Statistical Modelling of Neighbor Treatment Effects in Aquaculture Clinical Trials

In the design of clinical trials involving fish observed over time in tanks, there may be advantages in housing several treatment groups within the same tank. In particular, such “within-tank” designs will be more efficient than designs with treatment groups in separate tanks when substantial between-tank variability is expected. One potential problem with within-tank designs is that it may not be possible to include all treatments in one tank; in statistical terms this means that the blocks (tanks) are incomplete. In incomplete block designs, there may be a concern that the treatments present in the same tank (denoted here as “neighbors”) affect each other in their performance; thus the need for an assessment of neighbor effects. In this paper, we propose two statistical approaches to assess and account for neighbor effects. The first approach is based on a non-linear mixed model and the second involves cross-classified and multiple membership models. Both approaches are illustrated on simulated data as well as data from a clinical ISAV (Infectious Salmon Anaemia Virus) trial; corresponding computer code is available online.     

Impact of co-infection with Lepeophtheirus salmonis and Moritella viscosa on inflammatory and immune responses of Atlantic salmon (Salmo salar)

This study was conducted to determine the effects of a co-infection with Moritella viscosa at different exposure levels of sea lice Lepeophtheirus salmonis in Atlantic salmon (Salmo salar). M. viscosa (1.14 × 10⁶ cfu/ml) was introduced to all experimental tanks at 10 days post-lice infection (dpLs). Mean lice counts decreased over time in both the medium lice co-infection (31.5 ± 19.0 at 7 dpLs; 16.9 ± 9.3 at 46 dpLs) and high lice co-infection (62.0 ± 10.8 at 7 dpLs; 37.6 ± 11.3 at 46 dpLs). There were significantly higher mortalities and more severe skin lesions in the high lice co-infected group compared to medium lice co-infected group or M. viscosa-only infection. Quantitative gene expression analysis detected a significant upregulation of genes in skin from the high lice co-infection group consistent with severe inflammation (il-8, mmp-9, hep, saa). Skin lesions retrieved throughout the study were positive for M. viscosa growth, but these were rarely located in regions associated with lice. These results suggest that while M. viscosa infection itself may induce skin lesion development in salmon, co-infection with high numbers of lice can enhance this impact and significantly reduce the ability of these lesions to resolve, resulting in increased mortality.     

Prevalence of thermophilic Campylobacter species in cats and dogs in two animal shelters in Ireland

Rectal swabs or faecal samples for the isolation of Campylobacter species were taken from 120 dogs and cats in an animal shelter in which only one kitten showed signs of gastrointestinal disease, and rectal swabs were taken from 46 dogs, 22 of which showed signs of gastrointestinal disease, in another shelter. At the first shelter, the swabs from 24 of 47 dogs (51.1 per cent) and 36 of 48 cats (75 per cent) yielded a Campylobacter species. The rate of isolation was significantly higher from dogs and cats less than six months old, and significantly higher from cats than from dogs (P< or =0.05). At the second shelter Campylobacter species were isolated from 40 of 46 dogs (87 per cent), but there was no significant difference between the age groups. Campylobacter species were isolated from 19 (86.4 per cent) of the 22 dogs with signs of gastrointestinal disease and from 21 (87.5 per cent) of the 24 unaffected dogs. Several culture methods were applied to the samples collected from both shelters, and the combination significantly increased the recovery of Campylobacter species.     

Management and prevention of vitamin D deficiency rickets in captive-born juvenile chimpanzees (Pan troglodytes).

Vitamin D deficiency rickets was diagnosed in three juvenile chimpanzees (Pan troglodytes) raised indoors under skylights and consuming only breast milk. Two cases detected early had mild but characteristic radiographic changes. More advanced disease presented with florid x-ray features of rickets and pathologic fractures, as well as hypocalcemia, hypophosphatemia, and low serum 25-hydroxyvitamin D levels. Treatment by a single injection of vitamin D2 in sesame oil (slow release) followed by daily oral supplementation with vitamin D2 corrected the condition. On the basis of experience with these cases and comparison with rickets in humans, a prevention protocol for mother-reared, inside-housed, chimpanzee juveniles was developed. Injection with slow release vitamin D2 (5,000 IU i.m. once) at 4 mo of age, followed by oral supplementation of 400 IU vitamin D2 daily until weaning, prevents rickets in juvenile chimpanzees raised indoors.     

An investigation on the effect of transport and lairage on the faecal shedding prevalence of Escherichia coli O157 in cattle

The aim of the study was to investigate the effect of transport and lairage on the prevalence of Escherichia coli O157 faecal shedding and the subsequent contamination of beef carcasses. Individual rectal faecal samples were taken from two cohorts of cattle (109 and 59) at the farm before transport and at the abattoir post-transport and lairage. The entire outer and inner surfaces of the carcass of each animal were swabbed immediately following slaughter and dressing. The prevalence of E. coli O157 shedding in cattle sampled at farm, post-transport and lairage was 18% (20), 13% (14) and 12% (13) for cohort A and 1.7% (1), 1.7% (1) and 0 for cohort B, respectively. No E. coli O157 was recovered from the 168 dressed carcasses. In total, 98% (46 of 47) of the E. coli O157 isolates from cohort A were potentially pathogenic to man. Transport and lairage do not cause an increase in the prevalence of E. coli O157 faecal shedding in cattle. This study demonstrates that even positive cohorts of cattle may be slaughtered and processed to produce clean carcasses by following good hygienic practices.     

The prevalence and PCR detection of Salmonella contamination in raw poultry

Contaminated poultry meat has been identified as one of the principal foodborne sources of Salmonella. The development of rapid detection assays for Salmonella would enable official agencies and food industries to identify contaminated foodstuffs in a more timely manner. In addition, these diagnostic tools could allow more 'real time' decisions to be made regarding end product acceptability. In this study, a survey was carried out to determine the prevalence of Salmonella in raw broiler carcasses. A total of 198 neck skin samples were obtained from within 40 flocks at a commercial broiler slaughtering facility. The presence of Salmonella was assessed by traditional culture methods and by a Salmonella-specific polymerase chain reaction (PCR) test. Salmonella was recovered from 32 (16%) of all samples using traditional culture methods. In contrast, the PCR assay proved to be more sensitive and detected Salmonella DNA in 38 (19%) of the samples tested. The pathogen was detected in 45 (23%) of the 198 samples when culture and PCR results were combined. The sensitivity of the PCR test was also greater than culture when detecting Salmonella from within flocks (53% of flocks by PCR, 30% of flocks by culture). The combination of both tests revealed that 55% of the flocks were contaminated with Salmonella. The PCR assay proved to be a highly specific and sensitive method for detecting Salmonella and the incorporation of a routine PCR test in conjunction with standard culture could be effective in providing a more accurate profile of the prevalence of this pathogen in broiler carcasses.     

Prediction of calving date in beef cows by real-time ultrasonic scanning

Three hundred pregnant beef cows between 35 and 125 days of gestation were scanned ultrasonically and their calving dates were predicted from measurements of fetal parts. The mean difference between the actual and predicted calving dates was 0.9 day with a standard deviation of 9.0 days. The accuracy and precision of the prediction of calving date were sufficient to be of benefit in the management of cows in late pregnancy and at calving.