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United States Department of Agriculture

Agricultural Research Service

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NARMS -National Antimicrobial Resistance Monitoring System Animal Isolates
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Overview

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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 and Enterococcus were included in 2000.   

 

The 2009 NARMS Executive Report contains additional background information on sampling and testing methodology as well as summary data from all three components of the program.   

 

The goals and objectives of the monitoring program are to:

1.        Monitor trends in antimicrobial resistance among foodborne bacteria from humans, retail meats, and animals

2.        Disseminate timely information on antimicrobial resistance to promote interventions that reduce resistance  among foodborne bacteria

3.        Conduct research to better understand the emergence, persistence, and spread of antimicrobial resistance

4.        Assist the FDA in making decisions related to the approval of safe and effective antimicrobial drugs for animals

Information resulting from the monitoring program and follow-up outbreak investigations will be distributed to veterinarians, physicians, and food animal producer groups. Use of the information will be targeted to redirecting drug use so as to diminish the development and spread of resistance over the short term with directives involving long-term use developed in collaboration with the appropriate professional practitioner groups. Outbreak investigations and field studies will be initiated as a result of major shifts or changes in resistance patterns in either animal or human isolates.

 


Sampling and Testing Methods

A. Samples

 

Salmonella isolates from food animals at slaughter (1997-present): carcass rinsates (chicken), carcass swabs (turkey, cattle and swine), and ground products (chicken, turkey, and beef) were collected through USDA-FSIS’s Salmonella PR/HACCP verification testing program from all federally inspected plants throughout the United States.

 

Sampling methods used by FSIS for the PR/HACCP Salmonella verification testing program have changed since NARMS animal testing began. Before June of 2006, there were two phases of the FSIS regulatory program for Salmonella in raw products: non-targeted and targeted testing. Non-targeted samples were collected at establishments randomly selected from the population of eligible establishments, with a goal of scheduling every eligible establishment at least once a year. Targeted samples were collected from establishments that had a previously failed non-targeted sample set. Beginning in June of 2006,  sampling was scheduled using risk-based criteria designed to focus FSIS resources on establishments with the most samples positive for Salmonella and the greatest number of samples with serotypes most frequently associated with human salmonellosis1,2.

Recovery of Campylobacter (1998-present), E. coli (2000-present), and Enterococcus (2003-present) was through culture of chicken carcass rinsates.

 

Salmonella isolates from Sentinel Sites (1998-2006): State veterinary laboratories from various states including: California, Colorado, Florida, Iowa, Indiana, Nebraska, New York, Ohio, Oklahoma, Pennsylvania, Tennessee, Washington and Wisconsin participated in the NARMS program at various times by submitting isolates recovered from ill animals with an attempt to provide a geographic representation that complemented states submitting human isolates to CDC. 

 

Salmonella isolates from the National Veterinary Services Laboratories (1997-2005): To augment the numbers of diagnostic isolates, Salmonella isolates recovered from primary or secondary associated infections were obtained from the USDA-APHIS, National Veterinary Services Laboratories (NVSL) in Ames, IA.

 

B. Isolation

 

Salmonella isolation from slaughter samples was conducted at all three FSIS Regulatory Field Services Laboratories [Eastern (Athens, GA), Midwestern (St. Louis, MO) and Western (Alameda, CA)] following the “Isolation and Identification of Salmonella from Meat, Poultry, and Egg” as described in the Microbiology Laboratory Guidebook, section 42. 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 Guidebook (MLG)3. For the first half of 2001, ARS tested several isolation methods until a new method was adopted in July whereby Campylobacter was isolated by ARS from FSIS’ Eastern lab spent chicken carcass rinsates. Effective July 2011, FSIS implemented new Campylobacter performance standards for whole carcasses of young chickens (broilers) and began the isolation, identification and enumeration of Campylobacter as described in the FSIS MLG3. Campylobacter isolates were then given to ARS for susceptibility testing.

 

ARS started isolating E.coli and Enterococcus from these same rinsates in 2000 and 2003, respectively. Additionally, Enterococcus and Campylobacter speciation was 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 enterococci4. 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 described6.

 

E. Antimicrobial Susceptibility

 

Salmonella, Campylobacter, E.coli, and Enterococcus were tested using a semi-automated system (Sensitire®, Trek Diagnostic Systems, Inc., Cleveland, Ohio).  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 available7,8. For antimicrobial agents without CLSI approved standards, NARMS interpretive criteria as established by the NARMS working group were used. Antimicrobials tested and their breakpoints for Salmonella/E.coli, Campylobacter, and Enterococcus can be found on the following page: Antimicrobials tested: concentration ranges and breakpoints.

