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Article ; Online: Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing.

Harry T Child / Paul A O'Neill / Karen Moore / William Rowe / Hubert Denise / David Bass / Matthew J Wade / Matt Loose / Steve Paterson / Ronny van Aerle / Aaron R Jeffries

PLoS ONE, Vol 18, Iss 4, p e

2023 Volume 0284211

Abstract: Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and ... ...

Abstract	Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and transmission patterns of outbreaks and detect the emergence of novel variants that may impact the course of an epidemic. Population-level surveillance of viruses through genomic sequencing of wastewater captures unbiased lineage data, including cryptic asymptomatic and undiagnosed infections, and has been shown to detect infection outbreaks and novel variant emergence before detection in clinical samples. Here, we present an optimised protocol for quantification and sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in influent wastewater, used for high-throughput genomic surveillance in England during the COVID-19 pandemic. This protocol utilises reverse compliment PCR for library preparation, enabling tiled amplification across the whole viral genome and sequencing adapter addition in a single step to enhance efficiency. Sequencing of synthetic SARS-CoV-2 RNA provided evidence validating the efficacy of this protocol, while data from high-throughput sequencing of wastewater samples demonstrated the sensitivity of this method. We also provided guidance on the quality control steps required during library preparation and data analysis. Overall, this represents an effective method for high-throughput sequencing of SARS-CoV-2 in wastewater which can be applied to other viruses and pathogens of humans and animals.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A major locus confers triclabendazole resistance in Fasciola hepatica and shows dominant inheritance.

Nicola J Beesley / Krystyna Cwiklinski / Katherine Allen / Rebecca C Hoyle / Terry W Spithill / E James La Course / Diana J L Williams / Steve Paterson / Jane E Hodgkinson

PLoS Pathogens, Vol 19, Iss 1, p e

2023 Volume 1011081

Abstract: Fasciola hepatica infection is responsible for substantial economic losses in livestock worldwide and poses a threat to human health in endemic areas. The mainstay of control in livestock and the only drug licenced for use in humans is triclabendazole ( ... ...

Abstract	Fasciola hepatica infection is responsible for substantial economic losses in livestock worldwide and poses a threat to human health in endemic areas. The mainstay of control in livestock and the only drug licenced for use in humans is triclabendazole (TCBZ). TCBZ resistance has been reported on every continent and threatens effective control of fasciolosis in many parts of the world. To date, understanding the genetic mechanisms underlying TCBZ resistance has been limited to studies of candidate genes, based on assumptions of their role in drug action. Taking an alternative approach, we combined a genetic cross with whole-genome sequencing to localise a ~3.2Mbp locus within the 1.2Gbp F. hepatica genome that confers TCBZ resistance. We validated this locus independently using bulk segregant analysis of F. hepatica populations and showed that it is the target of drug selection in the field. We genotyped individual parasites and tracked segregation and reassortment of SNPs to show that TCBZ resistance exhibits Mendelian inheritance and is conferred by a dominant allele. We defined gene content within this locus to pinpoint genes involved in membrane transport, (e.g. ATP-binding cassette family B, ABCB1), transmembrane signalling and signal transduction (e.g. GTP-Ras-adenylyl cyclase and EGF-like protein), DNA/RNA binding and transcriptional regulation (e.g. SANT/Myb-like DNA-binding domain protein) and drug storage and sequestration (e.g. fatty acid binding protein, FABP) as prime candidates for conferring TCBZ resistance. This study constitutes the first experimental cross and genome-wide approach for any heritable trait in F. hepatica and is key to understanding the evolution of drug resistance in Fasciola spp. to inform deployment of efficacious anthelmintic treatments in the field.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Research data: (with research data) Offspring development and lifeâhistory variation in a water flea depends upon cloneâspecific integration of genetic, nonâgenetic and environmental cues

Harney, Ewan / Steve Paterson / Stewart J. Plaistow

Functional ecology. 2017 Oct., v. 31, no. 10

2017

Abstract: Theory predicts that offspring developmental strategies involve the integration of genetic, nonâgenetic and environmental âcuesâ. But it is unclear how cue integration is achieved during development, and whether this pattern is general or genotype ... ...

