Spatial and genotypic clustering of Salmonella over time in a swine production unit

Transmission patterns of Salmonella in a swine production unit were investigated by statistical analysis of the spatial distribution of isolates and the clustering of genotypes over a 12-week period. The study unit was a breeding-gestation building in a single-site farrow-to-finish swine production system. During the summer of 2003, 1746 pen floor samples were collected during 6 visits conducted at 2-week intervals. Genotyping was performed on the 107 Salmonella isolates obtained using repetitive sequence PCR (3 primers: REP, BOX, ERIC). Genetic similarity was evaluated by DNA fragment matching and hierarchical cluster analysis based on genetic similarities. For each visit, the distance at which spatial clustering of Salmonella isolates occurred was estimated using second order analyses. Significant spatial clustering of Salmonella up to a distance of 15.2m was identified for 4 of the 6 farm visits, those for which the prevalence of Salmonella was the highest. Cluster analysis of genetic similarities identified 4 groups of Salmonella isolates at the level of at least 85% similarity in rep-PCR fragment matching patterns. Genetic clusters were relatively homogeneous for time of visit, with each genetic cluster consisting of isolates from the same or temporally adjacent visits. The correlation between genetic similarity and spatial proximity between pairs of Salmonella isolates, and the correlation between these measures and differences in time of sampling, were evaluated using Mantel's r. There was a strong positive correlation (r=0.62, p<0.0001) between genetic distance and time of sampling, indicating evolution of the Salmonella population over time. For 4 of the 6 visits, a pattern of decreasing genetic similarity between isolates with increasing distance between sampling locations was apparent. However, when viewed over all 6 visits, Salmonella was concentrated in one area of the building and did not move in any specific direction. These results suggest that a particular genotype of Salmonella, if introduced in the breeding-gestation unit of a swine farm would evolve slowly over short time intervals; its spatial distribution would be limited primarily to adjacent or nearby pens. In this study spatial analysis (e.g., Ripley's K-function) and matrix correlation methods (e.g., Mantel's r) expanded upon cluster analysis of genotypic similarities to provide additional interpretable information regarding the spatial distances to which Salmonella is transmitted over time in swine production facilities.     

Multivariate similarity clustering analysis: a new method regarding biogeography and its application in global insects

A new method, multivariate similarity clustering analysis (MSCA) method, was established for biogeographical distribution analyzing. General similarity formula (GSF), the core of MSCA method, can be used to calculate the similarity coefficients between 2 and among any ≥ 3 geographical units. Taking the global insects as example, we introduced the steps to use of GSF and consequent clustering processes of this method in details. Firstly, geographical distributions of certain taxa (e.g. Insecta) were categorized into basic geographical units (BGUs); Secondly, similarity coefficients between 2 and among n BGUs were calculated using GSF. Thirdly, hierarchical clustering was conducted according to values of similarity coefficients (from high to low); then a clustering diagram was generated. Finally, a framework of biogeographical division map was established for the target taxa (e.g. Insecta). We concluded that the MSCA method was efficiently applied in analyzing the biogeographical distribution of given biological taxa; the geographical regions regarding global insects were categorized into 7 Realms with 20 sub-Realms based on the results of MSCA method.     

Summary of the first round analyses of the Second International Swine CD Workshop

The reactivity of 176 monoclonal antibodies (mAb) submitted to the Second International Swine CD Workshop, together with 19 internal standards, was analyzed by flow cytometry on 16 different cell types as a means of establishing the proper cell subset for later detailed clustering analyses. The exact CD subset reactivity of the 19 internal standard mAb had been characterized in the First International Swine CD Workshop. The flow cytometric analyses resulted in 40 data sets which were then subjected to statistical clustering using the Leukocyte Typing Database IV (LTDB4) software. As result of this work, 22 clusters were defined. After review of these results, panels of mAb from the defined first round clusters were assigned to cell subsets. The respective mAb in those first round clusters were then distributed to subset group researchers for further examination during the second round of the workshop.     

