Development and validation of a fully automated 2-dimensional imaging system generating body condition scores for dairy cows using machine learning.

Monitoring body condition score (BCS) is a useful management tool to estimate the energy reserves of an individual cow or a group of cows. The aim of this study was to develop and evaluate the performance of a fully automated 2-dimensional imaging system using a machine learning algorithm to generate real-time BCS for dairy cows. Two separate datasets were used for training and testing. The training dataset included 34,150 manual BCS (MAN_BCS) assigned by 5 experienced veterinarians during 35 visits at 7 dairy farms. Ordinal regression methods and deep learning architecture were used when developing the algorithm. Subsequently, the testing dataset was used to evaluate the developed BCS prediction algorithm on 4 of the participating farms. An experienced human assessor (HA1) visited these farms and performed 8 whole-milking-herd BCS sessions. Each farm was visited twice, allowing for 30 d (±2 d) to pass between visits. The MAN_BCS assigned by HA1 were considered the ground truth data. At the end of the validation study, MAN_BCS were merged with the stored automated BCS (AI_BCS), resulting in a testing dataset of 9,657 single BCS. A total of 3,817 cows in the testing dataset were scored twice 30 d (±2 d) apart, and the change in their BCS (ΔBCS) was calculated. A subset of cows at one farm were scored twice on consecutive days to evaluate the within-observer agreement of both the human assessor and the system. The manual BCS of 2 more assessors (HA2 and HA3) were used to assess the interobserver agreement between humans. Finally, we also collected ultrasound measurements of backfat thickness (BFT) from 111 randomly selected cows with available MAN_BCS and AI_BCS. Using the testing dataset, intra- and interobserver agreement for single BCS and ΔBCS were estimated by calculating the simple percentage agreement (PA) at 3 error levels and the weighted kappa (κw) for the exact agreement. A Bland-Altman plot was constructed to visualize the systematic and proportional bias. The association between MAN_BCS and AI_BCS and the BFT was assessed with Passing-Bablok regressions. The system had an almost perfect repeatability with a κw of 0.99. The agreement between MAN_BCS and AI_BCS was substantial, with an overall κw of 0.69. The overall PA at the exact, ± 0.25-unit, and ± 0.50-unit BCS error range between MAN_BCS and AI_BCS was 44.4%, 84.6%, and 94.8%, respectively, and greater than the PA obtained between HA1 and HA3. The Bland-Altman plot revealed a minimal systematic bias of -0.09 with a proportional bias at the extreme scores. Furthermore, despite the low κw of 0.20, the overall PA at the exact and ± 0.25-unit of BCS error range between MAN_BCS and AI_BCS regarding the ΔBCS was 45.7 and 88.2%, respectively. A strong linear relationship was observed between BFT and AI_BCS (ρ = 0.75), although weaker than that between BFT and MAN_BCS (ρ = 0.91). The system was able to predict single BCS and ΔBCS with satisfactory accuracy, comparable to that obtained between trained human scorers.

Variation in protein metabolism biomarkers during the transition period and associations with health, colostrum quality, reproduction, and milk production traits in Holstein cows.

The aims of this study were to assess (1) the variation of protein metabolism biomarkers and factors affecting them during the transition period, (2) the association of each biomarker with skeletal muscle reserves and their changes, and (3) the association of these biomarkers with postpartum health, colostrum quality, reproduction, and milk production. For this purpose, 238 multiparous Holstein cows from 6 herds were used in a prospective cohort study. Plasma concentrations of 3-methylhistidine (3-MH) and 1-methylhistidine (1-MH) and serum concentrations of total protein (TP), albumin (ALB), urea nitrogen (BUN), and creatinine (SCR) were determined for each cow at -21, -7, 7, 21, and 28 d relative to calving. Clinical diseases were recorded during the first 28 d postcalving, and presence of subclinical ketosis (scKET) was investigated at 7 and 21 d. Colostrum quality was estimated by Brix refractometry. Reproduction data by 150 d in milk (DIM) and milk production records were also available. Linear mixed models including the fixed effects of time point, herd, parity, body condition score (-21 d), duration of dry period and postparturient diseases were fitted to assess the variation in each biomarker's concentration. The association between the biomarkers' concentration during the prepartum period with the odds for each postparturient disease and for a combined trait (CD_1-28), defined as the presence of at least one clinical condition during the first 28 d after calving, were assessed with separate binary logistic models for time points -21 d and -7 d. The relationship of each biomarker's concentration with longissimus dorsi thickness (LDT) and the changes in LDT (ΔLDT) was assessed with pairwise correlations. Separate general linear models were used to assess the association of each biomarker with colostrum Brix values and milk production traits. Finally, the associated hazard for first artificial insemination (AI) and for pregnancy by 150 DIM (PREG_150DIM) was assessed with Cox proportional hazard models, whereas odds for pregnancy to the first AI (PREG_1stAI) were assessed with binary logistic models. The level of 3-MH was affected mainly by herd, time points, and their interaction. Higher 3-MH was associated with increased odds for metritis and CD_1-28, increased hazard for PREG_150 DIM and with increased milk production. 1-Methylhistidine was affected mainly by herd, scKET and occurrence of displaced abomasum. Higher 1-MH was associated with better colostrum quality, increased odds for scKET, increased hazard for first AI by 150 DIM and with decreased milk production. Both 3-MH and 1-MH were weakly to moderately negatively correlated with LDT and moderately to strongly negatively correlated with ΔLDT at the corresponding time periods. Additionally, higher TP was associated with increased odds for metritis and CD_1-28 and increased milk production, while higher ALB was associated with increased odds for scKET and increased milk production. Moreover, higher BUN was associated with decreased odds for scKET, increased odds for PREG_1stAI and increased milk production. Higher SCR was associated with decreased odds for retained fetal membranes, metritis, and CD_1-28. Periparturient protein metabolism is significantly associated with postpartum health, colostrum quality, reproduction, and milk production; mechanisms involved require further investigation.

