A new predilection site of Mycoplasma bovis: Postsurgical seromas in beef cattle

Mycoplasma bovis is a highly contagious bacterium, which predominantly causes chronic pneumonia, otitis and arthritis in calves and mastitis in adult cattle. In humans, Mycoplasma species have been associated with post-surgical infections. The present study aimed to identify the bacteria associated with three outbreaks of infected seromas after caesarian section in Belgian Blue beef cattle. A total of 10 cases occurred in three herds which were in close proximity of each other and shared the same veterinary practice. M. bovis could be cultured from seroma fluid in five of the six referred animals, mostly in pure culture and was isolated from multiple chronic sites of infection (arthritis and mastitis) as well. DNA fingerprinting of the isolates targeting two insertion sequence elements suggested spread of M. bovis from chronic sites of infection (udder and joints) to the postsurgical seromas. Identical genetic profiles were demonstrated in two animals from two separate farms, suggesting spread between farms. Mortality rate in the referred animals positive for M. bovis in a seroma was 80% (4/5), despite intensive treatment. A massive increase in antimicrobial use was observed in every affected farm. These observations demonstrate involvement of mycoplasmas in outbreaks of postsurgical seromas in cattle.

Beef CHAPA : cow/calf health & productivity audit.

"March 1996"--Cover of [pt. 6]

Quantification and prevalence of Salmonella in beef cattle presenting at slaughter

Aims: A survey to determine the prevalence and numbers of Salmonella in beef cattle presented for slaughter at abattoirs across Australia was conducted between September 2002 and January 2003. Methods and Results: Automated immunomagnetic separation (AIMS) was used for detection and isolation of Salmonella enriched from cattle faeces. Salmonella were enumerated from positive samples using a combination of the Most Probable Number (MPN) technique and AIMS. A total of 310 faecal samples were tested, 155 were from lot-fed cattle and 155 from grass-fed cattle. Salmonella spp. were isolated from 21 (6.8%) of the cattle and the prevalence amongst grass-fed cattle (4.5%) was not significantly different to that found in lot-fed cattle (9%). Counts of Salmonella in positive faeces varied from

Validation of assembled nucleic acid-based tests in diagnostic microbiology laboratories

Medical microbiology and virology laboratories use nucleic acid tests (NAT) to detect genomic material of infectious organisms in clinical samples. Laboratories choose to perform assembled (or in-house) NAT if commercial assays are not available or if assembled NAT are more economical or accurate. One reason commercial assays are more expensive is because extensive validation is necessary before the kit is marketed, as manufacturers must accept liability for the performance of their assays, assuming their instructions are followed. On the other hand, it is a particular laboratory's responsibility to validate an assembled NAT prior to using it for testing and reporting results on human samples. There are few published guidelines for the validation of assembled NAT. One procedure that laboratories can use to establish a validation process for an assay is detailed in this document. Before validating a method, laboratories must optimise it and then document the protocol. All instruments must be calibrated and maintained throughout the testing process. The validation process involves a series of steps including: (i) testing of dilution series of positive samples to determine the limits of detection of the assay and their linearity over concentrations to be measured in quantitative NAT; (ii) establishing the day-to-day variation of the assay's performance; (iii) evaluating the sensitivity and specificity of the assay as far as practicable, along with the extent of cross-reactivity with other genomic material; and (iv) assuring the quality of assembled assays using quality control procedures that monitor the performance of reagent batches before introducing new lots of reagent for testing.

Attachment of Shiga toxigenic Escherichia coli to beef muscle and adipose tissue

Shiga toxigenic Escherichia coli (STEC) serotypes are important foodborne pathogens that cause gastrointestinal disease worldwide. An understanding of how STEC strains attach to surfaces may provide insight into the potential persistence of and contamination with STEC in food environments. The initial attachment of a selection of STEC serotypes to beef muscle and adipose tissue was evaluated for isolates grown in planktonic and sessile culture. Initial experiments were performed to determine whether attachment differed among STEC strains and between the two modes of growth. Viable counts were obtained for loosely and strongly attached cells, and the strength of attachment (S-r) was calculated. All bacterial isolates grown in sessile culture attached in higher numbers to muscle and adipose tissue than did bacteria in planktonic cultures. For all attachment assays performed, mean concentrations for loosely attached cells were consistently higher than concentrations for strongly attached cells. The mean concentrations for strongly attached bacteria for planktonic and sessile cultures were significantly higher (P < 0.05) on adipose than on muscle tissue. However, some strains of STEC, particularly those from sessile culture, did not differ in their attachment to muscle or adipose tissue. S-r values were not significantly different (P > 0.05) among STEC isolates for all assays. No correlation was found between bacterial hydrophobicity and surface charge values (previously determined) and production of surface structures, viable counts, and S-r values. STEC grown in planktonic and sessile culture seems to behave differently with respect to attachment to muscle and adipose tissue. Cells in sessile culture may have a greater potential to strongly attach to meat surfaces.

