High-throughput sequencing of the chicken gut microbiome

The chicken ($Gallus$ $gallus$ $domesticus$) is the most abundant and widely distributed livestock animal with a global population of over 21 bill ion. A newly hatched broiler chick increases its body weight by 25% overnight and 50-fold over five weeks. The symbiotic, complex and variable community of the microbiome forms an important part of the gastrointestinal tract (gut). It is involved in gut development, biochemistry, immunology, physiology and non-specific resistance to infection. This study investigated the chicken gut microbiota using high-throughput 16S rRNA sequencing and culture-based techniques. There was specific interest in the proventriculus of which there is limited research currently in the literature and the caecum because it contains the highest density of bacterial cells in the gut at 10$^1$$^1$ per gram. The results showed no significant difference in the first stages of the gut which shared a low-diversity microbiota dominated by a few $Lactobacillus$ species. The microbiota becomes more diverse in the latter pa1ts of the small intestine where $C/ostridiales$ and $Enterobacteriaceae$ were present in higher numbers. The caecum was the most diverse organ with the majority of species belonging to Ruminococcaceae, Lachnospiraceae and $Alistipes$. A number of novel species were isolated from the chicken gut and six of these were whole-genome sequenced

A sensitive method for the recovery of Escherichia coli serogroup O55 including Shiga toxin-producing variants for potential use in outbreaks

AIM: Shiga toxin-producing Escherichia coli (STEC) cause bloody diarrhoea, kidney failure and occasionally death. However, identifying the source of infection caused by STEC other than serogroup O157 is hampered by availability of sensitive methods for detecting these pathogens. In this study we developed novel tools for detecting E. coli O55 that is potentially associated with human outbreaks. METHOD AND RESULTS: Overall specificity of immuno-magnetic separation (IMS) beads coated with anti-O55 serum was good with exception of cross reactivity with E. coli O22 and O23, which was eliminated using an O55 specific PCR. Limit of detection for E. coli O55 using O55-IMS-beads in spiked cattle faeces was on average 50 CFU ml-1 (range 1-90), and improved to <10 CFU ml-1 using the O55 specific PCR, following IMS on samples enriched for 2h with E. coli O55. Application of these tools to test cattle faeces collected on-farm allowed the isolation of O55:H19, which through whole genome sequencing was compared to STEC O55:H7 human outbreak strains. CONCLUSION: These tools provide a sensitive method which could be used to screen samples for STEC O55, whether environmental or human clinical. SIGNIFICANCE AND IMPACT OF THE STUDY: Several human outbreaks reported in England were caused by STEC O55:H7. Tools developed here could assist in identification of the environmental source for these isolates, which has not yet been established. This article is protected by copyright. All rights reserved

Draft Genome Sequences of Six Novel Bacterial Isolates from Chicken Ceca

The chicken is the most common domesticated animal and the most abundant bird in the world. However, the chicken gut is home to many previously uncharacterized bacterial taxa. Here, we report draft genome sequences from six bacterial isolates from chicken ceca, all of which fall outside any named species

Molecular characterization of extended spectrum cephalosporin resistant Escherichia coli isolated from livestock and in-contact humans in Southeast Nigeria

The rise in antimicrobial resistance (AMR) in bacteria is reducing therapeutic options for livestock and human health, with a paucity of information globally. To fill this gap, a One-Health approach was taken by sampling livestock on farms (n = 52), abattoir (n = 8), and animal markets (n = 10), and in-contact humans in Southeast Nigeria. Extended spectrum cephalosporin (ESC)-resistant (ESC-R) Escherichia coli was selectively cultured from 975 healthy livestock faecal swabs, and hand swabs from in-contact humans. Antimicrobial susceptibility testing (AST) was performed on all ESC-R E. coli. For isolates showing a multi-drug resistance (MDR) phenotype (n = 196), quantitative real-time PCR (qPCR) was performed for confirmation of extended-spectrum β-lactamase (ESBL) and carbapenemase genes. Whole-genome sequencing (WGS) was performed on a subset (n = 157) for detailed molecular characterisation. The results showed ESC-R E. coli was present in 41.2% of samples, with AST results indicating 48.8% of isolates were phenotypically MDR. qPCR confirmed presence of ESBL genes, with bla(CTX-M) present in all but others in a subset [bla(TEM) (62.8%) and bla(SHV) (0.5%)] of isolates; none harboured transferable carbapenemase genes. Multi-locus sequence typing identified 34 Sequence Types (ST) distributed among different sampling levels; ST196 carrying bla(CTX-M-55) was predominant in chickens. Large numbers of single nucleotide polymorphisms (SNPs) in the core genome of isolates, even within the same clade by phylogenetic analysis, indicated high genetic diversity. AMR genotyping indicated the predominant bla(CTX-M) variant was bla(CTX-M-15) (87.9%), although bla(CTX-M-55), bla(CTX-M-64,) and bla(CTX-M-65) were present; it was notable that bla(CTX-M-1), common in livestock, was absent. Other predominant AMR genes included: sul2, qnrS1, strB, bla(TEM-1b), tetA-v2, and dfrA14, with prevalence varying according to host livestock species. A bla(CTX-M-15) harbouring plasmid from livestock isolates in Ebonyi showed high sequence identity to one from river/sewage water in India, indicating this ESBL plasmid to be globally disseminated, being present beyond the river environment. In conclusion, ESC-R E. coli was widespread in livestock and in-contact humans from Southeast Nigeria. WGS data indicated the isolates were genetically highly diverse, probably representing true diversity of wild type E. coli; they were likely to be MDR with several harbouring bla(CTX-M-15.) Surprisingly, human isolates had highest numbers of AMR genes and pigs the least

