Veterinary Services 

Centers for Epidemiology and Animal Health April 2009 

_________________________________________________________________________________________________________________________ 

Commensal Enterococcus

on U.S. Swine Sites: 

Prevalence and Antimicrobial 

Drug Susceptibility 

Background

Enterococci are normal inhabitants of human and 

animal gastrointestinal tracts. These organisms 

have been known to cause human illnesses, such 

as meningitis, septicemia, endocarditis, arthritis, 

and pneumonia.1 2 3 Two species of Enterococcus,

E. faecalis and E. faecium, have been associated 

with foodborne illness in humans worldwide,4

although Enterococcus has not been identified as a 

major cause of foodborne illness in the United 

States. 

Food animals such as pigs can be reservoirs 

for E. faecium organisms, some of which may be 

resistant to antimicrobials. In addition, there is 

potential for resistance components of 

enterococci to be transferred to other bacteria, 

including those that cause human illness. In the 

United States, the emergence of Enterococcus

with resistance to gentamicin, penicillin, synercid, 

and vancomycin in humans has been a concern.5 

Enterococcus on U.S. swine sites 

In 2006, USDA’s National Animal Health 

Monitoring System (NAHMS) conducted a study on 

swine health and management practices from a 

random sample of swine production sites in 

17 States*. These States represented about 

94 percent of the U.S. pig inventory and 94 percent 

of U.S. pork producers with 100 or more pigs. 

Overall, 2,230 swine production sites participated in 

the first interview from July 1 to August 15, 2006. 

As part of Swine 2006, fecal samples were 

collected from pen floors on 135 sites. On each 

site, up to 15 fecal samples were collected from 

 

* Arkansas, Colorado, Iowa, Illinois, Indiana, Kansas, Michigan, 

Minnesota, Missouri, Nebraska, North Carolina, Oklahoma, Ohio, 

Pennsylvania, South Dakota, Texas, and Wisconsin.

pens containing grower/finisher pigs and cultured 

for Enterococcus. From September 5, 2006, 

through March 15, 2007, 1,362 samples were 

cultured for Enterococcus. 

Overall, at least one sample was found culturepositive for Enterococcus on 99.3 percent of sites, 

96.1 percent of barns, and 71.4 percent of pens.

Additionally, 69.0 percent of samples were culture 

positive. Between two and four different 

Enterococcus species were isolated on 

76.1 percent of sites. Some sites (12.7 percent) 

had as many as five or six different species 

isolated. Among the 940 isolates, there were 11 

different Enterococcus species; E. faecalis and E. 

faecium accounted for 35.3 percent of isolates. In 

addition, 71.1 and 33.3 percent of sites were 

positive for E. faecalis and E. faecium, respectively 

(table 1). 

Table 1. Percentage of Enterococcus Isolates and 

Percentage of Sites Positive for Enterococcus, by 

Species

Species

Percent 

Isolates 

Percent 

Sites 

E. hirae 29.6 71.1 

E. faecalis 27.4 71.1 

E.spp* 16.0 49.6 

E. faecium 7.9 33.3 

E. mundtii 7.7 16.3 

E. casseliflavus 3.0 15.6 

E. gallinarum 2.5 14.8 

E. avium 2.0 12.6 

E. durans 1.6 8.1 

E. solitarius 1.4 8.9 

E. saccharolyticus 0.8 5.9 

E. pseudoavium 0.1 0.7 

Total 100.0 NA 

*Species not identified.
Antimicrobial susceptibility 

All the available isolates were tested for 

resistance to a panel of 17 antimicrobial drugs.** 

Resistance break points used by the National 

Antimicrobial Resistance Monitoring System were 

used to classify isolates as susceptible, 

intermediate, or resistant. Of the 940 original 

isolates, 83 could not be re-grown from stocks and 

were not tested for susceptibility. Of the remaining 

857 isolates, resistance to lincomycin was most 

common (96.0 percent of isolates), followed by 

resistance to tetracycline (81.9 percent) and 

flavomycin (57.1 percent) [table 2]. 

No Enterococcus isolates were resistant to 

vancomycin or linezolid. Only 2.5 percent of 

isolates were resistant to gentamicin, and all of 

those isolates were E. faecalis. 

Table 2. Number and Percentage of Antimicrobial 

Resistance1

 Among Enterococcus Isolates 

Antimicrobial 

Number 

Resistant 

(n=857) Percent 

Lincomycin 823 96.0 

Tetracycline 702 81.9 

Flavomycin 489 57.1 

Tylosin 451 52.6 

Erythromycin 447 52.2 

Synercid2 ---- ---- 

Streptomycin 194 22.6 

Kanamycin 139 16.2 

Nitrofurantoin 71 8.3 

Penicillin 53 6.2 

Chloramphenicol 33 3.9 

Ciprofloxacin 26 3.0 

Tigecycline3 ---- ---- 

Gentamicin 21 2.5 

Daptomycin3 ---- ---- 

Linezolid 0 0.0 

Vancomycin 0 0.0 

1

Intermediate isolates were classified as not resistant. 2

E. faecalis is intrinsically (naturally) resistant to synercid. Among the 

 other 602 isolates, 162 (26.9%) were resistant. 

