California Dairy Farms Research Articles

Comparison of two methods for collecting antimicrobial usage in large dairy farms in Ohio and California

Quantification of on-farm antimicrobial use (AMU) is critical to correlate with patterns of antimicrobial resistance, surveil­lance programs and formulate interventions to optimize its use. Prior studies have used the empty drug container (EDC) method to quantify AMU; however, the method is labor-intensive and time-consuming. Therefore, this study aimed to compare it against farm treatment records (FTR) as a reliable method to collect on-farm AMU. We hypothesized a low level of agreement in on-farm treatment incidence (TI) obtained between these 2 different collection methods.

Microbial diversity in dairy manure environment under liquid-solid separation systems

ABSTRACT In dairy manure, a wide array of microorganisms, including many pathogens, survive and grow under suitable conditions. This microbial community offers a tremendous opportunity for studying animal health, the transport of microbes into the soil, air, and water, and consequential impacts on public health. The aim of this study was to assess the impacts of manure management practices on the microbial community of manure. The key novelty of this work is to identify the impacts of various stages of manure management on microbes living in dairy manure. In general, the majority of dairy farms in California use a flush system to manage dairy manure, which involves liquid-solid separations. To separate liquid and solid in manure, Multi-stage Alternate Dairy Effluent Management Systems (ADEMS) that use mechanical separation systems (MSS) or weeping wall separation systems (WWSS) are used. Thus, this study was conducted to understand how these manure management systems affect the microbial community. We studied the microbial communities in the WWSS and MSS separation systems, as well as in the four stages of the ADEMS. The 16S rRNA gene from the extracted genomic DNA of dairy manure was amplified using the NovoSeq Illumina next-generation sequencing platform. The sequencing data were used to perform the analysis of similarity (ANOSIM) and multi-response permutation procedure (MRRP) statistical tests, and the results showed that microbial communities among WWSS and MSS were significantly different (p < 0.05). These findings have significant practical implications for the design and implementation of manure management practices in dairy farms.

Effect of a dairy farmworker stewardship training program on antimicrobial drug usage in dairy cows

Antimicrobial use (AMU) is critical to preserving animal health and welfare. However, the development of antimicrobial resistance (AMR) represents a public health threat. Although most antimicrobials used on the farm require a veterinarian prescription, farmworkers make daily on-farm treatment decisions. Therefore, farmworker training is vital to promote responsible AMU. This research project aimed to evaluate the effect of farmworker antimicrobial stewardship (AMS) training on the quantity of AMU on dairy farms in Ohio and California. We hypothesized that farms receiving AMS training would have reduced AMU in dairy cattle compared with farms where training wasn't administered. We designed a quasiexperimental study with 18 conventional dairy farms enrolled in Ohio and California. Twelve farms received AMS training, and 6 farms did not. The AMS program included a 12-wk training focused on accurate identification of cows requiring antimicrobial treatment. We quantified AMU by collecting used drug containers, manually counted by researchers during farm visits. Treatment incidence (TI) was calculated using animal daily doses (ADD), and Poisson regression models were used to analyze the TI data. Disease incidence rate (DIR) in lactating cows was 2.2, 1.5, 1.0, 0.4, 0.3, 0.2, and 0.03/1,000 cow-days for mastitis, lameness, metritis, pneumonia, retained placenta, diarrheas, and other diseases (e.g., conjunctivitis, injuries), respectively. The highest TI by antimicrobial class (provided in ADD/1,000 cow-days) was cephalosporin (5.9), penicillin (5.2), tetracyclines (0.4), lincosamides (0.2), and sulfonamides (0.1). Among the trained farms using a within-treatment group analysis, no significant differences were observed in TI pre-intervention (10.9 ADD/1,000 cow-days) compared with TI postintervention (10.3 ADD/1,000 cow-days). Treatment incidence from the training group was 10.8 ADD/1,000 cow-days and although numerically lower, it was not significantly different compared with TI in the control groups at 13.9 ADD/1,000 cow-days (rate ratio = 0.77, CI = 0.25-2.38). Future research on AMS should incorporate farmworker training with social science approaches to overcome barriers and promote on-farm responsible use.

Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome

BackgroundThe goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge.ResultsAll three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The α diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted < 0.01) in the diversity of genera between CT and MET samples (R2 = 0.112, P = 0.003) and a non-significant difference between MET and PUS samples (R2 = 0.036, P = 0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella.ConclusionsThe results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased α-diversity but decreased β-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.

Evaluation of antimicrobial resistance and risk factors for recovery of intrauterine Escherichia coli from cows with metritis on California commercial dairy farms

Metritis is a major uterine disease in dairy cattle, typically oc­curring within 21 days post-partum, and the fourth most com­mon health issue in cows as identified by producers. Currently, little is known of MICs of intrauterine E. coli (EC) to common antimicrobial drugs used to treat metritis in California dairies. The goals of this study were to evaluate factors affecting recov­ery and antimicrobial resistance (AMR) in intrauterine E. coli in post-partum dairy cows with and without metritis from com­mercial California dairy farms.

Quantification of antimicrobial usage on dairy farms before, during and after the implementation of farmworker stewardship training

Antimicrobials are critical to preserving animal health and welfare. However, the development of antimicrobial resistance represents a public health threat. Veterinarians prescribe an­timicrobials, but farmworkers are responsible for making on-farm treatment decisions and their training is vital to promote responsible antimicrobial use (AMU). This research project aimed to describe and quantify AMU on large dairy farms in Ohio and California and evaluate the impact of farmworker antimicrobial stewardship (AMS) training on those metrics. We hypothesized that farms, where AMS training was adminis­tered, would have significantly lower AMU compared to farms where training was not administered.

Development of sulfonated and aminated poly (ethylene-vinyl alcohol) nanofibrous membrane as a solid phase extraction matrix for trace metal ions preconcentration from dairy wastewater for direct ICP-OES analyses

A robust nanofiber-based adsorbent was developed as a potential solid phase extraction matrix for adsorption and preconcentration of Al3+, Ni2+, Cu2+ and Cd2+ ions. This adsorbent was developed by amination and sulfonation of eletrospun poly (ethylene-vinyl alcohol) nanofibrous membranes (SF-EVOH NFM). Possessing porous structure, abundant active amine and sulfonate groups, the SF-EVOH NFM showed static maximum adsorption capacities of 350, 180, 140 and 125 mg.g−1 for Al3+, Cu2+, Ni2+, and Cd2+, respectively. The varied metal affinities toward the NFM are determined by the structural features of the metal ions and the NFM. More significantly, the NFM showed a dynamic column adsorption ratio of 99% with a 97% recovery of metal ions, revealing the features of efficient adsorption and release of metal ions by the unique structures of the SF-EVOH NFM. Furthermore, the SF-EVOH NFM demonstrated excellent stability and recyclability for up to 10 cycles. The NFM was applied as a solid phase extraction (SPE) filter to preconcentrate metal ions from wastewater samples collected from dairy farms in Central Valley California, USA. The preconcentrated solution released from the SF-EVOH NFM filter adsorbents could be directly tested by an ion-coupled plasma optical emission spectroscopy (ICP-OES) with a limit of detection (LOD) of 0.025 mg.L−1 and a relative standard deviation (RSD) < 5% for Al3+, highlighting the excellent performance of the NFM for enhanced instrumental monitoring applications of wastewater samples.