Abstract	Theory predicts that offspring developmental strategies involve the integration of genetic, nonâgenetic and environmental âcuesâ. But it is unclear how cue integration is achieved during development, and whether this pattern is general or genotype specific. In order to test this, we manipulated the maternal and offspring environments of three genetically distinct clones of the water flea Daphnia magna taken from different populations. We then quantified the effect that the genotype, maternal environment and the offspring environment had on the development and life histories of the three different clones. Mothers responded to the same maternal environments in different ways, resulting in cloneâspecific maternal effects on neonate size. Offspring responses to maternal cues varied according to the trait in question and were also clone specific. The integration of these maternal effects during development was highly context dependent in two clones but more consistent across environments in the third. Genetic, nonâgenetic and environmental cues contributed to offspring phenotypic variation in all three clones, but there was no general pattern linking traits to specific cues. In fact, two clones used different combinations of cues at different points in development to achieve similar phenotypic outcomes. Reaction norms for the age and size at which maturation was initiated differed among genotypes, between maternal environments and across current environments. Developmental transitions such as the decision to mature may thus play an important role in determining patterns of cue integration. Considering multiple traits during development demonstrated that variation in the integration of genetic, nonâgenetic and environmental cues was an important determinant of lifeâhistory variation among D. magna genotypes. This variation is likely to influence phenotypic evolution. A lay summary is available for this article.
Keywords	Daphnia magna ; clones ; evolution ; genotype ; life history ; maternal effect ; mothers ; neonates ; phenotype ; phenotypic variation ; progeny
Language	English
Dates of publication	2017-10
Size	p. 1996-2007.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Research data
Note	JOURNAL ARTICLE
ZDB-ID	2020307-X
ISSN	1365-2435 ; 0269-8463 ; 0269-8463
ISSN (online)	1365-2435
ISSN	0269-8463
DOI	10.1111/1365-2435.12887
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation.

James P J Hall / Rosanna C T Wright / Ellie Harrison / Katie J Muddiman / A Jamie Wood / Steve Paterson / Michael A Brockhurst

PLoS Biology, Vol 19, Iss 10, p e

2021 Volume 3001225

Abstract: Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly ... ...

Abstract	Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.
Keywords	Biology (General) ; QH301-705.5
Subject code	570 ; 572
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Endemic Hantavirus in Field Voles, Northern England

Anna G. Thomason / Michael Begon / Janette E. Bradley / Steve Paterson / Joseph A. Jackson

Emerging Infectious Diseases, Vol 23, Iss 6, Pp 1033-

2017 Volume 1035

Abstract: We report a PCR survey of hantavirus infection in an extensive field vole (Microtus agrestis) population present in the Kielder Forest, northern England. A Tatenale virus–like lineage was frequently detected (≈17% prevalence) in liver tissue. Lineages ... ...

Abstract	We report a PCR survey of hantavirus infection in an extensive field vole (Microtus agrestis) population present in the Kielder Forest, northern England. A Tatenale virus–like lineage was frequently detected (≈17% prevalence) in liver tissue. Lineages genetically similar to Tatenale virus are likely to be endemic in northern England.
Keywords	Microtus ; Microtus agrestis ; field vole ; hantavirus ; Tatenale virus ; United Kingdom ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Language	English
Publishing date	2017-06-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Fasciola hepatica demonstrates high levels of genetic diversity, a lack of population structure and high gene flow: possible implications for drug resistance

Beesley, Nicola J / Diana J.L. Williams / Jane Hodgkinson / Steve Paterson

International journal for parasitology. 2017 Jan., v. 47, no. 1

2017

Abstract: Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a ... ...

Abstract	Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations.
Keywords	adults ; alleles ; anthelmintics ; drug resistance ; Fasciola hepatica ; gene flow ; genetic variation ; genotype ; human health ; intermediate hosts ; liver flukes ; livestock and meat industry ; pastures ; population structure ; risk ; selfing ; snails ; zoonoses ; United Kingdom
Language	English
Dates of publication	2017-01
Size	p. 11-20.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	120518-3
ISSN	1879-0135 ; 0020-7519
ISSN (online)	1879-0135
ISSN	0020-7519
DOI	10.1016/j.ijpara.2016.09.007
Database	NAL-Catalogue (AGRICOLA)

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Article ; Research data: (with research data) Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteriaâplasmidâphage interaction

Harrison, Ellie / Andrew J. Spiers / James P. J. Hall / Michael A. Brockhurst / Steve Paterson

Molecular ecology. 2017 May, v. 26, no. 10

2017

Abstract: Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be ... ...

Abstract	Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities, bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here, we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage, SBW25Ï2, and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions.
Keywords	bacteria ; bacteriophages ; evolution ; horizontal gene transfer ; hosts ; interspersed repetitive sequences ; microbial communities ; plasmids ; prediction ; Pseudomonas fluorescens
Language	English
Dates of publication	2017-05
Size	p. 2757-2764.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Research data
Note	JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083 ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.14080
Database	NAL-Catalogue (AGRICOLA)

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Article: Increased socially mediated plasticity in gene expression accompanies rapid adaptive evolution

Pascoal, Sonia / Marlene Zuk / Michael G. Ritchie / Nathan W. Bailey / Nichola Rockliffe / Steve Paterson / Xuan Liu / Yongxiang Fang

Ecology letters. 2018 Apr., v. 21, no. 4

2018

Abstract: Recent theory predicts that increased phenotypic plasticity can facilitate adaptation as traits respond to selection. When genetic adaptation alters the social environment, socially mediated plasticity could cause coâevolutionary feedback dynamics that ...

