Effects of simplified group housing on behavior, welfare, growth performance, and health of preweaned dairy calves on a California dairy.

Most US dairy calves are raised in individual hutches for biocontainment purposes and to facilitate monitoring and handling of calves. However, individual hutches typically restrict calves' activity and social interactions. Previous studies showed that group housing (GH) is beneficial to calf welfare and is associated with social benefits. The adoption of GH on dairies is hindered by several concerns, with the primary concern being the potential for increased transmission of diseases due to heightened calf-to-calf contact. In light of this, our study aimed to compare the behavior, health, and growth outcomes of calves housed in groups of 3 to individually housed (IH) calves during the preweaning period. A total of 42 Holstein heifer calves on a commercial dairy in Northern California were enrolled in groups of 3 to different housing treatments; IH (n = 21) or GH (n = 21) between July and October 2020. Each treatment was composed of 7 groups of 3 calves each. Calves in the GH treatment were housed in groups of 3 from 6 to 10 d until 70 d of age. Individual pens consisted of one polyethylene hutch with a 1.5 m × 1.2 m outside exercise area. Group pens were constructed by assembling 3 polyethylene hutches with a 1.5 m × 3.6 m outside exercise area of wire panel fencing. Calves were weighed and measured for height at birth and weaning. Diarrhea and bovine respiratory disease (BRD) scores were recorded daily throughout the preweaning period. Cumulative incidence and hazard ratios were estimated for BRD and diarrhea for GH and IH. A mixed model with pen as a random effect was specified to evaluate the effect of treatment. Group-housed calves gained 0.64 ± 0.02 kg/d while IH calves gained 0.65 ± 0.02 kg/d. Similarly, there was no evidence for treatment differences in withers height gain in GH calves (0.22 ± 0.01 cm/d) compared with IH calves (0.21 ± 0.01 cm/d). The cumulative incidence of BRD based on the California scoring system in GH calves was 75 ± 9.68% compared with 66.66 ± 10.28% in IH calves. Group-housed calves had a BRD hazard of 1.14 times that of IH calves (95% CI: 1.21-2.40). The cumulative incidence of diarrhea (fecal score 3) in GH calves was 100% in comparison to 95.20% ± 4.66% in IH calves. The mean proportion of scan observations of calves feeding on concentrates was significantly higher in GH (0.145 ± 0.004/h) compared with IH calves (0.076 ± 0.003/h) during the preweaning period. The study results provide evidence that this simplified GH system provides benefits of GH without detrimental short-term effects on calf growth and health during the preweaning period.

Antimicrobial resistance of Escherichia coli from dairy farms participating in an antimicrobial stewardship educational program for farm employees.

Antimicrobial use in food-producing animals is under increasing scrutiny due to the potential effect on the selection of antimicrobial-resistant bacteria that may be transmitted to humans by direct contact, with the food chain, or the environment. Novel data monitoring commensal Escherichia coli from dairy farms is essential for understanding antimicrobial resistance (AMR) patterns and their association with herd health management practices. The objectives of this study were to: (1) compare the prevalence of antimicrobial resistance in the E. coli isolates from the hospital, fresh, and mid-lactation pens from 18 conventional dairy farms participating in an educational training program in antimicrobial stewardship practices in California and Ohio, and (2) to characterize the prevalence of antimicrobial resistance of commensal E. coli isolated from pooled fecal pat samples before and 3 mo after participating in the educational training program. Pooled fecal pat samples were collected from the hospital pen, the fresh pen (1 to 5 DIM), and the mid-lactation pens (90 to 150 DIM) on conventional dairies in CA (n = 9) and OH (n = 9). Fecal samples were collected as part of a larger study using a quasi-experimental design that assigned farms to the training intervention group (TG; 6 per state) or the control group (CG; 3 per state). For the TG, farm worker(s) identified as having the task of diagnosis and treatment of adult cows on the farm participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 mo after completing the intervention on each of the participating farms (n = 18), followed by culture for E. coli isolation and antimicrobial sensitivity testing using the broth microdilution methodology. Logistic regression models were used to evaluate the association between E. coli antimicrobial resistance patterns with the training intervention and farm-level factors. No effect was observed in the prevalence of resistant isolates between the control and intervention farms after the training was delivered. Isolates from the hospital pens were 2.48 (95% CI: 1.06-6.22, P = 0.03) and 5.61 (95% CI: 1.94-16.91, P < 0.001) times, more likely to be resistant to streptomycin and chloramphenicol, respectively, than isolates from the mid-lactation pens. Our findings indicate there was a higher prevalence of AMR in E. coli associated with the hospital pen within the farm, while the training program for 3 mo did not affect the prevalence of AMR in E. coli on the farms participating in the program. Further research efforts should be conducted to identify factors driving AMR at the pen level, as well as approaches that could be used to reduce the risk of disseminating AMR from sick pens to animals being housed and to other pens on the farm.