Assessing the environmental impact of resource recovery from dairy manure

Manure management is a major contributor to environmental impacts from large-scale dairy production. In this study, technologies for recovering energy, nutrients, and water from dairy manure were evaluated using life cycle assessment (LCA) and compared to conventional practices on California dairy farms. Six scenarios were evaluated: conventional manure management practices, anaerobic digestion (AD) for biogas recovery, and four scenarios for nutrients, energy, and water integrated recovery, called NEWIR. The NEWIR system consists of hydrothermal carbonization (HTC) for energy recovery via hydrochar, algae cultivation in the HTC aqueous product for nutrient recovery and production of protein-rich cattle feed, and water recovery from algae pond effluent via membrane distillation. Four NEWIR scenarios were evaluated, each with a different species of algae. Based on the results of the LCA, AD improves GHG emissions relative to conventional practices by 82%, but has similar eutrophication impacts, posing similar concerns for nutrient management as current practices. Results for the NEWIR system are highly dependent on the algae species used. Three of the four species evaluated (Chlamydomonas reinhardtii, Chlorella vulgaris, and Scenedesmus obliquus) improve GHG emissions by 420–500 kg CO2-eq. per functional unit, while net water consumption is increased by approximately 75% over AD and conventional practices Spirulina maxima requires more water and chemical inputs for cultivation than the other species, resulting in higher water use (21 times higher than baseline), though GHG emissions are still reduced by 85 kg CO2-eq. per functional unit relative to conventional practices. All NEWIR scenarios improve eutrophication impacts relative to AD and conventional practices by 16–46% for marine eutrophication and 18–99% for freshwater eutrophication, depending on the algae species used. The results suggest integrated resource recovery through NEWIR is a promising treatment method for manure to mitigate GHG emissions and improve nutrient management on large-scale farms. In addition, carbon and nutrient trading policies are discussed in relation to resource recovery technologies and their potential to incentivize producers to recover products from dairy manure.

Physiological responses of Holstein calves and heifers carrying the SLICK1 allele to heat stress in California and Florida dairy farms.

Inheritance of the SLICK1 allele of the prolactin receptor gene improves thermotolerance of lactating Holstein cows under humid heat stress conditions. The aim of this study was to investigate whether pre- and postweaning Holstein heifers carrying the SLICK1 allele would show physiological responses indicative of higher tolerance to heat stress in high- and low-humidity climates. A total of 101 heifer calves of two age groups heterozygous for the SLICK1 allele and 103 wild-type half-siblings were evaluated during July 2020 in 3 dairy farms in central California and 2 in south Florida. Dry bulb temperature and relative humidity data were recorded during evaluation and used to calculate the temperature-humidity index (THI). Physiological measurements were obtained between 1600 and 1900 h in California, and 1200 and 1400 h in Florida and included rectal temperature, respiration rate, skin temperature, and sweating rate. Data were analyzed via Generalized Linear Mixed Models including the main effects of genotype, state, group, sire, farm within state, and interactions, with THI included as a covariate. The correlations between THI and dependent variables were analyzed via linear regression. The average 24-h THI was higher in Florida compared with California (90 vs. 72, respectively); the main driver of the higher THI in Florida was the high relative humidity (average 85.6% in Florida vs. 36.7% in California). In Florida, the rectal temperature of slick calves was 0.4°C lower than non-slick calves (39.5 ± 0.1 vs 39.9 ± 0.1°C); no differences were detected between slick and non-slick calves in California. Regardless of genotype, heifer calves in Florida had higher respiration rate, higher rectal and skin temperatures, and lower sweating rate than in California. This study is the first to evaluate physiological responses of calves carrying the SLICK1 allele under heat stress conditions in different climates. Our findings demonstrate that the presence of this allele is associated with lower rectal temperatures in pre- and post-weaning Holstein females. According to the physiological parameters evaluated, calves raised in Florida appeared to be under more severe heat stress; in those conditions, the SLICK1 allele was advantageous to confer thermotolerance as evidenced by lower rectal temperature in slick animals.

Effectiveness of the Australian breeding value for heat tolerance at discriminating responses of lactating Holstein cows to heat stress.

Heat stress has negative consequences for milk production and reproduction of dairy cattle. These adverse effects are likely to increase because of climate change and anticipated increases in milk yield. Some of the variation among cows in ability to resist effects of heat stress is genetic. The current objective of this observational study was to assess the effectiveness of the Australian breeding value for heat tolerance (ABVHT) based on the decline in milk yield with heat stress for predicting cow differences in effects of heat stress on regulation of body temperature, milk production, and reproductive function. Genomic breeding values for heat tolerance were calculated for 12,487 cows from a single California dairy farm. Rectal temperature in the afternoon (1100-2045 h) was measured on a subset of 626 lactating cows with ABVHT ≥102 (heat tolerant) or <102 (heat sensitive). Rectal temperature was 0.12°C lower for heat-tolerant cows than heat-sensitive cows. Vaginal temperatures were measured every 15 min for 5 d in 118 cows with ABVHT ≥108 (extreme heat tolerant) or <97 (extreme heat sensitive). Vaginal temperature was 0.07°C lower for extreme heat-tolerant cows than extreme heat-sensitive cows. Lactation records for 4,703 cows with ABVHT were used to evaluate seasonal variation in first 90-d milk yield, fat percent, and protein percent for each ABVHT quartile. Overall, cows with higher ABVHT had lower milk yield, fat percentage, and protein percentage and higher first service pregnancy rate. There was no summer depression in production or reproduction or interactions between season and ABVHT quartile. We observed that ABVHT can successfully identify heat-tolerant cows that maintain lower body temperatures during heat stress. The lack of a pronounced seasonality in milk production or reproduction precluded evaluation of whether ABVHT is related to the magnitude of effect of heat stress on those traits.

