A.G.V. Teixeira

Molecular and epidemiological characterization of bovine intrauterine Escherichia coli

Escherichia coli are believed to be associated with postpartum metritis and endometritis but their role in the pathogenesis of both diseases is still undefined. In this study, uterine swabs for E. coli isolation were collected from 374 lactating Holstein cows housed on 4 commercial farms near Ithaca, New York. A total, 125 of 374 cows (33.4%) were positive for E. coli culture. Standard multiplex PCR protocols were used to screen the isolates for the presence of 32 virulence factor genes. Cows that had twin parturition were 4.4 times more likely to have intrauterine E. coli contamination than those that gave birth to single live female calves. Stillborn parturition and birth of single live male calves also increased the odds of intrauterine contamination by E. coli (3.7- and 1.6-fold, respectively) compared with birth of live female calves. Six virulence factors, common to extraintestinal and enteroaggregative E. coli, were found to be associated with metritis and endometritis: fimH, hlyA, cdt, kpsMII, ibeA, and astA. The virulence factor gene fimH was the most prevalent and the most significant: intrauterine E. coli carrying fimH and at least 1 of the other 5 identified virulence factors were pathogenic, and phylogenetic analysis based on the nucleotide sequence of DNA gyrase from 41 such IUEC revealed 2 clades.

Microbiota of Cow’s Milk; Distinguishing Healthy, Sub-Clinically and Clinically Diseased Quarters

The objective of this study was to use pyrosequencing of the 16S rRNA genes to describe the microbial diversity of bovine milk samples derived from clinically unaffected quarters across a range of somatic cell counts (SCC) values or from clinical mastitis, culture negative quarters. The obtained microbiota profiles were used to distinguish healthy, subclinically and clinically affected quarters. Two dairy farms were used for the collection of milk samples. A total of 177 samples were used. Fifty samples derived from healthy, culture negative quarters with a SCC of less than 20,000 cells/ml (group 1); 34 samples derived from healthy, culture negative quarters, with a SCC ranging from 21,000 to 50,000 cells/ml (group 2); 26 samples derived from healthy, culture negative quarters with a SCC greater than 50,000 cells/ml (group 3); 34 samples derived from healthy, culture positive quarters, with a SCC greater than 400,000 (group 4, subclinical); and 33 samples derived from clinical mastitis, culture negative quarters (group 5, clinical). Bacterial DNA was isolated from these samples and the 16S rRNA genes were individually amplified and pyrosequenced. All samples analyzed revealed great microbial diversity. Four bacterial genera were present in every sample obtained from healthy quarters (Faecalibacterium spp., unclassified Lachnospiraceae, Propionibacterium spp. and Aeribacillus spp.). Discriminant analysis models showed that samples derived from healthy quarters were easily discriminated based on their microbiota profiles from samples derived from clinical mastitis, culture negative quarters; that was also the case for samples obtained from different farms. Staphylococcus spp. and Streptococcus spp. were among the most prevalent genera in all groups while a general multivariable linear model revealed that Sphingobacterium and Streptococcus prevalences were associated with increased 10 log SCC. Conversely, Nocardiodes and Paenibacillus were negatively correlated, and a higher percentage of the genera was associated with a lower 10 log SCC.

Efficacy of formalin, copper sulfate, and a commercial footbath product in the control of digital dermatitis

The objective was to evaluate the relative efficacy of a novel, commercially available disinfectant agent (T-Hexx Dragonhyde HBC, Hydromer, Branchburg, NJ) compared with formalin and copper sulfate. The hypothesis was 2 sided; therefore, the hypothesis was that the new agent would be better or worse compared with the industry gold standard footbath agents, formalin and copper sulfate. The study was conducted in a large commercial dairy farm located near Ithaca, New York, from June 18, 2009 to October 26, 2009. Two identical studies were conducted, the first comparing Dragonhyde (5% solution, twice weekly) and formalin (5% solution, twice weekly) and the second comparing Dragonhyde (5% solution, twice weekly) and copper sulfate (10% solution, twice weekly). The study design was identical for both studies with 4 pens (physically identical), 2 treatments (Dragonhyde vs. formalin and Dragonhyde vs. copper sulfate), 2 periods (crossing over the treatment within pen), and 3 repeated measures (3 observations per cow: enrollment, wk 2, and wk 4). For study 1, 406 cows were enrolled (n=201 formalin and 205 Dragonhyde). For study 2, 356 cows were enrolled (n=189 copper sulfate and 167 Dragonhyde). The adjusted odds of digital dermatitis lesion (DDL) throughout the study period were analyzed by mixed logistic regression model. In study 1, the odds of DDL were 1.36 times higher for the formalin group compared with the Dragonhyde group. In study 2, the data were analyzed by a similar statistical model and the variable treatment did not significantly affect the overall prevalence of DDL. In conclusion, the performance of 3 hoof care products was evaluated and it was concluded that Dragonhyde performed better than formalin and that there was no difference between copper sulfate and Dragonhyde.

