Biology subjects

Dallman, T. J.

Publications and source records attributed to Dallman, T. J..

12 recordsLinked to original sources

bioRxiv2026

Exploring differences across pangenome-graph representations using Escherichia coli O157:H7 as a model

Pangenome graphs are increasingly used to represent population-scale bacterial diversity, yet construction methods span fundamentally different representation paradigms whose outputs and sensitivities to assembly quality remain poorly quantified. We systematically reviewed microbial pangenome graph tools and benchmarked six representative methods spanning gene-cluster, compacted coloured de Bruijn graph (ccDBG), multiple sequence alignment, and hybrid approaches. Using a repeat-rich Escherichia coli O157:H7 dataset with complete genomes and matched short-read data, we constructed graphs from identical inputs and observed orders-of-magnitude differences in graph size and fragmentation, indicating that global topology is driven by representation strategy. Varying completeness composition revealed that assembly fragmentation is a first-order determinant of graph structure: gene-cluster graphs contracted as draft assemblies replaced complete genomes, whereas unitig graphs expanded, with distinct degree-prevalence fingerprints across tools. Computational cost mirrored these shifts and depended strongly on completeness composition, including a pronounced runtime penalty for one ccDBG implementation on all-draft inputs. Finally, analysis of Shiga toxin loci showed that pangenome-level reconciliation does not reliably correct assembly artefacts at challenging multi-copy genes and that performance varies by locus. Together, these findings show that pangenome graphs are representation-dependent models of bacterial diversity, and that assembly completeness is a primary determinant of their topology, scalability, and locus-level accuracy. Authors SummaryBacterial populations are often described using "pangenome graphs," which aim to capture all genetic variation across many genomes in a single structure. However, different tools build these graphs in fundamentally different ways, and little is known about how those differences affect the results. In this study, we systematically compared several widely used approaches using a clinically important strain of Escherichia coli that is rich in repeated and mobile DNA. We found that the size, connectivity, and overall structure of the resulting graphs varied dramatically depending on the method used. Importantly, we also show that incomplete genome assemblies (common in large sequencing studies) strongly alter graph structure, and that different tools respond to incomplete data in different ways. In some cases, this affects the detection of medically relevant genes, including Shiga toxin genes linked to severe disease. Our results demonstrate that pangenome graphs are not interchangeable representations of bacterial diversity. Instead, their structure depends on both the method and the quality of the input data. We argue that researchers should choose graph-building tools carefully and report structural properties explicitly to ensure reproducible and interpretable results.

bioinformatics↗

bioRxiv2020

Emergence and global spread of Listeria monocytogenes main clinical clonal complex

Retracing microbial emergence and spread is essential to understanding the evolution and dynamics of pathogens. The bacterial foodborne pathogen Listeria monocytogenes clonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with listeriosis, and is strongly associated with cattle and dairy products. Here we analysed 2,021 Lm-CC1 isolates collected from 40 countries, since the first Lm isolation to the present day, to define its evolutionary history and population dynamics. Our results suggest that Lm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming in the 20th century. Lm-CC1 then firmly established at a local level, with limited inter-country spread. This study provides an unprecedented insight into Lm-CC1 phylogeography and dynamics and can contribute to effective disease surveillance to reduce the burden of listeriosis.

genomics↗

bioRxiv2020

Prophage-dependent recombination drives genome structural variation and phenotypic heterogeneity in Escherichia coli O157:H7