Antimicrobial stewardship on the dairy: Evaluating an on-farm framework for training farmworkers.

Dairy farmworkers are commonly responsible for disease diagnosis and routine treatment decisions for cattle. This highlights the importance of farmworkers' knowledge and skills to successfully implement judicious use of antimicrobials in livestock production systems. The main objectives of this project were to develop and evaluate an on-farm educational program for farmworkers in antimicrobial stewardship in adult dairy cattle. A longitudinal quasi-experimental study design was used, by enrolling 12 conventional dairy farms in the United States (6 in California and 6 in Ohio). Farmworkers responsible for treatment decisions on the farm (n = 25) participated in a didactic and hands-on 12-wk antimicrobial stewardship training program led by the investigators. All antimicrobial stewardship training materials were available in Spanish and English. Interactive short videos with audio were developed to cover the learning objectives for each of the 6 teaching modules: antimicrobial resistance, treatment protocols, visual identification of sick animals, clinical mastitis, puerperal metritis, and lameness. Pre- and post-training assessments were administered using an online training assessment tool to evaluate changes in knowledge and attitudes about antimicrobial stewardship practices. Cluster analysis and multiple correspondence analyses were conducted to evaluate the association among categorical variables for participants' level of change in knowledge and its association with language, farm size, and state. A 32% average increase in knowledge was observed through an assessment conducted after completing the antimicrobial stewardship training, compared with the pre-training assessment. A significant improvement in 7 of 13 attitude questions related to antimicrobial stewardship practices on the farm was observed. Knowledge and attitude scores of participants on antimicrobial stewardship and identification of sick animals significantly improved after completing the antimicrobial stewardship training. The results observed in this study support the relevance of antimicrobial stewardship training programs targeting farmworkers to improve antimicrobial drug use knowledge and skills.

Development of a clinical scoring system for bovine respiratory disease in weaned dairy calves.

Clinical scoring systems for bovine respiratory disease (BRD) in weaned dairy calves have been developed in the past with calves experimentally infected with specific respiratory pathogens. In this prevalent case control study, a BRD clinical scoring system for weaned calves was developed using field data from 689 dairy calves housed in group pens on 5 dairies in California. Of the 689 calves in the study, 89 were selected because they appeared sick based on the display of lethargy, depression, or separation from the group, whereas the remaining 600 were randomly selected. Clinical signs were recorded for all calves, and BRD case status was determined by thoracic auscultation and ultrasound examinations, which were interpreted in parallel. Of the 689 calves, 238 were identified as BRD cases. Five survey-adjusted generalized linear mixed models with a logit link function, calf as the unit of analysis, and dairy as a random intercept were assessed using 3-fold cross-validation. The best model chosen based on performance and parsimony contained the variables cough (2 points), abnormal respiration (1 point), low body condition (5 points), sunken eyes (4 points), and a 24-h ambient temperature range >15°C (1 point) with a 2-point cutoff for a BRD suspect score. An alternative model did not contain a score for the covariate 24-h ambient temperature range and had a 1-point cutoff. The best model was tested on 174 observations not used for model training and resulted in 77.0% screening sensitivity, 100% diagnostic sensitivity, and 61.9% specificity. Adding rectal temperature ≥39.2°C (102.5°F) as a second-tier test increased specificity to 76.7% and lowered the screening sensitivity to 64.8% and diagnostic sensitivity to 76.9%. The alternative model had a screening sensitivity of 84.2%, diagnostic sensitivity of 100%, and specificity of 45.7%. Adding rectal temperature ≥39.2°C (102.5°F) as a second-tier test for score-positive animals improved specificity of the alternative model to 62.6% while lowering its screening sensitivity to 70.5% and diagnostic sensitivity to 76.9%. Use of a 2-tier California BRD postweaning scoring system may provide producers and veterinarians with a new tool to monitor BRD in group-housed dairy calves. Furthermore, the scoring system may aid in judicious medical intervention for BRD cases and reduce unnecessary treatments of animals with antimicrobials.

WGS of intrauterine E. coli from cows with early postpartum uterine infection reveals a non-uterine specific genotype and virulence factors.