3

No resistance break points have been established for tigecycline 

 and daptomycin. There were 835 and 850 isolates at or below the 

 break point for susceptibility for tigecycline and daptomycin, 

respectively. 

Table 3 shows the percentage of isolates by the 

number of antimicrobials they were resistant to for 

E. faecium, E. faecalis, and all other Enterococcus

species. E. faecalis isolates were resistant to a 

 

** Chloramphenicol, ciprofloxacin, daptomycin, erythromycin, 

flavomycin, gentamicin, kanamycin, lincomycin, linezolid, 

nitrofurantoin, penicillin, streptomycin, synercid, tetracycline, 

tigecycline, tylosin, and vancomycin.

higher number of antimicrobials than E. faecium. 

For example, 35.2 percent of E. faecalis isolates 

were resistant to five or more antimicrobials, 

compared with only 25.7 percent of E. faecium 

isolates. 

 

Table 3. Number of Antimicrobials by Number and 

Percentage of Enterococcus Isolates Showing 

Resistance*

Percent 

Number 

Antimicrobials*

E. 

faecium

Isolates 

(n=74) 

E. faecalis

Isolates 

(n=255)

All Other 

Enterococcus 

spp. 

Isolates 

(n=528)

0 0.0 0.0 0.4 

1 8.1 7.1 3.6 

2 14.9 16.5 25.4 

3 35.1 5.9 19.5 

4 16.2 35.3 6.8 

5 2.7 12.6 8.3 

6 10.8 13.7 16.5 

7 5.4 8.6 7.2 

8 5.4 0.3 9.1 

9 0.0 0.0 2.2 

10 1.4 0.0 1.0 

Total 100.0 100.0 100.0 

*Intermediate isolates were classified as not resistant based on 15 

antimicrobials evaluated for E. faecium (dropping tigecycline and 

daptomycin) and based on 14 antimicrobials for E. faecalis (dropping 

tigecycline, daptomycin and dynercid). 

The resistance patterns of E. faecalis and

E. faecium isolates to four drugs are shown in 

table 4.5

 All isolates were susceptible to 

vancomycin. E. faecalis showed resistance to 

gentamicin, while E. faecium did not; the opposite 

was true for resistance to penicillin. 

Table 4. Species of Resistant Enterococcus Isolates 

and Resistance Patterns from Swine Feces 

Species 

Number 

Isolates 

Percent 

Species 

Isolates Resistance 

21 8.2 Gentamicin 

0 0.0 Penicillin Faecalis* 

(n=255) 0 0.0 Vancomycin 

0 0.0 Gentamicin 

9 12.2 Penicillin 

8 10.8 Synercid 

Faecium 

(n=74) 

0 0.0 Vancomycin 1

*E. faecalis is intrinsically (naturally) resistant to synercid.
Conclusions 

Given that Enterococcus spp. is a commensal 

organism that inhabits the gastrointestinal tract of 

many people and animals it is not surprising that it 

was frequently recovered on swine operations. 

E. faecalis is more common on swine sites, while 

the prevalence of E. faecium is much lower. 

Resistance of Enterococcus isolates to 

antimicrobial drugs on swine sites varies by 

bacterial species. 

References 

1 Murray, B.E. 1990. The life and times of the 

Enterococcus. Clin Microbiol Rev; 3(1):46-65. 

2 Lu, Hong-Zhou, Xin-Hua Weng, Haijing Li, YouKuan Yin, Mao-Yin Pang, and Yi-Wei Tang. 2002. 

Enterococcus faecium-related outbreak with 

molecular evidence of transmission from pigs to 

humans. J Clin Microbiol; 40(3):913–917. 

3 Kahn, C.M. (ed.). 2005. In: The Merck Veterinary 

Manual 9th ed. Merck & Co., Inc., Whitehouse 

Station, N.J. p. 585. 

4 Cliver, D.O. and H.P. Riemann (eds.). 2002. In: 

Foodborne Diseases 2nd ed. Academic Press, San 

Diego, Calif. p. 154. 

5 CDC. National Antimicrobial Resistance 

Monitoring System for Enteric Bacteria (NARMS): 

Human Isolates Final Report, 2004. Atlanta, 

Georgia: U.S. Department of Health and Human 

Services, CDC, 2007. p. 47-54. 

For more information, contact: 

USDA:APHIS:VS:CEAH 

NRRC Building B, M.S. 2E7 

2150 Centre Avenue 

Fort Collins, CO 80526-8117 

970.494.7000 

E-mail: NAHMS@aphis.usda.gov 

http://nahms.aphis.usda.gov

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