Association between a genetic index for digital dermatitis resistance and the presence of digital dermatitis, heel horn erosion, and interdigital hyperplasia in Holstein cows.

Digital dermatitis (DD) is a polybacterial disease endemic to most UK dairy farms. It poses a major financial and welfare threat and is characterized by high incidence and recurrence rates. We aimed to investigate the association between the UK EBV for resistance to digital dermatitis, the digital dermatitis index (DDI), and the frequency of DD, heel horn erosion (HHE), and interdigital hyperplasia (IH) in a population of Holstein dairy cows. We enrolled and genotyped 2,352 cows from 4 farms in a prospective cohort study. Foot lesion records were recorded by veterinary surgeons for each animal at 4 time points during a production cycle, starting at approximately 2 mo before calving and ending in late lactation. Importantly, these records were not used in the calculation of the DDI. Lesion records were matched to the animal's own DDI (n = 2,101) and their sire's DDI (n = 1,812). Digital dermatitis index values in our study population ranged from -1.41 to +1.2 and were transformed to represent distance from the mean expressed in SD. The relationship between the DDI and the presence of DD was investigated using a logistic regression model, with farm, parity, and a farm-parity interaction fitted as covariates. A multivariable logistic regression model was fitted to evaluate the relationship between HHE and DDI with farm fitted as a covariate. Finally, a univariable logistic regression model with DDI as explanatory variable was used to investigate the relationship between IH and DDI. The odds ratio of an animal being affected by DD was 0.69 for 1 SD increase in the animal's DDI (95% CI = 0.63-0.76). The odds of HHE and IH were 0.69 (95% CI = 0.62-0.76) and 0.58 (95% CI = 0.49-0.68) respectively for 1 SD increase in DDI. The adjusted probability of DD was 32% (95% CI = 27-36%) for cows with mean DDI value of 0, while it was 24% (95% CI = 20-29%) in cows with a DDI value of +1. Sire DDI breeding values were standardized in the same way and then binned into terciles creating an ordinal variable representing bulls of high, medium, and low genetic merit for DD resistance. The daughters of low genetic merit bulls were at 2.05 (95% CI = 1.60-2.64), 1.96 (95% CI = 1.53-2.50), and 2.85 (95% CI = 1.64-5.16) times greater odds of being affected by DD, HHE, and IH, respectively, compared with the daughters of high genetic merit bulls. The results of this study highlight the potential of digital dermatitis genetic indexes to aid herd management of DD, and suggest that breeding for resistance to DD, alongside environmental and management control practices, could reduce the prevalence of the disease.

A study on the use of thermal imaging as a diagnostic tool for the detection of digital dermatitis in dairy cattle.

Our aims were to (1) determine how interdigital skin temperature (IST), measured using infrared thermography, was associated with different stages of digital dermatitis (DD) lesions and (2) develop and validate models that can use IST measurements to identify cows with an active DD lesion. Between March 2019 and March 2020, infrared thermographic images of hind feet were taken from 2,334 Holstein cows across 4 farms. We recorded the maximum temperature reading from infrared thermographic images of the interdigital skin between the heel bulbs on the hind feet. Pregnant animals were enrolled approximately 1 to 2 mo precalving, reassessed 1 wk after calving, and again at approximately 50 to 100 d postpartum. At these time points, IST and the clinical stage of DD (M-stage scoring system: M1-M4.1) were recorded in addition to other data such as the ambient environmental temperature, height, body condition score, parity, and the presence of other foot lesions. A mixed effect linear regression model with IST as the dependent variable was fitted. Interdigital skin temperature was associated with DD lesions; compared to healthy feet, IST was highest in feet with M2 lesions, followed by M1 and M4.1 lesions. Subsequently, the capacity of IST measurements to detect the presence or absence of an active DD lesion (M1, M2, or M4.1) was explored by fitting logistic regression models, which were tested using 10-fold validation. A mixed effect logistic regression model with the presence of active DD as the dependent variable was fitted first. The average area under the curve for this model was 0.80 when its ability to detect presence of active DD was tested on 10% of the data that were not used for the model's training; an average sensitivity of 0.77 and an average specificity of 0.67 was achieved. This model was then restricted so that only explanatory variables that could be practically recorded in a nonresearch, external setting were included. Validation of this model demonstrated an average area under the curve of 0.78, a sensitivity of 0.88, and a specificity of 0.66 for 1 of the time points (precalving). Lower sensitivity and specificity were achieved for the other 2 time points. Our study adds further evidence to the relationship between DD and foot skin temperature using a large data set with multiple measurements per animal. Additionally, we highlight the potential for infrared thermography to be used for routine on-farm diagnosis of active DD lesions.