 

Quality control strains used for Salmonella and E. coli susceptibility testing included E. coli ATCC 25922, Enterococcus faecalis ATCC 29212, Pseudomonas aeruginosa ATCC 27853 and Staphylococcus aureus ATCC 29213. Campylobacter jejuni ATCC 33560 was used as a control for Campylobacter susceptibility testing. For Enterococcus testing, Enterococcus faecalis ATCC 29212 and ATCC 51299 were used.

 


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.


 

1 USDA/FSIS. 2008.  Serotypes Profile of Salmonella Isolates from Meat and Poultry Products.  Available at http://www.fsis.usda.gov/Science/Serotypes_Profile_Salmonella_Isolates/index.asp.  

 

2 USDA/FSIS. FSIS Scheduling Criteria for Salmonella Sets in Raw Classes of Product.  Available at http://www.fsis.usda.gov/PDF/Scheduling_Criteria_Salmonella_Sets.pdf.

3  USDA/FSIS. 2004. Isolation and Identification of Salmonella from Meat, Poultry, and Egg Products. Microbiological Lab Guidebook 4.03. Available at http://www.fsis.usda.gov/PDF/MLG_4_03.pdf

4 USDA/FSIS.  1998.  Isolation, Identification, And Enumeration Of Campylobacter jejuni/coli From Meat And Poultry Products.  Microbiology Laboratory Guidebook, chapter 6.  Available at http://www.fsis.usda.gov/ophs/Microlab/Mlgchp6.pdf

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

6 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.

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

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


Antimicrobials Tested: Concentration Ranges and Breakpoints

Breakpoints Used for Susceptibility Testing of Salmonella and E. coli1

 

 

Antimicrobial Concentration Range  (µg/ml)

Breakpoints (µg/ml)

CLSI Class2

Antimicrobial Agent

1997

1998

1999

2000

2001

2002-2003

2004-2010

2011-2012

Susceptible

Intermediate

Resistant

 

 Amikacin

4  -  32

4  -  32

4  -  32

4  -  32

4  -  32

0.5  -  4

0.5  -  64

NT

< 16

32

> 64

 Aminoglycosides

 Apramycin

2  -  16

2  -  16

2  -  32

2  -  32

2  -  32

NT

NT

NT

N/A

N/A

>32

 

 Gentamicin

0.25 -- 16

0.25 -- 16

0.25  -  16

0.25  -  16

0.25  -  16

0.25  -  16

0.25  -  16

0.25  -  16

< 4

8

> 16

 

 Kanamycin

16  -  64

16  -  64

16  -  64

16  -  64

16  -  64

8  -  64

8  -  64

8  -  64

< 16

32

> 64

 

 Streptomycin3

32  -  256

32  -  256

32  -  256

32  -  256

32  -  64

32  -  64

32  -  64

32  -  64

< 32

N/A

> 64

 β-Lactam/β-Lactamase
 Inhibitor Combinations

 Amoxicillin–          Clavulanic Acid

0.5/0.25  -  32/16

0.5/0.25  -  32/16

0.5/0.25  -  32/16

0.5/0.25  -  32/16

0.5/0.25  -  32/16

1/0.5  -  32/16

1/0.5  -  32/16

1/0.5  -  32/16

< 8 / 4

16/8

> 32 / 16

 Carbapenem

 Imipenem

NT

NT

NT

NT

0.25  -  8

NT

NT

NT

< 4

8

>16

 Carboxypenicillins

 Ticarcillin

2  -  128

2  -  128

NT

NT

NT

NT

NT

NT

< 16

32 - 64

>128

 Cephems

 Cephalothin

1 - 32

1 - 32

1 - 32

1 - 32

1 - 32

2 - 32

NT

NT

< 8

16

> 32

 

 Ceftiofur

0.5  -  16

0.5  -  16

0.5  -  16

0.5  -  16

0.5  -  16

0.12  -  8

0.12  -  8

0.12  -  8

< 2

4

> 8

 

 Cefoxitin

NT

NT

NT

4  -  32

4  -  32

0.5  -  16

0.5  -  32

0.5  -  32

≤ 8

16

> 32

 