Identifying the spatiotemporal clusters of plague occurrences in China during the Third Pandemic

Plague, a devastating infectious disease caused by Yersinia pestis, has killed millions of people in the past and is still active in the natural foci of the world today. Understanding the spatiotemporal patterns of plague outbreaks in history is critically important, as it may help to facilitate prevention and control of potential future outbreaks. In this study, we explored spatiotemporal clusters of human plague occurrences in China using a machine‐learning clustering method and reconstructed the potential transmission pattern during the Third Pandemic (1772–1964). We succeeded in identifying 6 clusters in the space domain (2D) and 13 clusters in the spatiotemporal domain (3D). Our results suggest that there were several temporal outbreaks and transmissions of plague in different spatial clusters. Together with the spatiotemporal nearest neighbor approach (ST‐NNA), this method could allow us to have a clearer look at the spatiotemporal patterns of plague.     

Phylogenetic analysis of Fusobacterium necrophorum, Fusobacterium varium and Fusobacterium nucleatum based on gyrB gene sequences

The nucleotide sequences of the DNA gyrase B subunit gene (gyrB) of Fusobacterium necrophorum subsp. necrophorum, F. necrophorum subsp. funduliforme and F. varium were determined and analyzed together with those of F. nucleatum subsp. nucleatum and F. nucleatum subsp. vincentii. On the phylogenetic tree constructed, the strains of each fusobacterial species formed distinct clusters with deep sublines. The degree of sequence similarity within each cluster was 93.2% or more, whereas similarities between clusters ranged from 70.1 to 72.7%. These clusters were recovered with 100% bootstrap probabilities and are in very good agreement with the species of Fusobacterium. These data suggest that gyrB is an accurate genealogical marker for the classification of the fusobacterial taxa considered in this study.     

Spatial and spatial-temporal clustering analysis of hemorrhagic disease in white-tailed deer in the southeastern USA: 1980-2003

We used the space-time K function and Kulldorff's scan statistic to analyze the spatial and spatial-temporal clustering of hemorrhagic disease (HD) in white-tailed deer in Alabama, Georgia, South Carolina, North Carolina, and Tennessee. The HD occurrence data were binary presence/absence data acquired annually on a county basis from 1980 to 2003. Space-time K function was employed to globally examine the existence of spatial-temporal clustering in the HD data. Three approaches of Kulldorff's scan statistic, i.e., spatial clustering analysis for the entire period, spatial-temporal clustering analysis, and spatial clustering analysis by individual years, were applied to detect potential HD clusters. Statistically significant spatial clusters and spatial-temporal clusters were detected in the five southeastern states during the 24-year study period. Some clusters were observed in multiple years. Clusters were most evident in west Alabama, south Alabama, central South Carolina, and along the border between South Carolina and North Carolina. The identification of HD clusters may provide a means to better understand the causal factors related to the HD outbreaks. Results also have potential application in improving or designing effective surveillance programs for this disease.     

基于神经网络集成的蚕茧干壳量无损检测方法研究

蚕茧无损检测中的核心问题是蚕茧干壳量的测定。利用虚拟仪器技术和神经网络集成技术研究了一种无损检测蚕茧干壳量的方法,并实现了数据采集和信号处理等功能。系统首先提取并选择蚕茧振动信号中与蚕蛹质量相关的特征值,再将选择的特征值训练BP神经网络和RBF神经网络,用训练得到的这两种类型网络作为神经网络集成的输入,以蚕蛹质量作为神经网络集成的输出。检测试验的结果表明该方法有效可行,最高检测准确率达到85.6%。     

Similar cefoxitin-resistance plasmids circulating in Escherichia coli from human and animal sources

