Lizeth Lacharme-Lora*, Siân V Owen*, Richard Blundell, Rocío Canals, Nicolas Wenner, Blanca Perez-Sepulveda, Wai Yee Fong, Rachel Gilroy, Paul Wigley, and Jay CD Hinton. 2019. “The use of chicken and insect infection models to assess the virulence of African Salmonella Typhimurium ST313.” PLOS Neglected Tropical Diseases, 13, 7, Pp. e0007540. Publisher's VersionAbstract
Over recent decades, Salmonella infection research has predominantly relied on murine infection models. However, in many cases the infection phenotypes of Salmonella pathovars in mice do not recapitulate human disease. For example, Salmonella Typhimurium ST313 is associated with enhanced invasive infection of immunocompromised people in Africa, but infection of mice and other animal models with ST313 have not consistently reproduced this invasive phenotype. The introduction of alternative infection models could help to improve the quality and reproducibility of pathogenesis research by facilitating larger-scale experiments. To investigate the virulence of S. Typhimurium ST313 in comparison with ST19, a combination of avian and insect disease models were used. We performed experimental infections in five lines of inbred and one line of outbred chickens, as well as in the alternative chick embryo and Galleria mellonella wax moth larvae models. This extensive set of experiments identified broadly similar patterns of disease caused by the African and global pathovariants of Salmonella Typhimurium in the chicken, the chicken embryo and insect models. A comprehensive analysis of all the chicken infection experiments revealed that the African ST313 isolate D23580 had a subtle phenotype of reduced levels of organ colonisation in inbred chickens, relative to ST19 strain 4/74. ST313 isolate D23580 also caused reduced mortality in chicken embryos and insect larvae, when compared with ST19 4/74. We conclude that these three infection models do not reproduce the characteristics of the systemic disease caused by S. Typhimurium ST313 in humans.
Siân V. Owen*, Blanca M. Perez-Sepulveda*, and Evelien M. Adriaenssens. 11/16/2018. “Detection of Bacteriophages: Sequence-Based Systems.” In Bacteriophages, Pp. 1-25. Springer. Publisher's VersionAbstract

The invention of sequencing technologies has fundamentally changed molecular biology, including the way we look at bacteriophages. In addition to investigating bacteriophage plaques, electron micrographs, or the phenotypes of different mutants, we are now able to explore the entire genetic potential encoded in their genomes. As of July 2018, over 6,000 complete phage genome sequences were published in public databases, with over 28,000 partial sequences available.

In this chapter, we give an overview of the latest technologies that can be used to determine phage genome sequences, ranging from short-read platforms which generally give multiple gigabases of sequence data to long-read technologies which have the potential to sequence a bacteriophage genome in one single read. We then look at applications of sequencing technologies in detecting bacteriophages, from a single gene, over entire genomes, to the community level.