Escherichia coli has been attributed to playing a major role in a cascade of events that affect the prevalence and severity of uterine disease in cattle. The objectives of this project were to (i) define the association between the prevalence of specific antimicrobial resistance and virulence factor genes in E. coli with the clinical status related to uterine infection, (ii) identify the genetic relationship between E. coli isolates from cows with diarrhea, with mastitis, and with and without metritis, and (iii) determine the association between the phenotypic and genotypic antimicrobial resistance identified on the E. coli isolated from postpartum cattle. Bacterial isolates (n = 148) were obtained from a larger cross-sectional study. Cows were categorized into one of three clinical groups before enrollment: metritis, cows with purulent discharge, and control cows. For genomic comparison, public genomes (n = 130) from cows with diarrhea, mastitis, and metritis were included in a genome-wide association study, to evaluate differences between the drug classes or the virulence factor category among clinical groups. A distinct E. coli genotype associated with metritis could not be identified. Instead, a high genetic diversity among the isolates from uterine sources was present. A virulence factor previously associated with metritis (fimH) using PCR was not associated with metritis. There was moderate accuracy for whole-genome sequencing to predict phenotypic resistance, which varied depending on the antimicrobial tested. Findings from this study contradict the traditional pathotype classification and the unique intrauterine E. coli genotype associated with metritis in dairy cows.IMPORTANCEMetritis is a common infectious disease in dairy cattle and the second most common reason for treating a cow with antimicrobials. The pathophysiology of the disease is complex and is not completely understood. Specific endometrial pathogenic Escherichia coli have been reported to be adapted to the endometrium and sometimes lead to uterine disease. Unfortunately, the specific genomic details of the endometrial-adapted isolates have not been investigated using enough genomes to represent the genomic diversity of this organism to identify specific virulence genes that are consistently associated with disease development and severity. Results from this study provide key microbial ecological advances by elucidating and challenging accepted concepts for the role of Intrauterine E. coli in metritis in dairy cattle, especially contradicting the existence of a unique intrauterine E. coli genotype associated with metritis in dairy cows, which was not found in our study.

Effect of Group Housing of Preweaned Dairy Calves: Health and Fecal Commensal Antimicrobial Resistance Outcomes.

The objectives of this study were to investigate the effects of group housing (three calves per group) on bovine respiratory disease (BRD), diarrhea and antimicrobial resistance (AMR) to fecal commensal Escherichia coli (EC) and enterococci/streptococci (ES). Our study comprised two arms, one experimental and one observational. In the experimental arm, preweaned calves on a California dairy were randomized to either individual (IND; n = 21) or group (GRP; n = 21) housing, using a modified California-style wooden hutch. The study period lasted from birth to 56 days of age, during which calves were health scored daily. Cumulative incidence and hazard ratios were estimated for disease. Antimicrobial resistance outcomes were assessed using a prospective cohort design; feces were collected from each calf three times per week and EC and ES were evaluated for AMR using the broth microdilution method against a panel of 19 antimicrobial drugs (AMD). Analysis of treatment records was used to select calves that had been exposed (EXP) to an AMD-treated calf. In GRP, exposure occurred when a calf was a hutchmate with an AMD-treated calf. In IND, exposure occurred when a calf was a neighbor with an AMD-treated calf (TRT). Age-matched unexposed calves (UNEXP) were then selected for comparison. Proportions of AMR in fecal commensals among EXP, UNEXP, and TRT calves were compared between GRP and IND. Accelerated failure time survival regression models were specified to compare differences in minimum inhibitory concentration (MIC) of fecal commensals between EXP and UNEXP calves within each of GRP and IND calves separately. Group calves had a BRD hazard 1.94 times greater that of IND calves (p = 0.03), using BRD treatment records as the outcome. For AMR in EC isolates, higher resistance to enrofloxacin was detected in enrofloxacin-EXP GRP isolates compared with enrofloxacin-EXP IND isolates, and UNEXP GRP calves had lower resistance to ceftiofur compared with enrofloxacin-EXP and enrofloxacin-TRT calves. A significant housing-by-time interaction was detected for EC ceftiofur MIC in EXP GRP calves at 4-14 days post exposure to enrofloxacin (MIC EXP-UNEXP: µg/mL (95% CI): 10.62 (1.17, 20.07)), compared with UNEXP calves. The findings of this study show an increase in BRD hazard for group-housed calves and an increase in ceftiofur resistance in group-housed calves exposed to an enrofloxacin-treated calf.

Effect of Intramammary Dry Cow Antimicrobial Treatment on Fresh Cow's Milk Microbiota in California Commercial Dairies.

