Attachment D_ResNARMS final.pdf

Attachment D

ResNARMS Final Report Temporal Co-occurrence of Antimicrobial Class Residue in tissue and

Antimicrobial Sensitivity Profile from Cecal Content Strains

Office of Public Health Science, Food Safety and Inspection Service United States Department of Agriculture

June 18, 2019

Objective: To determine temporal co-occurrence of the antimicrobial resistance profile from isolates obtained from cecal content and antimicrobial residue findings from paired kidney tissue samples obtained from dairy cows and young chicken tested as part of the National Residue Program.1

Background: ResNARMS was conducted to determine potential links, if any, between the antimicrobial resistance profiles of bacterial strains isolated from cecal content and drug residues present in the tissue samples collected from the same1,2. This pilot project was unique as it combined sampling from two independent FSIS surveillance programs3. The ResNARMS pilot project was implemented from June 1, 2017 to May 31, 2018 and supported the National Action Plan for Combating Antibiotic Resistant Bacteria (CARB) and the USDA Antimicrobial Resistance (AMR) Action Plan.

Methodology – Sampling, Laboratory and Data Analysis: Samples were collected by FSIS in-plant veterinarians following the guidance provided in FSIS Notice 23-171. Residues in animal kidney tissue samples were analyzed at FSIS laboratories using the FSIS methods routinely used in the National Residue Program (NRP) and described in FSIS Chemistry Laboratory Guidebook4. The target bacteria (Salmonella sp., Campylobacter sp., Enterococcus sp., and generic E. coli), were recovered and subjected to antimicrobial sensitivity testing as described in The National Antimicrobial Resistance Monitoring System Manual of Laboratory Methods5. Data from this study were curated to keep only complete matched pairs where we had both cecal content and kidney tissue results. Data was analyzed using R™ software package (R Development Core Team, 20196).

Results: Of the 2,477 samples collected from 282 establishments, 1,570 (63.4%) were from dairy cows and 907 (36.6%) were from young chickens. Target bacteria were isolated from cecal content at the following rate:

1 FSIS Notice 23-17(4/27/17) - FSIS Pilot for Residue Sampling to Complement the National Antimicrobial Resistance

Monitoring System Program, (https://www.fsis.usda.gov/wps/wcm/connect/5d7b7925-5284-496a-a017-c7b5d1e32935/23- 17.pdf?MOD=AJPERES&CONVERT_TO=url&CACHEID=5d7b7925-5284-496a-a017-c7b5d1e32935)

2 FSIS Directive 10,100.1 - FSIS Sampling for the National Antimicrobial Resistance Monitoring System (NARMS), (https://www.fsis.usda.gov/wps/wcm/connect/056b7ec7-5456-4325-ae55-1a73ddd6f348/10100.1.pdf?MOD=AJPERES)

3 NARMS and NRP: The U.S. National Residue Program (NRP) for Meat, Poultry, and Egg Products, administered by the U.S.

Department of Agriculture’s (USDA), Food Safety and Inspection Service (FSIS), is an interagency program designed to identify, rank, and analyze for chemical contaminants in meat, poultry, and egg products. The NARMS surveillance program has two sampling Sources from federally inspected slaughter and processing plants throughout the US; These include Pathogen Reduction/Hazard Analysis and Critical Control Point (PR/HACCP) Program (1997-Present) and Cecal Sampling Program (2013-Present).

4 Chemistry Laboratory Guidebook. https://www.fsis.usda.gov/wps/portal/fsis/topics/science/laboratories-and-procedures/guidebooks-and-methods/chemistry-laboratory-guidebook 5 https://www.fda.gov/media/101423/download 6 R Core Team (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

Attachment D

Salmonella, sp. 629 (27%) of which 71% were from dairy cows and 29% from young chicken;

Generic E. coli 845 (90.2%) of which 95% were from dairy cows and 5% from young chicken;

Enterococcus, sp. 908 (97%) of which 79% were from dairy cows and 21% from young chicken; and

Campylobacter, sp. 925 (40%) of which 62% were from dairy cows and 38% from young chicken.

Pan-susceptibility was identified in 388 (62%) of Salmonella, sp. isolates, 500 (61%) generic E. coli isolates, 322 (39%) Campylobacter, sp. isolates, and 50 (8%) Enterococcus, sp. isolates.

Only four matched pairs had both the presence of drug residues in the tissue and an antimicrobial resistance strain concurrently present in the same carcass. Of those, only one sample (#4, below in Table 1) showed a concurrent presence of a resistance profile for Sulfonamides (generic E. coli) and similar drug class residue (Sulfadimethoxine)7

Table 1: Description of AMR profiles vs residue (all from dairy cows).

Residue Pathogen (result)

AMR Profile Residue Concentration (ppb)

1 Desfuroylceftiofur Enterococcus

Lincomycin

140.92

2 Dihydrostreptomycin Enterococcus Lincomycin, Synercid

143.47

3 Gentamycin Sulfate Campylobacter Tetracycline 5.01 E. Coli Tetracycline 5.01

4 Sulfadimethoxine E. coli Sulfonamides, Tetracycline

44.56

Conclusion: Veterinary drug residue findings are highly uncommon observations, as documented by detecting only four (0.16%) residue positive samples from 2,477 samples tested. Antimicrobial resistant strains are also relatively uncommon in Salmonella, sp., and generic E. coli, as we identified 233(9.4%), 322(13%), 503 (20.3%), 581 (23.5%), and resistant strains to Salmonella, sp., generic E. coli, Campylobacter, sp., and Enterococcus, sp., respectively. Given the rarity of the positive findings, determining an association between drug residue presence and matching antimicrobial resistance would require a very large sample size. The testing of 2,477 paired samples, yielded only one outcome where the antimicrobial drug class (sulfa) was present in the tissue and as a resistance characteristic of a bacterial strain isolated from the cecal content from the same carcass. Subsequent studies could focus on examining samples taken from carcasses separated for veterinary exam and disposition due to pathological conditions identified during slaughter.

7 Note: This establishment has no other drug residue except the only one sample with Sulfadiethoxine.