The aim of this study was to determine the molecular epidemiology of cefoxitin-resistance Escherichia coli identified in cattle entering feedlots and determine if there were any similarities to E. coli causing human infections in Canadian hospitals. A total of 51 E. coli were isolated from a total of 2483 cattle entering four feedlots in southern Alberta, Canada. DNA fingerprinting using pulsed-field gel electrophoresis revealed thirty-two unique patterns with two major clusters observed comprised of Cluster A (11 strains) and Cluster B (7 strains). PCR and sequence analysis revealed 38 isolates (74.5%) harboured bla(CMY-2), whereas the remainder were found to contain mutations in the promoter region of the chromosomal ampC gene, which has been previously associated with cefoxitin resistance. No resistance to nalidixic acid, ciprofloxacin, or amikacin was observed in the clinical isolates. bla(CMY-2) harbouring plasmids were transferred to E. coli DH10B. All of the plasmids carrying bla(CMY-2) contained the A/C replicon and also harboured other resistance genes. Plasmid fingerprinting using BglII revealed 17 unique patterns with all but one clustering within 70% similarity. Comparison of the plasmid fingerprints to those isolated from human clinically significant E. coli in Canada during a similar time period [Mulvey, M.R., Bryce, E., Boyd, D.A., Ofner-Agostini, M., Land, A.M., Simor, A.E, Paton, S., 2005. The Canadian Hospital Epidemiology Committee, and The Canadian Nosocomial Infection Surveillance Program, Health Canada. Molecular characterization of cefoxitin resistant Escherichia coli from Canadian hospitals. Antimicrob. Agents Chemother. 49, 358-365] revealed four strains that harboured bla(CMY-2) A/C replicon type plasmid with fingerprint similarities of greater than 90% to the ones identified in E. coli from the cattle in this study. These findings highlight the potential linkage of multidrug resistant organisms in food producing animals and human infections in Canadian hospitals. The plasmids conferred resistance to multiple antibiotics which could limit options for the treatment of infections caused by these strains.     

Variation in Salmonella enteritidis RAPD-PCR patterns may not be due to genetic differences

Salmonella Enteritidis is a leading cause of gastroenteritis associated with consumption of contaminated poultry meat and eggs. Because pulsed-field gel electrophoresis (PFGE) has limited utility in distinguishing between clonal Salmonella Enteritidis isolates, random amplified polymorphic DNA (RAPD) PCR has been recommended as an alternative molecular fingerprinting tool. This study's objective was to determine whether increasing PCR stringency would improve the repeatability of RAPD DNA patterns based on assessment of target sites within the genome. An in silico PCR was performed to predict amplification products from an Salmonella Enteritidis genome sequence for three different RAPD primers (1247, 1283, and OPA4) and to determine whether any primer would be more likely to amplify variable regions within the genome. A comparison of within- and between-isolate similarities in RAPD patterns was performed using primer 1247, which was predicted by in silico analysis to yield a variable size range of amplicons. In order to reduce artifactual variability associated with the method, three different methods for template preparation were evaluated. All were found to provide comparable results with respect to the similarities observed with repeated analyses of the same Salmonella Enteritidis isolates (n = 18, P = 0.91). Although the median within-isolate similarity (76.0%) was significantly greater than the median between-isolate similarity (66.7%; P = 0.001), duplicate RAPD-PCR runs of the same Salmonella Enteritidis isolates produced DNA patterns that ranged in similarity between 61.5 and 100%. These results indicate that the repeatability of RAPD-PCR is insufficient to distinguish genetic differences among related and unrelated Salmonella Enteritidis isolates.     

抗蚜苜蓿品种(系)SSR标记的遗传多样性分析

用6对SSR引物对9个抗蚜苜蓿(Medicago spp.)品种(系)进行了遗传多样性检测,共检测到69个位点。多态位点百分率为91.3%(63个位点),平均等位基因数为1.913 0,平均有效等位基因数为1.482 2,平均遗传多样性指数为0.293 4,遗传距离为0.156 6～0.623 2。聚类分析结果表明:抗蚜品种M8和品系HA-3具有较近的亲缘关系,二者的相似系数最大,为0.855 0。而品种S7和X2亲缘关系较远,相似系数最小,为0.536 2。此外,高抗品系HA-3与低抗品种Hunter River的相似系数为0.739 1,其遗传背景差异性相对较大。     

