Use of underwater contactless ultrasonography to elucidate the internal anatomy and reproductive activity of manta and devil rays (family: Mobulidae).

The ability to visualise the internal anatomical structures of fish provides important information on their reproductive status and body condition and has made important contributions to many areas of fish biology. Obtaining information on the internal anatomy of fish has traditionally required euthanasia and dissection. Although ultrasonography is now increasingly used to study internal fish anatomy without the need for euthanasia, traditional techniques still require restraint and contact with the animal, both of which are known to cause stress. This has prompted the development of waterproof, contactless and portable equipment to allow ultrasonographic examinations to be carried out in free-swimming individuals, which also facilitates the application of this tool in wild populations of endangered species. This study reports the validation of this equipment using anatomical examinations of nine manta and devil ray (Mobulidae) specimens landed at fish markets in Sri Lanka. The species studied were Mobula kuhlii (n = 3), Mobula thurstoni (n = 1), Mobula mobular (n = 1), Mobula tarapacana (n = 1) and Mobula birostris (n = 3). The use of this equipment was further validated with ultrasonographic examinations in 55 free-swimming reef manta rays Mobula alfredi, which enabled maturity status to be quantified in 32 females. Structures successfully identified in free-swimming individuals were the liver, spleen, gallbladder, gastrointestinal tract, skeletal structures, developing follicles and uterus. The study demonstrated that ultrasonography provided a reliable method of determining both sexual maturity and gestational status in free-swimming M. alfredi. The methodology induced no detectable signs of disturbance to the animals involved and therefore offers a viable and practical alternative to invasive techniques currently used to study anatomical changes in both captive and wild marine organisms.

Overexpression of antibiotic resistance genes in hospital effluents over time.

Objectives: Effluents contain a diverse abundance of antibiotic resistance genes that augment the resistome of receiving aquatic environments. However, uncertainty remains regarding their temporal persistence, transcription and response to anthropogenic factors, such as antibiotic usage. We present a spatiotemporal study within a river catchment (River Cam, UK) that aims to determine the contribution of antibiotic resistance gene-containing effluents originating from sites of varying antibiotic usage to the receiving environment. Methods: Gene abundance in effluents (municipal hospital and dairy farm) was compared against background samples of the receiving aquatic environment (i.e. the catchment source) to determine the resistome contribution of effluents. We used metagenomics and metatranscriptomics to correlate DNA and RNA abundance and identified differentially regulated gene transcripts. Results: We found that mean antibiotic resistance gene and transcript abundances were correlated for both hospital ( ρ = 0.9, two-tailed P <0.0001) and farm ( ρ = 0.5, two-tailed P <0.0001) effluents and that two ß-lactam resistance genes ( bla GES and bla OXA ) were overexpressed in all hospital effluent samples. High ß-lactam resistance gene transcript abundance was related to hospital antibiotic usage over time and hospital effluents contained antibiotic residues. Conclusions: We conclude that effluents contribute high levels of antibiotic resistance genes to the aquatic environment; these genes are expressed at significant levels and are possibly related to the level of antibiotic usage at the effluent source.

Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment.

The aquatic environment has been implicated as a reservoir for antimicrobial resistance genes (ARGs). In order to identify sources that are contributing to these gene reservoirs, it is crucial to assess effluents that are entering the aquatic environment. Here we describe a metagenomic assessment for two types of effluent entering a river catchment. We investigated the diversity and abundance of resistance genes, mobile genetic elements (MGEs) and pathogenic bacteria. Findings were normalised to a background sample of river source water. Our results show that effluent contributed an array of genes to the river catchment, the most abundant being tetracycline resistance genes tetC and tetW from farm effluents and the sulfonamide resistance gene sul2 from wastewater treatment plant (WWTP) effluents. In nine separate samples taken across 3 years, we found 53 different genes conferring resistance to seven classes of antimicrobial. Compared to the background sample taken up river from effluent entry, the average abundance of genes was three times greater in the farm effluent and two times greater in the WWTP effluent. We conclude that effluents disperse ARGs, MGEs and pathogenic bacteria within a river catchment, thereby contributing to environmental reservoirs of ARGs.

Molecular characterization of poxviruses associated with tattoo skin lesions in UK cetaceans.

There is increasing concern for the well-being of cetacean populations around the UK. Tattoo skin disease (characterised by irregular, grey, black or yellowish, stippled cutaneous lesions) caused by poxvirus infection is a potential health indicatora potential health indicator for cetaceans. Limited sequence data indicates that cetacean poxviruses (CPVs) belong to an unassigned genus of the Chordopoxvirinae. To obtain further insight into the phylogenetic relationships between CPV and other Chordopoxvirinae members we partially characterized viral DNA originating from tattoo lesions collected in Delphinidae and Phocoenidae stranded along the UK coastline in 1998-2008. We also evaluated the presence of CPV in skin lesions other than tattoos to examine specificity and sensitivity of visual diagnosis. After DNA extraction, regions of the DNA polymerase and DNA topoisomerase I genes were amplified by PCR, sequenced and compared with other isolates. The presence of CPV DNA was demonstrated in tattoos from one striped dolphin (Stenella coeruleoalba), eight harbour porpoises (Phocoena phocoena) and one short-beaked common dolphin (Delphinus delphis) and in one 'dubious tattoo' lesion detected in one other porpoise. Seventeen of the 18 PCR positive skin lesions had been visually identified as tattoos and one as a dubious tattoo. None of the other skin lesions were PCR positive. Thus, visual identification had a 94.4% sensitivity and 100% specificity. The DNA polymerase PCR was most effective in detecting CPV DNA. Limited sequence phylogeny grouped the UK samples within the odontocete poxviruses (CPV group 1) and indicated that two different poxvirus lineages infect the Phocoenidae and the Delphinidae. The phylogenetic tree had three major branches: one with the UK Phocoenidae viruses, one with the Delphinidae isolates and one for the mysticete poxvirus (CPV group 2). This implies a radiation of poxviruses according to the host suborder and the families within these suborders.