This study used 16S rRNA sequencing to evaluate the effects of dry cow antimicrobial therapy on the udder milk microbiota by comparing the microbial populations in milk at dry-off (DRY) (~60 days before calving) and post-partum (FRESH) (4-11 days after calving) from cows receiving an intramammary antibiotic infusion prior to dry-off (IMT) and cows that did not receive treatment (CTL). Milk was collected from 23 cows from the IMT group and 27 cows from the CTL group. IMT and DRY samples had a greater correlation with the genera Brevibacterium and Amaricoccus, and the family Micrococcaceae, when compared to IMT and FRESH samples. CTL group samples collected at DRY had a greater correlation with the genera Akkermansia and Syntrophus, when compared to FRESH samples; no bacterial taxa were observed to have a significant correlation with FRESH samples in the CTL group. DRY samples collected from the CTL group had a greater correlation with the genus Mogibacterium when compared to IMT and CTL samples. For DRY samples collected from the IMT group, a greater correlation with the genus Alkalibacterium when compared to DRY and CTL samples, was observed. The lack of a correlation for FRESH samples between the CTL and IMT treatment groups indicated that intramammary antimicrobial dry cow therapy had no significant effect on the udder milk microbiota post-partum.

Factors Associated with Antimicrobial Stewardship Practices on California Dairies: One Year Post Senate Bill 27.

BACKGROUND: The current study is aimed at identifying the factors associated with antimicrobial drug (AMD) use and stewardship practices on conventional California (CA) dairies a year after CA Senate Bill 27. METHODS: Responses from 113 out of 1282 dairies mailed a questionnaire in 2019 were analyzed to estimate the associations between management practices and six outcomes including producer familiarity with medically important antimicrobial drugs (MIADs), restricted use of MIADs previously available over the counter (OTC), use of alternatives to AMD, changes in on-farm management practices, changes in AMD costs, and animal health status in dairies. RESULTS: Producers who reported having a veterinarian-client-patient relationship (VCPR) and tracking AMD withdrawal intervals had greater odds of being familiar with the MIADs. Producers who began or increased the use of preventive alternatives to AMD in 2019 had higher odds (OR = 3.23, p = 0.04) of decreased use of MIADs previously available OTC compared to those who did not. Changes in management practices to prevent disease outbreak and the use of diagnostics to guide treatment were associated with producer-reported improved animal health. In addition, our study identified record keeping (associated with familiarity with MIADs), use of alternatives to AMD (associated with management changes to prevent diseases and decreased AMD costs), and use of diagnostics in treatment decisions (associated with reported better animal health) as factors associated with AMD stewardship. CONCLUSIONS: Our survey findings can be incorporated in outreach education materials to promote antimicrobial stewardship practices in dairies.

2018 Survey of antimicrobial drug use and stewardship practices in adult cows on California dairies: post-Senate Bill 27.

BACKGROUND: A survey of California (CA) dairies was performed in spring 2018 to characterize antimicrobial stewardship practices, antimicrobial drug (AMD) use, and health management of adult cows on CA dairies since the implementation of the Veterinary Feed Directive (VFD) and the CA Senate Bill 27 (SB 27). Effective January 1, 2017, the U.S. Food and Drug Administration (FDA) implemented regulatory changes requiring veterinary oversight for therapeutic uses of medically-important antimicrobial drugs (MIADs) administered in feed (VFD) and water (veterinary prescription). Similarly, effective January 1, 2018, the CA legislature enacted California Food and Agricultural Code (FAC) 14400-14408, formerly known as Senate Bill 27 (SB 27) requiring veterinary prescriptions for all other dosage forms of MIADs. METHODS: The questionnaire consisted of 43 questions partitioned into three sections to assess herd information, management practices, and AMD use and perspectives. The questionnaire was mailed to 1,282 grade A licensed dairies in CA and 149 responses (11.6%) were collected from 19 counties across the three defined regions of CA: Northern CA (NCA), Northern San Joaquin Valley (NSJV), and Greater Southern CA (GSCA). RESULTS: Most dairies reported treating all dry cows with intramammary AMD and/or teat sealant at the end of a lactation (87.2%). In 92.3% of dairies, producers relied on the veterinarian for information about AMD used to treat cows. Treatment duration for cows treated with AMD was based on the drug manufacturer's label and veterinarian's instructions in most dairies (98.6%). Most respondents to the survey confirmed having a valid veterinarian-client-patient-relationship (VCPR) for their dairies (91.7%), participated in animal welfare audit programs (81.8%) and dairy quality assurance programs (52.9%). Approximately 98.6% respondents were aware that all uses of MIADs in livestock required a veterinary feed directive (VFD) or prescription and are no longer sold over-the-counter (OTC) in CA since January 1, 2018. Multiple factor analysis (MFA) was performed and identified seven components composed of 21 variables (questions) that explained 99.7% of the total variance in the data. Hierarchical cluster analysis on the principal coordinates of the MFA based on conventional dairy survey responses identified two clusters characterized as large conventional dairies (median herd size: 1,265 cows) and mid-sized conventional dairies (median herd size: 715 cows) mostly in GSCA and NSJV. The organic dairies grouped into a single cluster of median herd size of 325 cows mostly in NCA. CONCLUSIONS: The survey results contribute to the knowledge of AMD use and antimicrobial stewardship practices on CA dairies since the implementation of the SB 27 and VFD laws and provide useful information for future evaluation of resistance-related risk in adult cows.

