Statistical methods for geographical surveillance in veterinary epidemiology

Spatial clustering and cluster detection are statistical analysis developed to address relevant scientific hypothesis. The difficulty stays in the large number of alternative hypothesis due to the different mechanisms that could generate the anomalous cases aggregation. We review methods for marked point data (case/control) aimed to describe spatial intensity of disease risk, to test for randomness and to locate significant excesses. Bayesian Gaussian Spatial Exponential models are used to illustrate probabilistic aspects and the link with simpler non parametric tools are shown. We develop an informal guideline to the analysis and used data on faecal contamination and dog parasitic diseases in the city of Naples, Italy. Kernel density estimation resulted very sensitive to bandwidth choice and overemphasized localized excess, Ripley'K function and Cuzick-Edwards test were very consistent each other while the SatScan failed to detect excesses. The spatial range was around 600 meters and justifies several small clusters. Bayesian models were very powerful in reconstructing the phenomenon and allow inference on model parameters in good agreement with the non parametric analysis.     

Human enteric viruses in groundwater indicate offshore transport of human sewage to coral reefs of the Upper Florida Keys

To address the issue of human sewage reaching corals along the main reef of the Florida Keys, samples were collected from surface water, groundwater and coral [surface mucopolysaccharide layers (SML)] along a 10 km transect near Key Largo, FL. Samples were collected semi‐annually between July 2003 and September 2005 and processed for faecal indicator bacteria (faecal coliform bacteria, enterococci and Clostridium perfringens) and human‐specific enteric viruses (enterovirus RNA and adenovirus DNA) by (RT)‐nested polymerase chain reaction. Faecal indicator bacteria concentrations were generally higher nearshore and in the coral SML. Enteric viruses were evenly distributed across the transect stations. Adenoviruses were detected in 37 of 75 samples collected (49.3%) whereas enteroviruses were only found in 8 of 75 samples (10.7%). Both viruses were detected twice as frequently in coral compared with surface water or groundwater. Offshore, viruses were most likely to be found in groundwater, especially during the wet summer season. These data suggest that polluted groundwater may be moving to the outer reef environment in the Florida Keys.     

Fecundity and egg output by Toxocara canis in the red fox, Vulpes vulpes

The role of the red fox Vulpes vulpes in the dissemination of eggs of Toxocara canis into the environment is considered with reference to female worm fecundity and egg output in the faeces of infected foxes collected from four localities in southern England. A significant positive correlation was found between female worm size and the number of eggs in the uterus but there was no significant relationship between T. canis worm numbers and egg output in fox faeces. Reliable estimates of worm burdens in foxes could not, therefore, be determined from faecal egg counts alone. The highest mean egg output of 2145.0 epg recorded from adult foxes indicated that fox cubs are not necessarily the main sources of environmental contamination with T. canis eggs. Saturated magnesium sulphate was found to be a more effective flotation solution than zinc sulphate and sodium chloride for recovering eggs from fox faecal samples.     

Use of RNAlater® as a preservation method for parasitic coprology studies in wild-living chimpanzees

We evaluated the use of an RNA stabilisation buffer, RNAlater® (Ambion, Austin, Texas), as a preservation medium for parasitic coprology analysis of faecal samples collected from chimpanzees living in the wild (Pan troglodytes troglodytes). Thirty faecal samples collected in the forests of south-east Cameroon (Mambele area) from 2003 to 2011 were preserved in RNAlater® at −80 °C and analysed for their parasite content. We identified and counted parasitic elements and assessed their shape, size and morphology in relation to the storage time of the samples. We found that parasite elements were identifiable in RNAlater® preserved samples after as many as 7 years, showing that RNAlater® could be an effective and reliable preservation medium for coprology. Thus, its use could be an interesting way to optimise sample collection for several types of studies (parasitology and bacteriology/virology) at once, especially considering the logistically challenging and time-consuming field campaigns needed to obtain these faecal samples.     

Patterns in the distribution of fish communities across the Central Great Barrier Reef

Summary Changes in the structure of fish communities along a transect from the Australian mainland to the Coral Sea, in the Central region of the Great Barrier Reef, were examined. Visual censuses of fish were made on the outer reef slopes (0 to 13 m deep) of two inshore reefs, approximately 10 km offshore, three reefs on the mid-shelf, 50 km offshore, three reefs on the outer shelf, 100 km offshore, and three reefs in the Coral Sea approximately 200 km offshore. The Pomacentridae, Chaetodontidae, Acanthuridae and Scaridae were examined in detail—the Labridac, Siganidae and the lutjanid genus Caesio in less detail. Major changes in the composition of fish communities occurred along the transect (Fig. 3). There were differences in the composition of assemblages among replicate censuses within individual reefs and also differences between reefs at the same location on the transect but these differences were small compared to those among locations. The nature of the distribution of species across the transect differed between families (Figs. 4–6). Pomacentrid and chaetodontid species were significantly more restricted in distribution than acanthurids, scarids or labrids.     

