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United States Department of Agriculture

Agricultural Research Service

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2007 Veterinary Isolates Final Report- Accessible Version
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1 - Introduction, Materials and Methods and Data Analysis
2 - Antimicrobials and breakpoints
3 - Isolates tested- all organisms
4 - Salmonella (Tables 1 and 2)
5 - Salmonella (Tables 3 and 4)
6 - Salmonella (Table 5)
7 - Salmonella (Table 6)
8 - Salmonella (Table 7)
9 - Salmonella (Table 8)
10 - Salmonella (Tables 9-12)
11 - Salmonella (Tables 13-16)
12 - Campylobacter (All tables)
13 - E. coli (All tables)
Introduction, Materials and Methods and Data Analysis



                                                                                                             November 2008


I. Introduction


    In an effort to prospectively monitor the occurrence of antimicrobial resistance of zoonotic pathogens from human diagnostic specimens, retail meats and food animals, the National Antimicrobial Resistance Monitoring System (NARMS) was established in 1996 by the Food and Drug Administration’s Center for Veterinary Medicine in collaboration with the Center for Disease Control and Prevention (CDC), and the United States Department of Agriculture (USDA).


    The animal component of NARMS is housed within the Bacterial Epidemiology and Antimicrobial Resistance Research Unit (BEAR) of the Agricultural Research Service (ARS) in Athens, Georgia. The animal component of NARMS comprises the testing of isolates obtained from diagnostic animal specimens, healthy on-farm animals, and food-producing animals at slaughter. The panel of antimicrobial agents chosen is representative of common antimicrobials used in both human and veterinary medicine. Non-typhoid Salmonella was chosen as a sentinel organism of the animal component of NARMS which was launched in 1997.   Testing of Campylobacter isolates began in 1998 while Escherichia coli was included in 2000. In 2004, Enterococcus data was added.


    This report summarizes 2007 data for Salmonella, Campylobacter, E.coli, and Enterococcus isolates from food-producing animals at slaughter (carcass rinsates, carcass swabs, and ground products) obtained through USDA’s Food Safety and Inspection Service (FSIS) Pathogen Reduction: Hazard Analysis and Critical Control Point (PR/HACCP) verification testing program. When suitable, resistance trends are also included; however, due to the amount of data and complexity of analyses involved, all permutations are not represented.  Additional information on the animal component of NARMS including past annual reports, summary trend tables and graphs as well as a new component for interactive data analysis can be found on the NARMS Veterinary Isolates web page.


    The 2004 NARMS Executive Report also contains additional background information on sampling and testing methodology as well as summary data from all three components of the program.



II. Sampling and Testing Methods


A. Samples


    Salmonella isolates were recovered from food animals at slaughter: carcass rinsates (chicken), carcass swabs (turkey, cattle and swine), and ground products (chicken, turkey, and beef) collected through USDA-FSIS’s Salmonella PR/HACCP verification testing program from all federally inspected plants throughout the United States. Recovery of Campylobacter, E. coli, and Enterococcus was only attempted from chicken carcass rinsates. For this report, descriptions of isolates are confined by major animal species.


B. Isolation


    Salmonella isolation from slaughter samples was conducted at all three FSIS Regulatory Field Services Laboratories (Eastern, Midwestern and Western) following the Isolation and Identification of Salmonella from Meat, Poultry, and Egg procedures as described in the Microbiology Laboratory Guidebook, section 4.1  Positive isolates were forwarded by FSIS to the National Veterinary Services Laboratories (NVSL) for serotyping and were subsequently sent to the BEAR unit as serotyping results became available.  



     From 1998 to 2000, Campylobacter was isolated by FSIS using the method described in the FSIS Microbiology Laboratory Guidebook2. For the first half of 2001, ARS tested several isolation methods until a new method was adopted in July.  Since that time, Campylobacter has been isolated by ARS from FSIS’ Eastern lab spent chicken carcass rinsates. ARS started isolating E.coli and Enterococcus from these same rinsates in 2000 and 2003, respectively. In 2003, all Enterococcus isolates obtained were tested for susceptibility. From 2004 to 2006, a subset of Enterococcus isolates were selected for susceptibility testing with a maximum of 1,500 isolates tested each year. A total of 375 isolates were selected for each yearly quarter by selecting isolates from samples which also tested positive for Salmonella, E.coli and Enterococcus.  Additionally, all odd Enterococcus species found (avium, cecorum, malodoratus, and gilvus) were tested.  Any remaining isolates to test were selected by selecting 30% E. faecalis, 30% E. faecium, 10% E. durans, 10% E. hirae, 10% E. casseliflavus, and 10% E. gallinarum.  In 2007, all Enterococcus isolates obtained were tested for susceptibility.


     Additionally, Enterococcus and Campylobacter speciation was also performed as described below.


C. Enterococcus Speciation


    A species-specific multiplex PCR was performed on presumptive Enterococcus isolates which provided a simultaneous genus and species identification of 23 species of enterococci.3 Confirmed Enterococcus isolates of other species not identified with this procedure were labeled as ‘Enterococcus species’.