A description of interestrus and interservice intervals and associated fertility in 16 United Kingdom dairy herds.

Understanding the changes that have occurred in reproductive management and physiology of the dairy cow is necessary to reverse the trend of declining fertility. In this study we analyzed the intervals between estrus events, as detected using tail chalk, in a population of 6,092 dairy cows from 16 herds in the central United Kingdom. Intervals were categorized by absence or presence of an insemination at the first estrus event, being designated interestrus intervals and interservice intervals, respectively. Modal interestrus interval was 21 d, as has been commonly described. Interservice interval was significantly longer than interestrus interval, with a modal value of 22 d. Multivariable analysis identified explanatory variables for intervals between estrus events, with random effects modeling accounting for clustering within herds and within individual cows. Intraclass correlation coefficients indicated that herd identity has a negligible effect, whereas animal identity accounts for 9% of interval variation. Parity, days in milk, insemination at the first estrus of the interval, and interval number within lactation all affected the interval. Logistic regression modeling indicated that interval length is also associated with the outcome of pregnancy. These findings indicate that intervals following an insemination are both longer than previously described and longer than interestrus intervals with no insemination event. The data also suggest that longer interservice interval length may be more conducive to subsequent conception than shorter intervals. Several factors appear to influence interestrus events and further work is required to investigate the underlying physiological mechanisms of these phenomena.

The effect of intrauterine infusion of dextrose on clinical endometritis cure rate and reproductive performance of dairy cows.

The main objective of this study was to evaluate the intrauterine administration use of 200 mL of 50% dextrose solution as a treatment against clinical endometritis (CE); CE cure rate and reproductive performance were evaluated. Additionally, the association of several relevant risk factors, such as retained placenta (RP), metritis, CE, anovulation, hyperketonemia, and body condition score with reproductive performance, early embryonic mortality, and CE were evaluated. A total of 1,313 Holstein cows housed on 4 commercial dairy farms were enrolled in the study. At 7±3 DIM cows were examined for metritis and had blood collected to determine serum ß-hydroxybutyrate concentration. To determine if cows had ovulated at least once before 44±3 DIM, the presence of a corpus luteum was evaluated by ovarian ultrasonography at 30±3 DIM and at 44±3 DIM. At 30±3 DIM, CE was diagnosed using the Metricheck device (SimcroTech, Hamilton, New Zealand); cows with purulent or mucopurulent vaginal discharge were diagnosed as having CE. Cows diagnosed with CE (n=175) were randomly allocated into 2 treatment groups: treatment (intrauterine infusion of 200 mL of 50% dextrose) or control (no infusion). Clinical endometritis cows were re-evaluated as described above at 44±3 DIM, and cows that were free of purulent or mucopurulent vaginal discharge were considered cured. Intrauterine infusion of dextrose tended to have a detrimental effect on CE cure rate, and treatment did not have an effect on first-service conception rate and early embryonic mortality. A multivariable Cox's proportional hazard model was performed to evaluate the effect of several variables on reproductive performance; the variables RP, CE, parity, anovulation, and the interaction term between parity and anovulation were associated with hazard of pregnancy. Cows that did not have RP or CE were more likely to conceive than cows that were diagnosed with RP or CE. Cows that had RP were at 3.36 times higher odds of losing their pregnancy than cows that did not have RP. In addition, cows diagnosed with CE were at 2.16 higher odds of losing their pregnancy than cows without CE. In conclusion, intrauterine infusion of 200 mL of 50% dextrose solution as a treatment for CE had a strong statistical tendency to decrease CE cure rate, did not improve first-service conception rate and early embryonic mortality, and did not decrease calving-to-conception interval.

Short communication: Genetic characterization of digital cushion thickness.