The occurrence of Dirofilaria immitis, Borrelia burgdorferi, Ehrlichia canis and Anaplasma phagocytophium in dogs in China

A survey of the occurrence of Dirofilaria immitis, Borrelia burgdorferi, Ehrlichia canis and Anaplasma phagocytophium in dogs was undertaken in the People's Republic of China between October 2008 and October 2009. A total of 600 blood samples were taken from dogs in four cities in China: 300 in Beijing, 150 in Shenzhen, 30 in Shanghai and 120 in Zhengzhou. All samples were tested for the heartworm antigen and antibodies of canine B. burgdorferi, E. canis and A. phagocytophium by using the canine SNAP? 4Dx? test kit. The occurrence of D. immitis, B. burgdorferi, E. canis and A. phagocytophium was 1.17% (7/600), 0.17% (1/600), 2.17% (13/600) and 0.5% (3/600), respectively. In Shenzhen city 2% (3/150), 8.67% (13/150) and 2% (3/150) of samples were positive for D. immitis, E. canis and A. phagocytophium, respectively. The occurrence of heartworm antigen was 0.33% (1/300) in Beijing, 2.00% (3/150) in Shenzhen, 3.33% (1/30) in Shanghai and 1.67% (2/120) in Zhengzhou. We found E. canis and A. phagocytophium only at one site, Shenzhen, while the only occurrence of B. burgdorferi was at Beijing. In conclusion, the dog population in China is at potential risk for D. immitis, B. burgdorferi, E. canis and A. phagocytophium infection, the risk being especially high in southern China.     

A survey of intestinal helminths of well-cared-for dogs in Jamaica, and their potential public health significance

This study investigates the level of helminthic infestation in better-cared-for dogs in a middle-class community in suburban Kingston. A canine zoographic study was conducted, and fresh faecal deposits were collected and analysed for helminth life-cycle stages. The survey indicated that 73% (n = 93) of households in the study area owned one dog or more (mean = 1.4). Resident's attitudes towards canine management suggested that the dog population was, in general, restricted to the residential estate, and most owners claimed to have dewormed their dogs at least as young animals. Of 141 faecal specimens, 58% contained eggs or larvae of one or more of eight helminths: Uncinaria stenocephala (26%), Ancylostoma sp. (23%), Trichuris vulpis (9%), Toxocara canis (8%), Spirocerca lupi (6%), Strongyloides sp. (6%), Apophallus sp. (4%) and taeniids (1%). There was a high level of multiple infection in the host animals, with approximately one fifth of the infected samples containing three or more helminth types. Infection intensity was apparently low, but some dogs harboured heavy worm loads.     

“城-郊-乡”森林生态样带植被变化梯度分析

沿纽约市“市区－郊区－农区”１４０ｋｍ森林生态样带,对９个样地１９个样方的森林植被进行了研究。植被组成和结构沿样带变化明显,分异出城区森林、郊区森林和农区森林等不同类型,优势种替代明显,植物种类也形成了不同的生态类型。植被的梯度变化与人类活动密切相关,城市化对植被有重要影响。森林生态样带是研究人类活动对植被影响的好手段。     

The relationships between salmonellas and faecal indicator concentrations in two pools in the Australian wet/dry tropics.

The relationships between total coliform, faecal coliform, enterococci and salmonella concentrations were investigated at Berry and Howard Pools in the Australian wet/dry tropics. Both pools have catchments with minimal human activity and no major point source of faecal pollution. Forty-five indicator and salmonella enumerations were made from each pool over a 1 year period. Salmonellas were isolated from 69% and 96% of samples collected from Howard and Berry Pools respectively, the maximum (MPN) concentration was 110/100 ml. Native fauna were the primary salmonella source. Spearman rank correlations between indicator organisms and salmonella at Howard Pool were significant at the 5% level and approximated 0.6. At Berry Pool, total coliform and enterococci Spearman rank correlations with salmonella were also statistically significant, approximating 0.3; faecal coliforms and salmonella rankings, however, were unrelated. The higher correlation coefficients at Howard Pool were attributed to its small catchment (4 km2) and the more recent nature of faecal contamination compared with Berry Pool which has a catchment of 130 km2. The results highlight the spatial variability of the indicator/pathogen numerical relationship. Total coliform and enterococci counts, as indicators of faecal pollution, were similar and more consistent than faecal coliforms.     

