in North and South Dakota

During the February – December 2017 time period, none of the ground turkey samples tested positive for Salmonella, and only 1 for Campylobacter (Table 4). 

The Campylobacter isolate showed resistance against 2 of the 9 antibiotics against which it was tested. During this period, 50 E. coli isolates were obtained from ground turkey, with 22 of them being MDR. Antibiotic resistance of these E. coli isolates were most commonly toward tetracycline (66% of isolates resistant) and ampicillin (52%). Forty-two Enterococcus isolates were obtained from ground turkey during the same time period, with all but 4 of them MDR isolates. Antibiotic resistance for Enterococcus isolates was most commonly noted against lincomycin (95%) and tetracycline (79%).

Table 4. Antibiotic resistance in bacteria from ground turkey, North and South Dakota grocery stores, Feb. 2017 – December 2017.
   
# of antibiotics that isolates were resistant to
 
Bacteria
Total
0
1
2
3
4
5
6
7
8
# of MDR isolates
Salmonella
0
-
-
-
-
-
-
-
-
-
-
Campylobacter
1
-
-
1
-
-
-
-
-
-
0/1
E. coli
50
14
7
7
6
7
8
1
-
-
22/50
Enterococcus
42
-
-
4
12
4
13
2
5
2
38/42

Summary

South Dakota State University continues its important involvement with NARMS. This year’s work adds to the information about the prevalence of potentially illness-causing germs in poultry and other meat products in North and South Dakota. This year’s data indicates that the presence of Salmonella and Campylobacter in chicken and ground turkey continues to be relatively uncommon in the Dakotas. Comparing this data with contemporary national data (once it’s available) will provide even better information regarding food safety in the Dakotas.

The project is also measuring levels of antibiotic resistance in those germs and certain indicator germs. As changes occur in poultry production, monitoring germ resistance to antibiotics will become important to determine the effect, if any, of shifts and declines in antibiotic use in poultry production.