 Ceftriaxone

0.25  -  16

0.25  -  16

0.25  -  64

0.25  -  64

0.25  -  64

0.25  -  64

0.25  -  64

0.25  -  64

1

2

4

 Folate Pathway Inhibitors

 Sulfonamides   Sulfamethoxazole: 1998-2003/Sulfizoxazole: 2004-2009

128  -  512

128  -  512

128  -  512

128  -  512

128  -  512

16  -  512

16  -  256

16  -  256

≤ 256

N/A

> 512

 

 Trimethoprim– Sulfamethoxazole

0.12/2.4 - 4/76

0.12/2.4 - 4/76

0.12/2.4 - 4/76

0.12/2.4 - 4/76

0.12/2.4 - 4/76

0.12/2.4 - 4/76

0.12/2.4 - 4/76

0.12/2.4 - 4/76

≤ 2 / 38

N/A

> 4 / 76

 Macrolide

 Azithromycin3

NT

NT

NT

NT

NT

NT

NT

0.12  -  16

N/A

N/A

N/A

 Penicillins

  Ampicillin

2  -  64

2  -  64

2  -  32

2  -  32

2  -  32

1  -  32

1  -  32

1  -  32

< 8

16

> 32

 Phenicols

 Chloramphenicol

4  -  32

4  -  32

4  -  32

4  -  32

4  -  32

2  -  32

2  -  32

2  -  32

  8

16

> 32

 Florfenicol

NT

NT

2  -  16

NT

NT

NT

NT

NT

N/A

N/A

N/A

 Quinolones

 Ciprofloxacin

0.015  -  2

0.015  -  2

0.015  -  4

0.015  -  4

0.015  -  4

0.015  -  4

0.015  -  4

0.015  -  4

≤ 0.06

0.12 -0.5

> 1

 

 Nalidixic acid

4  -  64

4  -  64

4  -  256

4  -  256

4  -  64

0.5  -  32

0.5  -  32

0.5  -  32

≤ 16

N/A

> 32

 Tetracyclines

 Tetracycline

4  -  64

4  -  64

4  -  32

4  -  32

8  - 16

4  -  32

4  -  32

4  -  32

≤ 4

8

> 16

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1Breakpoints established by CLSI (Clinical and Laboratory Standards Institute) were used when available
2According to CLSI M100 document
3There are no CLSI breakpoints for streptomycin

NT=Not tested
NA=Not applicable


Breakpoints Used for Susceptibility Testing of Campylobacter1

 

 Antimicrobial Agent

Antimicrobial Concentration Range  (µg/ml) 1998-2004

Breakpoints (µg/ml) Etest (1998-2004)

Antimicrobial Concentration Range  (µg/ml) 2005-2012

Breakpoints (µg/ml) Microbroth Dilution (2005-2011)

 

 

Susceptible

Intermediate

Resistant

Susceptible

Intermediate

Resistant

CLSI Subclass2

 Aminoglycosides

 Gentamicin

0.016 - 256

< 4

8

> 16

0.12 - 32

< 2

4

> 8

 Lincosamides

 Clindamycin

0.016 - 256

< 0.5

1 - 2

> 4

0.03 - 16

< 2

4

> 8

 Macrolides

 Azithromycin

0.016 - 256

< 0.25

0.5 - 1

> 2

0.015 - 64

< 2

4

> 8

 Erythromycin

0.016 - 256

< 0.5

1 - 4

> 8

0.03 - 64

< 8

16

> 32

 Ketolides

 Telithromycin

NT

NT

NT

NT

0.015 - 8

< 4

8

> 16

 Phenicols

 Florfenicol

NT

NT

NT

NT

0.03 - 64

< 4

N/A

N/A

 Chloramphenicol

0.016 - 256

< 8

16

> 32

NT

NT

NT

NT

 Fluoroquinolones

 Ciprofloxacin

0.002 - 32

< 1

2

> 4

0.015 - 64

< 1

2

> 4

 Quinolones

 Nalidixic acid

0.016 - 256

< 16

N/A

> 32

4 - 64

< 16

32

> 64

 Tetracyclines

 Tetracycline

0.016 - 256

< 4

8

> 16

0.06 - 64

< 4

8

> 16

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1Breakpoints established by CLSI (Clinical and Laboratory Standards Institute)were used when available. CLSI breakpoints are only available
for erythromycin, ciprofloxacin, and tetracycline
2According to CLSI M100 document

