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The recent multistate outbreak of a multidrug-resistant (MDR) Salmonella Heidelberg strain from commercial poultry production highlights the need to better understand the reservoirs of these zoonotic pathogens within the commercial poultry production and processing environment. As part of a larger study looking at temporal changes in microbial communities within the major water tanks within a commercial processing facility, this paper identifies and characterizes Salmonella enterica isolated from the water in a final scalder tank at 3 times during a typical processing day: prior to the birds entering the tank (start), halfway through the processing day (mid), and after the final birds were scalded (end). Over 3 consecutive processing days, no Salmonella were recovered from start-of-day water samples, while a total of 56 Salmonella isolates were recovered from the mid-day and end-of-day scalder water samples. Traditional and newer PCR-based serotyping methods eventually identified these isolates as either group C3 S. Kentucky (n=45) and group B S. Heidelberg (n=11). While none of the S. Kentucky isolates possessed any resistances to the antimicrobials tested, all S. Heidelberg isolates were found to be multidrug resistant to 5 specific antimicrobials representing 3 antimicrobial classes. Due to the potential public health impact of S. Heidelberg and the recent nationwide poultry-associated outbreak of multidrug-resistant S. Heidelberg, future studies should focus on understanding the transmission and environmental growth dynamics of this serotype within the commercial poultry processing plant environment., (© 2015 Poultry Science Association Inc.)

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many environmental samples within these disciplines can be physiochemically and microbiologically unique (e.g., fecal and litter/bedding samples from the poultry production spectrum), appropriate and effective DNA extraction methods need to be carefully chosen. Therefore, a novel semi-automated hybrid DNA extraction method was developed specifically for use with environmental poultry production samples. This method is a combination of the two major types of DNA extraction: mechanical and enzymatic. A two-step intense mechanical homogenization step (using bead-beating specifically formulated for environmental samples) was added to the beginning of the "gold standard" enzymatic DNA extraction method for fecal samples to enhance the removal of bacteria and DNA from the sample matrix and improve the recovery of Gram-positive bacterial community members. Once the enzymatic extraction portion of the hybrid method was initiated, the remaining purification process was automated using a robotic workstation to increase sample throughput and decrease sample processing error. In comparison to the strict mechanical and enzymatic DNA extraction methods, this novel hybrid method provided the best overall combined performance when considering quantitative (using 16S rRNA qPCR) and qualitative (using microbiomics) estimates of the total bacterial communities when processing poultry feces and litter samples.

Differences in adoption of selected practices used in welfare assessment and audit programs were contrasted among organic (ORG; n=192) herds and similarly sized conventional grazing herds (CON-GR; n=36), and conventional nongrazing herds (CON-NG; n=64). Criteria from 3 programs were assessed: American Humane Association Animal Welfare Standards for Dairy Cattle, Farmers Assuring Responsible Management (FARM), and the Canadian Codes of Practice (CCP). Data were collected by trained study personnel during a herd visit and included information about neonatal care, dehorning, pain relief, calf nutrition, weaning, record keeping, use of veterinarians, and animal observations. Associations of management type (ORG, CON-GR, or CON-NG) with adoption of selected practice were assessed. Almost all farms (97%) met criteria suggested for age at weaning but fewer CON-NG farmers weaned calves at ≥5 wk of age compared with ORG and CON-GR farmers. Only 23% of farms met program requirements for use of pain relief during dehorning, and fewer CON-NG farmers used pain relief for calves after dehorning compared with ORG and CON-GR farmers. Calves on ORG farms were fed a greater volume of milk and were weaned at an older age than calves on CON-GR and CON-NG farms. Calves