Distribution of bulimulid land snails on the northern slope of Santa Cruz Island, Galapagos

The observations made along south-north transects on Santa Cruz Island's northern slope show that the distribution of bulimulid land snails follows a distinct zonation. Their zonation pattern is related to the well-marked plant zonation, the substrate and the important climatic gradient characterizing this area.
Live snails and shells belonging to 14 bulimulid taxa were collected along a transect (11 km long) starting from Cerro Puntudo, one of the island's highest points. Their distribution, the vegetal zonation and the rapid change in the climate observed along the transect are described.     

Growth determinations for unattached bacteria in a contaminated aquifer.

Growth rates of unattached bacteria in groundwater contaminated with treated sewage and collected at various distances from the source of contamination were estimated by using frequency of dividing cells and tritiated-thymidine uptake and compared with growth rates obtained with unsupplemented, closed-bottle incubations. Estimates of bacterial generation times [(In 2)/mu] along a 3-km-long transect in oxygen-depleted (0.1 to 0.7 mg of dissolved oxygen liter-1) groundwater ranged from 16 h at 0.26 km downgradient from an on-land, treated-sewage outfall to 139 h at 1.6 km and correlated with bacterial abundance (r2 = 0.88 at P less than 0.001). Partitioning of assimilated thymidine into nucleic acid generally decreased with distance from the contaminant source, and one population in heavily contaminated groundwater assimilated little thymidine during a 20-h incubation. Several assumptions commonly made when frequency of dividing cells and tritiated-thymidine uptake are used were not applicable to the groundwater samples.     

Growth determinations for unattached bacteria in a contaminated aquifer

Growth rates of unattached bacteria in groundwater contaminated with treated sewage and collected at various distances from the source of contamination were estimated by using frequency of dividing cells and tritiated-thymidine uptake and compared with growth rates obtained with unsupplemented, closed-bottle incubations. Estimates of bacterial generation times [(In 2)/mu] along a 3-km-long transect in oxygen-depleted (0.1 to 0.7 mg of dissolved oxygen liter-1) groundwater ranged from 16 h at 0.26 km downgradient from an on-land, treated-sewage outfall to 139 h at 1.6 km and correlated with bacterial abundance (r2 = 0.88 at P less than 0.001). Partitioning of assimilated thymidine into nucleic acid generally decreased with distance from the contaminant source, and one population in heavily contaminated groundwater assimilated little thymidine during a 20-h incubation. Several assumptions commonly made when frequency of dividing cells and tritiated-thymidine uptake are used were not applicable to the groundwater samples.     

Faecal contamination of drinking water sources of Dhaka city during the 2004 flood in Bangladesh and use of disinfectants for water treatment

AIMS: To describe the extent of faecal pollution and point of use water treatment strategy during and after the 2004 flood in Dhaka. METHODS: A total of 300 water samples were collected from 20 different drinking water sources in Kamalapur, Dhaka city from August 2004 to January 2005. The level of faecal contamination was estimated using measurements of faecal indicator bacteria (total coliforms, faecal coliforms and faecal streptococci) and isolation of Vibrio cholerae was carried out following standard procedures. Total dissolved solids, dissolved oxygen, hardness, chloride and pH were also monitored. The efficacy of four disinfectants including Halotab, Zeoline-200, alum potash and bleaching powder were tested as point of use water treatment agents. The unacceptable level of contamination of total coliforms (TC), faecal coliforms (FC) and faecal streptococci (FS) ranged from 23.8% to 95.2%, 28.6% to 95.2% and 33.3% to 90.0%, respectively. The isolation rates of V. cholerae O1 and O139 were both 0.33%, and non-O1/non-O139 was 7.0%. CONCLUSION: Water collected during and after floods was contaminated with TC, FC, FS and V. cholerae. Although alum potash, bleaching powder, Halotab and Zeoline-200 were all effective general disinfectants, Halotab and Zeoline-200 were superior to bleaching powder and alum potash against FC. SIGNIFICANCE AND IMPACT OF THE STUDY: During and after floods, point of use water treatment could reduce waterborne diseases among flood-affected people.     