D. Campylobacter Speciation



     Final confirmation and speciation were obtained using the Campylobacter BAX® PCR (DuPont Qualicon; Wilmington, DE).  This multiplex assay, specific for C. coli and C. jejuni, was performed according to manufacturer’s directions as previously described4.



E. Antimicrobial Susceptibility


     Salmonella, Campylobacter, E.coli, and Enterococcus were tested using a semi-automated system (Sensitire®, Trek Diagnostic Systems, Westlake, Ohio) to determine the minimum inhibitory concentration (MIC). Tables 1, 2 and 3 list antimicrobials tested and their breakpoints for Salmonella/E.coli, Campylobacter, and Enterococcus respectively.   Resistance trends for Campylobacter include data from 1998-2004 which was obtained using Etest® (AB Biodisk).  Antimicrobial resistance was determined using Clinical and Laboratory Standards Institute (CLSI, formerly NCCLS) standards, when available.5,6 For antimicrobial agents without CLSI approved standards, NARMS interpretive criteria as established by the NARMS working group were used.


     Quality control strains used for Salmonella and E.coli included E.coli ATCC 25922, Enterococcus faecalis ATCC 29212, and Staphylococcus aureus ATCC 29213. Campylobacter jejuni ATCC 33560 was used for Campylobacter testing while four strains were used for testing Enterococcus: Enterococcus faecalis ATCC 29212, Enterococcus faecalis ATCC 51299, E.coli ATCC 25922, and Staphylococcus aureus ATCC 29213.



F. Phage Typing 


     Salmonella Typhimurium and S. Typhimurium var. 5- isolates with resistance to at least ampicillin, chloramphenicol, sulfisoxazole and tetracycline were submitted to NVSL for phagetyping.



III. Data Analysis


     WHONET 5, a Microbiology Laboratory Database Software was used to categorize minimum inhibitory concentrations as resistant, intermediate susceptibility (when applicable), and susceptible according to CLSI established interpretive criteria (where available).  Duplicate isolates (same pathogen, sample, and species/serotype) were excluded from data analysis.  The 95% confidence interval was calculated following the Wilson interval with Continuity Correction method.  MIC distributions as well as resistance and intermediate susceptibility (when applicable) rates were tabulated by pathogen and food animal source.  For Salmonella, MIC distributions were also tabulated for the top serotypes tested for each animal source.  For Campylobacter, MIC distributions were tabulated separately for C. coli and C. jejuni.  Additionally, historical resistance rates by food animal source and organism are presented from 1997 through 2007 for Salmonella and from 2000 through 2007 for E.coli.  Resistance rates for Campylobacter are reported from 1998 through 2007 and are separated by species.   The frequency of S. typhimurium showing a resistance pattern to at least ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfisoxazole and tetracycline) or ACSuT (ampicillin, chloramphenicol, sulfisoxazole and tetracycline) as well as phage type distributions are reported separately for S. typhimurium and S. typhimurium var. 5- isolates.  The frequency and percentage of confirmed DT104 isolates is reported separately by food animal source from 1997 through 2007. Multiple antimicrobial resistance tabulations for all pathogens were limited to only those antimicrobials tested for all years (core antimicrobials).  The 14 core antimicrobials for Salmonella and E.coli were amikacin, gentamicin, kanamycin, streptomycin, ampicillin, amoxicillin/clavulanic acid, ceftiofur, ceftriaxone, sulfonamides (sulfamthoxazole/sulfisoxazole), trimethoprim/sulfamethoxazole, chloramphenicol, ciprofloxacin, nalidixic acid, and tetracycline.   The 7 core antimicrobials for Campylobacter were gentamicin, clindamycin, azithromycin, erythromycin, ciprofloxacin, nalidixic acid and tetracycline.









Mention of trade names or commercial products is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.



NARMS Veterinary Isolates Contact


Dr. Paula Fedorka-Cray

Research Leader, Bacterial Epidemiology and Antimicrobial Resistance

Research Unit

950 College Station Rd.

Athens, GA 30605




IV. References


1 USDA/FSIS. 2004. Isolation and Identification of Salmonella from Meat, Poultry, and Egg Products. Microbiological Lab Guidebook 4.03. Available at


2 USDA/FSIS.  1998.  Isolation, Identification, And Enumeration Of Campylobacter jejuni/coli From Meat And Poultry Products.  Microbiology Laboratory Guidebook, chapter 6.  Available at


3 Jackson, C. 2004. Use of a Genus- and Species-Specific Multiplex PCR for Identification of Enterococci. Journal of Clinical Microbiology, 42(8):3558-65.


4 Englen, M.D. and Paula J. Fedorka-Cray.  2002.  Evaluation of a Commercial Diagnostic PCR for the Identification of Campylobacter jejuni and Campylobacter coli.  Lett. Appl. Microbiol, 35:353-356.


5 NCCLS/CLSI. 2002. Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated from Animals.  Approved Standard, M31-A2. NCCLS, Wayne, PA.


6 CLSI. 2006. Performance Standards for Antimicrobial Susceptibility Testing; Sixteenth Informational Supplement (M100-S16). CLSI, Wayne, PA.




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Last Modified: 11/21/2008
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