scholarly journals Large-scale structure of brown rat (Rattus norvegicus) populations in England: effects on rodenticide resistance

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1458 ◽  
Author(s):  
Mohd Z.H. Haniza ◽  
Sally Adams ◽  
Eleanor P. Jones ◽  
Alan MacNicoll ◽  
Eamonn B. Mallon ◽  
...  
Keyword(s):  
Population Structure ◽  
Rattus Norvegicus ◽  
Large Scale ◽  
Animal Health ◽  
Pest Species ◽  
Resistance Mutations ◽  
Anticoagulant Rodenticides ◽  
Brown Rat ◽  
Negative Impacts ◽  
The Uk

The brown rat (Rattus norvegicus) is a relatively recent (<300 years) addition to the British fauna, but by association with negative impacts on public health, animal health and agriculture, it is regarded as one of the most important vertebrate pest species. Anticoagulant rodenticides were introduced for brown rat control in the 1950s and are widely used for rat control in the UK, but long-standing resistance has been linked to control failures in some regions. One thus far ignored aspect of resistance biology is the population structure of the brown rat. This paper investigates the role population structure has on the development of anticoagulant resistance. Using mitochondrial and microsatellite DNA, we examined 186 individuals (from 15 counties in England and one location in Wales near the Wales–England border) to investigate the population structure of rural brown rat populations. We also examined individual rats for variations of theVKORC1gene previously associated with resistance to anticoagulant rodenticides. We show that the populations were structured to some degree, but that this was only apparent in the microsatellite data and not the mtDNA data. We discuss various reasons why this is the case. We show that the population as a whole appears not to be at equilibrium. The relative lack of diversity in the mtDNA sequences examined can be explained by founder effects and a subsequent spatial expansion of a species introduced to the UK relatively recently. We found there was a geographical distribution of resistance mutations, and relatively low rate of gene flow between populations, which has implications for the development and management of anticoagulant resistance.

scholarly journals 1888. A Nationwide Outbreak of Invasive Pneumococcal Disease (IPD) Caused by a Novel Streptococcus Pneumoniae Serotype 2 (SP2) Clone in the PCV13 Era, in Israel

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S54-S54
Author(s):  
Ron Dagan ◽  
Shalom Ben-Shimol ◽  
Rachel Benisty ◽  
Gili Regev-Yochay ◽  
Merav Ron ◽  
...  
Keyword(s):  
Population Structure ◽  
Jewish Population ◽  
Pneumococcal Disease ◽  
Large Scale ◽  
Evolutionary Dynamics ◽  
Fold Increase ◽  
Population Based ◽  
Whole Genome ◽  
Single Strain ◽  
The Uk

Abstract Background IPD caused by Sp2 (non-PCV13 serotype) is relatively rare. However, Sp2 has a high potential for causing IPD including meningitis. Large-scale outbreaks of Sp2 IPD are rare and were not reported post-PCV implementation. We describe Sp2 IPD outbreak in Israel, in the PCV13 era, caused by a novel clone. Additionally, we analyzed the population structure and evolutionary dynamics of Sp2 during 2006–2018. Methods An ongoing, population-based, nationwide active surveillance, conducted since July 2009. PCV7/PCV13 were implemented in Israel in July 2009 and November 2010, respectively. All isolates were tested for antimicrobial susceptibility, PFGE, MLST and whole-genome sequencing (WGS). Results. Overall, 173 Sp2 IPD cases were identified; all isolates were analyzed by MLST (Figure 1). During 2016–2017, Sp2 caused 7.6% of all-IPD, a 7-fold increase compared with 2006–2015, and ranked second (after serotype 12F causing 12%) among IPD isolates. During 2006–2015, 98% (40/41) Sp2 IPD were caused by the previously reported global ST-1504 clone. The outbreak was caused by a novel clone ST-13578, not previously reported (Figure 2). WGS analysis confirmed that ST-13578 was related, but genetically distinct from ST-1504, observed exclusively before the outbreak. A single strain of clone ST-74 previously globally reported was identified in 2017–2018. An additional case was identified in an adult in the UK, following a family visit from Israel. The ST-13578 clone was identified only in the Jewish population and was mainly distributed in 3 of the 7 Israeli districts. All tested strains were penicillin-susceptible (MIC < 0.06 μg/mL). Conclusion To the best of our knowledge, this is the first widespread Sp2 outbreak since PCV13 introduction worldwide, caused by a novel clone ST-13578. The outbreak is still ongoing, although a declining trend was noted since 2017. Disclosures All Authors: No reported Disclosures.

scholarly journals Global population divergence and admixture of the brown rat ( Rattus norvegicus )