Laboratory-based simulation of freezing profiles of beef trim for Escherichia coli O157 survival determinations

This study was undertaken to develop a simple laboratory-based method for simulating the freezing profiles of beef trim so that their effect on E. coli 0157 survival could be better assessed. A commercially available apparatus of the type used for freezing embryos, together with an associated temperature logger and software, was used for this purpose with a -80 degrees C freezer as a heat sink. Four typical beef trim freezing profiles, of different starting temperatures or lengths, were selected and modelled as straight lines for ease of manipulation. A further theoretical profile with an extended freezing plateau was also developed. The laboratory-based setup worked well and the modelled freezing profiles fitted closely to the original data. No change in numbers of any of the strains was apparent for the three simulated profiles of different lengths starting at 25 degrees C. Slight but significant (P < 0.05) decreases in numbers (similar to 0.2 log cfu g(-1)) of all strains were apparent for a profile starting at 12 degrees C. A theoretical version of this profile with a freezing plateau phase extended from 11 h to 17 h resulted in significant (P < 0.05) decreases in numbers (similar to 1.2 log cfu g(-1)) of all strains. Results indicated possible avenues for future research in controlling this pathogen. The method developed in this study proved a useful and cost-effective way for simulating freezing profiles of beef trim. (c) 2005 Elsevier B.V. All rights reserved.

The "Beef" about Beef

The grading of beef has become a controversial issue, with both government and the cattle industry working to ensure uniformity. The author contends that meat quality, and the resulting tenderness, juiciness, and flavor desired by consumers, is being threatened by such pressures and actions.

The application of next generation sequencing to profile microbe related cheese quality defects

High throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencing-based approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbe-associated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.

A Loop-mediated Isothermal Amplification Method for Rapid Direct Detection and Differentiation of Non-pathogenic and Verocytotoxigenic Escherichia coli in Beef and Bovine Faeces

The aim of this study was to develop a multiplex loop-mediated isothermal amplification (LAMP) method capable of detecting Escherichia coli generally and verocytotoxigenic E. coli (VTEC) specifically in beef and bovine faeces. The LAMP assay developed was highly specific (100%) and able to distinguish between E. coli and VTEC based on the amplification of the phoA, and stx1 and/or stx2 genes, respectively. In the absence of an enrichment step, the limit of detection 50% (LOD50) of the LAMP assay was determined to be 2.83, 3.17 and 2.83-3.17 log CFU/g for E. coli with phoA, stx1 and stx2 genes, respectively, when artificially inoculated minced beef and bovine faeces were tested. The LAMP calibration curves generated with pure cultures, and spiked beef and faeces, suggested that the assay had good quantification capability. Validation of the assay, performed using retail beef and bovine faeces samples, demonstrated good correlation between counts obtained by the LAMP assay and by a conventional culture method, but suggested the possibility of false negative LAMP results for 12.5-14.7% of samples tested. The multiplex LAMP assay developed potentially represents a rapid alternative to culture for monitoring E.coli levels in beef or faeces and it would provide additional information on the presence of VTEC. However, some further optimisation is needed to improve detection sensitivity.

