Laura E. Green

The role of ecological theory in microbial ecology

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

Assessment of the welfare of dairy cattle using animal-based measurements: direct observations and investigation of farm records.

A protocol was developed by consultation with experts on the welfare of cattle to use direct observations of cattle and an examination of farm records to assess welfare. Fifty-three dairy farms in England were visited and assessed during the winter of 2000/01. The findings were compiled and the results of the welfare measurements were examined by 50 experts who indicated at what level they considered that improvement was required. More than 75 per cent of them considered that 32 of the 53 farms needed to take action to reduce the incidence of mastitis, and that at least 42 of the farms needed to take action to reduce the prevalence of lameness, overgrown claws, swollen and ulcerated hocks, and injuries from the environment.

Survey of the incidence and aetiology of mastitis on dairy farms in England and Wales

A survey of clinical and subclinical mastitis was carried out on 97 dairy farms in England and Wales, selected at random from members of a national milk recording scheme. The farmers were asked to collect aseptic milk samples from five consecutive cases of clinical mastitis and from five quarters with high somatic cell counts using a defined protocol, and they completed a questionnaire that included information on the cows sampled, the herd and the history of mastitis in the herd. The samples were collected throughout the year. The mean incidence of clinical mastitis was 47 cases per 100 cows per year (estimated from historic farm records) and 71 cases per 100 cows per year (estimated from the samples collected). Streptococcus uberis and Escherichia coli were isolated in pure culture from 23·5 per cent and 19·8 per cent, respectively, of the clinical samples; 26·5 per cent of the clinical samples produced no growth. The most common isolates from the samples with high cell counts were coagulase-negative staphylococci (15 per cent), S uberis (14 per cent) and Corynebacterium species (10 per cent). Staphylococcus aureus and coagulase-positive staphylococci together accounted for 10 per cent of the samples with high somatic cell counts; 39 per cent produced no bacterial growth.

A case control study of on-farm risk factors for tail biting in pigs

Abstract Tail biting is an abnormal behaviour of pigs that is thought to have a multi-factorial origin. It is considered an unpredictable event on farms and is hard to reproduce experimentally. Therefore, a novel approach involving a case control study was used to investigate risk factors for tail biting on commercial units in England. Ninety-two pig farms across England were visited over a period of 11 months. At each visit, the owner or the manager of the unit was interviewed and the unit inspected. Data were recorded on standard forms. Farms were categorised into those that had tail biting in at least one pig in the past 6 months and those that had not. Univariate and logistic regression analyses yielded the following main results. Adding straw in the creep area once or more per day decreased the risk of tail biting 10-fold. Keeping grower pigs on partially or fully slatted floors versus solid floor increased risks of tail biting (odds ratio (OR)=3.2). Using a feeding system with five or more grower pigs per feed space increased risks of tail biting (OR=2.7). A stocking density during the growing phase of 110kg/m 2 or greater increased risks of tail biting (OR=2.7). Farms that belonged to a holding of five or more pig units had an increased risk of tail biting (OR=3.5). As the number of pens per stockman increased by one, the risk of tail biting increased 1.06-fold. Tail biting was also associated with the following disease and production information: as the P2 back-fat value increased by 1mm, the risk of tail biting decreased by 1.5-fold; post-weaning mortality above 2.5% was associated with a 3.9-fold increase in the risk of tail biting; presence of respiratory diseases was associated with a 1.6-fold increase in the risk of tail biting. Tail docking was associated with a three-fold increase in the risk of tail biting. This study has identified and quantified some management practices on commercial farms that can be changed to decrease the risk of tail biting in growing and finishing pigs.

Multilocus Sequence Typing of Intercontinental Bovine Staphylococcus aureus Isolates

ABSTRACT A total of 258 bovine-associated Staphylococcus aureus isolates from the United States, Chile, and the United Kingdom, plus the reference isolate S. aureus Newbould 305 (NCIMB 702892), were analyzed by multilocus sequence typing (MLST). A collection of previously characterized United Kingdom isolates were also included in the analysis. The results demonstrated that MLST is suitable for the differentiation of bovine S. aureus isolates from various sites (milk, teat skin, milking machine unit liners, hands, and bedding) and countries. The theory of the host specificity of S. aureus is supported by the detection of a previously undescribed clonal complex that comprised 87.4% of the isolates studied, with representatives from all geographic locations investigated. This suggests that a single clonal group has achieved a widespread distribution and is responsible for the majority of infections. Some sequence types (STs; ST25, ST115, ST124, and ST126) demonstrated site specificity, as they were significantly (P < 0.05) associated with milk or teat skin.

Leg disorders in broiler chickens: prevalence, risk factors and prevention.