2016 ◽  
Vol 283 (1841) ◽  
pp. 20161762 ◽  
Author(s):  
Emily E. Puckett ◽  
Jane Park ◽  
Matthew Combs ◽  
Michael J. Blum ◽  
Juliet E. Bryant ◽  
...  
Keyword(s):  
Population Structure ◽  
Rattus Norvegicus ◽  
Population Divergence ◽  
Western North America ◽  
Westward Expansion ◽  
Fine Grained ◽  
Worldwide Distribution ◽  
Brown Rat ◽  
Commensal Rodents ◽  
Global Population

Native to China and Mongolia, the brown rat ( Rattus norvegicus ) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes.

scholarly journals Parallels, differences and lessons: a comparison of the management of foot-and-mouth disease and COVID-19 using UK 2001/2020 as points of reference

2020 ◽  
Vol 287 (1938) ◽  
pp. 20200906
Author(s):  
Keith Sumption ◽  
Theodore J. D. Knight-Jones ◽  
Melissa McLaws ◽  
David J. Paton
Keyword(s):  
Large Scale ◽  
Animal Health ◽  
Scientific Information ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Foot And Mouth ◽  
The Uk ◽  
Disease Free ◽  
Rapid Emergence ◽  
Critical Resources

Foot-and-mouth disease (FMD) is an extremely infectious viral infection of cloven-hoofed animals which is highly challenging to control and can give rise to national animal health crises, especially if there is a lack of pre-existing immunity due to the emergence of new strains or following incursions into disease-free regions. The 2001 FMD epidemic in the UK was on a scale that initially overwhelmed the national veterinary services and was eventually controlled by livestock lockdown and slaughter on an unprecedented scale. In 2020, the rapid emergence of COVID-19 has led to a human pandemic unparalleled in living memory. The enormous logistics of multi-agency control efforts for COVID-19 are reminiscent of the 2001 FMD epidemic in the UK, as are the use of movement restrictions, not normally a feature of human disease control. The UK experience is internationally relevant as few countries have experienced national epidemic crises for both diseases. In this review, we reflect on the experiences and lessons learnt from UK and international responses to FMD and COVID-19 with respect to their management, including the challenge of preclinical viral transmission, threat awareness, early detection, different interpretations of scientific information, lockdown, biosecurity behaviour change, shortage of testing capacity and the choices for eradication versus living with infection. A major lesson is that the similarity of issues and critical resources needed to manage large-scale outbreaks demonstrates that there is benefit to a ‘One Health’ approach to preparedness, with potential for greater cooperation in planning and the consideration of shared critical resources.

scholarly journals Contemporary work: Its meanings and demands

2017 ◽  
Vol 59 (2) ◽  
pp. 122-138 ◽  
Author(s):  
Patricia Findlay ◽  
Paul Thompson
Keyword(s):  
Performance Management ◽  
Work Performance ◽  
Large Scale ◽  
Qualitative Case Studies ◽  
Positive Elements ◽  
Contemporary Work ◽  
Market Factors ◽  
Negative Impacts ◽  
Nuanced Understanding ◽  
The Uk

This article addresses recurrent trends in the forces shaping work and its meanings. Using evidence from large-scale surveys and qualitative case studies it maps the changing picture of work and employment, particularly in the UK and Australia. It does so by focusing on insecurity, demanding work, performance management, work–life boundaries and dis/engagement. Whilst identifying a number of negative impacts of change such as growing insecurity and excessive work pressures, the article emphasises that these are trends, not universals, and don’t affect all workers or affect them in the same way. We need to be more careful about how trends are translated into overarching theoretical constructs that give a misleading picture. In policy terms, attention should be given to the intersection of labour process and labour market factors, the changing boundaries between and shared aspirations of ‘standard’ and ‘nonstandard’ workers, and to a more nuanced understanding of the positive elements of ‘bad’ jobs and the more negative elements of ‘good’ ones.

scholarly journals Revealing multi-scale population structure in large cohorts

2018 ◽  
Author(s):  
Alex Diaz-Papkovich ◽  
Luke Anderson-Trocmé ◽  
Simon Gravel
Keyword(s):  
Population Structure ◽  
Large Scale ◽  
Large Population ◽  
Computational Cost ◽  
General Purpose ◽  
Exploratory Analysis ◽  
Fine Scale ◽  
Using Data ◽  
The Uk ◽  
Unbalanced Sampling