The human zoonotic pathogen Escherichia coli O157 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157 serogroup and defines the phenotypic consequences of specific structural variants. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157 and by using both optical mapping and ONT long-read sequencing demonstrate that LCRs are generated in laboratory cultures started from a single colony and particular variants are selected during animal colonisation. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga toxin production, type 3 secretion and motility are affected by LCRs. In summary, E. coli O157 has acquired multiple prophage regions over time that act as genome engineers to continually produce structural variants of the genome. This structural variation is a form of epigenetic regulation that generates sub-population phenotypic heterogeneity with important implications for bacterial adaptation and survival. Author SummaryEscherichia coli has an open genome and has acquired genetic information over evolutionary time, often in the form of bacteriophages that integrate into the bacterial genome (prophages). E. coli O157 is a clonal serogroup that is found primarily in ruminants such as cattle but can cause life-threatening infections in humans. E. coli O157 isolates contain multiple prophages including those that encode Shiga-like toxins which are responsible for the more serious disease associated with human infections. We show in this study that many of these prophages exhibit large regions of sequence similarity that allow rearrangements to occur in the genome generating structural variants. These occur routinely during bacterial culture in the laboratory and the variants are detected during animal colonization. The variants generated can give the bacteria altered phenotypes, such as increased motility or toxin production which can be selected in specific environments and therefore represent a highly dynamic mechanism to generate variation in bacterial populations without a change in overall gene content.

microbiology↗

bioRxiv2020

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring of the emergence and spread of resistant clones at local and global scales.

microbiology↗

bioRxiv2020

Accessory genome dynamics and structural variation of Shigella from persistent infections

Shigellosis is a diarrhoeal disease caused mainly by Shigella flexneri and Shigella sonnei. Infection from Shigella is thought to be largely self-limiting, with short- to medium- term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM) associated shigellosis have been reported where Shigella of the same serotype were serially sampled from individuals between 1 to 1862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM associated S. flexneri and S. sonnei isolates serially sampled from individual patients at various days apart. We find that pairs likely associated with persistent carriage infection and with smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection and with greater SNP-distance. We also observed evidence of antimicrobial resistance (AMR) acquisition during persistent Shigella infection, specifically the gain of extended spectrum beta-lactamase genes in two pairs associated with persistent carriage. Finally, we explored chromosomal structural variations and rearrangements in seven (5 chronic and 2 reinfection associated) pairs of S. flexneri 3a isolates from a MSM-associated epidemic sublineage, which revealed variations at several common regions across pairs. These variations were mediated by insertion sequence (IS) elements which facilitated plasticity of genetic material with a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes in Shigella during persistent infection. ImportanceShigella spp are Gram-negative bacteria that are the etiological agent of shigellosis, the second most common cause of diarrhoeal illness globally, particularly among children under the age of 5 in low-income countries. In high-income countries, an alternative transmission pathway of sexually transmissible disease among men who have sex with men (MSM) is emerging as the dominant presentation of the disease. Within MSM we have captured prolonged infection and/or recurrent infection with shigellae of the same serotype, challenging the belief that Shigella infection is short-lived, and confers homologous serotypic immunity. Using this recently-emerged transmission scenario we comprehensively characterise the genomic changes that occur over the course of individual infection with Shigella and uncover a distinct functional profile of variable genome regions in these globally important pathogens.

microbiology↗

bioRxiv2020

Ecological niche adaptation of a bacterial pathogen associated with reduced zoonotic potential

