No abstract

There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.

In New Zealand, the introduced honey bee (Apis mellifera) is a valuable production animal, providing pollination services for horticultural crops and significant export volumes of honey, especially m anuka honey. Honey bees in New Zealand are free from a number of significant diseases and pests such as European foulbrood, acarine disease, small hive beetle, Israeli acute paralysis virus and tropilaelaps mites. We sought to determine the health status of honey bees in New Zealand using a longitudinal study that followed 60 beekeepers over 2.5 years, ascertaining disease and pest status in their elected study apiary and interviewing them every spring and autumn. Participant beekeepers accounted for the management of approximately 12% of the beehives registered in New Zealand. Differences in beekeeping practices were observed between the North Island and the South Island. Nosema ceranae was found almost exclusively on the North Island and did not displace Nosema apis over the course of the study. Lotmaria passim showed a reverse-phase seasonality to nosema, peaking in autumn at near 100% prevalence. The prevalence of Varroa in apiaries varied seasonally between 45.0% and 46.7% in spring and between 65.0% and 69.5% in autumn, with most infestation rates below 3 mites per 100 bees. The detection rate of symptomatic American foulbrood disease during our hive inspections was very low, between 0.00% and 0.85% hive-level prevalence dependent on the season. This study sets a foundation for understanding honey bee health in New Zealand.

The impacts of foot‐and‐mouth disease (FMD) on food security in developing countries are difficult to quantify due to the scarcity of accurate data on the prevalence and incidence of affected villages. This is partly due to resource constraints as well as the logistical challenges of conducting regular diagnostic testing in remote locations. In this study, we used descriptive analysis and latent class analysis (LCA) models to analyse data collected during a field survey of 160 villages in central Myanmar in the Mandalay and Sagaing Regions over the 2012–2016 time period. We evaluated the performance of verbal reports made by village householders and headmen against serological data to retrospectively determine the FMD‐infection status of our study area and to identify factors contributing to under‐reporting. Blood samples were collected from approximately 30 cattle per village in both the 6‐ to 18‐month age range and over 18‐month age range to distinguish between recent and historic exposure. Village householders were asked to identify pictures of FMD‐affected cattle amongst pictures of cattle affected with other common endemic diseases to assess the accuracy of their verbal reporting. The serological results confirmed that FMD is endemic in central Myanmar with village‐level seroprevalence estimated at 56% for animals 6–18 months of age and 80% when all age groups were considered together. Most village householders were familiar with the clinical signs of FMD‐affected cattle (72%). Based on the results from the LCA models, the village headman had a sensitivity of 77% and specificity of 75% for identifying FMD outbreaks in their village, whereas individual householders had a higher sensitivity and lower specificity of 80% and 56%, respectively. The level of disagreement between the different sources was correlated with the total number of cattle in the village and may potentially be worse in villages where endemic FMD may have led to a high level of natural immunity in cattle and subsequent masking of clinical signs. However, other regional effects such as the intensity of FMD extension efforts cannot be ruled out. Overall, the results suggest that verbal reports of FMD outbreaks from village headmen may be a useful tool to integrate into active FMD surveillance programmes in developing countries.

Foot and mouth disease (FMD) is endemic in the Lao People's Democratic Republic (PDR) and it causes economic loss to smallholder husbandry systems. An intervention programme based on a risk‐based partial vaccination strategy was implemented in three provinces of Lao PDR (Champasak, Savannakhet and Xiangkhouang) to immunise domestic cattle and buffalo during 2016–2020. Two cross‐sectional surveys were conducted in 2016/17 and 2020 to evaluate the impact of the vaccination programme on the prevalence of FMD virus exposure and clinical incidence of the disease. A total of 212 villages were visited during the two surveys, collecting 1609 household‐level questionnaire results and 5931 blood samples of domestic cattle and buffalo. Blood samples were tested for the presence of antibodies to the non‐structural proteins of FMD virus, and seroprevalence of 42.5 and 47.5% in 2016/17 and 2020, respectively were found. Multivariable regression analysis indicated that the efficacy of the FMD vaccination programme for reducing FMD virus circulation varied by province. In general, the incidence of clinical FMD increased toward the end of the 5‐year intervention period, coinciding with a reduction of vaccine coverage in the last 2 years of the period. The findings suggest that the risk‐based vaccination strategy achieved a marginally protective effect against the circulation of FMD virus with the possible limiting factors being operational constraints of public veterinary services, lack of farmers’ compliance and unsustainable funding. We conclude that consistent resource availability and higher vaccination coverage is required to successfully control FMD with a risk‐based vaccination strategy in Lao PDR.