AbstractGenetic structure in large cohorts results from technical, sampling and demographic variation. Visualisation is therefore a first step in most genomic analyses. However, existing data exploration methods struggle with unbalanced sampling and the many scales of population structure. We investigate an approach to dimension reduction of genomic data that combines principal components analysis (PCA) with uniform manifold approximation and projection (UMAP) to succinctly illustrate population structure in large cohorts and capture their relationships on local and global scales. Using data from large-scale genomic datasets, we demonstrate that PCA-UMAP effectively clusters closely related individuals while placing them in a global continuum of genetic variation. This approach reveals previously overlooked subpopulations within the American Hispanic population and fine-scale relationships between geography, genotypes, and phenotypes in the UK population. This opens new lines of investigation for demographic research and statistical genetics. Given its small computational cost, PCA-UMAP also provides a general-purpose approach to exploratory analysis in population-scale datasets.Author summaryBecause of geographic isolation, individuals tend to be more genetically related to people living nearby than to people living far. This is an example of population structure, a situation where a large population contains subgroups that share more than the average amount of DNA. This structure can tell us about human history, and it can also have a large effect on medical studies. We use a newly developed method (UMAP) to visualize population structure from three genomic datasets. Using genotype data alone, we reveal numerous subgroups related to ancestry and correlated with traits such as white blood cell count, height, and FEV1, a measure used to detect airway obstruction. We demonstrate that UMAP reveals previously unobserved patterns and fine-scale structure. We show that visualizations work especially well in large datasets containing populations with diverse backgrounds, which are rapidly becoming more common, and that unlike other visualization methods, we can preserve intuitive connections between populations that reflect their shared ancestries. The combination of these results and the effectiveness of the strategy on large and diverse datasets make this an important approach for exploratory analysis for geneticists studying ancestral events and phenotype distributions.

scholarly journals Scalable probabilistic PCA for large-scale genetic variation data

2019 ◽  
Author(s):  
Aman Agrawal ◽  
Alec M. Chiu ◽  
Minh Le ◽  
Eran Halperin ◽  
Sriram Sankararaman
Keyword(s):  
Principal Component Analysis ◽  
Population Structure ◽  
Genetic Variation ◽  
Principal Components ◽  
Large Scale ◽  
Principal Component ◽  
Uk Biobank ◽  
Genome Wide ◽  
Variation Data ◽  
The Uk

AbstractPrincipal component analysis (PCA) is a key tool for understanding population structure and controlling for population stratification in genome-wide association studies (GWAS). With the advent of large-scale datasets of genetic variation, there is a need for methods that can compute principal components (PCs) with scalable computational and memory requirements. We present ProPCA, a highly scalable method based on a probabilistic generative model, which computes the top PCs on genetic variation data efficiently. We applied ProPCA to compute the top five PCs on genotype data from the UK Biobank, consisting of 488,363 individuals and 146,671 SNPs, in less than thirty minutes. Leveraging the population structure inferred by ProPCA within the White British individuals in the UK Biobank, we scanned for SNPs that are not well-explained by the PCs to identify several novel genome-wide signals of recent putative selection including missense mutations in RPGRIP1L and TLR4.Author SummaryPrincipal component analysis is a commonly used technique for understanding population structure and genetic variation. With the advent of large-scale datasets that contain the genetic information of hundreds of thousands of individuals, there is a need for methods that can compute principal components (PCs) with scalable computational and memory requirements. In this study, we present ProPCA, a highly scalable statistical method to compute genetic PCs efficiently. We systematically evaluate the accuracy and robustness of our method on large-scale simulated data and apply it to the UK Biobank. Leveraging the population structure inferred by ProPCA within the White British individuals in the UK Biobank, we identify several novel signals of putative recent selection.

Q fever (Coxiella burnetii) reservoir in wild brown rat (Rattus norvegicus) populations in the UK

Parasitology ◽  
1995 ◽  
Vol 110 (1) ◽  
pp. 31-35 ◽  
Author(s):  
J. P. Webster ◽  
G. Lloyd ◽  
D. W. Macdonald
Keyword(s):  
Coxiella Burnetii ◽  
Rattus Norvegicus ◽  
Q Fever ◽  
Causal Agent ◽  
Captive Population ◽  
High Seroprevalence ◽  
Brown Rat ◽  
Wild Rats ◽  
The Uk

Seroprevalence ofCoxiella burnetii, the causal agent of Q fever in humans, was examined in wild brown rat populations from 4 Oxfordshire farmsteads (n= 127), 9 Somerset homesteads (n= 98), and 1 captive enclosure (n= 88) in the UK. Seroprevalence ranged between 7 and 53%, the lowest being within the captive population and the highest on dairy farmsteads with sheep present. This is the first reported investigation ofC. burnetiiin wild rats outside India. We suggest that the high Seroprevalence among rats (i) provides evidence that wild rats constitute an important reservoir forC. burnetiiin the UK, and (ii) explains why cats, as frequent predators of rats, are so important in the epidemiology of this disease.

Sign in / Sign up

Export Citation Format

Share Document