Evaluation of antimicrobial resistance and risk factors for recovery of intrauterine Escherichia coli from cows with metritis on California commercial dairy farms

The goals of this study were to evaluate factors affecting recovery and antimicrobial resistance (AMR) in intrauterine E. coli in post-partum dairy cows with and without metritis from commercial California dairy farms. Using a cross-sectional study design, a total of 307 cows were sampled from 25 farms throughout California, from which a total of 162 intrauterine E. coli isolates were recovered. During farm visits, cows within 21 days post-partum were categorized in one of three clinical presentation groups before enrollment: metritis (MET, n = 86), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; cows with purulent discharge (PUS, n = 106), defined as a non-fetid purulent or mucopurulent vaginal discharge; and control cows, (CTL, n = 115) defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge. Cows diagnosed as MET had significantly higher odds for recovery of E. coli compared to cows diagnosed as CTL (OR = 2.16, 95% CI: 1.17–3.96), with no significant difference observed between PUS and CTL, and PUS and MET. An increase in days in milk (DIM) at the time of sampling was significantly associated with a decrease in the odds ratio for E. coli recovery from intrauterine swabs (OR = 0.94, 95% CI: 0.89–0.98). All intrauterine E. coli were resistant to ampicillin (AMP), with an AMR prevalence of 30.2% and 33.9% observed for chlortetracycline and oxytetracycline, respectively. Only 8.6% of isolates were resistant to ceftiofur (CEFT), one of the most common drugs used to treat cows on farms sampled. No significant difference in the prevalence of AMR was observed among clinical groups at the individual cow level. At the farm level, a significantly higher odds for isolating intrauterine E. coli resistant to chlortetracycline (OR: 2.6; 95% CI: 3.7–58.0) or oxytetracycline (OR: 1.9; 95% CI: 1.4–33.8) was observed at farms that used an intrauterine infusion of oxytetracycline as a treatment for metritis when compared to those farms that did not use this practice. Findings from this study indicate the need for further research supporting a broader understanding of farm practices driving AMR in cows with metritis, as well as data to increase the accuracy of breakpoints for AMR classification of intrauterine E. coli from cattle.

Dynamic changes in fecal bacterial microbiota of dairy cattle across the production line

BackgroundMicrobiota play important roles in the gastrointestinal tract (GIT) of dairy cattle as the communities are responsible for host health, growth, and production performance. However, a systematic characterization and comparison of microbial communities in the GIT of cattle housed in different management units on a modern dairy farm are still lacking. We used 16S rRNA gene sequencing to evaluate the fecal bacterial communities of 90 dairy cattle housed in 12 distinctly defined management units on a modern dairy farm.ResultsWe found that cattle from management units 5, 6, 8, and 9 had similar bacterial communities while the other units showed varying levels of differences. Hutch calves had a dramatically different bacterial community than adult cattle, with at least 10 genera exclusively detected in their samples but not in non-neonatal cattle. Moreover, we compared fecal bacteria of cattle from every pair of the management units and detailed the number and relative abundance of the significantly differential genera. Lastly, we identified 181 pairs of strongly correlated taxa in the community, showing possible synergistic or antagonistic relationships.ConclusionsThis study assesses the fecal microbiota of cattle from 12 distinctly defined management units along the production line on a California dairy farm. The results highlight the similarities and differences of fecal microbiota between cattle from each pair of the management units. Especially, the data indicate that the newborn calves host very different gut bacterial communities than non-neonatal cattle, while non-neonatal cattle adopt one of the two distinct types of gut bacterial communities with subtle differences among the management units. The gut microbial communities of dairy cattle change dramatically in bacterial abundances at different taxonomic levels along the production line. The findings provide a reference for research and practice in modern dairy farm management.

