Surveillance for lumpy skin disease and foot and mouth disease in the Kimberley, Western Australia

We quantified the sensitivity of surveillance for lumpy skin disease (LSD) and foot and mouth disease (FMD) in cattle in the Kimberley region of Western Australia. We monitored producer and veterinary activity with cattle for 3 years commencing January 2020. Each year, ~274,000 cattle of 685,540 present on 92 pastoral leases (stations) were consigned to other stations, live export or slaughter. Veterinarians examined 103,000 cattle on the stations, 177,000 prior to live export, and 10,000 prior to slaughter. Detection probabilities for the disease prior to transport or during veterinary procedures and inspections were elicited by survey of 17 veterinarians working in Northern Australia. The veterinarians estimated the probabilities that they would notice, recognise, and submit samples from clinical cases of LSD and FMD, given a 5% prevalence of clinical signs in the herd. We used scenario tree methodology to estimate monthly surveillance sensitivity of observations made by producers and by veterinarians during herd management visits, pre-export inspections, and ante-mortem inspections. Average monthly combined sensitivities were 0.49 for FMD and 0.37 for LSD. Sensitivity was high for both diseases during the dry season and low in the wet season. We estimated the confidence in freedom from the estimated surveillance sensitivity given one hypothetically infected herd, estimated probability of introduction, and prior confidence in freedom. This study provided assurance that the Kimberley is free of these diseases and that routine producer and veterinary interactions with cattle are adequate for the timely detection of the disease should they be introduced.

Ostreid herpesvirus-1 microvariant surveillance in Pacific oysters (Magallana gigas, Thunberg, 1793) in Australia in 2011

OBJECTIVE

To demonstrate that OsHV-1 microvariant was limited to the known infected areas in New South Wales at the time of the survey in 2011.

DESIGN

A 2-stage survey to demonstrate probability of infection at 2% design prevalence within oyster growing regions and to detect at least one infected region (4% design prevalence) with 95% confidence.

SAMPLE POPULATION

Magallana gigas in nominated oyster growing regions in New South Wales, South Australia and Tasmania as approved by the Aquatic Consultative Committee on Emergency Animal Diseases and documented in a national surveillance plan.

PROCEDURE

Field sampling for active surveillance and laboratory selection of appropriate tissues using methods to minimize potential for cross contamination. Published methods for qPCR and conventional PCR for OsHV-1 microvariant. Stochastic analysis of survey results to demonstrate probability of detection in the areas tested.

RESULTS AND CONCLUSIONS

OsHV-1 microvariant was not detected in a total 4121 samples according to the case definition developed for the survey. However, in NSW a screening qPCR for OsHV-1 detected 13 samples that reacted. These samples were negative at 2 laboratories in the qPCR and conventional PCR assays used in the case definition for the survey. We concluded that oyster production areas of Australia outside the infected area in NSW met the criteria for self-declaration of freedom at the time of the survey in 2011.

CLINICAL RELEVANCE

This activity illustrated achievements in surveillance for an emerging emergency animal pathogen where epidemiological and test validation data were limited, but where data was required to inform the emergency disease response. It also illustrated the challenges faced by investigators in interpreting surveillance results using tests with limited validation. It was guided by and has informed improvements in surveillance and emergency disease preparedness.

A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

BACKGROUND

Sugarcane bagasse is a major source of lignocellulosic biomass, yet its economic potential is not fully realised. To add value to bagasse, processing is needed to gain access to the embodied recalcitrant biomaterials. When bagasse is stored in piles in the open for long periods it is colonised by microbes originating from the sugarcane, the soil nearby or spores in the environment. For these microorganisms to proliferate they must digest the bagasse to access carbon for growth. The microbial community in bagasse piles is thus a potential resource for the discovery of useful and novel microbes and industrial enzymes. We used culturing and metabarcoding to understand the diversity of microorganisms found in a uniquely undisturbed bagasse storage pile and screened the cultured organisms for fibre-degrading enzymes.