on CON-GR farms were dehorned at a younger age compared with calves on ORG and CON-NG farms. The calving area was shared with lactating cows for a larger proportion of ORG herds compared with conventional herds. About 30% of herds met welfare program criteria for body condition score but only about 20% met criteria for animal hygiene scores. The least proportion of cows with hock lesions was observed on ORG farms. Regular use of veterinarians was infrequent for ORG herds. Results of this study indicate that most of the organic and conventional farms enrolled in this study would have been unlikely to achieve many criteria of audit and assessment programs currently used in the US dairy industry., (Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The objective of this study was to evaluate the presence of methicillin-resistant Staphylococcus aureus and coagulase-negative Staphylococcus spp. in bulk tank milk samples from 288 organic and conventional dairy farms located in New York, Wisconsin, and Oregon from March 2009 to May 2011. Due to recent publications reporting the presence mecC (a mecA homolog not detected by traditional mecA-based PCR methods), a combination of genotypic and phenotypic approaches was used to enhance the recovery of methicillin-resistant organisms from bulk tank milk. In total, 13 isolates were identified as methicillin resistant: Staph. aureus (n=1), Staphylococcus sciuri (n=5), Staphylococcus chromogenes (n=2), Staphylococcus saprophyticus (n=3), Staphylococcus agnetis (n=1), and Macrococcus caseolyticus (n=1). The single methicillin-resistant Staph. aureus isolate was identified from an organic farm in New York, for an observed 0.3% prevalence at the farm level. The methicillin-resistant coagulase-negative staphylococci prevalence was 2% in the organic population and 5% in the conventional population. We did not identify mecC in any of the isolates from our population. Of interest was the relatively high number of methicillin-resistant Staph. sciuri recovered, as the number of isolates from our study was considerably higher than those recovered from other recent studies that also assessed milk samples. Our research suggests that the presence of a potential methicillin-resistant Staphylococcus reservoir in milk, and likely the dairy farm population in the United States, is independent of the organic or conventional production system., (Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

Background: The objective of this study was to identify associations between the concentration of Mycobacterium avium subsp. paratuberculosis (MAP) antibodies in bulk milk and potential risk factors in herd management and herd characteristics, explaining high MAP antibody titers in milk. An extensive questionnaire was administered to 292 organic and conventional dairy farms from New York, Wisconsin and Oregon. Bulk milk samples were taken from each farm for MAP enzyme-linked immunosorbent assay (ELISA). A general linear model was constructed with MAP ELISA value as the outcome variable and the management factors and herd characteristics as independent variables, while at the same time controlling for the study design variables of state, herd size, and production system (organic or conventional). High bulk tank MAP ELISA value may be due to either a high prevalence of MAP in a herd with many cows contributing to the antibody titer or due to a few infected cows that produce large quantities of antibodies., Results: Results of the regression models indicated that bulk milk ELISA value was associated with season of sampling and the presence or absence of protocols for managing MAP-positive cows. The concentration of MAP antibodies in bulk milk varied seasonally with a peak in the summer and low concentrations in the winter months. When compared to farms that had never observed clinical Johne's disease, keeping MAP-positive cows or only culling them after a period of delay was associated with an increase in optical density., Conclusions: The seasonal variation in MAP antibody titers, with a peak in the summer, may be due to a seasonal increase in MAP-bacterial load. Additionally, seasonal calving practices may contribute to seasonal fluctuations in MAP antibody titers in bulk tank milk. Keeping MAP-positive cows increases the antibody titer in bulk milk, likely due to direct antibody production in the infected cow and indirect triggering of antibody production in herdmates.