Dairy cow lameness is a serious animal welfare issue. It is also a significant cause of economic losses, reducing reproductive efficiency and milk production and increasing culling rates. The digital cushion is a complex structure composed mostly of adipose tissue located underneath the distal phalanx and has recently been phenotypically associated with incidence of claw horn disruption lesions (CHDL); namely, sole ulcers and white line disease. The objective of this study was to characterize digital cushion thickness genetically and to investigate its association with body condition score (BCS), locomotion score (LOCO), CHDL, and milk production. Data were collected from 1 large closely monitored commercial dairy farm located in upstate New York; 923 dairy cows were used. Before trimming, the following data were collected by a member of the research team: BCS, cow height measurement, and LOCO. Presence or not of CHDL (sole ulcer or white line disease, or both) was recorded at trimming. Immediately after the cows were hoof trimmed, they underwent digital sonographic B-mode examination for the measurement of digital cushion thickness. Factors such as parity number, stage of lactation, calving date, mature-equivalent 305-d milk yield (ME305MY), and pedigree information were obtained from the farm's dairy management software (DairyCOMP 305; Valley Agricultural Software, Tulare, CA). Univariate animal models were used to obtain variance component estimations for each studied trait (CHDL, BCS, digital cushion thickness average, LOCO, height, and ME305MY) and a 6-variate analysis was conducted to estimate the genetic, residual, and phenotypic correlations between the studied traits. The heritability estimate of DCTA was 0.33±0.09, whereas a statistically significant genetic correlation was estimated between DCTA and CHDL (-0.60±0.29). Of the other genetic correlations, significant estimates were derived for BCS with LOCO (-0.49±0.19) and ME305MY (-0.48±0.20). Digital cushion thickness is moderately heritable and genetically strongly correlated with CHDL.

Association of digital cushion thickness with sole temperature measured with the use of infrared thermography.

The main objective of this study was to investigate the association between digital cushion thickness and sole temperature measured by infrared thermography. Data were collected from 216 lactating Holstein cows at 4 to 10d in milk (DIM). Cows were locomotion scored and sole temperature was measured after claw trimming (a minimum delay of 3 min was allowed for the hoof to cool) using an infrared thermography camera. Temperature was measured at the typical ulcer site of the lateral digit of the left hind foot. Immediately after the thermographic image was obtained, the thickness of the digital cushion was measured by ultrasonography. Rumen fluid samples were collected with a stomach tube and sample pH was measured immediately after collection. Additionally, a blood sample was obtained and used for measurements of serum concentrations of ß-hydroxybutyrate (BHBA), nonesterified fatty acids (NEFA), and haptoglobin. To evaluate the associations of digital cushion thickness with sole temperature, a linear regression model was built using the GLIMMIX procedure in SAS software (SAS Institute Inc., Cary, NC). Sole temperature was the response variable, and digital cushion thickness quartiles, locomotion score group, rumen fluid pH, rumen fluid sample volume, environmental temperature, age in days, and serum levels of NEFA, BHBA, and haptoglobin were fitted in the model. Only significant variables were retained in the final model. Simple linear regression scatter plots were used to illustrate associations between sole temperature (measured by infrared thermography at the typical ulcer site) and environmental temperature and between NEFA and BHBA serum levels and haptoglobin. One-way ANOVA was used to compare rumen fluid pH for different locomotion score groups and for different digital cushion quartiles. Results from the multivariable linear regression model showed that sole temperature increased as locomotion scores increased and decreased as digital cushion thickness increased. These results were adjusted for environmental temperature, which was significantly associated with sole temperature. Serum levels of NEFA, BHBA, and haptoglobin were not associated with sole temperature. However, significant correlations existed between serum levels of NEFA and haptoglobin and between serum levels of BHBA and haptoglobin. Rumen fluid pH was not associated with either locomotion score or digital cushion thickness. In conclusion, we show here that digital cushion thickness was associated with sole temperature in cows at 4 to 10 DIM.

Effect of trace mineral supplementation on selected minerals, energy metabolites, oxidative stress, and immune parameters and its association with uterine diseases in dairy cattle.

The objective of this study was to evaluate the relationship between selected minerals' serum levels, energy metabolites, oxidative stress indicators, IL-8 and haptoglobin levels, and the potential for uterine diseases. Additionally, we investigated the effect of injectable trace mineral supplementation (ITMS) on metabolism, immune function, and animal health under field conditions involving a dairy herd with high milk production. The study was conducted in 1 dairy farm located near Ithaca, New York, with 270 multiparous cows were enrolled from October 3, 2012 until January 10, 2013. Cows were randomly allocated into 1 of 2 treatments groups: ITMS or control. Cows randomly assigned to the ITMS group received 2 injections of trace minerals at 230 and 260 d of gestation; each injection contained 300 mg of Zn, 50mg of Mn, 25mg of Se, and 75 mg of Cu. Retained placenta (RP) and metritis were diagnosed and treated by trained farm personnel. Clinical endometritis evaluation was performed by the investigators. Blood mineral levels, plasma nonesterified fatty acids and serum ß-hydroxybutyrate concentrations, plasma IL-8 concentrations, serum haptoglobin concentration, and serum superoxidase dismutase and plasma glutathione peroxidase activities were measured at various time points before and after calving. Four groups of mixed general linear models were fitted to the data using MIXED procedure of SAS. Injectable trace mineral-supplemented cows had increased serum concentration of Cu, Se, and Zn. Conversely, ITMS did not affect energy metabolites or immune and oxidative stress parameters. Serum concentration of Ca, Cu, K, Mg, Mo, Ps, Pt, Se, and Zn varied according to days relative to parturition. Cows with RP had reduced serum concentrations of Ca, Mg, Mo, and Zn when compared with cows without RP. Cows affected with metritis had significantly lower serum concentrations of Ca, Mo, soluble P, total P, Se, and Zn than nonaffected cows. Serum concentration of Ca, Cu, Mo, and Zn were reduced in cows diagnosed with endometritis in comparison to nonaffected ones.