Broiler (meat) chickens have been subjected to intense genetic selection. In the past 50 years, broiler growth rates have increased by over 300% (from 25 g per day to 100 g per day). There is growing societal concern that many broiler chickens have impaired locomotion or are even unable to walk. Here we present the results of a comprehensive survey of commercial flocks which quantifies the risk factors for poor locomotion in broiler chickens. We assessed the walking ability of 51,000 birds, representing 4.8 million birds within 176 flocks. We also obtained information on approximately 150 different management factors associated with each flock. At a mean age of 40 days, over 27.6% of birds in our study showed poor locomotion and 3.3% were almost unable to walk. The high prevalence of poor locomotion occurred despite culling policies designed to remove severely lame birds from flocks. We show that the primary risk factors associated with impaired locomotion and poor leg health are those specifically associated with rate of growth. Factors significantly associated with high gait score included the age of the bird (older birds), visit (second visit to same flock), bird genotype, not feeding whole wheat, a shorter dark period during the day, higher stocking density at the time of assessment, no use of antibiotic, and the use of intact feed pellets. The welfare implications are profound. Worldwide approximately 2×1010 broilers are reared within similar husbandry systems. We identify a range of management factors that could be altered to reduce leg health problems, but implementation of these changes would be likely to reduce growth rate and production. A debate on the sustainability of current practice in the production of this important food source is required.

Cross-sectional study of the prevalence of feather pecking in laying hens in alternative systems and its associations with management and disease.

A cross-sectional study of risk factors for feather pecking in layings hens in alternative systems was carried out in July 1998. A total of 637 questionnaires were sent out to farmers and producer groups and, after two reminders, the final response rate was 51.5 per cent. The outcome variable was feather pecking after point of lay. Over 55 per cent of the farmers reported that feather pecking had occurred in the last depopulated flock. This outcome was compared with the management procedures reported by flock managers by using univariate statistics. Factors associated with feather pecking with a significance ≤0.05 were then tested in two logistic regression models. In the first model the following factors were associated with an increased risk of feather pecking: less than 50 per cent of the flock using the outdoor area on a fine and sunny day, the occurrence of egg peritonitis and the occurrence of infectious bronchitis. The direction of the association between feather pecking and these infectious diseases was unclear, so in the second model only factors which were consistent throughout the laying period were tested. The following factors were associated with an increased risk of feather pecking: less than 50 per cent of the flock using the outdoor area on a fine and sunny day; three or more changes of diet during lay; the inspection of the flock by one person; an absence of loose litter at the end of lay; a temperature in the hen house of less than 20°C; turning the lights up when the flock was inspected; and the use of bell-drinkers. It is concluded that some of these factors could inhibit foraging and dust-bathing behaviour and others may increase competition or frustration, both of these changes having been shown experimentally to initiate feather pecking behaviour.

National intervention study of mastitis control in dairy herds in England and Wales

An intervention study was carried out on 52 dairy farms in England and Wales to determine whether the implementation of a well-specified mastitis control plan in herds with an incidence of clinical mastitis of more than 35 cases per 100 cows per year would reduce the incidence of clinical mastitis, and also reduce the incidence of increases in the somatic cell counts of individual cows. A clearly defined plan for the diagnosis and control of mastitis was developed by two veterinary specialists from the research literature. The herds were randomly allocated to receive the plan either at the start of the study (intervention herds) or after one year (control herds). Data on mastitis management and the farm environment were collected during farm visits. After one year there was a significant 22 per cent reduction in the proportion of cows affected with clinical mastitis on the intervention farms compared with the control farms. There were also significant reductions of approximately 20 per cent in the incidence of clinical mastitis and in the occurrence of increases in the somatic cell counts of individual cows from below, to above 200,000 cells/ml.

Risk factors associated with the prevalence of footrot in sheep from 1999 to 2000

A postal survey of the techniques being used for the treatment and control of footrot in sheep flocks between November 1999 and October 2000 was conducted in England and Wales in November 2000. Of the 392 questionnaires circulated, 251 (64 per cent) were returned, and 209 of these were usable. Negative binomial regression analysis indicated that the isolation of bought-in sheep, and the separation and individual treatment of diseased sheep with parenteral antibiotics, foot trimming and topical foot sprays were associated with a significantly lower prevalence of footrot in a flock. In contrast, ewe flocks which were routinely foot trimmed more than once a year had a significantly higher prevalence of footrot. No evidence was found that footbathing a flock reduced the level of footrot, except on the 14 per cent of farms where the penning and race facilities for footbathing were reported by the farmer to be excellent. Vaccination had no significant beneficial effect on the level of footrot in a flock.

Risk factors for lamb mortality on UK sheep farms.

Data on neonatal-lamb mortality and flock history were recorded by veterinary students working on 108 sheep farms in the UK in Spring 1997. The mean reported mortality incidence risk was 10.0% (median 9%; inter-quartile range 5.9-12.3%). The outcomes were incidence risks of stillbirth, perinatal (within 24h of birth) mortality and postnatal (>24h after birth) mortality. Exposures were screened for univariable associations with mortality risk. Logistic binomial multiple regressions adjusted for confounding, with farm as a random effect. This study has raised hypotheses for management factors associated with lamb mortality that warrant further study. Intensive rearing systems appear to be associated with increased perinatal and postnatal mortality, although housing ewes at lambing was associated with a decreased risk of stillbirth. High perinatal mortality also was associated with poor mothering-pen hygiene, flocks that foster more lambs, and failure to provide appropriate nursing for sick lambs. Larger flocks, poor ewe condition at breeding, and flocks with higher ewe-replacement rates were associated with higher postnatal mortality.