In the past decade, the demand for organic agricultural products has increased rapidly in the United States and worldwide. Milk quality research is of major interest to both consumers and dairy farmers alike. However, scientific data on milk quality, herd management methods, and animal welfare on organic farms in the United States has been lacking before the research from this study. The objective of this study was to evaluate the association of bulk tank milk somatic cell count (SCC) with management characteristics on organic and conventional dairy farms in New York, Oregon, and Wisconsin. Data from similarly sized organic farms (n=192), conventional nongrazing farms (n=64), and conventional grazing farms (n=36) were collected at a single farm visit. Of the 292 farms visited, 290 bulk tank milk samples were collected. Overall, no difference in SCC was observed between the conventional and organic grazing systems. Two models were created to assess the effects of various management and herd characteristics on the logarithmic transformation of the SCC (LSCC), one using data from all herds and one using data from organic herds only. From the total herd model, more grain fed per cow per day was negatively associated with LSCC, whereas a positive bulk tank culture for Staphylococcus aureus and years that a farmer reported being in the dairy business were both positively associated with LSCC. In the organic herd model, a seasonal effect indicated that LSCC tended to increase in the summer and decrease in the winter. Grain fed per cow per day, the use of anionic salts in transition-cow diets, the use of gloves during milking, and regular use of a quarantine unit at milking were all negatively associated with LSCC. Similar to the total herd model, a Staph. aureus-positive bulk tank culture was positively associated with LSCC in the organic model. Standard plate count was also positively associated with LSCC in the organic model. Several variables that were associated with management using external resources were combined to create an external input score. In the total herd model, use of more external resources was negatively associated with LSCC. Conventional herds in the study tended to use more outside management resources than organic herds., (Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The objective of this study was to evaluate management characteristics on organic and similarly sized conventional dairy farms located in New York, Wisconsin, and Oregon. Data from 192 organic farms (ORG), 64 conventional nongrazing farms (CON-NG), and 36 conventional grazing farms (CON-GR) were collected during farm visits and were size-matched and analyzed. The average lactation number of animals on ORG and CON-GR farms was 2.6 lactations, which was greater than that on CON-NG farms (2.3 lactations). A greater percentage of first-lactation heifers were found on conventional farms than on ORG farms. Facilities used by adult animals, including housing and milking facilities, did not differ among the grazing systems. Cattle on conventional farms were fed approximately twice as much grain as cattle on ORG farms and had greater milk production. Little difference was found for the average reported somatic cell count and standard plate count, suggesting that milk quality is not dependent on grazing system. Milking procedures were similar across all 3 grazing systems, indicating that an industry standard now exists for milking and that milk quality problems will need to be addressed with other management problems in mind. Although some disease prevention measures were commonly utilized on ORG farms, such as keeping a closed herd and having a written record of treatments administered to the animals, the use of outside support and vaccinations were found to be less prevalent on organic farms than on conventional farms., (Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The purpose of this study was to assess the association of bulk tank milk standard plate counts, bulk tank coliform counts (CC), and the presence of Staphylococcus aureus in bulk tank milk with various management and farm characteristics on organic and conventional dairy farms throughout New York, Wisconsin, and Oregon. Data from size-matched organic farms (n=192), conventional nongrazing farms (n=64), and conventional grazing farms (n=36) were collected at a single visit for each farm. Of the 292 farms visited, 290 bulk tank milk samples were collected. Statistical models were created using data from all herds in the study, as well as exclusively for the organic subset of herds. Because of incomplete data, 267 of 290 herds were analyzed for total herd modeling, and 173 of 190 organic herds were analyzed for the organic herd modeling. Overall, more bulk tanks from organic farms had Staph. aureus cultured from them (62% of organic herds, 42% conventional nongrazing herds, and 43% of conventional grazing herds), whereas fewer organic herds had a high CC, defined as ≥50 cfu/mL, than conventional farms in the study. A high standard plate count (×1,000 cfu/mL) was associated with decreased body condition score of adult cows and decreased milk production in both models. Several variables were significant only in the model created using all herds or only in organic herds. The presence of Staph. aureus in the bulk tank milk was associated with fewer people treating mastitis, increased age of housing, and a higher percentage of cows with 3 or fewer teats in both the organic and total herd models. The Staph. aureus total herd model also showed a relationship with fewer first-lactation animals, higher hock scores, and less use of automatic takeoffs at milking. High bulk tank CC was related to feeding a total mixed ration and using natural service in nonlactating heifers in both models. Overall, attentive management and use of outside resources were useful with regard to CC on organic farms. In all models except the organic CC model, we observed an association with the average reported somatic cell count from 3 mo before the herd visit, indicating that many of the regularly tested milk quality parameters are interconnected. In conclusion, we found that conventional and organic farms are similar in regard to overall herd management, but each grazing system faces unique challenges when managing milk quality., (Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)