Clinical Mastitis Incidence in Compost Bedded Pack Barns as Compared to Freestall Barns

2014 Annual Report for OS13-070

Project Type: On-Farm Research
Funds awarded in 2013: $13,750.00
Projected End Date: 12/31/2014
Region: Southern
State: Kentucky
Principal Investigator:
Dr. Jeffrey Bewley
University of Kentucky

Clinical Mastitis Incidence in Compost Bedded Pack Barns as Compared to Freestall Barns


A comparison of compost bedded pack barn and deep-bedded sand freestall barn dairy herds to determine if differences exist regarding cow health and comfort.  To date, no significant differences between mastitis incidence, cow cleanliness, or lameness have been noted.  Bacterial data from the compost bedded pack barns has also been collected to determine how management of the barns affects health and cleanliness.  No analysis has been run at this time, but shifts in population based on moisture content and internal compost temperature have been observed.

Objectives/Performance Targets

Objective 1: Cow Health and Welfare Dynamics, Key Personnel: Bewley, Arnold, Coyne

Data will be collected from ten farms participating in a comprehensive field study for 2 years.  The following data will be collected and compared with compost success metrics (Objective 2):


  1. Establish cow and herd level benchmark monitoring criteria (including somatic cell counts, clinical mastitis incidence, mastitis pathogen prevalence, immune status, digital dermatitis incidence, estrus detection rates, culling rates, locomotion scores, hygiene scores, and teat end-condition scores).  Emphasis will be placed on standards for animal care outlined in the National Dairy FARM (Farmers Assuring Responsible Management) Animal Care Guide).


  1. Dairy producers in the project will be asked to rank important cow and herd based criteria for judging compost bedded pack barn performance. Periodic feedback will be requested from producers throughout the project.
  2. Monthly bacteriological evaluation of sampled compost material from compost bedded pack barns will be conducted including total bacterial and fungal counts; staphylococcus counts; streptococcus counts; and coliform counts (fecal and total (240 samples collected for 10 farms over a 2 year period).
  3. Aseptic quarter milk samples will be collected from all clinical mastitis cases from 10 farms to evaluate mastitis pathogen prevalence within this system and compare to pack bacteria levels.
  4. Daily bulk tank milk yields and number of cows milked will be collected to determine average milk yield for each farm.
  5. Individual animal somatic cell counts and milk yields will be collected from Dairy Herd Improvement Association records.
  6. Herd level estrus detection and culling rates will be collected from Dairy Herd Improvement Association records.
  7. Monthly locomotion, hygiene, hock scores, and teat end condition scores will be assessed by the animal sciences graduate student using the standards established in the National Dairy FARM (Farmers Assuring Responsible Management) Animal Care Guide.
  8. Immunological analysis of blood and milk samples including markers for antigen presenting cells (CD14), adhesion molecules present particularly neutrophil activation (CD18), and a marker on dendritic cells, important antigen presenting cells (DEC205) will be collected to assess animal immunological status.


  1. Compost Bedded Pack Sample Collection & Culture. On a monthly basis, shortly after routine mixing of the compost, composite samples from at least five locations in each barn will be collected at depths of 0-6, 6-12, and 12-18 inches (0-15, 15-30, 30-46 cm) and transported to UK where it will be stored at 4 C until use . At UK the samples will be mixed, and a representative portion sent to Regulatory Services for nutrient analysis. Portions of the remaining samples will be suspended in buffer, shaken to release bound microbes, diluted, and plated in triplicate on SMA or PDA  agar (for isolation of bacteria and fungi, respectively). After incubation at 25 C for a period of at least one week the colony forming units representing viable bacteria and fungi in the samples will be counted. Repeated measures analysis of colony forming units for each compost depth will be performed to assess the effect of barn, time, and position on the microbial properties of the compost. These values will be related to chemical properties of the compost at each sample period.


