Determination of neonatal serum immunoglobulin G concentrations associated with mortality during the first 4 months of life in dairy heifer calves.

Colostral administration practices on dairy farms have significantly improved over the last 15-20 years resulting in prevalence of calves ingesting insufficient colostrum decreasing from 35-40% to 19%. Despite these improvements, the serum immunoglobulin G (IgG) concentration of ≥ 1000 g/dl and serum total protein (TP) concentrations of ≥ 5. 2 g/dl are considered indicative of adequate transfer of immunity. We hypothesised that the current serum IgG concentrations of ≥ 1000 mg/dl is too low to indicate adequate transfer of colostral immunity on modern dairies. The objective of this study was to determine the serum IgG and TP concentrations indicating adequate transfer of passive immunity in dairy heifer calves. A cohort study of 1290 heifers from a calf raising facility for 48 dairy farms was performed. Heifers were assigned into strata based on serum IgG and TP concentrations. Mortality events were recorded for the heifers for 4 months. Interval likelihood ratios for mortality were calculated for heifers in each stratum of serum IgG or TP concentrations. Logistic regression to predict probability of mortality events was performed. Estimates of probability of survival were evaluated using survival analysis. Serum strata of ≤ 1500, 1501-2000 or >2500 were not significant predictors of mortality during the 120 d of rearing. Serum IgG concentration was not a significant predictor of hazard for mortality. In contrast to previous studies, serum IgG and TP concentrations of 2001-2500 mg/dl and 5.8-6.3 g/dl respectively, were considered optimum for indicating adequate passive transfer of colostral immunity in dairy calves based on the likelihood ratios. On dairies with optimum colostral feeding practices, serum IgG and TP concentrations of 2001-2500 mg/dl and 5.8-6.3 g/dl are recommended as endpoints to indicate adequate passive immunity in dairy calves.

Refractometer assessment of colostral and serum IgG and milk total solids concentrations in dairy cattle.

BACKGROUND: Estimation of the quantity of colostral IgG or serum IgG absorbed following ingestion of colostrum by calves is essential for monitoring the effectiveness of colostrum feeding practices on dairy farms. Milk total solids concentrations determination is a critical part of quality assessment of nonsaleable whole milk prior to feeding to calves. To date, on-farm methods to assess colostral IgG, serum IgG or milk total solids concentrations have been performed separately with various instruments. The objective of this study was to evaluate the diagnostic performance of a single electronic, hand-held refractometer for assessing colostral and serum IgG concentrations and milk total solids in dairy cattle. Colostral IgG, serum IgG and milk total solids concentrations were determined by the refractometer. Corresponding analysis of colostral and serum IgG concentrations were determined by radial immunodiffusion (RID) while milk total solids were determined by spectrophotometry. Sensitivity and specificity of the refractometer for colostrum and serum samples were calculated as determined by RID. Sensitivity and specificity of the refractometer for milk samples was calculated as determined by spectrophotometry. RESULTS: The sensitivity of the refractometer was 1 for colostral IgG, serum IgG and milk total solids determinations. Specificity of the refractometer was 0.66, 0.24 and 0 for colostral IgG, serum IgG and milk total solids determinations, respectively. The refractometer underestimated colostral IgG, serum IgG and milk total solids concentrations compared to the concentrations determined by RID or spectrophotometry. CONCLUSIONS: The refractometer was an acceptable, rapid, convenient on-farm method for determining colostral IgG and milk total solids. The refractometer was not an acceptable method for determination of serum IgG concentrations as it severely underestimated the serum IgG concentrations.

Rumen sampling methods bias bacterial communities observed.

The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey the bacterial and some archaeal. Oral stomach tubing a cow to collect a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method (oral stomach tubing vs cannulated grab sample), as well as rumen fraction type (liquid vs solid), bias the bacterial and archaeal communities observed. Liquid samples were further divided into liquid strained through cheesecloth and unstrained. Fecal samples were also collected to determine how these differed from the rumen sample types. The abundance of major archaeal communities was not different at the family level in samples acquired via rumen cannula or stomach tube. In contrast to the stable archaeal communities across sample type, the bacterial order WCHB1-41 (phylum Kiritimatiellaeota) was enriched in both liquid strained and unstrained samples as well as the family Prevotellaceae as compared to grab samples. However, these liquid samples had significantly lower abundance of Lachnospiraceae compared with grab samples. Solid samples strained of rumen liquid most closely resembled the grab samples containing both rumen liquid and solid particles obtained directly from the rumen cannula; therefore, inclusion of particulate matter is important for an accurate representation of the rumen bacteria. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with grab samples.