Isotopic Signatures of Methane Emissions From Dairy Farms in California’s San Joaquin Valley

AbstractIn this study, we present seasonal atmospheric measurements of δ13CCH4 from dairy farms in the San Joaquin Valley of California. We used δ13CCH4 to characterize emissions from enteric fermentation by measuring downwind of cattle housing (e.g., freestall barns, corrals) and from manure management areas (e.g., anaerobic manure lagoons) with a mobile platform equipped with cavity ring‐down spectrometers. Across seasons, the δ13CCH4 from enteric fermentation source areas ranged from −69.7 ± 0.6 per mil (‰) to −51.6 ± 0.1‰ while the δ13CCH4 from manure lagoons ranged from −49.5 ± 0.1‰ to −40.5 ± 0.2‰. Measurements of δ13CCH4 of enteric CH4 suggest a greater than 10‰ difference between cattle production groups in accordance with diet. Isotopic signatures of CH4 were used to characterize enteric and manure CH4 from downwind plume sampling of dairies. Our findings show that δ13CCH4 measurements could improve the attribution of CH4 emissions from dairy sources at scales ranging from individual facilities to regions and help constrain the relative contributions from these different sources of emissions to the CH4 budget.

Quantification of antibiotic resistance genes and mobile genetic in dairy manure.

BackgroundAntibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure.MethodsThis study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLSB) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1).ResultsPrevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.

Treatment practices after calving-related events on 45 dairy farms in California

Retained fetal membranes (RFM), dystocia, and twinning are common postpartum events that increase the risk of metritis, impair reproductive performance, and contribute to antimicrobial use on dairies. The overall objective of this study was to describe treatment decisions after RFM, severe dystocia (cesarean section and fetotomy), nonsevere dystocia (nonmechanical and mechanical assistance to extract the calf), and twinning. A total of 44 dairies from California's San Joaquin Valley (39 Holstein and 6 Jersey or crossbreed herds) with 450 to 9,500 lactating cows were enrolled in this study. Researchers visited each dairy once to observe cow-side fresh cow health evaluations and to interview health evaluators and maternity workers, using a standardized survey tool. The survey included questions about antimicrobial (class, dose, and duration) and nonantimicrobial therapies for calving-related events. Antimicrobial therapy was used in all 44 dairies to treat RFM at 24 (n = 23), 48 (n = 10), or 72 h (n = 5) after calving, or when puerperal metritis signs were observed (n = 6). Antimicrobial therapy was used after all severe dystocia cases, and after nonsevere dystocia (n = 27) and twinning (n = 15). Ceftiofur products were the most common antimicrobial class; they were used to treat RFM cases (n = 29), nonsevere dystocia (n = 13), and twinning (n = 10). Supportive therapy for calving-related events included nonantimicrobial intrauterine treatments, nonsteroidal antiinflammatory drugs, oxytocin, i.v. calcium, or oral drenches. Our study highlights opportunities to reduce extra-label use of antimicrobials in postpartum cows affected with RFM, and the need for education and outreach efforts on judicious use of antimicrobials. Furthermore, antimicrobial treatment choices differed largely across dairies, indicating a need to reach consensus and promote standardized practices within the industry.

Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California.

The objectives of this study were to characterize overall genomic antibiotic resistance profiles of fecal Escherichia coli and Enterococcus spp. from dairy cattle at different production stages using whole-genome sequencing and to determine the association between antimicrobial resistance (AMR) phenotypes and their corresponding genotypes. The Comprehensive Antibiotic Resistance Database (CARD) and ResFinder, two publicly available databases of antimicrobial resistance genes, were used to annotate isolates. Based on the ResFinder database, 27.5% and 20.0% of tested E. coli isolates (n = 40) harbored single and ≥3 antimicrobial resistance genes, respectively; for Enterococcus spp., we observed 87.8% and 8.2%, respectively. The highest prevalence of AMR genes in E. coli was for resistance to tetracycline (27.5%), followed by sulphonamide (22.5%) and aminoglycoside (20.0%); the predominant antimicrobial resistance genes in Enterococcus spp. targeted macrolide drugs (77.6%). Based on the CARD database, resistance to ≥3 antimicrobial classes was observed in all E. coli and 77.6% in Enterococcus spp. isolates. A high degree of agreement existed between the resistance phenotype and the presence of resistance genes for various antimicrobial classes for E. coli but much less so for isolates of Enterococcus. Consistent with prior work, fecal E. coli and Enterococcus spp. isolates from calves harbored a wide spectrum of resistance genes, compared to those from cattle at other production stages, based on the cross-sectional samples from the studied farm.

Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk.

Contagious bovine mastitis caused by Mycoplasma bovis and other Mycoplasma species including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma canadense is an economical obstacle affecting many dairy herds throughout California and elsewhere. Routine bacteriological culture-based assays for the pathogens are slow and subject to false-positive results due to the presence of the related, non-pathogenic species Acholeplasma laidlawii. To address the need for rapid and accurate detection methods, a new TaqMan multiplex, quantitative real-time PCR (qPCR) assay was developed that targets the 16S rRNA gene of Mycoplasma, rpoB gene of M. bovis, and the 16S to 23S rRNA intergenic transcribed spacer (ITS) region of A. laidlawii. qPCR amplification efficiency and range of detection were similar for individual assays in multiplex as when performed separately. The multiplex assay was able to distinguish between M. bovis and A. laidlawii as well as detect Mycoplasma spp. collectively, including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma canadense, Mycoplasma arginini and Mycoplasma alkalescens. In milk, the lower limit of detection of M. bovis, M. californicum, and A. laidlawii with the multiplex assay was between 120 to 250 colony forming units (CFU) per mL. The assay was also able to simultaneously detect both M. bovis and A. laidlawii in milk when present in moderate (103 to 104 CFU/mL) to high (106 to 107 CFU/mL) quantities. Compared to laboratory culture-based methods, the multiplex qPCR diagnostic specificity (Sp) was 100% (95% CI [86.8–100]; n = 26) and diagnostic sensitivity (Se) was 92.3% (95% CI [74.9–99.1]; n = 26) for Mycoplasma species in milk samples collected from California dairy farms. Similarly, the Sp was 100% (95% CI [90.5–100]; n = 37) and Se was 93.3% (95% CI [68.1–99.8]; n = 15) for M. bovis. Our assay can detect and distinguish among M. bovis, other prevalent Mycoplasma spp., and non-pathogenic Acholeplasma laidlawii for effective identification and control of mycoplasma mastitis, ultimately supporting dairy cattle health and high-quality dairy products in California.

Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach

BackgroundUnderstanding the effects of herd management practices on the prevalence of multidrug-resistant pathogenic Salmonella and commensals Enterococcus spp. and Escherichia coli in dairy cattle is key in reducing antibacterial resistant infections in humans originating from food animals. Our objective was to explore the herd and cow level features associated with the multi-drug resistant, and resistance phenotypes shared between Salmonella, E. coli and Enterococcus spp. using machine learning algorithms.MethodsRandomly collected fecal samples from cull dairy cows from six dairy farms in central California were tested for multi-drug resistance phenotypes of Salmonella, E. coli and Enterococcus spp. Using data on herd management practices collected from a questionnaire, we built three machine learning algorithms (decision tree classifier, random forest, and gradient boosting decision trees) to predict the cows shedding multidrug-resistant Salmonella and commensal bacteria.ResultsThe decision tree classifier identified rolling herd average milk production as an important feature for predicting fecal shedding of multi-drug resistance in Salmonella or commensal bacteria. The number of culled animals, monthly culling frequency and percentage, herd size, and proportion of Holstein cows in the herd were found to be influential herd characteristics predicting fecal shedding of multidrug-resistant phenotypes based on random forest models for Salmonella and commensal bacteria. Gradient boosting models showed that higher culling frequency and monthly culling percentages were associated with fecal shedding of multidrug resistant Salmonella or commensal bacteria. In contrast, an overall increase in the number of culled animals on a culling day showed a negative trend with classifying a cow as shedding multidrug-resistant bacteria. Increasing rolling herd average milk production and spring season were positively associated with fecal shedding of multidrug- resistant Salmonella. Only six individual cows were detected sharing tetracycline resistance phenotypes between Salmonella and either of the commensal bacteria.DiscussionPercent culled and culling rate reflect the increase in culling over time adjusting for herd size and were associated with shedding multidrug resistant bacteria. In contrast, number culled was negatively associated with shedding multidrug resistant bacteria which may reflect producer decisions to prioritize the culling of otherwise healthy but low-producing cows based on milk or beef prices (with respect to dairy beef), amongst other factors. Using a data-driven suite of machine learning algorithms we identified generalizable and distant associations between antimicrobial resistance in Salmonella and fecal commensal bacteria, that can help develop a producer-friendly and data-informed risk assessment tool to reduce shedding of multidrug-resistant bacteria in cull dairy cows.