  1. Clinical Mastitis Sample Collection & Culture

Bacteriological cultures and SCC will be collected for all quarters when any quarter is diagnosed with clinical mastitis. Approximately 5 ml of milk will be collected aseptically from all four quarters of a cow diagnosed with clinical mastitis. These samples will be frozen and shipped weekly for bacterial evaluation. Samples will be taken aseptically according to procedures recommended by the National Mastitis Council (Hogan et al., 1999).  Teat ends will be washed thoroughly, dried with individual disposable paper towels, and then cleaned with 70% isopropyl alcohol swabs. Milk samples for microbiological analysis will be collected into sterile pop-cap tubes and taken directly to the lab or kept frozen until evaluation. Another 5 ml of milk will be sampled from each quarter for SCC samples, which will be taken directly after bacteriological cultures are taken in non-sterile pop-cap tubes. These samples will be preserved and refrigerated until taken to UK’s Regulatory Services.  Milk samples will be examined following procedures recommended by the National Mastitis Council (Oliver et al., 2004b) and as described by Oliver et al. (1994). Briefly, foremilk samples (10 ml) from each mastitis sample will be plated onto one quadrant of a trypticase soy agar plate supplemented with 5% defibrinated sheep blood (Becton Dickinson and Company, Franklin Lakes, NJ). Plates will be incubated at 37°C and bacterial growth will be observed at 24-hr intervals for 3d.  Bacteria on primary culture medium will be identified tentatively according to colony morphologic features, hemolytic characteristics, and catalase test.  Isolates identified presumptively as staphylococci will be tested for coagulase by the tube coagulase method (Remel, Lenexa, KS), Mannitol salt (Becton Dickinson and Company) and DNase agar (Becton Dickinson and Company).  Isolates identified presumptively as streptococci will be evaluated for growth in 6.5% NaCl, hydrolysis of esculin and CAMP-reaction.  Streptococcal organisms will be identified to the species level using the API 20 Strep System (bioMérieux Inc.).  Gram-negative isolates were evaluated by their biochemical reactions on the following: MacConkey agar (Becton Dickinson and Company), triple sugar iron agar (Becton Dickinson and Company), urea agar (Becton Dickinson and Company), oxidase (Becton Dickinson and Company), motility, indole and ornithine decarboxylase (Becton Dickinson and Company) and identified to the species level using the API 20E System (bioMérieux Inc.).


  1. DHIA and Cow Observations.

Daily bulk tank milk yields will be collected from milk cooperatives along with number of milking cows to calculate average daily milk yield.  Dairy Herd Improvement Association records (DHIA) will be utilized to collect individual animal somatic cell counts, milk yields, estrus detection rates, and culling rates.  These metrics will help in relating compost performance to herd-based metrics used in daily management by dairy producers.  Lastly, locomotion, hygiene, hock scores, and teat end condition scores will be collected monthly from each cooperating farm (n=10) by a graduate student using the standards for each subjective measurement established in the National Dairy FARM (Farmers Assuring Responsible Management) Animal Care Guide (NMPF, 2009).


Compost bedded pack collection and culture – samples have been taken from 8 compost bedded barns throughout Kentucky on a bi-weekly basis since May 14, 2013. The samples were taken from 9 predetermined places in each barn to gain a pooled representative sample for each barn at each sampling period.  These samples were sent to the University of Kentucky Regulatory Services lab for moisture, P, K, Ca, Mg, Zn, Cu, Mn, and Fe concentrations.  Four of these farms were also used for bacterial analysis – Bacillus species, Streptococcus species, Staphylococcus species, Klebsiella species, and coliform species were identified.  

  1. Clinical mastitis sample collection was done by farm owners or employees from May 2013 until May 3, 2014 on 7 sand freestall herds and 8 compost bedded pack herds.  Aseptic collection tubes and alcohol were provided to each farmer for the length of the study.  Samples were frozen and picked up bi-weekly for culture analysis at the University of Kentucky.  Samples were plated on a nutrient media, then speciation was done through gram staining and Vitek analysis.  Results were returned to farm personnel the week after culturing to aid in management decisions.

3. DHIA data has been collected to the present from May 2013 for SCC, milk yield, and lactating herd number.  Cow observations of locomotion, hygiene, and hock status have been done bi-weekly on 50 cows in herds with more than 50 cows and on all cows if herd number was less than 50.  Co-op data of bulk tank SCC has been collected for most of the herds included in the study from May 2013 until present.      