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. Methods: We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study. Results: The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2. Discussion: The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines.

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.

Milk with and without lactoferrin can influence intestinal damage in a pig model of malnutrition.

Malnutrition remains a leading contributor to the morbidity and mortality of children under the age of five worldwide. However, the underlying mechanisms are not well understood necessitating an appropriate animal model to answer fundamental questions and conduct translational research into optimal interventions. One potential intervention is milk from livestock that more closely mimics human milk by increased levels of bioactive components that can promote a healthy intestinal epithelium. We tested the ability of cow milk and milk from transgenic cows expressing human lactoferrin at levels found in human milk (hLF milk) to mitigate the effects of malnutrition at the level of the intestine in a pig model of malnutrition. Weaned pigs (3 weeks old) were fed a protein and calorie restricted diet for five weeks, receiving cow, hLF or no milk supplementation daily from weeks 3-5. After three weeks, the restricted diet induced changes in growth, blood chemistry and intestinal structure including villous atrophy, increased ex vivo permeability and decreased expression of tight junction proteins. Addition of both cow and hLF milk to the diet increased growth rate and calcium and glucose levels while promoting growth of the intestinal epithelium. In the jejunum hLF milk restored intestinal morphology, reduced permeability and increased expression of anti-inflammatory IL-10. Overall, this pig model of malnutrition mimics salient aspects of the human condition and demonstrates that cow milk can stimulate the repair of damage to the intestinal epithelium caused by protein and calorie restriction with hLF milk improving this recovery to a greater extent.

Comparison of serum immunoglobulin G half-life in dairy calves fed colostrum, colostrum replacer or administered with intravenous bovine plasma.

In calves, passive immunity of immunoglobulins can be acquired through ingestion of colostrum or colostrum replacers. Plasma can been used to supplement immunoglobulins in healthy or sick calves. Serum half-life of colostral derived immuglobulin G (IgG) is estimated to be 20 days. Half-life of IgG is important in determining response to antigens and timing of vaccination in calves. To date studies evaluating half-life of colostrum replacer or plasma derived IgG are lacking. The objectives of this study were to compare the serum half-life of IgG derived from colostrum, colostrum replacer and plasma in dairy calves reared up to 35 days of age. Thirty Jersey calves were randomly assigned to receive colostrum or colostrum replacer by oroesophageal tubing or plasma by intravenous administration. Serum samples were collected at 2, 5, 7, 10, 14, 21, 28 and 35 days. Serum IgG concentrations were determined by radial immunodiffusion. The results indicated that half-life for IgG in colostrum fed (28.5 days) or plasma transfused calves (27.3 days) was longer than colostrum replacer fed calves (19.1 days). Further studies are required to evaluate pathogen specific immunoglobulins in order to recommend vaccination timing in calves fed colostrum replacers.

Comparison of colostrum feeding by nipple bottle versus oroesophageal tubing in Holstein dairy bull calves.

OBJECTIVE: To compare the apparent efficiency of absorption of IgG and failure of passive transfer of immunity rates between calves fed colostrum by nipple bottle (NB) and oroesophageal tubing (OET). DESIGN: Randomized controlled study. ANIMALS: 26 Holstein bull calves (age, 4 to 8 hours). PROCEDURES: Calves were randomly assigned to receive colostrum by either NB or OET. Pooled colostrum was used for feeding each group of calves. Calves received either a maximum of 4 L of colostrum fed through an NB over a period of 20 minutes or an equivalent volume of colostrum fed by OET. Subsequently, a pair of similarly aged calves received similar volumes of colostrum with similar immunoglobulin concentrations. Colostrum was fed only once. Thereafter, calves were fed 2 L of milk replacer every 12 hours. All calves survived to at least 48 hours of age. Serum samples were collected prior to feeding colostrum and at 48 hours of age for determination of serum immunoglobulin concentrations. RESULTS: There were no differences in failure of passive transfer of immunity rates and apparent efficiency of absorption of IgG between calves fed by NB or OET. Volume of colostrum fed was the only significant variable in determining failure of passive transfer of immunity in calves at 48 hours. CONCLUSIONS AND CLINICAL RELEVANCE: Reported advantages and disadvantages of either feeding method are likely to be of minimal practical relevance in achieving adequate passive transfer of immunity in calves when calves are fed a similar volume of colostrum with comparable immunoglobulin concentrations.