Microbiological assessment of indoor air quality at different hospital sites

Poor hospital indoor air quality (IAQ) may lead to hospital-acquired infections, sick hospital syndrome and various occupational hazards. Air-control measures are crucial for reducing dissemination of airborne biological particles in hospitals. The objective of this study was to perform a survey of bioaerosol quality in different sites in a Portuguese Hospital, namely the operating theater (OT), the emergency service (ES) and the surgical ward (SW). Aerobic mesophilic bacterial counts (BCs) and fungal load (FL) were assessed by impaction directly onto tryptic soy agar and malt extract agar supplemented with antibiotic chloramphenicol (0.05%) plates, respectively using a MAS-100 air sampler. The ES revealed the highest airborne microbial concentrations (BC range 240-736 CFU/m(3) CFU/m(3); FL range 27-933 CFU/m(3)), exceeding, at several sampling sites, conformity criteria defined in national legislation [6]. Bacterial concentrations in the SW (BC range 99-495 CFU/m(3)) and the OT (BC range 12-170 CFU/m(3)) were under recommended criteria. While fungal levels were below 1 CFU/m(3) in the OT, in the SW (range 1-32 CFU/m(3)), there existed a site with fungal indoor concentrations higher than those detected outdoors. Airborne Gram-positive cocci were the most frequent phenotype (88%) detected from the measured bacterial population in all indoor environments. Staphylococcus (51%) and Micrococcus (37%) were dominant among the bacterial genera identified in the present study. Concerning indoor fungal characterization, the prevalent genera were Penicillium (41%) and Aspergillus (24%). Regular monitoring is essential for assessing air control efficiency and for detecting irregular introduction of airborne particles via clothing of visitors and medical staff or carriage by personal and medical materials. Furthermore, microbiological survey data should be used to clearly define specific air quality guidelines for controlled environments in hospital settings.

Melhoria da qualidade de jerked beef pela substituição de nitrito de sódio por extratos naturais de própolis e erva mate como agente antioxidante

Jerked beef, an industrial meat product obtained from beef with the addition of sodium chloride and curing salts and subjected to a maturing and drying process is a typical Brazilian product which has been gradually discovered by the consumer. The replacement of synthetic antioxidants by natural substances with antioxidant potential due to possible side effects discovered by lab tests, consumer health, is being implemented by the meat industry. This study aimed to evaluate the lipid oxidation of jerked beef throughout the storage period by replacing the sodium nitrite by natural extracts of propolis and Yerba Mate. For jerked beef processing brisket was used as raw material processed in 6 different formulations: formulation 1 (control - in nature), formulation 2 (sodium nitrite - NO), formulation 3 (Yerba Mate - EM), formulation 4 (propolis extract - PRO), formulation 5 (sodium nitrite + Yerba Mate - MS + NO), formulation 6 (propolis extract + sodium nitrite - PRO + NO). The raw material was subjected to wet salting, dry salting (tombos), drying at 25°C, packaging and storage in BOD 25°C. Samples of each formulation were taken every 7 days for analysis of lipid oxidation by the TBARS method. In all formulations, were carried out analysis of chemical composition at time zero and sixty days of storage. The water activity analysis and color (L *, a *, b *) was monitored at time zero, thirty and sixty days of storage. The Salmonella spp count, Coliform bacteria, Termotolerant coliforms and coagulase positive staphylococci were taken at time zero and sixty days. The activity of natural antioxidants evaluated shows the decline of lipid oxidation up to 2.5 times compared with the product in natura and presented values with no significant differences between treatments NO and EM, confirming the potential in minimize lipid oxidation of Jerked beef throughout the 60 days of storage. The results also showed that yerba mate has a higher antioxidant capacity compared to the propolis except the PRO + NO formulation. When associated with yerba mate with sodium nitrate, TBARS values become close to values obtained only for the control samples with the addition of sodium nitrite. The proximal composition of the formulations remained within the standards required in the IN nº22/2000 for jerked beef. Samples that differ significantly at 5% are directly related to the established type of formulation. The count of microorganisms was within the standards of the DRC nº12/2001 required for matured meat products. The intensity of the red (a*) decreased with storage time and increase the intensity of yellow (b*) indicates a darkening of the product despite L* also have been increased. These results suggest that yerba mate is a good alternative to meat industry in reducing healing addition salts when associated with another antioxidant.

