Genomic analysis of the population structure of Paenibacillus larvae in New Zealand.

New Zealand is a remote country in the South Pacific Ocean. The isolation and relatively late arrival of humans into New Zealand has meant there is a recorded history of the introduction of domestic species. Honey bees (Apis mellifera) were introduced to New Zealand in 1839, and the disease American foulbrood was subsequently found in the 1870s. Paenibacillus larvae, the causative agent of American foulbrood, has been genome sequenced in other countries. We sequenced the genomes of P. larvae obtained from 164 New Zealand apiaries where American foulbrood was identified in symptomatic hives during visual inspection. Multi-locus sequencing typing (MLST) revealed the dominant sequence type to be ST18, with this clonal cluster accounting for 90.2% of isolates. Only two other sequence types (with variants) were identified, ST5 and ST23. ST23 was only observed in the Otago area, whereas ST5 was limited to two geographically non-contiguous areas. The sequence types are all from the enterobacterial repetitive intergenic consensus I (ERIC I) genogroup. The ST18 and ST5 from New Zealand and international P. larvae all clustered by sequence type. Based on core genome MLST and SNP analysis, localized regional clusters were observed within New Zealand, but some closely related genomes were also geographically dispersed, presumably due to hive movements by beekeepers.

A four-decade profile of apicultural demographics and production in New Zealand, 1980-2020.

The demand for honey and pollination services has continued to grow in many countries worldwide, including New Zealand. This has influenced changes in the demographics of the managed population of honey bees (Apis mellifera). We examined historical data to describe how the apicultural demographics in New Zealand have changed temporally and geographically in the four decades to 2020. We also describe trends in honey production and the economic value of pure honey exported from New Zealand between 2000 and 2020. Our findings suggest that commercial apiculture has been key to the intensification of beekeeping in New Zealand during the study period. This is supported by evidence showing pronounced expansion of beekeeping operations among those with more than 1,000 colonies. The intensification has resulted in the density of apiaries increasing threefold across New Zealand during the four decades. While higher numbers of colonies per area produced higher volumes of honey, there was no corresponding improvement in production efficiency. Honey yields per apiary or colony, as indicators of production efficiency, appear to decline from the mid-2000s. The volume of pure honey export increased over 40-fold, a magnitude approximately ten times higher than that of production increase. This reflects a substantial increase in returns from honey exports, mostly driven by the price of manuka honey. Our findings add to a pool of information to support evidence-based decision making to enhance honey bee health and develop the apicultural industry in New Zealand.

Uptrend in global managed honey bee colonies and production based on a six-decade viewpoint, 1961-2017.

We conducted a retrospective study to examine the long-term trends for the global honey bee population and its two main products: honey and beeswax. Our analysis was based on the data collected by the Food and Agriculture Organization of the United Nations from 1961 to 2017. During this period, there were increases in the number of managed honey bee colonies (85.0%), honey production (181.0%) and beeswax production (116.0%). The amount of honey produced per colony increased by 45.0%, signifying improvements in the efficiency for producing honey. Concurrently, the human population grew by 144.0%. Whilst the absolute number of managed colonies increased globally, the number per capita declined by 19.9% from 13.6 colonies per 1000 population in 1961 to 10.9 colonies per 1000 population in 2017. Beeswax had a similar trend as the global production per capita reduced by 8.5% from 8.2 to 7.5 kg per 1000 population. In contrast, the global honey production per capita increased by 42.9% at the global level. The global human population growth outpaced that of managed honey bee colonies. Continuation of this trend raises the possibility of having a shortfall of pollinators to meet the increasing consumer demand for pollinated crops. To mitigate these challenges locally driven solutions will be key as influencing factors differed geographically.

Impact of risk-based partial vaccination on clinical incidence and seroprevalence of foot and mouth disease in Lao PDR.

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.

Does land use affect pathogen presence in New Zealand drinking water supplies?

Four microbes (Campylobacter spp., Escherichia coli, Cryptosporidium spp. and Giardia spp.) were monitored in 16 waterways that supply public drinking water for 13 New Zealand towns and cities. Over 500 samples were collected from the abstraction point at each study site every three months between 2009 and 2019. The waterways represent a range from small to large, free flowing to reservoir impoundments, draining catchments of entirely native vegetation to those dominated by pastoral agriculture. We used machine learning algorithms to explore the relative contribution of land use, catchment geology, vegetation, topography, and water quality characteristics of the catchment to determining the abundance and/or presence of each microbe. Sites on rivers draining predominantly agricultural catchments, the Waikato River, Oroua River and Waiorohi Stream had all four microbes present, often in high numbers, throughout the sampling interval. Other sites, such as the Hutt River and Big Huia Creek in Wellington which drain catchments of native vegetation, never had pathogenic microbes detected, or unsafe levels of E. coli. Boosted Regression Tree models could predict abundances and presence/absence of all four microbes with good precision using a wide range of potential environmental predictors covering land use, geology, vegetation, topography, and nutrient concentrations. Models were more accurate for protozoa than bacteria but did not differ markedly in their ability to predict abundance or presence/absence. Environmental drivers of microbe abundance or presence/absence also differed depending on whether the microbe was protozoan or bacterial. Protozoa were more prevalent in waterways with lower water quality, higher numbers of ruminants in the catchment, and in September and December. Bacteria were more abundant with higher rainfall, saturated soils, and catchments with greater than 35% of the land in agriculture. Although modern water treatment protocols will usually remove many pathogens from drinking water, several recent outbreaks of waterborne disease due to treatment failures, have highlighted the need to manage water supplies on multiple fronts. This research has identified potential catchment level variables, and thresholds, that could be better managed to reduce the potential for pathogens to enter drinking water supplies.

Game Meat Consumption and Foodborne Illness in Japan: A Web-Based Questionnaire Survey.

HIGHLIGHTS: Game meat represents a unique source of foodborne illness in humans. A Web-based survey about game meat consumption was completed by 50,000 respondents. The odds of illness were greater among consumers of raw game meat than processed meat. The greater the number of game meat types consumed, the higher the prevalence of illness. Those who hunted and prepared bear, boar, and deer meat were likely to get ill.

Environmental bio-monitoring with high-throughput sequencing.

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.

Spatiosurvival analysis of mortality on smallholder dairy farms in Tanga and Iringa regions of Tanzania.

A combination of survival and spatial analyses was applied to a dataset containing cattle mortalities on smallholder dairy farms in two separate regions (Tanga and Iringa) of Tanzania. Cattle mortality data for the year 1998 were collected retrospectively during the period January to April 1999. The objectives of the current study were, firstly, to quantify the hazard of mortality and, secondly, to investigate whether there was a spatial pattern in the variation that was unaccounted for in the hazard of mortality. A Cox regression model with farm as a frailty term was used to quantify the hazard of mortality. Geostatistical techniques were used to explore the first- and second-order spatial distribution of the farm frailty term. A total of 1,790 cattle from 400 randomly sampled smallholder dairy farms were included in the study. The overall mortality incidence rate for the study was 11.8 per 100 animal years (95% CI 10.0-13.8). The hazard of mortality for male cattle was 2.4 (95% CI 1.7-3.4) times higher than that of female cattle. There was evidence of a first-order spatial pattern, i.e., a tendency for farms with higher frailty to aggregate.