Disa L Hammarlöf, Carsten Kröger, Siân V Owen, Roc{\'ıo Canals, Lizeth Lacharme-Lora, Nicolas Wenner, Anna E Schager, Timothy J Wells, Ian R Henderson, Paul Wigley, and others. 2018. “Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella.” Proceedings of the National Academy of Sciences, 115, 11, Pp. e2614–e2623.
Disa L Hammarlöf*, Carsten Kröger*, Siân V Owen*, Rocío Canals, Lizeth Lacharme-Lora, Nicolas Wenner, Anna E Schager, Timothy J Wells, Ian R Henderson, Paul Wigley, and others. 2018. “Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella.” Proceedings of the National Academy of Sciences, Pp. 201714718. Publisher's VersionAbstract
Salmonella enterica serovar Typhimurium ST313 is a relatively newly emerged sequence type that is causing a devastating epidemic of bloodstream infections across sub-Saharan Africa. Analysis of hundreds of Salmonella genomes has revealed that ST313 is closely related to the ST19 group of S Typhimurium that cause gastroenteritis across the world. The core genomes of ST313 and ST19 vary by only ∼1,000 SNPs. We hypothesized that the phenotypic differences that distinguish African Salmonella from ST19 are caused by certain SNPs that directly modulate the transcription of virulence genes. Here we identified 3,597 transcriptional start sites of the ST313 strain D23580, and searched for a gene-expression signature linked to pathogenesis of Salmonella We identified a SNP in the promoter of the pgtE gene that caused high expression of the PgtE virulence factor in African S. Typhimurium, increased the degradation of the factor B component of human complement, contributed to serum resistance, and modulated virulence in the chicken infection model. We propose that high levels of PgtE expression by African S Typhimurium ST313 promote bacterial survival and dissemination during human infection. Our finding of a functional role for an extragenic SNP shows that approaches used to deduce the evolution of virulence in bacterial pathogens should include a focus on noncoding regions of the genome.
Siân V Owen. 2017. “Exploring the prophage biology of Salmonella enterica serovar Typhimurium ST313”.
Philip M Ashton, Siân V Owen, Lukeki Kaindama, Will PM Rowe, Chris R Lane, Lesley Larkin, Satheesh Nair, Claire Jenkins, Elizabeth M de Pinna, Nicholas A Feasey, and others. 2017. “Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa.” Genome medicine, 9, 1, Pp. 1–13.
Siân V. Owen*. 2017. “Exploring the prophage biology of Salmonella enterica serovar Typhimurium ST313.” Institute of Integrative Biology, University of Liverpool. Publisher's VersionAbstract
In the past 30 years, Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of ~390,000 people each year. The disease is largely caused by a recently described sequence type of Salmonella Typhimurium: ST313. Comparative genomic analysis showed that the ST313 lineage is closely-related to the ancestral gastroenteritis-associated Typhimurium sequence type ST19, but carries a distinct prophage repertoire. I hypothesised that prophages contribute to the biology of this clinically-relevant ST. In this thesis I show that the African ST313 representative strain D23580 contains 5 full length prophages. Prophage BTP1 and BTP5 are undescribed, novel prophages specific to African ST313 strains, whilst Gifsy-2, ST64B and Gifsy-1 are well-characterised prophages found in other strains of S. Typhimurium. Of the five prophages, only BTP1 and BTP5 showed evidence for functional phage production, and mutations responsible for the inactivation of Gifsy-2, ST64B and Gifsy-1 were identified. The BTP1 prophage spontaneously induced at a prolific rate, estimated to result in the phage-mediated lysis of approximately 0.2% of the lysogenic cell population. A GFP reporter system was developed to visualise the spontaneous induction of the BTP1 prophage at the single-cell level. Though the BTP5 phage could not be studied using traditional plaque assay methodology, there was evidence that the BTP5 prophage was capable of forming viable BTP5 phage that could lysogenise naïve hosts. I analysed the genomes of recently discovered ST313 isolates from the UK and show that ST313 in the UK represents a distinct population of antibiotic susceptible strains associated with gastrointestinal infection. Additionally, analysis of the UK-ST313 genomes indicated that the BTP1 and BTP5 prophages were acquired independently by the two African ST313 lineages, showing convergent evolution to acquire and conserve the BTP1 and BTP5 prophages. Finally I present evidence that the prophages, in particular BTP5, effect the global gene expression of ST313, and the ST313-td gene of BTP1 mediates lysogenic conversion by functioning as a superinfection immunity factor against infection by Salmonella phage P22. The implications of these findings for understanding the pathogen in terms of ecological niche, host range and invasiveness in humans is discussed.
Siân V Owen*, Nicolas Wenner, Rocío Canals, Angela Makumi, Disa L Hammarlöf, Melita A Gordon, Abram Aertsen, Nicholas A Feasey, and Jay CD Hinton. 2017. “Characterization of the prophage repertoire of African Salmonella Typhimurium ST313 reveals high levels of spontaneous induction of novel phage BTP1.” Frontiers in microbiology, 8, Pp. 235. Publisher's VersionAbstract
In the past 30 years, Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of an estimated 390,000 people each year. The disease is predominantly caused by a recently described sequence type of Salmonella Typhimurium: ST313, which has a distinctive set of prophage sequences. We have thoroughly characterized the ST313-associated prophages both genetically and experimentally. ST313 representative strain D23580 contains five full-length prophages: BTP1, Gifsy-2D23580, ST64BD23580, Gifsy-1D23580, and BTP5. We show that common S. Typhimurium prophages Gifsy-2, Gifsy-1, and ST64B are inactivated in ST313 by mutations. Prophage BTP1 was found to be a functional novel phage, and the first isolate of the proposed new species "Salmonella virus BTP1", belonging to the P22virus genus. Surprisingly, ∼109 BTP1 virus particles per ml were detected in the supernatant of non-induced, stationary-phase cultures of strain D23580, representing the highest spontaneously induced phage titer so far reported for a bacterial prophage. High spontaneous induction is shown to be an intrinsic property of prophage BTP1, and indicates the phage-mediated lysis of around 0.2% of the lysogenic population. The fact that BTP1 is highly conserved in ST313 poses interesting questions about the potential fitness costs and benefits of novel prophages in epidemic S. Typhimurium ST313.
Matthew Faulkner, Jorge Rodriguez-Ramos, Gregory F Dykes, Siân V Owen, Selene Casella, Deborah M Simpson, Robert J Beynon, and Lu-Ning Liu. 2017. “Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes.” Nanoscale, 9, 30, Pp. 10662–10673. Publisher's VersionAbstract
Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional β-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single β-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact β-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial β-carboxysomes that likely serve as the β-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional β-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of β-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of β-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering.
Philip M Ashton*, Siân V Owen*, Lukeki Kaindama, Will PM Rowe, Chris R Lane, Lesley Larkin, Satheesh Nair, Claire Jenkins, Elizabeth M de Pinna, Nicholas A Feasey, and others. 2017. “Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa.” Genome medicine, 9, 1, Pp. 92. Publisher's VersionAbstract


The ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified.