2018 Survey of factors associated with antimicrobial drug use and stewardship practices in adult cows on conventional California dairies: immediate post-Senate Bill 27 impact.

BACKGROUND: Antimicrobial drugs (AMD) are critical for the treatment, control, and prevention of diseases in humans and food-animals. Good AMD stewardship practices and judicious use of AMD are beneficial to the preservation of animal and human health from antimicrobial resistance threat. This study reports on changes in AMD use and stewardship practices on California (CA) dairies, following the implementation of CA Senate Bill 27 (SB 27; codified as Food and Agricultural Code, FAC 14400-14408; here onward referred to as SB 27), by modeling the associations between management practices on CA conventional dairies and seven outcome variables relating to AMD use and stewardship practices following SB 27. METHODS: A survey questionnaire was mailed to 1,282 grade A licensed dairies in CA in spring of 2018. Responses from 132 conventional dairies from 16 counties were included for analyses. Multivariate logistic regression models were specified to explore the associations between survey factors and six outcome variables: producers' familiarity with the Food and Drug Administration's (FDA), Silver Spring, WA, USA medically important antimicrobial drugs (MIAD) term; change in over-the-counter (OTC) AMD use; initiation or increased use of alternatives to AMD; changes to prevent disease outbreaks; changes in AMD costs; and better animal health post SB 27. We employed machine learning classification models to determine which of the survey factors were the most important predictors of good-excellent AMD stewardship practices of CA conventional dairy producers. RESULTS: Having a valid veterinary-client-patient-relationship, involving a veterinarian in training employees on treatment protocols and decisions on AMDs used to treat sick cows, tracking milk and/or meat withdrawal intervals for treated cows, and participating in dairy quality assurance programs were positively associated with producers' familiarity with MIADs. Use or increased use of alternatives to AMDs since 2018 was associated with decreased use of AMDs that were previously available OTC prior to SB 27. Important variables associated with good-excellent AMD stewardship knowledge by CA conventional dairy producers included having written or computerized animal health protocols, keeping a drug inventory log, awareness that use of MIADs required a prescription following implementation of SB 27, involving a veterinarian in AMD treatment duration determination, and using selective dry cow treatment. CONCLUSIONS: Our study identified management factors associated with reported AMD use and antimicrobial stewardship practices on conventional dairies in CA within a year from implementation of SB 27. Producers will benefit from extension outreach efforts that incorporate the findings of this survey by further highlighting the significance of these management practices and encouraging those that are associated with judicious AMD use and stewardship practices on CA conventional dairies.

2019 Survey of Antimicrobial Drug Use and Stewardship Practices in Adult Cows on California Dairies: Post Senate Bill 27.

Antimicrobial resistance (AMR) is a global issue for both human and animal health. Antimicrobial drug (AMD) use in animals can contribute to the emergence of AMR. In January 2018, California (CA) implemented legislation (Senate Bill 27; SB 27) requiring veterinary prescriptions for medically important AMD use in food animals. The objective of our survey was to characterize AMD use, health management, and AMD stewardship practices of adult cows on CA dairies since the implementation of SB 27. In 2019, we mailed a questionnaire to 1282 California dairies. We received a total of 131 (10.2%) survey responses from 19 counties in CA. Our results showed that 45.6% of respondents included a veterinarian in their decision on which injectable AMD to purchase. Additionally, 48.8% of dairy producers included a veterinarian in their decision on which AMDs were used to treat sick cows. The majority (96.8%) of dairy producers were aware that all uses of medically important AMDs require a prescription. Approximately 49% of respondents agreed or strongly agreed that AMD use in livestock does not cause problems in humans. The survey documents antimicrobial use and stewardship practices in CA's dairy industry and focus areas for future research and education.

Estimating the Rates of Acquisition and loss of Resistance of Enterobacteriaceae to Antimicrobial Drugs in Pre-Weaned Dairy Calves.