伊犁绢蒿荒漠不同退化阶段草地土壤种子库分析

采用萌发试验研究了伊犁绢蒿(Seriphidium transillense)荒漠不同退化阶段草地土壤种子库的变化特征,以期为干旱、半干旱地区退化草地生态系统恢复提供参考依据。结果表明:伊犁绢蒿荒漠土壤种子库共有14个物种,分属8个科;从未退化阶段到重度退化阶段种子库密度由684粒·m^-2下降到443粒·m^-2,而在极度退化阶段种子库密度却升高至758粒·m^-2;种子库在空间垂直分布上表现为随土壤深度的增加而减少,有67%的种子集中在土壤表层。种子库物种丰富度和多样性指数在不同退化阶段之间变化不大,但均匀度指数呈现先上升后下降的趋势;不同退化阶段种子库间的相似性表现为随退化程度相差距离越远其土壤种子库相似性越低,土壤种子库与地上植被的Jaccard相似性指数介于0.11~0.21之间,处于极不相似水平。     

Studies on Composition and Diversity of Species Based on Different Habitats along the Delingha-Hala Lake北大核心CSCD

To explore the diversity and spatial distribution pattern of community species in the Qaidam Basin, we calculated the species composition and diversity index of plant communities in five different habitats, and analyzed the relationship between species diversity and altitude in different habitats. The results showed that 79 species of plants were recorded in the area along Delingha-Hala Lake, and the main dominant families included Compositae, Gramineae, Leguminosae, and Cruciferae. The species diversity of different habitat types had similarities, but also differences. According to the results of the community similarity in species composition, the species composition similarity between the alpine cushion vegetation and the alpine Potentilla fruticosa shrub meadow was the highest, while that of the alpine Kobresia myosuroides and the weedy meadow was the lowest. The species richness and diversity of the community showed a trend of first decreasing and then increasing with the altitude increasing, but the uniformity remained stable. In addition, the community species diversity in the middle-altitude area was the highest, and the community species diversity in the low-altitude area was slightly higher than that in the high-altitude area. The main reasons for the difference in species composition and diversity in different habitats were the hydrothermal conditions and species competitiveness. © 2019 Authors. All rights reserved.     

德令哈-哈拉湖沿线不同生境下群落的物种组成及其多样性

为探讨柴达木盆地的群落物种的多样性和空间分布格局,本文以德令哈-哈拉湖沿线区域为研究对象,测定了5种不同生境下群落的物种组成和多样性指数,并分析了不同生境下群落物种多样性与海拔的关系。结果表明：该区域共记录了79种植物,菊科、禾本科、豆科、十字花科为当地的优势科种。不同生境类型的物种多样性具有相似性,但也存在差异性。从物种组成的群落相似性结果来看,高寒垫状植被与高寒金露梅（Potentilla fruticosa）灌丛草甸的物种组成相似性最高,而与高寒嵩草（Kobresia myosuroides）、杂类草草甸的物种组成相似性最低。随着海拔升高,群落物种丰富度和多样性呈先降低后增加的趋势,但均匀度保持稳定;中海拔区域的群落物种多样性最高,低海拔区域的群落物种多样性略高于高海拔区域,而造成不同生境群落物种组成和多样性差异的主要原因是水热条件和物种竞争力。     

Spatial and temporal patterns of pig herds diagnosed with Postweaning Multisystemic Wasting Syndrome (PMWS) during the first two years of its occurrence in Denmark