乌兰巴托-锡林浩特样带草地植被特征与水热因子的关系

2012年夏季,研究人员对蒙古高原长约1100km的乌兰巴托—锡林浩特草地样带开展考察,获取了46个样地的物种数量、地上生物量等数据;基于全球GHCN(全球历史气象网络)数据集,提取了样带夏季(6—8月)月均温度和降水总量;继而根据自然地理和行政区边界,将草地样带大致分成北部(蒙古国乌兰巴托—蒙古国艾日格)、中部(蒙古国艾日格—中国苏尼特左旗)和南部(中国苏尼特左旗—中国锡林浩特),开展了分析。研究表明:(1)样带夏季平均温度的空间分布形态呈现明显的倒"U"型分布,南北两端温度较低,中部温度较高;夏季降水量在空间上的分布形态则与之相反,呈现南北两端降水量较高,中部降水量较低的正"U"型分布;(2)样带上植物物种数量、地上生物量的空间分布形态均呈现正"U"型分布,即在生态景观类型为典型温性草原的样带南部和北部地区,其生物多样性、地上生物量明显好于呈现为温性荒漠草原、温性荒漠景观的样带中部地区。(3)相关分析体现了大尺度(高原样带尺度)上植被特征与水热环境因子间的关系:植物物种数量、地上生物量与夏季月均温度均呈现负相关,而与夏季降水总量则呈现正相关关系。(4)偏相关分析反映了局地小尺度上植被特征与水热环境因子间的关系:温度和降水要素对于植物物种数量、地上生物量均呈现正相关。     

黑龙江省乌裕尔河流域丹顶鹤等珍稀涉禽航空调查报告

利用Y-11型单翼轻型飞机,航高100米,航速140公里/小时,采用且测全区调查方法,对黑龙江省乌裕尔河流域丹顶鹤等涉禽进行了航空调查,续航里程2184公里,调查面积共计为209,000公顷。结果发现调查区内有丹顶鹤(Orus japoncnsis)173只,白枕鹤(Grus vipio)19只,白鹤(Grus leucogeraous)24只,白鹳(Ciconia ciconia)19只等。     

Faecal prevalence,distribution and risk factors associated with canine soil-transmitted helminths contaminating urban parks across Australia

Dog parks provide an ideal urban space where dogs and their owners can exercise, play, and socialise in a safe environment. However, these parks can also increase the risk of exposure to a series of infectious agents including canine soil-transmitted helminths (cSTHs) such as hookworms, roundworms, Strongyloides stercoralis, and Trichuris vulpis, which are endemic to Australia. In this study, we collected 1581 canine faecal samples in 190 urban parks across Australia and subjected these to faecal floatation and multiplex real-time PCRs (qPCR) to detect a range of cSTHs. In total, 44.2% of the parks sampled were contaminated with at least one species of cSTH, with hookworms being the most prevalent parasites (10.2%) followed by Trichuris spp. (1.3%) and Strongyloides spp. (1.2%). This is the first large-scale study investigating the contamination of urban parks with cSTHs in Australia, and the first nation-wide study to demonstrate the occurrence of Strongyloides spp. in canine faecal samples from urban areas in the country. This study reveals a high rate of contamination with cSTHs in dog parks in urban Australia, most of which having proven zoonotic potential. Preventive measures, including awareness-raising educational programmes promoting responsible pet ownership, should be encouraged to minimise the health risks associated with cSTHs for both dogs and humans.     

FLOTAC, a novel apparatus for a multivalent faecal egg count technique

Faecal egg count (FEC) techniques are widely used for parasitological diagnosis in humans and animals. They are also used to measure the prevalence and intensity of infections for epidemiological surveys, to quantify the efficacy of chemotherapies, and to detect anthelmintic resistance. They assess the number of parasitic elements (eggs, larvae, oocysts) present in the faecal samples, expressed per gram of faeces, and are based on the microscopic examination of an aliquot of faecal suspension from a known volume of a faecal sample. In the present paper a novel multivalent FEC technique, the FLOTAC technique, is described. It is based on flotation in centrifuge and translation of the apical portion of the floating suspension, and gives eggs/larvae/oocyst counts in quantities of faeces up to 1 gram. A novel apparatus, the FLOTAC, has been developed and patented in order to carry out this technique. It is a cylindrical-shaped device, made of unbreakable plastic, and holds two sample flotation chambers, which are 5 ml each for a total volume of 10 ml, with two ruled grids (18 x 18 mm). Each grid contains 12 equidistant ruled lines that are transparent, and hence permit the counting of parasitic elements under them. The FLOTAC apparatus is also very useful in order to recover parasitic elements after flotation.     

