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

Veterinary Services

Centers for Epidemiology and Animal Health May 2011 

_________________________________________________________________________________________________________________________ 

Clostridium difficile on U.S. 

Dairy Operations 

Disease caused by Clostridium difficile is linked most 

commonly to nosocomial (hospital-acquired) infections in 

humans, especially when antibiotics are administered 

that alter normal gastrointestinal flora. Humans develop 

a spectrum of disease after infected with some strains of 

C. difficile. Symptoms range from mild diarrhea to lifethreatening toxic megacolon and pseudo-membranous 

colitis (Weese, 2010). Even though C. difficile is typically 

seen as a nosocomial infection, there are increasing 

reports of community acquired infections. 

C. difficile is a spore-forming organism which can survive 

in the environment for long periods and can be ingested 

by animals or humans through contaminated foodstuffs 

and water (Yaeger et al., 2002). C. difficile has also been 

associated with clinical disease in young pigs and dairy 

calves (Yaeger et al., 2002; Hammitt et al., 2008). 

Shedding of C. difficile bacteria in animal feces can 

occur in the absence of clinical signs (Weese, 2010). In 

addition, some strains of C. difficile have been isolated 

from ground beef, ground pork, and ground veal 

purchased from retail markets in Canada which could 

serve as a source of infection in humans (RodriguezPalacios et al., 2007; Weese et al., 2009). To date, there 

has been little information available on the distribution 

and characteristics of C. difficile on various types of 

livestock operations across the United States. 

Dairy 2007 study 

The U.S. Department of Agriculture’s National 

Animal Health Monitoring System (NAHMS) conducted 

the Dairy 2007 study, which focused on dairy health and 

management practices in 17 States.1

 These States 

represented 79.5 percent of U.S. dairy operations and 

82.5 percent of U.S. dairy cows. The operations were 

divided into 3 herd-size categories based on the number 

of milk cows present: small (fewer than 100 cows), 

medium (100 to 499 cows), and large (500 or more 

cows). One objective of the Dairy 2007 study was to 

determine the prevalence of C. difficile in the feces of 

dairy cows presumed to be healthy on U.S. dairy 

operations. 

 

1 States/Regions: 

West: California, Idaho, New Mexico, Texas, Washington 

East: Indiana, Iowa, Kentucky, Michigan, Minnesota, Missouri, New 

York, Ohio, Pennsylvania, Vermont, Virginia, and Wisconsin 

C. difficile prevalence 

During the Dairy 2007 study, testing for C. difficile 

was performed on 118 dairy operations across the 17 

participating States. Individual cow fecal samples were 

taken via rectal retrieval for culture.2

Overall, 1,858 fecal samples from dairy cows were 

tested for the presence of C. difficile. Of the 1,858 fecal 

samples tested, C. difficile was isolated from 29 samples 

(1.6 percent) [table 1]. At least 1 positive sample was 

found on 15 of the 118 operations (12.7 percent). 

 

Table 1. Number and percentage of samples and 

operations tested for C. difficile, by test result 

Samples 

Tested 

Operations 

Tested 

Test 

Result Number Percent Number Percent 

Positive 29 1.6 15 12.7 

Negative 1,829 98.4 103 87.3 

Total 1,858 100.0 118 100.0 

 

2

 Culture methods available in Thitaram et al. (2011).

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

Sample-level results

Herd size and region

Sample-level prevalence estimates are shown in 

tables 2 and 3. Overall, the prevalence of C. difficile in 

fecal samples was low. Only 1.6 percent of fecal 

samples from cows were positive (table 2). The 

proportion of samples positive was different by herd size 

where a higher percentage of small herds were positive 

for C. difficile compared with medium herds (p=0.04). 

Table 2. Number of samples tested and number and 

percentage of samples positive for C. difficile, by 

herd size 

Herd Size (number of dairy cows) 

Small 

(fewer 

than 100) 

Medium 

(100–499) 

Large 

(500 or 

more) Total 

Number 

samples 

tested 

580 759 519 1,858 

Number 

samples 

positive 

19 3 7 29 

Percent 

samples 

positive 

3.3 0.4 1.4 1.6 

There was no significant regional difference in the 

percentage of samples positive for C. difficile (p=0.18) 

[table 3].

