United States Department of Agriculture • Animal and Plant Health Inspection Service • Safeguarding American Agriculture 

Veterinary Services 

Centers for Epidemiology and Animal Health May 2014 

_________________________________________________________________________________________________________________________ 

Enterococcus on U.S. Sheep and 

Lamb Operations 

Background 

 

Enterococcus is a normal bacterial (commensal) 

inhabitant of human and animal gastrointestinal tracts. 

Disease caused by Enterococcus in food-producing 

animals is uncommon, but Enterococcus is occasionally 

associated with mastitis in dairy animals. 

In hospital settings, enterococci are a common 

cause of infections in humans, especially after surgery. 

Two species of enterococci, E. faecalis and E. faecium, 

are responsible for most human disease caused by 

enterococci. Combined, these two species are 

responsible for 12 percent of all hospital-acquired 

infections in the United States and constitute a 

significant public health risk (Hancock and Gilmore, 

2006). 

Enterococcus species have natural resistance 

mechanisms to several classes of antimicrobials. In 

addition, Enterococcus readily acquires resistance to 

antimicrobials through mutations or acquisition of 

resistance genes (Hammerum et al., 2010). In both the 

United States and Europe, research indicates that the 

patterns of antimicrobial resistance in Enterococcus 

isolates from animals and humans differ (Mannu et al., 

2003). This finding suggests that production animals are 

an uncommon source for human infections. However, 

there are concerns that resistance components of 

enterococci in animals could be transferred to other 

bacteria, including those that cause human illness. The 

purpose of this information sheet is to describe the 

species distribution and antimicrobial susceptibility of 

Enterococcus in U.S. sheep and lambs. 

Enterococcus on U.S. sheep and lamb 

operations

For the Sheep 2011 study, the U.S. Department of 

Agriculture’s National Animal Health Monitoring System 

(NAHMS) collected data on sheep health and 

management practices from a representative sample of 

operations in 22 of the Nation’s major sheep-producing 

States.* 

 

* California, Colorado, Idaho, Iowa, Kansas, Kentucky, Michigan, 

Minnesota, Missouri, Montana, New Mexico, New York, Ohio, Oregon, 

Pennsylvania, South Dakota, Texas, Utah, Virginia, Washington and 

Wyoming. 

Collectively, these operations represented 85.5 percent 

of the ewe inventory and 70.1 percent of U.S. farms with 

ewes. 

During the Sheep 2011 study, 247 operations 

provided composite fecal samples for Enterococcus

testing. Composite samples consisted of two pellets from 

each of up to six animals up to 2 years of age. These 

samples were combined to make up a single sample. Up 

to five composite samples were collected on each 

operation. A total of 1,133 composite samples were 

collected from March 14 to June 30, 2011. Of the 

composite samples tested, 1,108 (97.8 percent) were 

positive for Enterococcus. 

In addition to composite samples, 95 of the 247 

operations provided fecal samples from individual 

animals up to 2 years of age. Individual-animal samples 

consisted of up to four fecal pellets collected directly 

from the rectum of each animal tested. Up to 15 fecal 

samples from individual animals were submitted per 

operation. Of the 688 individual samples collected, 646 

(93.9 percent) were positive for Enterococcus. 

Species identification was performed on 1,746 

Enterococcus isolates. One species was identified per 

sample. Eight isolates were not typed because of 

difficulty in regrowing isolates after initial testing. The 

most common species isolated was E. hirae, which 

accounted for over 60 percent of the positive composite 

and individual samples (table 1). In total, nine different 

species of Enterococcus were identified. An additional 

11 isolates contained Enterococcus species not 

otherwise specified because the PCR methodology used 

was unable to identify other species. E. faecium and 

E. faecalis together made up 9.1 percent of the isolates 

and were found on 35.2 percent of operations. 
United States Department of Agriculture • Animal and Plant Health Inspection Service • Safeguarding American Agriculture 

Table 1. Percentage of Enterococcus species

identified in positive samples, by sample type 

 Percent 

 Sample Type 

Species 

Composite 

(n=1,100)

Individual 

(n=646)

Any 

(n=1,746)

E. hirae 69.2 60.4 65.9 

E. mundtii 9.3 15.2 11.5 

E. casseliflavus 6.5 10.2 7.9 

E. faecalis 6.1 4.5 5.5 

E. faecium 3.2 4.3 3.6 

E. gallinarum 3.5 3.2 3.4 

E. durans 1.0 0.9 1.0 

Ent. spp. 0.7 0.5 0.6 

E. avium 0.4 0.3 0.4 

E. porcinus 0.1 0.5 0.2 

Total 100.0 100.0 100.0 

All 247 operations had at least one composite 

sample test positive for Enterococcus, and all 95 

operations from which individual samples were collected 

had at least one individual-animal sample test positive 

for Enterococcus. At least one E. hirae isolate was found 

on slightly over 95 percent of operations (table 2). 

