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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Monitoring of Antimicrobial Resistance in Food Animal Production

Location: Bacterial Epidemiology & Antimicrobial Resistance Research

2013 Annual Report

1a. Objectives (from AD-416):
1. To elucidate and provide descriptive data, such as prevalence and/or trends, including antimicrobial susceptibilities, and molecular subtyping for foodborne pathogens in food animals through the animal sampling arm of the NARMs program. The project will (1) continue to improve the standardization and quality control of methods used; and (2) where appropriate and necessary re-evaluate and/or develop improved sampling strategies to answer priority questions for NARMS in food animal production that are consistent with the overall NARMS goals and objectives as described on the NARMS web site. 2. Be a national resource of enteric bacterial isolates and resistance data for food animals from NARMS and US-VetNet. This resource will facilitate the identification and characterization of antimicrobial resistance as it emerges. Further, it will facilitate the identification and implementation of any new research needs by the complementary research project within this Unit. It is expected that the project will be highly responsive to requests for data from FDA-CVM, USDA-FSIS, and other stakeholders.

1b. Approach (from AD-416):
Continual comparison and evaluation of existing culture methodology and quality control of methods. Where appropriate and necessary re-evaluate and/or develop improved sampling strategies to answer priority questions for NARMS in food animal production that are consistent with the overall NARMS goals and objectives as described on the NARMS web site.

3. Progress Report:
In collaboration with a scientist in the Poultry Microbiology Safety Research Unit we completed studies on the effect of different broth and agar plating media as well as the impact of pH on the recovery of Salmonella serotypes from various sample types. Additional studies with other serotypes are planned. Lab personnel passed all proficiency testing and staff were recertified for PFGE. In collaboration with four University partners, the on-farm swine pilot was completed, data were summarized and presented to the FDA; each University partner was also given their state reports. Additional characterizations of isolates are being completed. In collaboration with a scientist in the Egg Quality and Safety Research Unit, we have begun sampling layer houses utilizing different caging systems. These houses were either newly constructed or renovated and were sampled prior to placement of birds; sampling has continued at measured intervals over time. The goal is to track both the emergence of Salmonella and Campylobacter within the birds and environment and more importantly the emergence and dissemination of antimicrobial resistance. Both the NAHMS Feedlot and NAHMS swine studies were completed in FY2012; however, we have continued to speciate and conduct antimicrobial susceptibility testing on Campylobacter isolates, speciate the enterococci isolates from the Swine study, conduct PFGE on the Salmonella isolates from the Swine study, and summarize the data. Collaborations are continuing with USDA-APHIS scientists in Fort Collins, CO and Ames, IA to complete the susceptibility testing and prepare manuscripts. Antimicrobial susceptibility testing on USDA-FSIS HACCP regulatory isolates for use in the NARMS program was conducted at the request of FSIS and FDA. Staff members also trained and transferred knowledge and know-how related to antimicrobial susceptibility testing to FSIS personnel; complete data sets were also transferred to FSIS. NARMS and VetNet data were used to assist the FSIS and the Centers for Disease Control foodborne outbreaks investigations and by FSIS to use in their predictive analytics model and for their regulatory testing programs. As a result of insufficient funds we did not accept data from VetNet collaborating centers, begin PFGE of methicillin staph aureus, or use a second enzyme on Campylobacter isolates. The Unit culture collection now consists of over 125,000 well characterized isolates of Salmonella, Campylobacter, E. coli, Enterococcus, Listeria, Staphylococcus aureus, and Clostridium difficile, including control strains dating back to the early 1990’s. Isolates are maintained and used by scientists within and ARS. Isolates were furnished to collaborators by use of a material transfer agreement. These isolates are invaluable for present and future research needs to assess the emergence/development/transmission of antimicrobial resistance genes.

4. Accomplishments

Review Publications
McDermott, P., Whichard, J., Cray, P.J., Tate, H., Karp, B., Haro, J.H., Plumblee, J. 2011. Highlights of the NARMS 2009 Executive Report. Available:

Cox Jr, N.A., Cason, J.A., Buhr, R.J., Richardson, K.E., Richardson, L.J., Rigsby, L.L., Cray, P.J. 2013. Variations in preenrichment pH of poultry feed and feed ingredients after incubation periods up to 48 hours. Journal of Applied Poultry Research. 22(2):190-195.

Sohn, M., Himmelsbach, D.S., Barton , F.E., Cray, P.J. 2009. Flourescence spectroscopy for rapid detection and classification of bacterial pathogens. Applied Spectroscopy. 63(11):1251-1255.

Lombard, J.E., Beam, A.L., Nifong, E.M., Fossler, C.P., Kopral, C.A., Dargatz, D.A., Wagner, B.A., Erdman, M.M., Cray, P.J. 2012. Comparison of individual, pooled, and composite fecal sampling methods for detection of Salmonella on U.S. dairy operations. Journal of Food Protection. 75(9):1562-1571.

Folster, J.P., Pecic, G., Singh, A., Duval, B., Rickert, R., Ayers, S., Abbott, J., Mcglinchey, B., Bauer-Turpin, J., Haro, J.H., Hise, K., Zhao, S., Cray, P.J., Whichard, J., Mcdermott, P.F. 2012. Characterization of extended-spectrum cephalosporin-resistant Salmonella enterica serovar Heidelberg isolated from food animals, retail meat, and humans in the United States 2009. Foodborne Pathogens and Disease. 9(7):638-645.

Molla, B., Byrne, M., Abley, M.J., Matthews, J., Jackson, C.R., Cray, P.J., Sreevatsan, S., Wang, P., Wondwossen, G. 2012. Epidemiology and genotypic characteristics of Methicillin-Resistant Staphylococcus aureus strains of porcine origin. Journal of Clinical Microbiology. 50(11):3687-3693.

Last Modified: 10/17/2017
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