Abstract	Recent theory predicts that increased phenotypic plasticity can facilitate adaptation as traits respond to selection. When genetic adaptation alters the social environment, socially mediated plasticity could cause coâevolutionary feedback dynamics that increase adaptive potential. We tested this by asking whether neural gene expression in a recently arisen, adaptive morph of the field cricket Teleogryllus oceanicus is more responsive to the social environment than the ancestral morph. Silent males (flatwings) rapidly spread in a Hawaiian population subject to acoustically orienting parasitoids, changing the population's acoustic environment. Experimental altering cricketsâ acoustic environments during rearing revealed broad, plastic changes in gene expression. However, flatwing genotypes showed increased socially mediated plasticity, whereas normalâwing genotypes exhibited negligible expression plasticity. Increased plasticity in flatwing crickets suggests a coevolutionary process coupling socially flexible gene expression with the abrupt spread of flatwing. Our results support predictions that phenotypic plasticity should rapidly evolve to be more pronounced during early phases of adaptation.
Keywords	acoustics ; evolutionary adaptation ; gene expression ; gene expression regulation ; genotype ; males ; parasitoids ; phenotypic plasticity ; plasticity ; prediction ; rearing ; social environment ; Teleogryllus oceanicus
Language	English
Dates of publication	2018-04
Size	p. 546-556.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	LETTER
ZDB-ID	1441608-6
ISSN	1461-0248 ; 1461-023X
ISSN (online)	1461-0248
ISSN	1461-023X
DOI	10.1111/ele.12920
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Transcriptome-wide analysis reveals different categories of response to a standardised immune challenge in a wild rodent

Klara M. Wanelik / Mike Begon / Elena Arriero / Janette E. Bradley / Ida M. Friberg / Joseph A. Jackson / Christopher H. Taylor / Steve Paterson

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 11

Abstract: Abstract Individuals vary in their immune response and, as a result, some are more susceptible to infectious disease than others. Little is known about the nature of this individual variation in natural populations, or which components of immune pathways ...

Abstract	Abstract Individuals vary in their immune response and, as a result, some are more susceptible to infectious disease than others. Little is known about the nature of this individual variation in natural populations, or which components of immune pathways are most responsible, but defining this underlying landscape of variation is an essential first step to understanding the drivers of this variation and, ultimately, predicting the outcome of infection. We describe transcriptome-wide variation in response to a standardised immune challenge in wild field voles. We find that genes (hereafter 'markers') can be categorised into a limited number of types. For the majority of markers, the response of an individual is dependent on its baseline expression level, with significant enrichment in this category for conventional immune pathways. Another, moderately sized, category contains markers for which the responses of different individuals are also variable but independent of their baseline expression levels. This category lacks any enrichment for conventional immune pathways. We further identify markers which display particularly high individual variability in response, and could be used as markers of immune response in larger studies. Our work shows how a standardised challenge performed on a natural population can reveal the patterns of natural variation in immune response.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: From the animal house to the field

Elena Arriero / Klara M Wanelik / Richard J Birtles / Janette E Bradley / Joseph A Jackson / Steve Paterson / Mike Begon

PLoS ONE, Vol 12, Iss 8, p e

Are there consistent individual differences in immunological profile in wild populations of field voles (Microtus agrestis)?

2017 Volume 0183450

Abstract: Inbred mouse strains, living in simple laboratory environments far removed from nature, have been shown to vary consistently in their immune response. However, wildlife populations are typically outbreeding and face a multiplicity of challenges, ... ...

Abstract	Inbred mouse strains, living in simple laboratory environments far removed from nature, have been shown to vary consistently in their immune response. However, wildlife populations are typically outbreeding and face a multiplicity of challenges, parasitological and otherwise. In this study we seek evidence of consistent difference in immunological profile amongst individuals in the wild. We apply a novel method in this context, using longitudinal (repeated capture) data from natural populations of field voles, Microtus agrestis, on a range of life history and infection metrics, and on gene expression levels. We focus on three immune genes, IFN-γ, Gata3, and IL-10, representing respectively the Th1, Th2 and regulatory elements of the immune response. Our results show that there was clear evidence of consistent differences between individuals in their typical level of expression of at least one immune gene, and at most all three immune genes, after other measured sources of variation had been taken into account. Furthermore, individuals that responded to changing circumstances by increasing expression levels of Gata3 had a correlated increase in expression levels of IFN-γ. Our work stresses the importance of acknowledging immunological variation amongst individuals in studies of parasitological and infectious disease risk in wildlife populations.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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