The objective of this study was to investigate the effect of the antimicrobial drugs (AMD) on the shedding of resistant Enterobacteriaceae in feces of pre-weaned dairy calves. The AMD considered were ceftiofur, administered parenterally, and neomycin sulfate added in milk replacer and fed to calves during the first 20 days of life. Fifty-five calves, aged one to three days, were enrolled and followed to 64 days. Fecal samples were collected three times/week and treatments recorded daily. Enterobacteriaceae were quantified for a subset of 33 calves using spiral plating on plain, ceftiofur supplemented, and neomycin supplemented MacConkey agar. Negative binomial models were used to predict the association between treatment with AMD and the gain and loss of Enterobacteriaceae resistance over time. Acquisition of resistance by the Enterobacteriaceae occurred during treatment and peaked between days three to four post-treatment before decreasing to below treatment levels at days seven to eight post-treatment. Acquisition of neomycin resistance was observed on the first sampling day (day four from the start of feeding medicated milk replacer) to day eight, followed by cyclical peaks until day 29, when the Enterobacteriaceae counts decreased below pre-treatment. Enterobacteriaceae resistance against both AMD increased after AMD administration and didn't return to pre-therapeutic status until seven or more days after therapy had been discontinued. The study findings provide valuable insights into the dynamics of Enterobacteriaceae under routine AMD use in calves.

Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows.

BACKGROUND: This study describes the occurrence of antimicrobial resistance (AMR) in commensal Escherichia coli and Enterococcus/Streptococcus spp. (ES) isolated from fecal samples of dairy cows and assesses the variation of AMR profiles across regions and seasons following the implementation of the Food and Agricultural Code (FAC) Sections 14400-14408 (formerly known as Senate Bill, SB 27) in California (CA). METHODS: The study was conducted on ten dairies distributed across CA's three milk sheds: Northern California (NCA), Northern San Joaquin Valley (NSJV), and the Greater Southern California (GSCA). On each study dairy, individual fecal samples were collected from two cohorts of lactating dairy cows during the fall/winter 2018 and spring/summer 2019 seasons. Each cohort comprised of 12 cows per dairy. The fecal samples were collected at enrollment before calving (close-up stage) and then monthly thereafter for four consecutive time points up to 120 days in milk. A total of 2,171 E. coli and 2,158 ES isolates were tested for antimicrobial susceptibility using the broth microdilution method against a select panel of antimicrobials. RESULTS: The E. coli isolates showed high resistance to florfenicol (83.31% ± 0.80) and sulphadimethoxine (32.45%), while resistance to ampicillin (1.10% ± 0.21), ceftiofur (1.93% ± 0.29), danofloxacin (4.01% ± 0.42), enrofloxacin (3.31% ± 0.38), gentamicin (0.32% ± 0.12) and neomycin (1.61% ± 0.27) had low resistance proportions. The ES isolates were highly resistant to tildipirosin (50.18% ± 1.10), tilmicosin (48% ± 1.10), tiamulin (42%) and florfenicol (46% ± 1.10), but were minimally resistant to ampicillin (0.23%) and penicillin (0.20%). Multidrug resistance (MDR) (resistance to at least 1 drug in ≥3 antimicrobial classes) was observed in 14.14% of E. coli isolates and 39% of ES isolates. Escherichia coli isolates recovered during winter showed higher MDR prevalence compared to summer isolates (20.33% vs. 8.04%). A higher prevalence of MDR was observed in NSJV (17.29%) and GSCA (15.34%) compared with NCA (10.10%). CONCLUSIONS: Our findings showed high rates of AMR to several drugs that are not labeled for use in lactating dairy cattle 20 months of age or older. Conversely, very low resistance was observed for drugs labeled for use in adult dairy cows, such as cephalosporins and penicillin. Overall, our findings identified important differences in AMR by antimicrobial class, region and season.

Components of a risk assessment tool for prevention and control of bovine respiratory disease in preweaned dairy calves.

Bovine respiratory disease (BRD) is the leading natural cause of death in US beef and dairy cattle, causing the annual loss of more than 1 million animals and financial losses in excess of $700 million. The multiple etiologies of BRD and its complex web of risk factors necessitate a herd-specific intervention plan for its prevention and control on dairies. Hence, a risk assessment is an important tool that producers and veterinarians can utilize for a comprehensive assessment of the management and host factors that predispose calves to BRD. The current study identifies the steps taken to develop the first BRD risk assessment tool and its components, namely the BRD risk factor questionnaire, the BRD scoring system, and a herd-specific BRD control and prevention plan. The risk factor questionnaire was designed to inquire on aspects of calf-rearing including management practices that affect calf health generally, and BRD specifically. The risk scores associated with each risk factor investigated in the questionnaire were estimated based on data from two observational studies. Producers can also estimate the prevalence of BRD in their calf herds using a smart phone or tablet application that facilitates selection of a true random sample of calves for scoring using the California BRD scoring system. Based on the risk factors identified, producers and herd veterinarians can then decide the management changes needed to mitigate the calf herd's risk for BRD. A follow-up risk assessment after a duration of time sufficient for exposure of a new cohort of calves to the management changes introduced in response to the risk assessment is recommended to monitor the prevalence of BRD.