Effect of grape seed extract on oxidative, color and sensory stability of pre-cooked, frozen, re-heated beef sausage model system

The processing of meats at the factory level can trigger the onset of lipid oxidation, which can lead to meat quality deterioration. Warmed over flavor is an off-flavor, which is associated with oxidative deterioration in meat. To avoid or delay the auto-oxidation process in meat products, synthetic and natural antioxidants have been successfully used. Grape (Vitis Vinifera) is of special interest due to its high content of phenolic compounds. Grape seed extract sold commercially as a dietary supplement, has the potential to reduce lipid oxidation and WOF in cooked ground beef when added at 1%. The objective of study 1 was to compare the antioxidant activity of natural antioxidants including grape seed extract and some herbs belonging to the Lamiaciae family: rosemary (Rosmarinus Officinalis), sage (Salvia Officinalis) and oregano (Origanum Vulgare) with commercial synthetic antioxidants like BHT, BHA, propyl gallate and ascorbic acid using the ORAC assay. All sample solutions were prepared to contain 1.8 gm sample/10 ml solvent. The highest antioxidant activity was observed for the grape seed extract sample (359.75 µM TE), while the lowest was observed for BHA, propyl gallate and rosemary also showed higher antioxidant potential with ORAC values above 300 μmol TE/g. ORAC values obtained for ascorbic acid and Sage were between 250-300μ mol TE/g while lowest values were obtained for Butylated Hydroxytoluene (28.50 µM TE). Based on the high ORAC values obtained for grape seed extract, we can conclude that byproducts of the wine/grape industry have antioxidant potential comparable to or better than those present in synthetic counterparts. The objective of study 2 was to compare three levels of grape seed extract (GSE) to commonly used antioxidants in a pre-cooked, frozen, stored beef and pork sausage model system. Antioxidants added for comparison with control included grape seed extract (100, 300, 500 ppm), ascorbic acid (AA, 100 ppm of fat) and propyl gallate (PG, 100 ppm of fat). Product was formed into rolls, frozen, sliced into patties, cooked on a flat griddle to 70C, overwrapped in PVC, and then frozen at –18C for 4 months. GSE- and PG-containing samples retained their fresh cooked beef odor and flavor longer (p<0.05) than controls during storage. Rancid odor and flavor scores of GSE-containing samples were lower (p<0.05) than those of controls after 4 months of storage. The L* value of all samples increased (p<0.05) during storage. Thiobarbituric acid reactive substances (TBARS) of the control and AA-containing samples increased (p<0.05); those of GSE-containing samples did not change significantly (p>0.05) over the storage period.

Integrative genomic, epigenetic and metabolomic characterization of beef from grass-fed Angus steers

Beef constitutes a main component of the American diet and still represent the principal source of protein in many parts of the world. Currently, the meat market is experiencing an important transformation; consumers are increasingly switching from consuming traditional beef to grass-fed beef. People recognized products obtained from grass-fed animals as more natural and healthy. However, the true variations between these two production systems regarding various aspects remain unclear. This dissertation provides information from closely genetically related animals, in order to decrease confounding factors, to explain several confused divergences between grain-fed and grass-fed beef. First, we examined the growth curve, important economic traits and quality carcass characteristics over four consecutive years in grain-fed and grass-fed animals, generating valuable information for management decisions and economic evaluation for grass-fed cattle operations. Second, we performed the first integrated transcriptomic and metabolomic analysis in grass-fed beef, detecting alterations in glucose metabolism, divergences in free fatty acids and carnitine conjugated lipid levels, and altered β-oxidation. Results suggest that grass finished beef could possibly benefit consumer health from having lower total fat content and better lipid profile than grain-fed beef. Regarding animal welfare, grass-fed animals may experience less stress than grain-fed individuals as well. Finally, we contrasted the genome-wide DNA methylation of grass-fed beef against grain-fed beef using the methyl-CpG binding domain sequencing (MBD-Seq) method, identifying 60 differentially methylated regions (DMRs). Most of DMRs were located inside or upstream of genes and displayed increased levels of methylation in grass-fed individuals, implying a global DNA methylation increment in this group. Interestingly, chromosome 14, which has been associated with large effects on ADG, marbling, back fat, ribeye area and hot carcass weight in beef cattle, allocated the largest number of DMRs (12/60). The pathway analysis identified skeletal and muscular system as the preeminent physiological system and function, and recognized carbohydrates metabolism, lipid metabolism and tissue morphology among the highest ranked networks. Therefore, although we recognize some limitations and assume that additional examination is still required, this project provides the first integrative genomic, epigenetic and metabolomics characterization of beef produced under grass-fed regimen.