Veterinary Services 

Centers for Epidemiology and Animal Health January 2009 

_________________________________________________________________________________________________________________________

Escherichia coli on U.S. 

Swine Sites—Antimicrobial 

Drug Susceptibility 

Background 

E. coli are normal (commensal) flora of the intestines of 

humans and animals, including swine. While many 

subtypes of E. coli are harmless, others—such as E. coli

O157:H7—can cause disease. Foodborne E. coli 

infections have been attributed to the consumption of 

undercooked hamburger and raw (unpasteurized) milk, 

as well as contaminated fruits, vegetables, water, and 

exposure to live animals and their environments.1

 

However, past studies have shown that it is uncommon 

for swine to shed E. coli O157:H7.2 

Although not necessarily pathogenic, commensal 

E. coli residing in the intestinal tracts of humans and 

animals may contain genes for resistance to 

antimicrobials. If the animal becomes infected with 

pathogenic bacteria, it is possible for the antimicrobial 

resistance genes to be transferred to those bacteria and 

thus render treatment with those antimicrobials 

ineffective. Understanding antimicrobial susceptibility of 

commensal E. coli can help identify emerging patterns of 

resistance that may also occur in disease-causing 

organisms. 

E. coli 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 with 100 or more pigs in 

17 States*

. These States represented approximately 

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

pork producers with 100 or more pigs. 

 

* States 

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

Minnesota, Missouri, Nebraska, North Carolina, Ohio

Oklahoma, Pennsylvania, South Dakota, Texas and Wisconsin.

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 pens containing 

grower/finisher pigs and cultured for E. coli. From 

September 5, 2006, through March 15, 2007, 1,362 

samples were cultured for E. coli. 

Overall, at least one sample was found culturepositive for commensal E. coli on 100 percent of sites, 

98.7 percent of barns, and 96.6 percent of pens. 

Additionally, 94.9 percent of samples were culture 

positive. These isolates were tested for resistance to a 

panel of 15 antimicrobial drugs.** Resistance break 

points used by the National Antimicrobial Resistance 

Monitoring System were used to classify isolates as 

susceptible, intermediate, or resistant. 

Antimicrobial susceptibility 

A total of 1,292 fecal samples were positive for 

E. coli and subjected to susceptibility testing. Two 

isolates died before susceptibility testing. Overall, 5.5 

percent (71 of the remaining 1,290 E. coli isolates) were 

susceptible to all antimicrobial drugs tested. All isolates 

were susceptible to amikacin, ceftriaxone, ciprofloxacin, 

and naladixic acid. 

Resistance to tetracycline was most common 

(91.5 percent of isolates), followed by sulfisoxazole 

(44.8 percent). Table 1 depicts the frequency of 

resistance among the 1,290 isolates to the 

15 antimicrobial drugs tested. 

 

** Amikacin, amoxicillin/clavulanic acid, ampicillin, cefoxitin, ceftiofur, 

ceftriaxone, chloramphenicol, ciprofloxacin, gentamicin, kanamycin, 

naladixic acid, streptomycin, sulfisoxazole, tetracycline, and 

trimethoprim/sulfamethoxazole.
Table 1. Number and Percentage of E. coli Isolates 

Resistant* to the Following Antimicrobials 

Antimicrobial Number Percent 

Tetracycline 1,180 91.5 

Sulfisoxazole 578 44.8 

Ampicillin 362 28.1 

Kanamycin 334 25.9 

Streptomycin 304 23.6 

Chloramphenicol 170 13.2 

Trimethoprim/ 

sulfamethoxazole 64 5.0 

Amoxicillin/ 

clavulanic acid 29 2.2 

Gentamicin 25 1.9 

Cefoxitin 20 1.6 

Ceftiofur 15 1.2 

Naladixic acid 0 0 

Ciprofloxacin 0 0 

Ceftriaxone 0 0 

Amikacin 0 0 

*Intermediate isolates were classified as not resistant.

Overall, 94.5 percent of isolates were resistant to at 

least one antimicrobial drug, and 62.6 percent were 

resistant to more than one antimicrobial drug. The 

highest percentage of isolates (31.9 percent) showed 

resistance to only one drug (table 2). Eleven isolates 

(0.8 percent) were resistant to 7 or more drugs. 

Table 2. Number of Antimicrobials by Number and 

Percentage of E. coli Isolates Showing Resistance* 

Number of 

Antimicrobials 

Number 

E. coli Isolates 

Percent 

E. coli Isolates 

0 71 5.5 

1 411 31.9 

2 247 19.1 

3 246 19.1 

4 195 15.1 

5 86 6.7 

6 23 1.8 

7 or more 11 0.8 

Total 1,290 100.0 

*Intermediate isolates were classified as not resistant.

The following six antimicrobial resistance patterns 

accounted for over one-half of isolates (55.7 percent): 

tetracycline alone (30.3 percent); sulfisoxazole and 

tetracycline (6.5 percent); kanamycin, streptomycin, 

sulfisoxazole, and tetracycline (5.5 percent); ampicillin 

and tetracycline (5.0 percent); ampicillin, sulfisoxazole, 

and tetracycline (4.8 percent); and streptomycin and 

tetracycline (3.6 percent). 

Conclusions 

Although over 60 percent of E. coli isolates were 

resistant to more than one antimicrobial, less than 

1 percent were resistant to seven or more antimicrobials. 

References 

1 Rangel, J.M., P.H. Sparling, C. Crowe, P.M. Griffin, 

and D.L. Swerdlow. 2005. Epidemiology of Escherichia 

coli O157:H7 outbreaks, United States, 1982–2002. 

Emerg Infect Dis; 11:603-609. 

2 Fratamico, P.M., L.K. Bagi, E.J. Bush, and B.T. Solow. 

2004. Prevalence and characterization of Shiga toxinproducing Escherichia coli in swine feces recovered in 

the National Animal Health Monitoring System's Swine 

2000 study. Appl Environ Microbiol; 70:7173-7178. 

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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