Feeding high amounts of almond hulls to lactating cows

California is the leading state for the production of almonds, with more than 400,000 bearing hectares of orchards that produced approximately 1 billion kilograms of shelled nuts in 2017. Almond hulls (AH) are a regional by-product feedstuff fed predominantly to dairy cattle in California. A 2012 study surveyed 40 dairy farms in California and found that 39 out of 104 total mixed rations contained AH, with a mean daily feeding rate of 1.45 kg/cow. In 2017, approximately 2 billion kilograms of AH was produced. At a feeding rate of 1.45 kg/cow daily, even if all 1.7 million lactating cows in California are consuming AH, there will be a surplus of AH on the market as the approximately 130,000 nonbearing hectares come into nut production. Therefore, the potential of feeding varying amounts of AH to lactating dairy cows was investigated using 12 Holstein cows with 4 primiparous and 8 multiparous cows. The dietary treatments were 4 total mixed rations containing 0, 7, 13, or 20% AH. The AH used contained 12.8% crude fiber (as-is basis), which was below the 15% legal limit set by state feed regulations. Diets were formulated so that as the inclusion rate of AH increased, the amount of steam-flaked corn and soyhull pellets decreased and soybean meal inclusion increased. Experimental design was a replicated 4 × 4 Latin square. Diet had a cubic effect on actual milk yield, energy-corrected milk yield, and dry matter intake, with the 7% AH diet having the highest values and the 13% AH diet having the lowest. The percent and yield of total solids and the yields of lactose and fat did not differ with diet, but percent and yield of protein declined linearly with increased AH inclusion, and fat percent increased linearly. Apparent total-tract digestibilities of dry matter and organic matter were higher with the inclusion of AH in the diet. Total percentage of the day spent ruminating increased linearly with higher amounts of AH. Overall, this work demonstrated that AH can be fed at varying amounts, up to 20% of the diet, to lactating dairy cows to support high levels of milk production and that increasing amounts of AH (up to 20%) in the diet could lead to improved digestibility and milk fat percentage but decreased milk protein production.

Development of an on-farm model to predict flow of fecal volatile solids to the liquid and solid handling systems of commercial California dairy farms

A source of methane (CH4) emissions from dairy farms arefecal volatile solids (VS) produced by cattle, which is impacted by herd size, cattle type, feed intake/composition and farm management practices. Where cattle deposit fecal VS in their pen is important in this regard since that deposited on concrete, which will be handled and stored in a liquid form, is a likely source of CH4 emissions, whereas fecal VS deposited on drylot surfaces will be handled and stored in a dry form and is a minor source of CH4 emissions. Our objective was to create a model to assist dairy farmers and regulators make informed evaluations of impacts of dairy farm management practices on potential CH4 emissions from fecal VS. Evaluation of initial model outputs led to on-farm data collection of the model inputs which influenced predicted fecal VS entering the liquid and solid manure handling systems. A key input limitation was lack of information on cattle fecal deposition locations within pens. Data collection used four dairy farms to measure time that cattle spent on concrete surfaces within day among season, as well as other model inputs. The final model, populated with collected data, showed that lactating cattle contribute the overwhelming proportion of fecal VS, 77% in the composite dairy farms, and that a composite freestall dairy farm had 65% of total fecal VS deposited on concrete annually with the remainder on drylot surfaces. In contrast, a composite drylot dairy farm had 37% of fecal VS deposited on concrete annually.