Factors associated with pleurisy in pigs: a case-control analysis of slaughter pig data for England and Wales.

UNLABELLED: A case-control investigation was undertaken to determine management and health related factors associated with pleurisy in slaughter pigs in England and Wales. METHODS: The British Pig Executive Pig Health Scheme database of abattoir pathology was used to identify 121 case (>10% prevalence of pleurisy on 3 or more assessment dates in the preceding 24 months) and 121 control units (≤5% prevalence of pleurisy on 3 or more assessment dates in the preceding 24 months). Farm data were collected by postal questionnaire. Data from respondents (70 cases and 51 controls) were analysed using simple logistic regression models with Bonferroni corrections. Limited multivariate analyses were also performed to check the robustness of the overall conclusions. RESULTS AND CONCLUSIONS: Management factors associated with increased odds of pleurisy included no all-in all-out pig flow (OR 9.3, 95% confidence interval [CI]: 3.3-29), rearing of pigs with an age difference of >1 month in the same airspace (OR 6.5 [2.8-17]) and repeated mixing (OR 2.2 [1.4-3.8]) or moving (OR 2.2 [1.5-3.4]) of pigs during the rearing phase. Those associated with decreased odds of pleurisy included filling wean-to-finish or grower-to-finish systems with piglets from ≤3 sources (OR 0.18 [0.07-0.41]) compared to farrow-to-finish systems, cleaning and disinfecting of grower (ORs 0.28 [0.13-0.61] and 0.29 [0.13-0.61]) and finisher (ORs 0.24 [0.11-0.51] and 0.2 [0.09-0.44]) accommodation between groups, and extended down time of grower and finisher accommodation (OR 0.84 [0.75-0.93] and 0.86 [0.77-0.94] respectively for each additional day of downtime). This study demonstrated the value of national-level abattoir pathology data collection systems for case control analyses and generated guidance for on-farm interventions to help reduce the prevalence of pleurisy in slaughter pigs.

Integrating contact network structure into tuberculosis epidemiology in meerkats in South Africa: Implications for control.

Empirical studies that integrate information on host contact patterns with infectious disease transmission over time are rare. The aims of this study were to determine the relative importance of intra-group social interactions in the transmission of tuberculosis (TB; Mycobacterium bovis infection) in a population of wild meerkats (Suricata suricatta) in South Africa, and to use this information to propose an evidence-based intervention strategy to manage this disease. Detailed behavioural observations of all members of eight meerkat groups (n=134 individuals) were made over 24 months from January 2006 to December 2007. Social network analysis of three types of interaction (aggression, foraging competitions and grooming) revealed social structure to be very stable over time. Clustering of interactions was positively correlated with group size for both aggression (r=0.73) and grooming interactions (r=0.71), suggesting that infections may spread locally within clusters of interacting individuals but be limited from infecting all members of large groups by an apparent threshold in connections between different clusters. Repeated biological sampling every three months of all members of one social group (n=37 meerkats) was undertaken to quantify individual changes in M. bovis infection status. These empirical data were used to construct a dynamic network model of TB transmission within a meerkat group. The results indicated that grooming (both giving and receiving) was more likely than aggression to be correlated with M. bovis transmission and that groomers were at higher risk of infection than groomees. Intervention strategies for managing TB in meerkats that focus on those individuals engaging in the highest amount of grooming are therefore proposed.

Accuracy of three diagnostic tests for determining Mycobacterium bovis infection status in live-sampled wild meerkats (Suricata suricatta).

Accurate diagnosis of Mycobacterium bovis infection (bovine tuberculosis [bTB]) in live animals is notoriously problematic. The aim of the present study was to evaluate the diagnostic potential of 2 new serologic tests (multiantigen print immunoassay [MAPIA] and lateral flow immunoassay rapid test [RT]) in comparison with mycobacterial culture of tracheal washes for determining M. bovis infection status in a free-ranging population of wild meerkats (Suricata suricatta). During a longitudinal study lasting 2.5 years, 240 individually identifiable meerkats were each sampled up to 8 times under anesthesia every 3 months. Diagnostic accuracy was determined through Bayesian and maximum likelihood estimations of sensitivity, specificity, and likelihood ratios for each diagnostic test when used independently and in parallel to classify the disease status of individual meerkats in the absence of a gold standard. Culture of tracheal washes was highly specific (0.99; 95% confidence interval [CI] = 0.77, 1.00) but of low sensitivity (0.36; 95% CI = 0.24, 0.50) for diagnosing M. bovis-infected individuals. The longitudinal nature of the study with repeated sampling of the same individual animals served simultaneously to improve chances of detecting infection and increase confidence in a negative result in individual animals repeatedly testing negative. Although MAPIA and RT were individually of limited diagnostic use, interpreting the results of these 2 tests in parallel produced estimates of sensitivity (0.83; 95% CI = 0.67, 0.93) and specificity (0.73; 95% CI = 0.62, 0.82) high enough to usefully inform decision making when determining exposure to bTB in wild meerkats and potentially other species in which bTB poses a diagnostic challenge.