RESULTS

Samples collected from 60 to 80 cm deep in the bagasse pile showed hemicellulose and partial lignin degradation. One hundred and four microbes were cultured from different layers and included a high proportion of oleaginous yeast and biomass-degrading fungi. Overall, 70, 67, 70 and 57% of the microbes showed carboxy-methyl cellulase, xylanase, laccase and peroxidase activity, respectively. These percentages were higher in microbes selectively cultured from deep layers, with all four activities found for 44% of these organisms. Culturing and amplicon sequencing showed that there was less diversity and therefore more selection in the deeper layers, which were dominated by thermophiles and acid tolerant organisms, compared with the top of pile. Amplicon sequencing indicated that novel fungi were present in the pile.

CONCLUSIONS

A combination of culture-dependent and independent methods was successful in exploring the diversity in the bagasse pile. The variety of species that was found and that are known for biomass degradation shows that the bagasse pile was a valuable selective environment for the identification of new microbes and enzymes with biotechnological potential. In particular, lignin-modifying activities have not been reported previously for many of the species that were identified, suggesting future studies are warranted.

Escherichia coli and Salmonella spp. isolated from Australian meat chickens remain susceptible to critically important antimicrobial agents

The World Health Organisation has defined "highest priority critically important antimicrobials" (CIAs) as those requiring the greatest control during food production. Evidence demonstrating that restricted antimicrobial usage prevents the emergence of resistance to CIA's amongst pathogenic and commensal organisms on a production system-wide scale would strengthen international efforts to control antimicrobial resistance (AMR). Therefore, in a designed survey of all major chicken-meat producers in Australia, we investigated the phenotypic AMR of E. coli (n = 206) and Salmonella (n = 53) from caecal samples of chickens at slaughter (n = 200). A large proportion of E. coli isolates (63.1%) were susceptible to all tested antimicrobials. With regards to CIA resistance, only two E.coli isolates demonstrated resistance to fluoroquinolones, attributed to mutations in the quinolone resistance-determining regions of gyrA. Antimicrobial resistance was observed for trimethoprim/sulfamethoxazole (8.7%), streptomycin (9.7%), ampicillin (14.1%), tetracycline (19.4%) and cefoxitin (0.5%). All Salmonella isolates were susceptible to ceftiofur, chloramphenicol, ciprofloxacin, colistin, florfenicol, gentamicin and tetracycline. A low frequency of Salmonella isolates exhibited resistance to streptomycin (1.9%), ampicillin (3.8%), and cefoxitin (11.3%). AMR was only observed among Salmonella Sofia serovars. None of the Salmonella isolates exhibited a multi-class-resistant phenotype. Whole genome sequencing did not identify any known resistance mechanisms for the Salmonella isolates demonstrating resistance to cefoxitin. The results provide strong evidence that resistance to highest priority CIA's is absent in commensal E. coli and Salmonella isolated from Australian meat chickens, and demonstrates low levels of resistance to compounds with less critical ratings such as cefoxitin, trimethoprim/sulfamethoxazole, and tetracycline. Apart from regulated exclusion of CIAs from most aspects of livestock production, vaccination against key bacterial pathogens and stringent biosecurity are likely to have contributed to the favorable AMR status of the Australian chicken meat industry. Nevertheless, industry and government need to proactively monitor AMR and antimicrobial stewardship practices to ensure the long-term protection of both animal and human health.

A preliminary study to estimate contact rates between free-roaming domestic dogs using novel miniature cameras