The clinical syndrome Postweaning Multisystemic Wasting Syndrome (PMWS) in pigs has emerged globally during the last decade. In October 2001, the first pig herd diagnosed with PMWS was reported in Denmark, and since then the number of herds diagnosed with PMWS has increased markedly. The etiology of PMWS is not well understood, but increased knowledge of the causal factors is prerequisite for applying preventive interventions. In this study we described the temporal (time of diagnosis), spatial (location of herds) and spatio-temporal pattern of Danish pig herds diagnosed with PMWS during the first two years after the first herd was diagnosed, and we tested for spatial and spatio-temporal clustering using scan statistics. The study population consisted of pig herds that during the study period (October 2001-September 2003) performed diagnostic submissions to the two major veterinary diagnostic laboratories in Denmark (6724 herds). Of these, 277 herds were diagnosed with PMWS. Two statistically significant spatial clusters of herds diagnosed with PMWS were identified. These clusters included 11% and 8% of the study herds, respectively. Within these two clusters the relative risk for a herd to be diagnosed with PMWS was twice as high as expected. One statistically significant spatio-temporal cluster was identified between February and May 2002. We discuss different hypotheses that could explain why pig herds diagnosed with PMWS were clustered both spatially and spatio-temporally, and conclude that the results support the hypothesis that PMWS is caused by introduction of a new, unidentified, pathogen into the Danish pig production.     

Regression analysis with nested effects in epidemiological studies: Assessment of a method eliminating one level of clustering

The analysis of binary data originating from clustered observations is often a problem in epidemiological studies. In most epidemiological studies on cattle, clustering occurs at two levels: cows are clustered within herds and lactation records are clustered within cows. This paper proposes and assesses a method of eliminating one level of clustering in regression analysis.

Data from an observational study were used to assess the relationships between health disorders and culling, by means of logistic regression analysis, in two different ways. In the Random One Lactation (ROL) analysis, ten random selections of one lactation record per cow were done. Logistic regression analysis was performed in each sample separately. Results showed qualitative and quantitative variations between the ten final models. From the ten random samples, a disease was considered as significantly associated with culling, if present in at least four final models. Using a single random sample might give incomplete information. In the All Lactations (AL) analysis, all the available lactation records were included in one model, despite the dependency between lactations.

The two methods generally agreed. All diseases significantly related in the AL analysis, except one, were also significantly associated with culling with the ROL analysis. However, differences in the regression coefficients between the ROL and the AL analyses showed the importance of dispersion parameters.     

Geographic distribution of BSE in Switzerland

Visual evaluation of the occurrence of BAB (born after ban) cases pointed towards spatial clustering. Therefore a statistical analysis of spatial case clustering was conducted using GIS technology. In the initial analysis, all 376 cases (135 BAB, 241 BBB/born before ban) diagnosed through mid of March 2001 were investigated using the spatial scan statistic. Two clusters of BBB cases were identified in the western part of Switzerland, and two clusters of BAB cases in the eastern part. Epidemiological investigations performed within the BAB clusters showed an increased pig density in these cluster regions. Pig density is considered an indicator for the probability of contamination of cattle feed with feed containing meat-and-bone meal that is intended for other species (cross-contamination). In an updated cluster analysis including all cases reported until end of June 2002 (data set B), clusters were identified in the same regions as previously. It was shown that the BAB clusters occurred in different time periods. The small scale differences in cluster size and location are discussed, with an emphasis on the implications for following epidemiological investigations.     

Phylogenetic analysis of subgroup J avian leucosis virus from broiler and native chickens in Taiwan during 2000-2002

Subgroup J avian leucosis virus (ALV-J) causes great economic losses in the poultry industry. One in 3 grandparent farms was closed due to ALV-J infection in 1998 in Taiwan. The remaining 2 farms were forced to import breeding chicks from different breeding companies afterwards. We report on the ALV-J infection status among these breeders, their progeny and Taiwan native chickens during 2000-2002. The weekly mortality for the male line among the infected breeders was higher than that for the female line. Sixty-three percent (5/8) of the broiler flocks were infected with ALV-J. The surface (SU) portion of the env gene from the ALV-J field isolates was cloned and sequenced. The phylogenetic results show that all of the isolates fell into 2 clusters. Unexpectedly, the isolates from the same breeds fell into different clusters, with a cluster including isolates from different breeding companies. ALV-Js from native chickens crossbred with imported chickens were placed into the same clusters as those from the imported breeds. The high similarities observed in different ALV-J isolates suggest that different ALV-Js were mixed in the pedigree generations in different breeding lines.     