4. A mid-study benchmark report was created and distributed to producers in January 2014 to inform producers in each of the barn types how they ranked compared to other producers on the study.

5. 2014 – statistical analysis has begun to determine statistical significance

6. May 3, 2014 – last day of sample collection

Impacts and Contributions/Outcomes

Abstract submitted for 2014 National ADSA meeting

Somatic cell counts, mastitis infection prevalence, and mastitis pathogen distribution in compost bedded pack and sand freestall farms

Eckelkamp, E.A., J.L. Taraba, R.J. Harmon, K.A. Akers, and J.M. Bewley, University of Kentucky, Lexington


The objective of this research was to describe the relationships among SCS, mastitis infection prevalence (MIP, percent of cows with SCS>3.9), and mastitis pathogen distribution (MPD) in 8 compost bedded pack (CB) and 7 sand freestall (SF) farms in Kentucky from May 2013 to January 2014.  The same observer evaluated cow hygiene scores (HYS, Cook and Reinemann, 2007) bi-weekly for 50 cows per herd.  Throughout the study, producers collected aseptic milk samples from all quarters displaying clinical mastitis signs for bacteriological culturing.  Test-day SCC and MIP were obtained from DHIA.  The MIXED procedure of SAS (SAS Institute, Inc., Cary, NC) was used to assess fixed effects of barn type (BT), maximum ambient temperature (MT), and HYS on SCS and MIP.  Stepwise backward elimination removed non-significant interactions (P≥0.05) with main effects remaining in the model regardless of significance. A χ2 analysis was conducted using the FREQ procedure of SAS to determine MPD between BT.  Maximum temperature × BT was a predictor of MIP (P<0.05).  As MT increased, MIP increased more rapidly in CB than in SF (P<0.05).  Calculated MIP LSMeans(±SE) for CB and SF herds were 28.68 ± 2.17% and 25.49 ± 2.21%, respectively (P<0.05).  Hygiene score and BT × MT were predictors of SCS (P<0.05).  With increasing MT, herd SCS increased more rapidly in CB than in SF (P<0.05).  Somatic cell score LSMeans(±SE) for CB and SF were 4.25 ± 0.16 and 3.97 ± 0.17 cells/mL, respectively (P≥0.05).  Table 1 summarizes MPD frequency by BT.  Results of this study demonstrate potential challenges for managing mastitis in CBP.

Table 1.  Frequencies of pathogens isolated from clinical mastitis cases in compost bedded pack (CB) barns and sand freestall (SF) barns1,2  


Pathogen isolated1


(Total number of cases = 232)

(Mean number of  cows  = 1208)


(Total number of cases = 117)

(Mean number of cows = 629)

Coagulase negative staphylococci



Environmental streptococci



Escherichia coli



Gram-positive Bacillus species



Staphylococcus aureus



Yeast species



Klebsiella species



Other gram-negative species



Other gram-positive species



No growth



Contaminated samples



Missing samples



1 Number of pathogens isolated per species (percent of total samples per barn type).

2 χ2 analysis indicated no significant differences for mastitis pathogen distribution between barn types (P≥0.05). 


This research will enhance understanding of the relationship between compost bedded pack barns and cow health, focusing on mastitis and lameness.  It will also give us insight into the differences between the systems and potential improvements regarding either disease.  The length of this study provides a unique opportunity to include the effect of season in each type of barn, and identify areas that may need to be improved.  The effect to date on clinical mastitis and SCC of the barn has not been significant.  This indicates other areas in each of the systems need to be explored for cause or prevention of mastitis, since housing environment by itself is not the determining factor.



Dr. Michelle Arnold

[email protected]
Extension Veterinarian
1490 Bull Lea Rd.
Lexington, KY 40511
Office Phone: 8592577190
Elizabeth Eckelkamp

[email protected]
Project Manager
408 WP Garrigus Building
Lexington, KY 40546
Office Phone: 3374017697
Dr. Joseph Taraba

[email protected]
Extension Professor
128 CE Barnhart Building
Lexington, KY 40546
Office Phone: 8592573000216