Isolation and Characterization of Faecalibacterium prausnitzii from Calves and Piglets

The goal of our study was to isolate and characterize Faecalibacterium prausnitzii from fecal samples of healthy calves and piglets, in order to develop a novel probiotic for livestock animals. We identified 203 isolates of Faecalibacterium sp., which were clustered in 40 genetically distinct groups. One representative isolate from each cluster was selected for further characterization. The concentrations of the short chain fatty acids (SCFA) acetate, butyrate, propionate and isobutyrate in the culture media were measured by gas chromatography. We observed reduction in the concentration of acetate followed by concomitant increase in the concentration of butyrate, suggesting that the isolates were consuming acetate present in the media and producing butyrate. Butyrate production correlated positively with bacterial growth. Since butyrate has many benefits to the colonic epithelial cells, the selection of strains that produce higher amounts of butyrate is extremely important for the development of this potential probiotic. The effect of pH and concentration of bile salts on bacterial growth was also evaluated in order to mimic the conditions encountered by F. prausnitzii in vivo. The optimal pH for growth ranged between 5.5 and 6.7, while most isolates were inhibited by of the lowest concentration of bile salts tested (0.1%). Antimicrobial resistance profile showed that most isolates of Faecalibacterium sp. were resistant against ciprofloxacin and sulfamethoxazole-trimethoprim. More than 50% of the isolates were resistant to tetracycline, amikacin, cefepime and cefoxitin. A total of 19 different combinations of multidrug resistance were observed among the isolates. Our results provide new insights into the cultural and physiological characteristics of Faecalibacterium prausnitzii illustrating large variability in short chain fatty acid production, in vitro growth, sensitivity to bile salts, and antibiotic resistance and suggesting that future probiotic candidates should be carefully studied before elected for in vivo studies.

The bovine colostrum microbiome and its association with clinical mastitis

In an effort to characterize colostrum microbial diversity and its potential associations with early-lactation clinical mastitis, we used high-throughput sequencing of the 16S rRNA gene to investigate the bovine colostrum microbiome. A prospective observational study was conducted that included 70 Holstein cows; colostrum samples were collected from all 4 mammary gland quarters. Colostrum samples were categorized according to whether the quarter was diagnosed (CMC) or not diagnosed (NCMC) with clinical mastitis during the first 30 d postpartum. Colostrum samples were dominated by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria, and Tenericutes phyla, with the 6 most common taxa [order (o), family (f), and genus (g)] being g_Staphylococcus, g_Prevotella, f_Ruminococcaceae, o_Bacteroidales, o_Clostridiales, and g_Pseudomonas. The colostrum microbiota of primiparous cows was significantly richer (higher number of bacterial species) than that of multiparous cows, and differences in colostrum taxonomic structure between parities were also observed. The microbial community of NCMC samples of primiparous cows was significantly more diverse than that of CMC samples, and the relative abundances of the Tenericutes and Fusobacteria phyla as well as the Mycoplasma and Fusobacterium genera were significantly higher in NCMC than in CMC samples of primiparous cows. The colostrum core microbiome, defined as the bacterial taxa common to all colostrum samples examined, was composed of 20 taxa and included bacterial genera already known to be associated with mastitis (e.g., Staphylococcus, Mycoplasma, and Streptococcus spp.). Our results indicate that the colostrum microbiome of primiparous cows differs from that of multiparous cows, and it harbors some diversity and taxonomic markers of mammary gland health specific to primiparous cows only.

The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media.