Genetic variability of avian Escherichia coli strains evaluated by enterobacterial repetitive intergenic consensus and repetitive extragenic palindromic polymerase chain reaction

In this study, we tested the capability of enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP) polymerase chain reaction (PCR) to detect genetic diversity among Escherichia coli strains isolated from chickens bearing clinical signs of colibacillosis and compared the genotypes so obtained with the O:H serotypes and virulence of those strains. The DNAs from 50 avian E. coli strains and from E. coli ATCC 25922 were used to amplify ERIC and REP sequences. DNA from avian strains produced from 8 to 17 bands by ERIC-PCR and from 6 to 20 bands by REP-PCR; E. coli ATCC produced 11 bands by both methods. ERIC and REP-PCR showed good discriminating power, and the dendograms based on the different patterns revealed extensive genetic diversity among the avian strains. Those strains were allocated into four major clonal clusters, each one with 60% of similarity by ERIC and REP-PCR, and those clusters corresponded to strains with different degrees of pathogenicity. However, 56% of the pathogenic strains (28/50) belonged to two out of three major clonal clusters, and 86% of the nonpathogenic strains tended to group in one cluster and one subgroup. The 32 serotypes detected were distributed in all clusters, and within a serogroup, different DNA fingerprints were observed; however, strains with same serotypes tended to form clusters with similarity coefficients greater than 80%. These results suggest that no specific serotype and genotype is responsible for colibacillosis and that REP and ERIC-PCR are reproducible techniques that can improve the studies needed to clarify the pathways to the pathogenesis of colibacillosis.     

Descriptive analysis and spatial epidemiology of porcine reproductive and respiratory syndrome (PRRS) for swine sites participating in area regional control and elimination programs from 3 regions of Ontario

The objectives of this study were to describe demographics, basic biosecurity practices, ownership structure, and prevalence of porcine reproductive and respiratory syndrome (PRRS) in swine sites located in 3 regions in Ontario, and investigate the presence of spatial clustering and clusters of PRRS positive sites in the 3 regions. A total of 370 swine sites were enrolled in Area Regional Control and Elimination projects in Niagara, Watford, and Perth from 2010 to 2013. Demographics, biosecurity, and site ownership data were collected using a standardized questionnaire and site locations were obtained from an industry organization. Status was assigned on the basis of available diagnostic tests and/or assessment by site veterinarians. Spatial dependence was investigated using the D-function, the spatial scan statistic test and the spatial relative risk method. Results showed that the use of strict all-in all-out (AIAO) pig flow and shower before entry are uncommon biosecurity practices in swine sites, but a larger proportion of sites reported having a Danish entry. The prevalence of PRRS in the 3 regions ranged from 17% to 48% and localized high and low risk clusters were detected. Sites enrolled in the PRRS control projects were characterized by membership in multiple and overlapping ownership structures and networks, which complicates the way the results of monitoring and disease management measures are communicated to the target population.     

Genetic conservation of five endangered Spanish donkey breeds

The genetic diversity of most livestock species is being reduced, and it is not possible to preserve all of these livestock breeds. In order to preserve as much of the genetic diversity as possible, we must first have a robust method of measuring genetic diversity among breeds. Three different methods of study that graphically represent relationships among breeds are presented; Weitzman's method, principal component analysis (PCA) and a neighbour‐joining tree with allele sharing. Diversity was evaluated on the basis of 15 microsatellite markers typed over a total of 513 DNA samples collected from five Spanish donkey breeds. Breed differentiation was confirmed by the clustering based on the genetic distances between individuals, which essentially grouped all individuals in discrete clusters. The genetic distance among breeds was used to measure the global diversity of the set in breeds considered, and to evaluate the marginal loss of diversity attached to each breed. The Catalana breed appeared to be the most ‘unique’ in the set considered. In addition to this, the usefulness of global evaluations of diversity using molecular markers to choose breeds is worthy of conservation.