Pattern of land mosaics affecting butterfly assemblage at Mt Ikoma, Osaka, Japan

We studied the effects of habitat mosaics on butterfly assemblage on multiple spatial scales: landscape, landscape element, local habitat, and microhabitat, based on the transect counts conducted along a 3.84 km route. The transect route, including 21 local habitats, passed through two distinct areas: 1.65 km of a secondary deciduous Quercus forest and the grove of a shrine in Hiraoka, and 2.19 km of a mosaic of secondary deciduous Quercus forest, grassland, and farmland in Narukawa. The diversity of the landscape elements and species richness were higher in Narukawa than in Hiraoka; the landscape mosaic enhanced the species richness in Narukawa. However, the diversity indices and specialist species (univoltine tree feeder) were decreased in this mosaic landscape. The species richness at local habitats was also increased by the mosaic of microhabitats, such as the herbaceous layer, glade, and mantle in the local habitats, whereas it was decreased by an abundant shrub layer. The ratios of species richness to abundance in the local habitats were lower than expected based on random sampling from the total of Hiraoka and Narukawa. This means that local assemblages were non-random samples from an assemblage on the landscape or regional scale, and were made up by the process of habitat selection of butterfly species in the assemblages on the landscape or regional scale. For conservation of butterfly assemblages, we recommend that woodlands should be kept without fragmentation, but with glades or small grasslands, and with clearance of the shrub layer along the path.     

A high‐throughput and quantitative hierarchical oligonucleotide primer extension (HOPE)‐based approach to identify sources of faecal contamination in water bodies

As faecal contamination of recreational and drinking water impairs the water quality and threatens public health, water bodies are routinely monitored for faecal coliforms to detect contamination. However, faecal coliforms are facultative anaerobes that survive and reproduce in ambient waters, and their presence does not depict the origin of contamination. Therefore, the use of Bacteroides‐Prevotella 16S rRNA gene to perform faecal source tracking has been proposed and applied. Here, we demonstrate the use of a new molecular method termed hierarchical oligonucleotide primer extension (HOPE) to simultaneously detect human‐associated Bacteroides spp. and three clusters of cow‐, pig‐ and dog‐specific uncultivated Bacteroidales. The method correctly identifies the origin of faecal contamination when tested against human, cow, pig and dog faeces (n = 17, 17, 16 and 13 respectively), and in waters contaminated with faeces of known origins. Subsequent tests with a total of 21 blind samples show that HOPE is able to accurately indicate single or multiple sources of faecal contamination originating from pigs, cows and humans in 81% of the blind samples. HOPE can further correctly detect and identify faecal contamination in five sampling sites located along a canal in southern Taiwan, and the results are validated against conventional faecal coliform tests and quantitative PCR. Overall, this study demonstrates HOPE as a quantitative and high‐throughput method that can identify sources of faecal contamination.     

Gradients in richness and turnover of a forest passerine's diet prior to breeding: A mixed model approach applied to faecal metabarcoding data

Rather little is known about the dietary richness and variation of generalist insectivorous species, including birds, due primarily to difficulties in prey identification. Using faecal metabarcoding, we provide the most comprehensive analysis of a passerine's diet to date, identifying the relative magnitudes of biogeographic, habitat and temporal trends in the richness and turnover in diet of Cyanistes caeruleus (blue tit) along a 39 site and 2° latitudinal transect in Scotland. Faecal samples were collected in 2014–2015 from adult birds roosting in nestboxes prior to nest building. DNA was extracted from 793 samples and we amplified COI and 16S minibarcodes. We identified 432 molecular operational taxonomic units that correspond to putative dietary items. Most dietary items were rare, with Lepidoptera being the most abundant and taxon‐rich prey order. Here, we present a statistical approach for estimation of gradients and intersample variation in taxonomic richness and turnover using a generalised linear mixed model. We discuss the merits of this approach over existing tools and present methods for model‐based estimation of repeatability, taxon richness and Jaccard indices. We found that dietary richness increases significantly as spring advances, but changes little with elevation, latitude or local tree composition. In comparison, dietary composition exhibits significant turnover along temporal and spatial gradients and among sites. Our study shows the promise of faecal metabarcoding for inferring the macroecology of food webs, but we also highlight the challenge posed by contamination and make recommendations of laboratory and statistical practices to minimise its impact on inference.