Evaluation of four commercial tests for detecting ceftiofur in waste milk bulk tank samples.

The objective of this study was to identify factors affecting the accuracy of four commercial tests for ceftiofur drug residue in milk samples from bulk tank waste milk (WM). WM samples were collected from 12 California dairy farms which were initially tested using liquid chromatography (LC-MS/MS) to confirm their negative status for drug residues above the FDA established tolerance/safe levels. The milk samples were also tested for fat, protein, lactose, solids non-fat (SNF), somatic cell count (SCC), coliform count, and standard plate count (SPC). Each WM sample was divided into two aliquots, one labeled as negative for drug residues (WMN) and the second spiked with ceftiofur as positive for ceftiofur residues (WMPos). Both types of WM samples were tested to evaluate the performance of 4 commercially available tests: Penzyme® Milk Test, SNAP® ß-lactam, BetaStar® Plus and Delvo SP-NT®. Three assays in triplicates for the WMN and WMPos were conducted for each WM sample. Test were evaluated using sensitivity, specificity, positive predictive value, negative predictive value and positive likelihood ratio. Kruskal-Wallis method was used to evaluate the effect of milk quality parameters on true positive (TP) and false negative (FN) test results. All WMPos samples were identified as positive by all four tests, rendering 100% sensitivity for each test. The specificity for Penzyme, BetaStar, Delvo, and SNAP tests were 59.2, 55.5, 44.4, and 29.6, respectively. Overall, all tests correctly identified samples with ceftiofur residues (WMPos), as shown by 100% sensitivity. Greater variability was observed regarding identification of samples free of any drug residue, with Penzyme and BetaStar having the highest risk for correctly identifying TN samples. Our findings indicate that when selecting commercial tests to detect drug residues in WM, milk quality parameters must be considered if the aim is to reduce FP test results.

Optimizing accuracy of sampling protocols to measure nutrient content of solid manure.

Precise applications of manure to cropland can help optimize productivity and minimize environmental nutrient losses. Applying manure precisely is a challenge because the nutrient content of manures is inherently variable and the accuracy of sampling protocols are unknown. This study aimed to quantify the accuracy of sampling protocols for static solid manure piles considering both the number and depth of grab samples entering a composite sample. Over 35 grab samples were collected from each of ten static piles of dairy manure in California's Central Valley. Grab samples were individually analyzed for dry matter (DM), ash, total nitrogen, potassium, and phosphorous concentrations. Resampling simulations quantified the precision and bias of sampling protocols varying in both grab sample number and depth. Results showed that number of grab samples required for measurements to meet an accuracy standard of ±10% of the true value varied significantly by pile makeup. Over 25 grab samples were often required for multi-source manure piles, where an average of six grab samples were required from single source piles. The DM concentration of manure piles decreased at depths greater than 0.4 m, and sampling simulations showed that measurements were biased unless 70-80% of grab samples were collected from the pile interior. Both the number and location of grab samples necessary to create a representative composite require resource investments by farmers, and should be considered to manage nutrient applications cropland.

Fecal Microbial Communities in a Large Representative Cohort of California Dairy Cows.

Improved sequencing and analytical techniques allow for better resolution of microbial communities; however, the agriculture field lacks an updated analysis surveying the fecal microbial populations of dairy cattle in California. This study is a large-scale survey to determine the composition of the bacterial community present in the feces of lactating dairy cattle on commercial dairy operations. For the study, 10 dairy farms across northern and central California representing a variety of feeding and management systems were enrolled. The farms represented three typical housing types including five freestall, two drylot and three pasture-based management systems. Fresh feces were collected from 15 randomly selected cows on each farm and analyzed using 16S rRNA gene amplicon sequencing. This study found that housing type, individual farm, and dietary components significantly affected the alpha diversity of the fecal microbiota. While only one Operational Taxonomic Unit (OTU) was common among all the sampled individuals, 15 bacterial families and 27 genera were shared among 95% of samples. The ratio of the families Coriobacteriaceae to Bifidobacteriaceae was significantly different between housing types and farms with pasture fed animals having a higher relative abundance of Coriobacteriaceae. A majority of samples were positive for at least one OTU assigned to Enterobacteriaceae and 31% of samples contained OTUs assigned to Campylobacter. However, the relative abundance of both taxa was <0.1%. The microbial composition displays individual farm specific signatures, but housing type plays a role. These data provide insights into the composition of the core fecal microbiota of commercial dairy cows in California and will further generate hypotheses for strategies to manipulate the microbiome of cattle.