We analysed the whole genome sequences of S. Typhimurium isolates from UK patients that were generated following the introduction of routine whole-genome sequencing (WGS) of Salmonella enterica by Public Health England in 2014.


We found that 2.7% (84/3147) of S. Typhimurium from patients in England and Wales were ST313 and were associated with gastrointestinal infection. Phylogenetic analysis revealed novel diversity of ST313 that distinguished UK-linked gastrointestinal isolates from African-associated extra-intestinal isolates. The majority of genome degradation of African ST313 lineage 2 was conserved in the UK-ST313, but the African lineages carried a characteristic prophage and antibiotic resistance gene repertoire. These findings suggest that a strong selection pressure exists for certain horizontally acquired genetic elements in the African setting. One UK-isolated lineage 2 strain that probably originated in Kenya carried a chromosomally located bla CTX-M-15, demonstrating the continual evolution of this sequence type in Africa in response to widespread antibiotic usage.


The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in this important sequence type. This study highlights the power of routine WGS by public health agencies to make epidemiologically significant deductions that would be missed by conventional microbiological methods. We speculate that the niche specialisation of sub-Saharan African ST313 lineages is driven in part by the acquisition of accessory genome elements.

TR Connor, SV Owen, G Langridge, S Connell, S Nair, S Reuter, TJ Dallman, J Corander, KC Tabing, S Le Hello, and others. 2016. “What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.” mBio, 7, 4, Pp. e00527–16.
Thomas R Connor, Siân V Owen, Gemma Langridge, Steve Connell, Satheesh Nair, Sandra Reuter, Timothy J Dallman, Jukka Corander, Kristine C Tabing, Simon Le Hello, and others. 2016. “What’s in a name? Species-wide whole-genome sequencing resolves invasive and noninvasive lineages of Salmonella enterica serotype Paratyphi B.” MBio, 7, 4, Pp. e00527–16. Publisher's VersionAbstract
For 100 years, it has been obvious that Salmonella enterica strains sharing the serotype with the formula 1,4,[5],12:b:1,2—now known as Paratyphi B—can cause diseases ranging from serious systemic infections to self-limiting gastroenteritis. Despite considerable predicted diversity between strains carrying the common Paratyphi B serotype, there remain few methods that subdivide the group into groups that are congruent with their disease phenotypes. Paratyphi B therefore represents one of the canonical examples in Salmonella where serotyping combined with classical microbiological tests fails to provide clinically informative information. Here, we use genomics to provide the first high-resolution view of this serotype, placing it into a wider genomic context of the Salmonella enterica species. These analyses reveal why it has been impossible to subdivide this serotype based upon phenotypic and limited molecular approaches. By examining the genomic data in detail, we are able to identify common features that correlate with strains of clinical importance. The results presented here provide new diagnostic targets, as well as posing important new questions about the basis for the invasive disease phenotype observed in a subset of strains.
Shabarinath Srikumar, Carsten Kröger, Magali Hébrard, Aoife Colgan, Sian V Owen, Sathesh K Sivasankaran, Andrew DS Cameron, Karsten Hokamp, and Jay CD Hinton. 2015. “RNA-seq brings new insights to the intra-macrophage transcriptome of Salmonella Typhimurium.” PLoS pathogens, 11, 11, Pp. e1005262.
Shabarinath Srikumar, Carsten Kröger, Magali Hébrard, Aoife Colgan, Siân V Owen, Sathesh K Sivasankaran, Andrew DS Cameron, Karsten Hokamp, and Jay CD Hinton. 2015. “RNA-seq brings new insights to the intra-macrophage transcriptome of Salmonella Typhimurium.” PLoS pathogens, 11, 11, Pp. e1005262. Publisher's VersionAbstract

Salmonella enterica serovar Typhimurium is arguably the world’s best-understood bacterial pathogen. However, crucial details about the genetic programs used by the bacterium to survive and replicate in macrophages have remained obscure because of the challenge of studying gene expression of intracellular pathogens during infection. Here, we report the use of deep sequencing (RNA-seq) to reveal the transcriptional architecture and gene activity of Salmonella during infection of murine macrophages, providing new insights into the strategies used by the pathogen to survive in a bactericidal immune cell. We characterized 3583 transcriptional start sites that are active within macrophages, and highlight 11 of these as candidates for the delivery of heterologous antigens from Salmonella vaccine strains. A majority (88%) of the 280 S. Typhimurium sRNAs were expressed inside macrophages, and SPI13 and SPI2 were the most highly expressed pathogenicity islands. We identified 31 S. Typhimurium genes that were strongly up-regulated inside macrophages but expressed at very low levels during in vitro growth. The SalComMac online resource allows the visualisation of every transcript expressed during bacterial replication within mammalian cells. This primary transcriptome of intra-macrophage S.-Typhimurium describes the transcriptional start sites and the transcripts responsible for virulence traits, and catalogues the sRNAs that may play a role in the regulation of gene expression during infection.