Information on contacts between individuals within a population is crucial to inform disease control strategies, via parameterisation of disease spread models. In this study we investigated the use of dog-borne video cameras–in conjunction with global positioning systems (GPS) loggers–to both characterise dog-to-dog contacts and to estimate contact rates. We customized miniaturised video cameras, enclosed within 3D-printed plastic cases, and attached these to nylon dog collars. Using two 3400 mAh NCR lithium Li-ion batteries, cameras could record a maximum of 22 hr of continuous video footage. Together with a GPS logger, collars were attached to six free roaming domestic dogs (FRDDs) in two remote Indigenous communities in northern Australia. We recorded a total of 97 hr of video footage, ranging from 4.5 to 22 hr (mean 19.1) per dog, and observed a wide range of social behaviours. The majority (69%) of all observed interactions between community dogs involved direct physical contact. Direct contact behaviours included sniffing, licking, mouthing and play fighting. No contacts appeared to be aggressive, however multiple teeth baring incidents were observed during play fights. We identified a total of 153 contacts–equating to 8 to 147 contacts per dog per 24 hr–from the videos of the five dogs with camera data that could be analysed. These contacts were attributed to 42 unique dogs (range 1 to 19 per video) which could be identified (based on colour patterns and markings). Most dog activity was observed in urban (houses and roads) environments, but contacts were more common in bushland and beach environments. A variety of foraging behaviours were observed, included scavenging through rubbish and rolling on dead animal carcasses. Identified food consumed included chicken, raw bones, animal carcasses, rubbish, grass and cheese. For characterising contacts between FRDD, several benefits of analysing videos compared to GPS fixes alone were identified in this study, including visualisation of the nature of the contact between two dogs; and inclusion of a greater number of dogs in the study (which do not need to be wearing video or GPS collars). Some limitations identified included visualisation of contacts only during daylight hours; the camera lens being obscured on occasion by the dog’s mandible or the dog resting on the camera; an insufficiently wide viewing angle (36°); battery life and robustness of the deployments; high costs of the deployment; and analysis of large volumes of often unsteady video footage. This study demonstrates that dog-borne video cameras, are a feasible technology for estimating and characterising contacts between FRDDs. Modifying camera specifications and developing new analytical methods will improve applicability of this technology for monitoring FRDD populations, providing insights into dog-to-dog contacts and therefore how disease might spread within these populations.

QTLs for stomatal and photosynthetic traits related to salinity tolerance in barley

BACKGROUND

Stomata regulate photosynthesis and transpiration, and these processes are critical for plant responses to abiotic stresses such as salinity. A barley double haploid population with 108 lines derived from a cross between CM72 (salt-tolerant) and Gairdner (salt-sensitive) was used to detect quantitative trait loci (QTLs) associated with stomatal and photosynthetic traits related to salinity tolerance.

RESULTS

A total of 11 significant QTLs (LOD > 3.0) and 11 tentative QTLs (2.5 < LOD < 3.0) were identified. These QTLs are distributed on all the seven chromosomes, except 5H and explain 9.5-17.3% of the phenotypic variation. QTLs for biomass, intercellular CO2 concentration, transpiration rate and stomatal conductance under control conditions co-localised together. A QTL for biomass also co-located with one for transpiration rate under salinity stress. A linkage was found between stomatal pore area and gas exchange. A QTL for salinity tolerance also co-localised with QTLs for grain yield and biomass on chromosome 3H. Based on the draft barley genome, the candidate genes for salinity tolerance at this locus are proposed.

CONCLUSIONS

The lack of major QTLs for gas exchange and stomatal traits under control and saline conditions indicates a complex relationship between salinity and leaf gas exchange due to the fact that these complex quantitative traits are under the control of multiple genes.

Predicted Spatial Spread of Canine Rabies in Australia

Modelling disease dynamics is most useful when data are limited. We present a spatial transmission model for the spread of canine rabies in the currently rabies-free wild dog population of Australia. The introduction of a sub-clinically infected dog from Indonesia is a distinct possibility, as is the spillover infection of wild dogs. Ranges for parameters were estimated from the literature and expert opinion, or set to span an order of magnitude. Rabies was judged to have spread spatially if a new infectious case appeared 120 km from the index case. We found 21% of initial value settings resulted in canine rabies spreading 120km, and on doing so at a median speed of 67 km/year. Parameters governing dog movements and behaviour, around which there is a paucity of knowledge, explained most of the variance in model outcomes. Dog density, especially when interactions with other parameters were included, explained some of the variance in whether rabies spread 120km, but dog demography (mean lifespan and mean replacement period) had minimal impact. These results provide a clear research direction if Australia is to improve its preparedness for rabies.