Sire predicted transmitting ability for conformation and yield traits and previous lactation incidence of foot lesions as risk factors for the incidence of foot lesions in Holstein cows.

The aims of the present study were (1) to investigate the repeatability of foot lesions [sole ulcers (SU), white line disease (WLD), and digital dermatitis (DD)] across multiple lactations, (2) to evaluate the effect of foot lesions on cow survivability and milk production across multiple lactations, and (3) to investigate the role of sire predicted transmitting ability (PTA) for conformation and production traits as risk factors for the incidence of SU, WLD, and DD. Data were collected from a dairy farm located in Cayuga County, New York. A total of 11,442 cows having first calved during the period from May 13, 2001, to March 26, 2012, were enrolled in the study. Data regarding sire genetic evaluations were obtained from DairyBulls.com (http://www.DairyBulls.com). Lameness was detected and treated and lesions were recorded into a dairy record database (DairyCOMP 305; Valley Agricultural Software, Tulare, CA) by trained farm employees. All demographic, production, and foot lesion data were extracted from DairyCOMP 305 and merged with the sires' PTA information to form a unique database. Mixed logistic regression, general linear mixed, and multivariable Cox proportional hazards models were used to analyze the data. Sole ulcers, WLD, and DD incidence was significantly higher for cows affected with SU, WLD, or DD in previous lactations. Cows affected with WLD or DD during the first lactation had significantly higher WLD or DD incidence during the second and the third lactations. Cows affected with SU or WLD during their first lactation had significantly lower milk production during the second lactation and cows diagnosed with SU, WLD, or DD during their second lactation had higher second-lactation mature-equivalent 305-d milk yield. Sire PTA for milk and protein yield were significantly associated with the incidence of SU, WLD, and DD and incidence of SU and WLD, respectively. Sire PTA for several conformation traits were found to be associated with SU, WLD, and DD incidence. Cows that were affected with SU or WLD during their first lactation were at 1.18 or 1.43 higher hazard of culling than unaffected cows, respectively. In summary, we conclude that SU, WLD, and DD are highly repeatable across lactations and that high genetic merit for milk and protein production as well as milk production (phenotype) were significantly associated with higher risk of SU, WLD, and DD. Additionally, sire PTA for several conformation traits were significantly associated with their daughters' foot lesion incidence.

The effect of prepartum intravaginal bacteriophage administration on the incidence of retained placenta and metritis.

The objective of this study was to evaluate the effect of prepartum intravaginal administration of an anti-Escherichia coli bacteriophage cocktail on uterine health and reproductive performance of lactating dairy cows. The study was conducted on a commercial dairy farm located near Ithaca, New York, from March to September 2012, and 107 cows were enrolled. The cows were divided randomly into 2 groups (treatment and control); treatment group cows were submitted to 3 intravaginal administrations of 20 mL of a bacteriophage cocktail including 10 different phages in a lysate with titration of approximately 10(9) plaque-forming units, on d 230, 260, and 275 of gestation. Control cows were not treated with a placebo, and physical examination and sample collection was conducted equally for both groups. Vaginal swabs were collected at d 230, 260, and 275 d of gestation, cervical swabs were collected at 3±1 d in milk, and blood was collected at 275 d of gestation for nonesterified fatty acids and interleukin (IL)-6 serum level measurements and at 10 DIM for ß-hydroxybutyrate and IL-6 serum level measurements. The bacteriophage cocktail significantly increased the incidence of retained placenta and metritis. Swab samples were cultured for E. coli and no difference was found between treatment and control groups. The lysate contained 6×10(9) IU of lipopolysaccharide/mL and could have caused prepartum overstimulation of toll-like receptor-4 (TLR4)-chemokine pathway, leading to a weaker immune response. However, IL-6 was not affected by treatment, although sample size was insufficient to prove a treatment effect on the suppression of the chemokine cascade and innate immune system. Bacteriophage treatment had an excellent bactericidal effect in previous in vitro trials; however, special attention must be given to production of the cocktail to obtain a purified solution free of E. coli bacterial products and fragments, particularly lipopolysaccharide.

Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis.