Molecular characterization of extended spectrum cephalosporin resistant Escherichia coli isolated from livestock and in-contact humans in Southeast Nigeria

The rise in antimicrobial resistance (AMR) in bacteria is reducing therapeutic options for livestock and human health, with a paucity of information globally. To fill this gap, a One-Health approach was taken by sampling livestock on farms (n = 52), abattoir (n = 8), and animal markets (n = 10), and in-contact humans in Southeast Nigeria. Extended spectrum cephalosporin (ESC)-resistant (ESC-R) Escherichia coli was selectively cultured from 975 healthy livestock faecal swabs, and hand swabs from in-contact humans. Antimicrobial susceptibility testing (AST) was performed on all ESC-R E. coli. For isolates showing a multi-drug resistance (MDR) phenotype (n = 196), quantitative real-time PCR (qPCR) was performed for confirmation of extended-spectrum β-lactamase (ESBL) and carbapenemase genes. Whole-genome sequencing (WGS) was performed on a subset (n = 157) for detailed molecular characterisation. The results showed ESC-R E. coli was present in 41.2% of samples, with AST results indicating 48.8% of isolates were phenotypically MDR. qPCR confirmed presence of ESBL genes, with blaCTX-M present in all but others in a subset [blaTEM (62.8%) and blaSHV (0.5%)] of isolates; none harboured transferable carbapenemase genes. Multi-locus sequence typing identified 34 Sequence Types (ST) distributed among different sampling levels; ST196 carrying blaCTX-M-55 was predominant in chickens. Large numbers of single nucleotide polymorphisms (SNPs) in the core genome of isolates, even within the same clade by phylogenetic analysis, indicated high genetic diversity. AMR genotyping indicated the predominant blaCTX-M variant was blaCTX-M-15 (87.9%), although blaCTX-M-55, blaCTX-M-64, and blaCTX-M-65 were present; it was notable that blaCTX-M-1, common in livestock, was absent. Other predominant AMR genes included: sul2, qnrS1, strB, blaTEM-1b, tetA-v2, and dfrA14, with prevalence varying according to host livestock species. A blaCTX-M-15 harbouring plasmid from livestock isolates in Ebonyi showed high sequence identity to one from river/sewage water in India, indicating this ESBL plasmid to be globally disseminated, being present beyond the river environment. In conclusion, ESC-R E. coli was widespread in livestock and in-contact humans from Southeast Nigeria. WGS data indicated the isolates were genetically highly diverse, probably representing true diversity of wild type E. coli; they were likely to be MDR with several harbouring blaCTX-M-15. Surprisingly, human isolates had highest numbers of AMR genes and pigs the least

Wordsworth's Gothic politics : a study of the poetry and prose, 1794-1814

This thesis argues for the deep implication of William Wordsworth’s writings over the period 1794 to 1814 in contemporary discourses of the Gothic. My investigation pivots upon the analogy offered in the preface to The Excursion (1814) between the incomplete epic poem The Recluse and a ‘gothic Church’, and aims, through a reconstruction of its literary and historical contexts, to establish the interpretative value of this figure in reading Wordsworth. I begin with a survey of previous critical approaches to, and a new close reading of, Wordsworth’s Gothic figure for his œuvre. I then trace the history of Gothic as a term in British public discourse since the English Revolution, showing how its contested status in the Revolution controversy of the 1790s inflects such texts as the preface to Lyrical Ballads (1800), the ‘Liberty’ sonnets of Poems, in Two Volumes (1807), and the Preamble to The Prelude. I then move to a series of detailed historical readings of Wordsworth’s key Gothic texts, starting with Salisbury Plain (1794). Recovering the network of associations that made Salisbury Plain legible to Wordsworth in 1793-4 as a map of British history, I show how the poem first subverts and then restores the English Gothic narrative of ‘Celtic night’ giving way to ‘present grandeur’. I then turn to Wordsworth’s Burkean prose tract on the Napoleonic Wars in Spain, The Convention of Cintra (1809), reading it in the context of the Gothic imagery of the conflict, and then arguing on this basis that it forms a vital part of the ‘gothic Church’ of The Recluse. Building upon this reading, I then argue that The Excursion’s advocacy of Andrew Bell’s ‘Madras’ system of ‘tuition by the scholars themselves’ shows Wordsworth’s progressive Gothic politics in action. In concluding, I turn to reconsider, in the light of the preceding chapters, in what sense Wordsworth can be called a Gothic poet.EThOS - Electronic Theses Online ServiceCarnegie Trust for the Universities of ScotlandGBUnited Kingdo