Table 2. Percentage of operations by Enterococcus 

species identified and by sample type 

 Percent 

 Sample type 

Species 

Composite 

(n=247)

Individual 

(n=95)

Any 

(n=247)

E. hirae 95.1 93.7 95.5 

E. mundtii 27.9 58.9 41.7 

E. casseliflavus 22.3 38.9 32.0 

E. faecalis 19.8 23.2 24.3 

E. faecium 11.3 20.0 15.7 

E. gallinarum 12.6 16.8 16.6 

E. durans 4.0 6.3 6.5 

Ent. spp. 3.2 3.2 4.5 

E. avium 2.0 2.1 2.4 

E. porcinus 0.4 3.2 1.6 

Any enterococci 100.0 100.0 100.0 

Isolates showed somewhat high levels of resistance 

to tetracycline: depending on the species of 

Enterococcus, 30.2 to 47.6 percent of isolates were 

resistant to tetracycline. Ciprofloxacin resistance was 

present in over one-third of E. faecium isolates 

(36.5 percent). Vancomycin resistance is of particular 

interest because it is commonly used to treat humans 

with enterococcal infections. None of the isolates 

demonstrated resistance to vancomycin. Resistance to 

quinupristin/dalfopristin (Synercid®) is also important 

because it used to treat humans infected with 

vancomycin-resistant E. faecium. The percentages of 

Synercid-resistant isolates in E. faecium and other 

enterococci were 14.3 and 4.5 percent, respectively. 

Most operations (85.4 percent) had at least one 

tetracycline-resistant isolate, and all operations had at 

least one lincomycin-resistant isolate. 

Table 3. Percentage of resistant Enterococcus

isolates and percentage of operations with at least 

one resistant isolate, by antimicrobial and by 

species 

Antimicrobial 

E. 

faecalis

(n=96)

E. 

faecium

(n=63)

Other 

enterococci 

(n=1585)3

Operation

level 

enterococci 

(n=247)4

Chloramphenicol 1.0 1.6 0.2 1.6 

Ciprofloxacin 0.0 36.5 0.9 13.0 

Daptomycin 3.1 1.6 28.1 68.4 

Erythromycin 7.3 7.9 1.0 7.7 

Gentamicin 1.0 0.0 0.1 1.2 

Kanamycin 6.3 3.2 0.8 3.6 

Lincomycin1 99.0 55.6 89.1 100.0 

Linezolid 0.0 0.0 0.0 0.0 

Nitrofurantoin 0.0 27.0 0.6 9.3 

Penicillin 0.0 1.6 0.1 1.2 

Quinupristin/ 

Dalfopristin 93.82

 14.3 4.5 36.0 

Streptomycin 7.3 3.2 1.1 6.1 

Tetracycline 30.2 47.6 46.6 85.4 

Tigecycline 1.0 0.0 0.4 2.4 

Tylosin 7.3 1.6 1.3 6.9 

Vancomycin 0.0 0.0 0.0 0.0 

1 Enterococcus exhibits natural resistance to lincosamides such as 

lincomycin, so a high level of resistance is expected. 2 E. faecalis exhibits natural resistance to quinupristin/dalfopristin (Synercid), 

so a high level of resistance is expected. 

3

Two “Other enterococci” isolates were not viable at the time of susceptibility 

testing. Thus, the total of isolates in table 3 (1,744) is not the same as the 

number of isolates in table 1 (1746). 

4 Percentage of flocks in which at least one Enterococcus isolate was 

resistant (of any Enterococcus species).
United States Department of Agriculture • Animal and Plant Health Inspection Service • Safeguarding American Agriculture 

Conclusions 

 

Nearly all sheep in this study were carrying 

Enterococcus, which was expected since it is a normal 

inhabitant of the intestinal tract of mammals. E. hirae

was found in over 60 percent of all samples and was the 

most commonly identified Enterococcus species. The 

species typically associated with human infections— 

E. faecalis and E. faecium—were relatively uncommon 

and were found in less than 10 percent of all samples. 

No evidence was found of vancomycin resistance in 

samples tested. This finding suggests that U.S. sheep 

are not a significant source of vancomycin-resistant 

enterococci, which are of concern to human health. 

References

Hammerum AM, Lester CH, Heuer OE. 2010. 

Antimicrobial-resistant enterococi in animals and meat: a 

human health hazard? Foodborne Pathogen Disease

7(10):1137–1146. 

Hancock LE, Gilmore MS. 2006. Pathogenicity of 

Enterococci. In Fischetti RPMNVA, Ferretti JJ, Portnoy 

DA, Rood JI, eds., Gram-positive pathogens. ASM 

Press, Washington, DC, p 299–311. 

Mannu L, et al., 2003. Comparison of the incidence of 

virulence determinants and antibiotic resistance between 

Enterococcus faecium strains of dairy, animal and 

clinical origin. International Journal of Food Microbiology

88(2–3):291–304. 

____________________ 

For more information, contact: 

USDA–APHIS–VS–CEAH–NAHMS 

NRRC Building B, M.S. 2E7 

2150 Centre Avenue 

Fort Collins, CO 80526-8117 

970.494.7000 

http://www.aphis.usda.gov/nahms

#690.0514 

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