BACKGROUND: Cryptosporidium parvum is the main cause of calf scour worldwide. With limited therapeutic options and research compared to other Apicomplexa, it is important to understand the parasites' biology and interactions with the host and microbiome in order to develop novel strategies against this infection. The age-dependent nature of symptomatic cryptosporidiosis suggests a link to the undeveloped immune response, the immature intestinal epithelium, and its associated microbiota. This led us to hypothesise that specific features of the early life microbiome could predict calf susceptibility to C. parvum infection. RESULTS: In this study, a single faecal swab sample was collected from each calf within the first week of life in a cohort of 346 animals. All 346 calves were subsequently monitored for clinical signs of cryptosporidiosis, and calves that developed diarrhoea were tested for Rotavirus, Coronavirus, E. coli F5 (K99) and C. parvum by lateral flow test (LFT). A retrospective case-control approach was taken whereby a subset of healthy calves (Control group; n = 33) and calves that went on to develop clinical signs of infectious diarrhoea and test positive for C. parvum infection via LFT (Cryptosporidium-positive group; n = 32) were selected from this cohort, five of which were excluded due to low DNA quality. A metagenomic analysis was conducted on the faecal microbiomes of the control group (n = 30) and the Cryptosporidium-positive group (n = 30) prior to infection, to determine features predictive of cryptosporidiosis. Taxonomic analysis showed no significant differences in alpha diversity, beta diversity, and taxa relative abundance between controls and Cryptosporidium-positive groups. Analysis of functional potential showed pathways related to isoprenoid precursor, haem and purine biosynthesis were significantly higher in abundance in calves that later tested positive for C. parvum (q ≤ 0.25). These pathways are either absent or streamlined in the C. parvum parasites. Though the de novo production of isoprenoid precursors, haem and purines are absent, C. parvum has been shown to encode enzymes that catalyse the downstream reactions of these pathway metabolites, indicating that C. parvum may scavenge those products from an external source. CONCLUSIONS: The host has previously been put forward as the source of essential metabolites, but our study suggests that C. parvum may also be able to harness specific metabolic pathways of the microbiota in order to survive and replicate. This finding is important as components of these microbial pathways could be exploited as potential therapeutic targets for the prevention or mitigation of cryptosporidiosis in bovine neonates.

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions.

BACKGROUND: Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms. RESULTS: We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation. CONCLUSIONS: Collectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes. Video Abstract.

Patterns of neck metastasis and occult neck disease during recurrent laryngeal cancer.

OBJECTIVE: Numerous factors are considered to impact on the rate of complications during salvage total laryngectomy procedures. Neck dissection could be one of these factors. This study analysed the pattern of lymph node metastasis and rate of occult neck disease during salvage total laryngectomy as well as the impact of neck dissection on survival and complication rates. METHOD: This was a retrospective analysis of a prospectively maintained laryngectomy database in two large tertiary teaching hospitals. RESULTS: The rate of occult neck disease was 11.1 per cent. Most cases with occult neck disease had rT4 disease. Patients with complications, advanced tumour stage and positive margins had a significant decrease in overall survival. Patients receiving elective neck dissection did not have any survival benefit. Positron emission tomography-computed tomography showed a very high specificity and negative predictive value. CONCLUSION: According to the low risk of occult neck disease when using contemporary imaging techniques as well as the lack of impact on survival, conservative management of the neck should be considered for crT1-T3 recurrence.

A novel diagnostic technique to determine uterine health of Holstein cows at 35 days postpartum.

The objectives were (1) to evaluate the association of uterine lavage sample optical density (ULSOD) with uterine health, and (2) to estimate and evaluate a threshold value that will maximize the accuracy of ULSOD as a diagnostic tool for clinical endometritis. The study enrolled 1,742 cows from 3 dairy farms located near Ithaca, New York. The samples were collected at 35 ± 3 d in milk (DIM) by using low-volume uterine lavage. Cows with a purulent or mucopurulent secretion in the sample were diagnosed with clinical endometritis, whereas a subgroup of all studied cows was examined for cytological evidence of inflammation by endometrial cytology. Data for ULSOD measured at different wavelengths (200, 352, 620, 790, 860, and 960 nm) were available for 554 cows; all 1,742 cows had data for ULSOD measured at 620 nm (ULSOD(620)). Incidences of clinical endometritis, metritis, and retained placenta were 10, 15.2, and 5.6%, respectively. The ULSOD(620) was associated with clinical endometritis. Receiver operating characteristic (ROC) analysis of the accuracy of optical density in the detection of clinical endometritis was conducted for ULSOD measured at different wavelengths; ULSOD(620) was selected for further analysis because it presented the best ROC curve to detect clinical endometritis. The recommended threshold for ULSOD(620) ROC was 0.058, where the sensitivity and specificity were 76.3 and 78.3%, respectively. The ROC analysis of the accuracy of optical density in the detection of endometritis defined as a percentage of neutrophils in the uterine lavage samples higher than 18% was conducted for ULSOD(620). The recommended threshold was 0.059, where the sensitivity and specificity were 100 and 82.2%, respectively. Cows with ULSOD(620) ≤ 0.058 were 1.21 times more likely to conceive than cows with ULSOD(620) >0.058; moreover, the median calving-to-conception interval for cows that had ULSOD(620) ≤ 0.058 was 122 d compared with 148 d for cows that had ULSOD(620) >0.058. Cows that were positive for Arcanobacterium pyogenes, diagnosed with metritis, or had retained placenta had 4.0, 1.4, and 1.7 times higher odds of having ULSOD(620) >0.058, respectively. Cows with ULSOD(620) >0.058 had a higher percentage of neutrophils in the uterine lavage samples than cows with ULSOD(620) ≤ 0.058. Uterine lavage sample optical density measured at 620 nm can be used as an objective indicator of uterine health in dairy cows, principally for clinical endometritis.