Table 3. Number of samples tested and number and 

percentage of samples positive for C. difficile, by 

region 

 Region 

 West East 

Number 

samples tested 282 1,576 

Number 

samples positive 8 21 

Percent 

samples positive 2.8 1.3 

Operation-level results 

Herd size and region

The operation-level prevalence for C. difficile varied 

by herd size (p=0.04). A lower percentage of medium 

operations (4.3 percent) had at least one sample positive 

for C. difficile compared with small and large operations 

(22.2 and 14.3 percent, respectively) [table 4]. 

Table 4. Number of operations tested and number 

and percentage of operations with at least one 

sample positive for C. difficile, by herd size 

Herd Size (number of dairy cows) 

Small 

(fewer 

than 100) 

Medium 

(100–499) 

Large 

(500 or 

more) Total 

Number 

operations 

tested 

36 47 35 118 

Number 

operations 

positive 

8 2 5 15 

Percent 

operations 

positive 

22.2 4.3 14.3 12.7 

There was no significant regional difference in the 

percentage of operations positive for C. difficile (p=0.07) 

[table 5]. 

Table 5. Number of operations tested and number 

and percentage of operations with at least one 

sample positive for C. difficile, by region 

 Region 

 West East 

Number 

operations 

tested 

19 99 

Number 

operations 

positive 

5 10 

Percent 

operations 

positive 

26.3 10.1 
United States Department of Agriculture • Animal and Plant Health Inspection Service • Safeguarding American Agriculture 

Summary

There was a difference in C. difficile results by herd 

size at the sample and herd levels. Because 

confounding factors may be present (e.g., average herd 

size differs by region), these univariate associations 

need to be explored further with statistical models or 

additional studies. 

The recovery of C. difficile from feces on livestock 

operations warrants further investigation. Not all strains 

of C. difficile appear to have the same propensity to 

cause disease. Therefore, isolates from this study will be 

further characterized to determine how related these 

isolates are to those causing human disease. Further 

characterization of C. difficile isolates, including 

molecular typing and additional epidemiological studies, 

is needed to ascertain if a relationship exists between 

food animal isolates and those from humans in order to 

determine the potential for foodborne disease. 

References

Hammitt MC, Bueschel DM, Keel MK, Glock RD, Cuneo 

P, DeYoung DW, Reggiardo C, Trinh HT, Songer 

JG. 2008. A possible role for Clostridium difficile in 

the etiology of calf enteritis. Vet Microbiol.127(3–

4):343–352. 

Rodriguez-Palacios A, Staempfli HR, Duffield T, Weese 

JS. 2007. Clostridium difficile in retail ground meat, 

Canada. Emerg Infect Dis.13(3):485–487.

Thitaram SN, Frank JF, Lyon SA, Siragusa GR, Bailey 

JS, Lombard JE, Haley CA, Wagner BA, Dargatz 

DA, Fedorka-Cray PJ. 2011. Clostridium difficile

from healthy food animals: optimized isolation and 

prevalence. J Food Prot 74(1):130–133. 

Weese JS. 2010. Clostridium difficile in food—innocent 

bystander or serious treat? Clin Microbiol Infect 16: 

3–10. 

Weese JS, Avery BP, Rousseau J, Reid-Smith RJ. 2009. 

Detection and enumeration of Clostridium difficile

spores in retail beef and pork. Appl Environ 

Microbiol 75(15):5009–5011. 

Yaeger M, Funk N, Hoffman L. 2002. A survey of agents 

associated with neonatal diarrhea in Iowa swine 

including Clostridium difficile and porcine 

reproductive and respiratory syndrome virus. J Vet 

Diagn Invest 14(4):281–287.

AHPIS acknowledges the contributions of the USDAARS Bacterial Epidemiology and Antimicrobial 

Resistance Research Unit for their participation in the 

Dairy 2007 study. 

____________________ 

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 

Email: NAHMS@aphis.usda.gov 

http://nahms.aphis.usda.gov 

#599.0411 

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