The upper respiratory tract (URT) hosts a complex microbial community of commensal microorganisms and potential pathogens. Analyzing the composition and nature of the healthy URT microbiota and how it changes over time will contribute to a better understanding of the pathogenesis of pneumonia and otitis. A longitudinal study was conducted including 174 Holstein calves that were divided in four groups: healthy calves, calves diagnosed with pneumonia, otitis or both diseases. Deep pharyngeal swabs were collected on days 3, 14, 28, and 35 of life, and next-generation sequencing of the 16S rRNA gene as well as quantitative PCR was performed. The URT of Holstein dairy calves aged 3 to 35 days revealed to host a highly diverse bacterial community. The relative abundances of the bacterial genera Mannheimia, Moraxella, and Mycoplasma were significantly higher in diseased versus healthy animals, and the total bacterial load of newborn calves at day 3 was higher for animals that developed pneumonia than for healthy animals. Our results corroborate the existing knowledge that species of Mannheimia and Mycoplasma are important pathogens in pneumonia and otitis. Furthermore, they suggest that species of Moraxella can potentially cause the same disorders (pneumonia and otitis), and that high neonatal bacterial load is a key contributor to the development of pneumonia.

Effect of an injectable trace mineral supplement containing selenium, copper, zinc, and manganese on immunity, health, and growth of dairy calves

The objective of this study was to evaluate the effect of 2 subcutaneous injections of a multimineral preparation, each containing 60 mg of zinc, 10mg of manganese, 5mg of selenium, and 15 mg of copper at 3 and 30 d after birth on immunity, health, and growth of dairy calves during the preweaning period. The study was conducted in upstate New York in 2 commercial dairy farms. A total of 790 Holstein heifer calves were randomly allocated at birth into 1 of 2 treatments: trace mineral supplement (TMS) treated or control. Blood samples were collected at 3, 14, and 35 d after birth to evaluate glutathione peroxidase (GPx) activity, superoxide dismutase (SOD) activity, haptoglobin, and neutrophil and monocyte function. Incidence of diseases and average daily gain was evaluated in the first 50 d of life. At 14 d of life, TMS-treated calves had increased neutrophil activity compared with control calves. Moreover, TMS-treated calves had greater GPx activity on d 14 after birth than control calves. The TMS treatment reduced the incidence of diarrhea (TMS=41.7% vs. control=49.7%) and combined incidence of pneumonia or otitis or both (TMS=41.7% vs. control=49.1%). Additionally, GPx was greater for calves diagnosed with otitis at d 35 after birth. However, calves diagnosed with pneumonia had decreased GPx activity at d 35 after birth. Serum SOD and haptoglobin concentrations were not affected by treatment or disease. Moreover, no effects were observed on average daily gain and survivability between TMS-treated and control calves during the preweaning period. Supplementation with trace minerals at 3 and 30 d of life increased neutrophil function and GPx activity and reduced the incidence of health disorders.

Thoracic ultrasound assessment of lung consolidation at weaning in Holstein dairy heifers: Reproductive performance and survival

The objective of this study was to determine the association of lung consolidation at weaning with later reproductive performance and survival. Ultrasonography of the lungs was performed at 60 d of life in recently weaned Holstein heifer calves from a single farm in New York State. Thoracic screening covered the right 2nd through 10th and left 3rd through 9th intercostal spaces and was performed using a 6.2-MHz linear transducer. Each calf was classified as not having lung consolidation (hyperechoic line with reverberation artifact with or without comet tail) or with lung consolidation (any detectable heterogeneous hypoechoic area). A total of 613 heifer calves were enrolled in the study, with 489 (79.8%) classified as not having lung consolidation and 124 (20.2%) classified as having lung consolidation. No difference in mortality was observed from 60 to 350 d of life between heifers with lung consolidation (1.6%) and without lung consolidation (2.0%). Six hundred and one nulliparous Holsteins became eligible for insemination at 350 d of life; the hazard of being removed from the herd between 350 d of life and first calving for heifers with lung consolidation at weaning was higher (hazard ratio = 4.7, 95% confidence interval = 2.1 to 10.7). Additionally, heifers without lung consolidation tended to have improved pregnancy to first artificial insemination (62.0%) compared with heifers with lung consolidation (52.5%). Overall reproductive performance was also affected as heifers with lung consolidation at 60 d of life had a lower hazard of pregnancy compared with those without lung consolidation (hazard ratio = 0.7, 95% confidence interval = 0.6 to 0.8). From 601 animals that entered the breeding period, 565 entered the milking herd and were followed during the first 3 mo of lactation. No differences in weekly average milk production were observed between animals with or without lung consolidation at weaning. Our results show that heifers with lung consolidation at weaning were less likely to get pregnant and more likely to be culled before their first parturition than heifers without lung consolidation; this difference did not continue into first lactation milk production, risk of culling, or reproductive performance.

Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics

Bovine respiratory disease (BRD) is a multifactorial disorder responsible for severe economic losses in dairy and feedlot herds. Advances in next-generation sequencing mean that microbial communities in clinical samples, including non-culturable bacteria, can be characterized. Our aim was to evaluate the microbiota of the upper respiratory tract of healthy calves and calves with BRD using whole-genome sequencing (shotgun metagenomics). We performed deep nasopharyngeal swabs on 16 Holstein heifer calves (10 healthy and 6 diagnosed with BRD during the study) at 14 and 28 d of life in 1 dairy herd near Ithaca, New York. Total DNA was extracted, and whole-genome sequencing was performed using the MiSeq Illumina platform (Illumina Inc., San Diego, CA). Samples included 5 predominant phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Tenericutes. At the genus level, we observed differences between groups for Pseudomonas spp. At the species level, Mannheimia haemolytica was the most abundant bacterium detected. We detected significant differences between groups of calves in the relative abundance of Pseudomonas fluorescens. Pasteurella multocida was among the 20 most abundant species, and Moraxella catarrhalis, commonly associated with pneumonia in humans, was detected in all groups. Analysis of resistance to antibiotics and compounds profiling revealed differences in cobalt-zinc-cadmium resistance. Further research to elucidate the role of Moraxella catarrhalis in BRD is warranted. Genes that were resistant to cobalt-zinc-cadmium, observed mostly in calves with BRD, might be associated with difficulties in antibiotic treatment.

Evaluation of the effects of ultraviolet light on bacterial contaminants inoculated into whole milk and colostrum, and on colostrum immunoglobulin G

Raw milk and colostrum can harbor dangerous microorganisms that can pose serious health risks for animals and humans. According to the USDA, more than 58% of calves in the United States are fed unpasteurized milk. The aim of this study was to evaluate the effect of UV light on reduction of bacteria in milk and colostrum, and on colostrum IgG. A pilot-scale UV light continuous (UVC) flow-through unit (45 J/cm(2)) was used to treat milk and colostrum. Colostrum and sterile whole milk were inoculated with Listeria innocua, Mycobacterium smegmatis, Salmonella serovar Typhimurium, Escherichia coli, Staphylococcus aureus, Streptococcus agalactiae, and Acinetobacter baumannii before being treated with UVC. During UVC treatment, samples were collected at 5 time points and bacteria were enumerated using selective media. The effect of UVC on IgG was evaluated using raw colostrum from a nearby dairy farm without the addition of bacteria. For each colostrum batch, samples were collected at several different time points and IgG was measured using ELISA. The UVC treatment of milk resulted in a significant final count (log cfu/mL) reduction of Listeria monocytogenes (3.2 ± 0.3 log cfu/mL reduction), Salmonella spp. (3.7 ± 0.2 log cfu/mL reduction), Escherichia coli (2.8 ± 0.2 log cfu/mL reduction), Staph. aureus (3.4 ± 0.3 log cfu/mL reduction), Streptococcus spp. (3.4 ± 0.4 log cfu/mL reduction), and A. baumannii (2.8 ± 0.2 log cfu/mL reduction). The UVC treatment of milk did not result in a significant final count (log cfu/mL) reduction for M. smegmatis (1.8 ± 0.5 log cfu/mL reduction). The UVC treatment of colostrum was significantly associated with a final reduction of bacterial count (log cfu/mL) of Listeria spp. (1.4 ± 0.3 log cfu/mL reduction), Salmonella spp. (1.0 ± 0.2 log cfu/mL reduction), and Acinetobacter spp. (1.1 ± 0.3 log cfu/mL reduction), but not of E. coli (0.5 ± 0.3 log cfu/mL reduction), Strep. agalactiae (0.8 ± 0.2 log cfu/mL reduction), and Staph. aureus (0.4 ± 0.2 log cfu/mL reduction). The UVC treatment of colostrum significantly decreased the IgG concentration, with an observed final mean IgG reduction of approximately 50%. Development of new methods to reduce bacterial contaminants in colostrum must take into consideration the barriers imposed by its opacity and organic components, and account for the incidental damage to IgG caused by manipulating colostrum.