The effect of intrauterine administration of mannose or bacteriophage on uterine health and fertility of dairy cows with special focus on Escherichia coli and Arcanobacterium pyogenes.

The objective of this study was to evaluate the effects of intrauterine administration of 50 g of ultrapure mannose or a bacteriophage cocktail and the presence of Escherichia coli and Arcanobacterium pyogenes in the uterine lumen on uterine health and reproductive performance of lactating dairy cows. The study was conducted on a commercial dairy farm located near Ithaca, New York, from May 4 to January 20, 2011, and 597 cows were enrolled. The cows were divided randomly into 3 treatment groups, and treatments were administered at 2 ± 1 d in milk (DIM). Treatment 1 consisted of intrauterine administration of 50 g of ultrapure mannose powder divided in 4 pills; treatment 2 consisted of intrauterine administration of a bacteriophage cocktail that included 4 different phages in one pill, with a dose of approximately 107 plaque-forming units; and treatment 3 consisted of intrauterine administration of one empty pill (control). Intrauterine fluid swabs were collected on day of treatment and at 10 ± 3 DIM; uterine lavage samples were collected at 35 ± 3 DIM. Swabs and uterine lavage samples were cultured for E. coli and A. pyogenes. The intrauterine administration of mannose and bacteriophage did not affect uterine health, reproduction performance, or outcome of intrauterine secretion cultures for E. coli and A. pyogenes. Prevalence of intrauterine E. coli at 2 ± 1 DIM and A. pyogenes at 2 ± 1, 10 ± 3, and 35 ± 3 were affected by retained placenta. Additionally, prevalence of intrauterine E. coli at 10 ± 3 and A. pyogenes at 35 ± 3 DIM were associated with metritis, and cows that were diagnosed with clinical endometritis at 35 ± 3 DIM had greater prevalence of intrauterine E. coli at 2 ± 1 DIM and A. pyogenes at 35 ± 3 DIM. Furthermore, cows positive for E. coli at 2 ± 1 and 10 ± 3 DIM and for A. pyogenes at 10 ± 3 DIM had 1.63, 2.34, and 1.54 increased odds of having metritis. Cows positive for A. pyogenes at 35 ± 3 DIM and for E. coli at 2 ± 1 DIM had 19.8 and 2.66 higher odds of being diagnosed with clinical endometritis, respectively. Additionally, cows negative for E. coli at 2 ± 1 DIM were 1.39 times more likely to conceive than cows positive cows for E. coli.

Skeletal muscle and adipose tissue reserves and mobilisation in transition Holstein cows: Part 1 Biological variation and affecting factors.

Nutrient deficit during the periparturient period leads to mobilisation of body energy and protein reserves. Research regarding fat reserves and mobilisation is extensive, while, on the contrary, investigation of muscle mobilisation during the periparturient period is limited. The aim of this cohort study was to simultaneously investigate the biological variation of skeletal muscle and subcutaneous fat reserves together with their mobilisation in transition Holstein cows of different herds, using ultrasonography, and to assess potential affecting factors. For this purpose, ultrasound measurements of longissimus dorsi muscle thickness (LDT) and backfat thickness (BFT) from 238 multiparous cows of six dairy farms were obtained at six time points across the transition period (from 21 days pre- to 28 days postpartum). Concentrations of serum creatinine and non-esterified fatty acids were determined in order to confirm the loss of muscle mass and adipose tissue, respectively. Cases of clinical postparturient diseases and subclinical ketosis (scKET) during the first 28 days postcalving were recorded. Cows mobilised on average 32.8% and 37.3% of LDT and BFT reserves, respectively. Large between-cow variation was observed for both the onset and the degree of mobilisation. Time point, initial body condition score and parity were the most important predictors of LDT variation. Cows diagnosed with metritis (MET) had lower LDT postpartum and mobilised more muscle depth compared to cows not diagnosed with MET. Initial BCS, time point, initial BW (estimated by heart girth measurement) and parity were the most important predictors of BFT variation. Cows diagnosed with MET mobilised more backfat between -7d and 7d compared to cows not diagnosed with MET. Cows with scKET mobilised more backfat between 7- and 21 days postpartum compared to healthy ones. Variation of subcutaneous fat and skeletal muscle reserves during the transition period was large and affected by herd and several cow-level factors.

Skeletal muscle and adipose tissue reserves and mobilisation in transition Holstein cows: Part 2 association with postpartum health, reproductive performance and milk production.