Developing risk models of Cryptosporidium transport in soils from vegetated, tilted soilbox experiments.

Transport of Cryptosporidium parvum through macroporous soils is poorly understood yet critical for assessing the risk of groundwater contamination. We developed a conceptual model of the physics of flow and transport in packed, tilted, and vegetated soilboxes during and immediately after a simulated rainfall event and applied it to 54 experiments implemented with different soils, slopes, and rainfall rates. Using a parsimonious inverse modeling procedure, we show that a significant amount of subsurface outflow from the soilboxes is due to macropore flow. The effective hydraulic properties of the macropore space were obtained by calibration of a simple two-domain flow and transport model that accounts for coupled flow in the matrix and in the macropores of the soils. Using linear mixed-effects analysis, macropore hydraulic properties and oocyst attenuation were shown to be associated with soil bulk density and rainfall rate. Macropore flow was shown to be responsible for bromide and C. parvum transport through the soil into the underlying pore space observed during the 4-h experiments. We confirmed this finding by conducting a pair of saturated soil column studies under homogeneously repacked conditions with no macropores in which no C. parvum transport was observed in the effluent. The linear mixed-effects and logistic regression models developed from the soilbox experiments provide a basis for estimating macropore hydraulic properties and the risk of C. parvum transport through shallow soils from bulk density, precipitation, and total shallow subsurface flow rate. The risk assessment is consistent with the reported occurrence of oocysts in springs or groundwater from fractured or karstic rocks protected only by shallow overlying soils.

Optimizing accuracy of protocols for measuring dry matter and nutrient yield of forage crops.

Farmers around the world must precisely manage nutrients applied to and removed from crop fields to maintain production and without causing nutrient pollution. This study is the first to quantify the baseline accuracy of current industry measurement protocols and achievable accuracy from intensifying protocols for measuring dry matter (DM), nitrogen (N), potassium (K), and phosphorus (P) yields from forage crops harvested for silage. The 'true' DM and nutrient yields of three fields each of corn, sorghum, and small grain were intensively measured by weighing and sampling every truckload of harvested forage. Simulations quantified the accuracy of practical sampling protocols by repeatedly subsampling the complete dataset for each field to measure average truckload weight and average DM and nutrient concentrations. Then uncertainty was propagated to DM, N, P, and K yield calculations using standard error equations. Yields measured using current industry protocols diverged from the true yields of some fields by more than ±40%, emphasizing the need for improved protocols. This study shows that improving average DM and nutrient concentration measurements is unlikely to improve accuracy of yield measurements if average load weight is not precisely measured. Accuracy did not come within 27% of true yields without weighing all truckloads on some fields even when DM and nutrient concentration measurements were perfectly accurate. Once all truckloads were weighed, the timing of forage sample collection to measure average DM concentration had the greatest impact on accuracy; precision improved by an average of 6.2% when >3 samples were evenly spaced throughout the harvest compared to the same number of consecutive samples. All crop fields are affected by within field variation in growing conditions that results in heterogeneity in DM and nutrient yield. Globally, this study provides foundational methodology to quantitatively evaluate and improve yield measurement protocols that ultimately support sustainable crop production.

Transport of Cryptosporidium parvum oocysts through vegetated buffer strips and estimated filtration efficiency.

Vegetated buffer strips were evaluated for their ability to remove waterborne Cryptosporidium parvum from surface and shallow subsurface flow during simulated rainfall rates of 15 or 40 mm/h for 4 h. Log(10) reductions for spiked C. parvum oocysts ranged from 1.0 to 3.1 per m of vegetated buffer, with buffers set at 5 to 20% slope, 85 to 99% fescue cover, soil textures of either silty clay (19:47:34 sand-silt-clay), loam (45:37:18), or sandy loam (70:25:5), and bulk densities of between 0.6 to 1.7 g/cm(3). Vegetated buffers constructed with sandy loam or higher soil bulk densities were less effective at removing waterborne C. parvum (1- to 2-log(10) reduction/m) compared to buffers constructed with silty clay or loam or at lower bulk densities (2- to 3-log(10) reduction/m). The effect of slope on filtration efficiency was conditional on soil texture and soil bulk density. Based on these results, a vegetated buffer strip comprised of similar soils at a slope of or=3 m should function to remove >or=99.9% of C. parvum oocysts from agricultural runoff generated during events involving mild to moderate precipitation.