Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings.

Holstein cows were killed at three physiological stages, prepartum (-7 d, n = 10), early lactation (63 d, n = 7), and late lactation (269 d, n = 8), for determination of chemical composition and prediction of energy changes during lactation. Cows were weighed, slaughtered, and separated into five or six fractions, including carcass, gastrointestinal tract, mammary gland, uterus, and fetus (if present); the remainder was noncarcass. Live BW and weight of all empty body components except fat were unaffected by physiological stage. Empty body fat was reduced 42.3 kg for the early lactation cows compared with that of prepartum cows. Fat-free matter was similar across physiological stages; however, the water content of fat-free matter was greater for the prepartum and early lactation cows than for late lactation cows. In early lactation cows, the percentages of total protein were less in carcass and greater in gastrointestinal tissue than in prepartum and late lactation cows, but fat distribution was not affected. The energy values of 9.2 and 5.57 Mcal/kg for fat and protein in tissue, respectively, were determined by regression and used to apportion energy associated with fat, .925, and protein, .07, during lactation using data adjusted for ash. A maximum loss of 442 Mcal of tissue energy by approximately 77 DIM was determined by regression of empty body energy on DIM).

Preparturient heifers (n = 561) from 9 herds in 6 US states and 1 Canadian province were enrolled in a study to test the hypothesis that prepartum intramammary therapy would cure existing intramammary infections (IMI) and lead to increased milk production, reduced linear somatic cell count (LSCC), and improved reproductive performance. Mammary secretions were collected 10 to 21 d before expected calving from each quarter. Heifers were then assigned by identification number to receive intramammary therapy consisting of infusion of one tube per mammary quarter of a lactating cow commercial antibiotic preparation containing cephapirin or to a nontreated control group. Overall, 34.1% of mammary quarters were infected with a mastitis pathogen before parturition and 63.4% of heifers had at least one mammary quarter infected. The coagulase-negative staphylococci (CNS) caused the majority (74.8%) of prepartum IMI. Coagulase-positive staphylococci, environmental streptococci, and coliforms accounted for 24.5% of prepartum infections. Treatment had a significant effect on the cure rate of infected mammary quarters. Mammary quarters that were infected prepartum and treated with antibiotics had a 59.5% efficacy of cure rate and the percentage reduction in heifers with IMI was 51.9. Control quarters had a spontaneous cure rate of 31.7%. Treatment did not significantly affect milk production or LSCC in the first 200 d of lactation; however, there was a significant treatment by herd interaction for milk production. Quarters cured of either CNS or major pathogens had a lower LSCC in the first 200 d of lactation. No significant effect on services per conception or days open between treatment and control groups was observed. This trial demonstrated that prepartum intramammary antibiotic therapy did reduce the number of heifer IMI postpartum. Milk production, LSCC, and reproductive performance during the first 200 d of the first lactation were not significantly affected by treatment. Given these results, use of prepartum intramammary antibiotic therapy in heifers as a universal strategy to increase milk production in first-lactation dairy cows may not be warranted.

The rate and extent of estimated energy mobilization and the relationship between fat depth at the rib and thurl and body condition score (BCS) were investigated in Jersey and Holstein cows in early lactation. Twenty-six cows were paired by breed, parity, and calving date, and were individually fed a total mixed ration ad libitum from parturition through 120 d in milk. Feed intake and milk production were measured daily; body weight (BW), BCS, subcutaneous fat depth, milk composition, and concentration of plasma nonesterified fatty acids were measured every 2 wk. Estimated tissue energy balance (TEB) was calculated using 1989 NRC equations. Net energy intake was greater in early lactation for Holsteins compared with Jerseys, 37.8 and 28.2 Mcal/d, respectively. Milk energy was greater for Holsteins relative to Jerseys, 30.5 versus 21.2 Mcal/d. Fat depth and BCS did not differ between breeds. A positive relationship existed between fat depth and BCS for Jerseys; however, there was no significant relationship for Holsteins. The best-fit regression model for predicting TEB for Holsteins and Jerseys in early lactation included week of lactation, milk composition, and BCS. Jerseys remained in negative TEB for a shorter period of time relative to Holsteins. The TEB nadir was -6.19 and -12.9 Mcal/d, for Jerseys and Holsteins, respectively. Expressed as a proportion of metabolic BW (BW(0.75)), net energy intake did not differ between breeds, yet milk energy and estimated tissue energy loss were greater for Holsteins compared with Jerseys.

To develop equations for predicting body composition, mature Holstein cows (n = 21) were slaughtered at three physiological stages (-7, 63, and 269 d postpartum) after consecutive intravenous dosing with urea and D2O. Blood was sampled at 0 and 12 min after dosing with urea for determination of urea space and from 0 to 72 h after dosing with D2O. Empty body water and total body water were estimated by dilution kinetics for D2O using two- and one-compartment models, respectively. At slaughter, body components were ground, sampled, and freeze-dried for chemical analysis. Prediction of empty body water by urea space was not an improvement over the prediction by body weight alone. Prediction by D2O dilution explained 73 and 87% of the variation in empty and total body water, respectively. Estimated body protein, as determined from empty body water, predicted actual body protein with an error of 4.7 kg. Daily DMI explained 84% of the variation in the DM of the gastrointestinal tract contents (DM fill). Estimations of empty body fat (R2 = .85) and empty body energy (R2 = .89) from D2O dilution were capable of detecting significant differences in body fat (42.9 kg) and body energy (375 Mcal) across physiological stages and might be useful for prediction of body composition changes during the lactation cycle.