The aim of this study was, for the first time, to simultaneously assess the association of skeletal muscle and subcutaneous fat reserves and their mobilisation, measured by ultrasonography, with the incidence of specific postparturient health, reproduction, and milk production traits. For this purpose, ultrasound measurements of longissimus dorsi thickness (LDT) and backfat thickness (BFT) from 238 multiparous cows from 6 dairy farms were obtained at 6 time points during the transition period (from 21 days pre- to 28 days postpartum). In each case, LDT and BFT measurements at each time point and LDT and BFT mobilisation variables at each study period were assessed simultaneously. Cases of specific clinical postparturient diseases and subclinical ketosis were recorded. An additional disease trait was used, defined as the presence or absence of at least one clinical condition after calving (CD_1-28). The associated disease odds with LDT/BFT variables were assessed with binary logistic regression models. The associated hazard for 1st artificial insemination (AI) and for pregnancy by 150 days-in-milk (PREG_150DIM) was assessed with Cox proportional hazard models. Moreover, binary logistic models were used to assess the associated odds for pregnancy to 1stAI (PREG_1stAI). Finally, association with 30d, 100d and 305d milk yield was assessed with linear regression models. Increased muscle depth during transition was negatively associated with odds for metritis and CD_1-28, while associations with odds for subclinical ketosis were inconclusive. Moreover, increased LDT reserves were associated with greater hazard for 1st AI by 150 days-in-milk, but results were inconclusive regarding odds for PREG_1stAI. Increased LDT mobilisation was associated with increased odds for metritis. Increased BFT reserves were positively associated with odds for metritis, CD_1-28 and subclinical ketosis and with decreased hazard for PREG_150DIM. Increased BFT mobilisation was associated with increased odds for subclinical ketosis and with decreased odds for PREG_1stAI and decreased hazard for PREG_150DIM. Cows with moderate BFT reserves performed better. Finally, increased BFT mobilisation during -21d to -7d from parturition was associated with less milk by 30d and 100d. On the contrary, increased BFT mobilisation during -7d to 7d was associated with more milk by 305d. Metabolism of muscle and fat tissue during transition period was differently associated with different postparturient health, reproduction and milk production traits. In general, greater muscle mass and moderate fat reserves with limited muscle and fat mobilisation were associated with better performance.

Establishing and integrating a transoral robotic surgery programme into routine oncological management of head and neck cancer - a UK perspective.

BACKGROUND: The introduction of transoral robotic surgery into routine management of patients is complex. It involves organisational, logistical and clinical challenges. This study presents our experience of implementing such a programme and provides a blueprint for other centres willing to establish similar services. METHODS: Implementation of the robotic surgery programme focused on several key domains: training, logistics, governance, multidisciplinary team awareness, pre-operative imaging, anaesthesia, post-operative care, finance, patient selection and consent. Programme outcomes were evaluated by assessing operative outcomes of the first 117 procedures performed. RESULTS: The success of the transoral robotic surgery programme has been possible because of the scrupulous planning phase before the first procedure, and the time invested on team awareness and training. CONCLUSION: Implementation of a new transoral robotic surgery service has led to: the development of a dedicated transoral robotic surgery patient care protocol, the performance of progressively more complex procedures, the inclusion of transoral robotic surgery training and the establishment of several research projects.

The dysbiosis of ovine foot microbiome during the development and treatment of contagious ovine digital dermatitis.

BACKGROUND: Contagious Ovine Digital Dermatitis (CODD) is an emerging and common infectious foot disease of sheep which causes severe welfare and economic problems for the sheep industry. The aetiology of the disease is not fully understood and control of the disease is problematic. The aim of this study was to investigate the polybacterial aetiopathogenesis of CODD and the effects of antibiotic treatment, in a longitudinal study of an experimentally induced disease outbreak using a 16S rRNA gene amplicon sequencing approach. RESULTS: CODD was induced in 15/30 experimental sheep. During the development of CODD three distinct phenotypic lesion stages were observed. These were an initial interdigital dermatitis (ID) lesion, followed by a footrot (FR) lesion, then finally a CODD lesion. Distinct microbiota were observed for each lesion in terms of microbial diversity, clustering and composition. Porphyromonadaceae, Family XI, Veillonellaceae and Fusobacteriaceae were significantly associated with the diseased feet. Veillonellaceae and Fusobacteriaceae were most associated with the earlier stages of ID and footrot rather than CODD. Following antibiotic treatment of the sheep, the foot microbiota showed a strong tendency to return to the composition of the healthy state. The microbiota composition of CODD lesions collected by swab and biopsy methods were different. In particular, the Spirochaetaceae family were more abundant in samples collected by the biopsy method, suggesting that these bacteria are present in deeper tissues of the diseased foot. CONCLUSION: In this study, CODD presented as part of a spectrum of poly-bacterial foot disease strongly associated with bacterial families Porphyromonadaceae, Family XI (a family in Clostridiales also known as Clostridium cluster XI), Veillonellaceae and Fusobacteriaceae which are predominately Gram-negative anaerobes. Following antibiotic treatment, the microbiome showed a strong tendency to return to the composition of the healthy state. The composition of the healthy foot microbiome does not influence susceptibility to CODD. Based on the data presented here and that CODD appears to be the severest end stage of sheep infectious foot disease lesions, better control of the initial ID and FR lesions would enable better control of CODD and enable better animal welfare.