NT=Not tested
NA=Not applicable

Breakpoints Used for Susceptibility Testing of Enterococcus1

CLSI Subclass2

Antimicrobial Agent

Antimicrobial Concentration Range  (µg/ml)

Breakpoints  (µg/ml)

2003

2004-2005

2006-2008

2009-2012

Susceptible

Intermediate

Resistant

Aminoglycoside

Gentamicin

128 - 1024

128 - 1024

128 - 1024

128 - 1024

≤ 500

N/A

> 500

Kanamycin

128 - 1024

128 - 1024

128 - 1024

128 - 1024

≤ 512

N/A

> 1024

Streptomycin

512 - 2048

512 - 2048

512 - 2048

512 - 2048

≤ 1000

N/A

> 1000

Glycopeptide

Vancomycin

0.5-32

0.5 - 32

0.5 - 32

0.25 - 32

≤ 4

8 - 16

> 32

Glycylcycline

Tigecycline

NT

NT

0.015 - 0.5

0.015 - 0.5

≤ 0.25

N/A

N/A4

Ionophore coccidiostat

Salinomycin

1 - 32

NT

NT

NT

≤8

 -

≥16

Lincosamides

Lincomycin

1 - 32

1 - 32

1 - 32

1 - 8

≤ 2

4

≥ 8

Lipopeptide

Daptomycin

NT

0.5 - 16

0.5 - 16

0.25 - 16

≤ 4

N/A

N/A5

Macrolide

Erythromycin

0.5 - 8

0.5 - 8

0.5 - 8

0.25 - 8

≤ 0.5

1 - 4

≥ 8

Tylosin

0.25 - 32

0.25 - 32

0.25 - 32

0.25 - 32

≤ 8

16

≥32

Nitrofuran

Nitrofurantoin

2 - 128

2 - 128

2 - 64

2 - 64

≤ 32

64

≥128

Oxazolidinones

Linezolid

0.5 - 8

0.5 - 8

0.5  -  8

0.5 - 8

≤ 2

4

≥ 8

Penicillin

Penicillin

0.5 - 16

0.5 - 16

0.5 - 16

0.25 - 16

≤ 8

N/A

≥ 16

Phenicol

Chloramphenicol

2 - 32

2 - 32

2 - 32

2 - 32

≤ 8

16

≥ 32

Phosphoglycolipid

Flavomycin

1 - 32

1 - 32

1 - 16

NT

≤ 8

16

≥ 32

Polypeptide

Bacitracin

8 - 128

8 - 128

NT

NT

≤ 16

32

≥ 64

Quinolone

Ciprofloxacin

0.12 - 4

0.12 - 4

0.12 - 4

0.12 - 4

≤ 1

2

≥ 4

Streptogramin

Quinupristin/Dalfoprisitin

1 - 32

1 - 32

1 - 32

0.5 - 32

≤ 1

2

≥ 4

Tetracycline

Tetracycline

4 - 32

4 - 32

4 - 32

1 - 32

≤ 4

8

≥ 16

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1Breakpoints established by CLSI (Clinical and Laboratory Standards Institute)were used when available
2According to CLSI M100 document
3For the aminoglycosides, breakpoints refer to high-level aminoglycoside resistance
4For tigecycline, only a susceptible breakpoint (≤ 0.25 µg/ml) has been established
5For daptomycin, only a susceptible breakpoint (≤ 4 µg/ml) has been established

NT=Not tested
NA=Not applicable



NARMS Data

There are four different ways in which the NARMS Animal Isolate data can be viewed:

 

I. Comprehensive Annual Reports:  Beginning in 2005 Annual Reports contain summary data for all organisms tested from slaughter samples: chicken, turkey, swine and cattle.  Previous years’ data can be found under Section II. Summary Tables and Reports (below).

 

2011

2010

2009 

2008 

2007 

2006

2005

 

II. Summary Tables and Reports: Summary tables facilitate access to individual organism data summarized by major animal sources, clinical status and years. 

 

III. Interactive Data Query Page:  These are currently unavailable due to the template change of ARS websites. We are sorry for the inconvenience.

 

IV. 508 Compliant Accessible Data: To the extent possible, this section provides information available in section III which is compliant with Section 508 accessibility standards. Further expansions are being developed. 

 

 

 

 

 


Last Modified: 6/3/2014