The emergence of new bacterial pathogens is a continuing challenge for agriculture and food safety. Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of foodborne illness worldwide, with pigs a major zoonotic reservoir. Two variants, S. Typhimurium phage type U288 and monophasic S. Typhimurium (S. 4,[5],12:i:-) ST34 emerged and have accounted for the majority of isolates from pigs in the UK in the past two decades, but have distinct host range and risk to food safety. ST34 accounts for over 50% of all S. Typhimurium infections in people while U288 less than 2%. U288 and ST34 form distinct phylogenetic clusters within S. Typhimurium, defined by approximately 600 SNPs within their 5 Mbp genomes. Evolution of the U288 clade from an LT2-like ancestor was characterised by the acquisition of AMR genes, insertions and deletions in the virulence plasmid pU288-1, and the accumulation of polymorphisms, some of which resulted in truncation of coding sequences. U288 isolates exhibited lower growth rate and viability following desiccation compared to ST34 isolates, characteristics that could affect transmission through the food chain. U288 and ST34 isolates exhibited distinct outcomes of infection in the murine model of colitis, and colonised pigs in a manner that affected the disease symptoms and distribution in organs. U288 infection was more disseminated in the lymph nodes while ST34 were recovered in greater numbers in the intestinal contents. These data are consistent with the evolution of S. Typhimurium U288 adaptation to pigs that may determine their reduced zoonotic potential. ImportanceBacterial pathogens continually evolve to exploit new ecological niches as they emerge due to human activity including agricultural, medical or societal practice. The consequences of the emergence of new pathogens may affect outcome of infection and risk to human or animal health. Genome sequence can resolve the population structure, identify variants that are evolving as they enter a new niche, and pinpoint potential functional divergence. We report a variant S. Typhimurium that adapted to a unique niche distinct to that occupied by a second S. Typhimurium variant circulating in the same pig populations. Adaptation was accompanied by phenotypic and genotypic changes consistent with a more invasive lifestyle and a decreased zoonotic potential observed in the epidemiological record. Our findings suggest that pathogen genotypic variation may be useful in estimating zoonotic potential and threat to livestock welfare.

microbiology↗

bioRxiv2019

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and disseminated disease worldwide. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. A robust fully parsimonious phylogenetic tree constructed from recombination purged variation in the whole genome sequence of 131 diverse strains of S. Typhimurium revealed population structure composed of two high order clades ( and {beta}) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade {beta} predominantly contained subclades associated with wild avian species, with the notable exception of a subclade containing the DT204/49 complex. The contrasting epidemiology of and {beta} strains was reflected in a distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification associated with invasiveness of host adapted serotypes. Gene flux was predominantly driven by acquisition, loss or recombination of prophage. The acquisition of large genetic islands (SGI-1 and 4) was limited to two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) in clade . Together, our data are consistent with the view that a broad host range common ancestor of S. Typhimurium diversified with clade lineages remained largely associated with multiple domesticated animal species, while clade {beta} spawned multiple lineages that underwent diversifying selection associated with adaptation to various niches, predominantly in wild avian species.

genomics↗

bioRxiv2019

Persistent transmission of shigellosis in England is associated with a recently emerged multi-drug resistant strain of Shigella sonnei

BackgroundWhole genome sequencing has enhanced surveillance and facilitated detailed monitoring of transmission of Shigella species in England.\n\nMethodsWe undertook an epidemiological and phylogenetic analysis of isolates from all cases of shigellosis referred to Public Health England between 2015 to 2018 to explore recent strain characteristics and transmission dynamics of Shigella species.\n\nResultsOf the 4950 confirmed cases of shigellosis identified during this period, the highest proportion of isolates were S. sonnei (54.4%), followed by S. flexneri (39.2%), S. boydii (4.1%) and S. dysenteriae (2.2%). Most cases were adults (82.9%) and male (59.5%), and 34.9% cases reported recent travel outside the UK. Throughout the study period diagnoses of S. flexneri and S. sonnei were most common in men with no history of recent travel abroad. Species prevalence was not static with cases of S. flexneri in men decreasing from 2015-2016, and the number of cases of S. sonnei increasing from 2017. Phylogenetic analysis showed this recent increase in S. sonnei was attributed to a novel clade exhibiting resistance to ciprofloxacin and azithromycin, which had emerged from a Central Asia sub-lineage.\n\nConclusionsDespite changes in species prevalence, Shigella diagnoses in England are persistently the most common in adult males without reported travel history, consistent with sexual transmission amongst men who have sex with men. The trend in increasing ciprofloxacin resistance, in addition to plasmid-mediated azithromycin resistance, in S. sonnei is of significant public health concern with respect to transmission of multi-drug resistant gastrointestinal pathogens and the risk of treatment failures.\n\nSummaryShigella diagnoses in England are most prevalent amongst men who have sex with men. S. sonnei exhibiting resistance to both azithromycin and ciprofloxacin has replaced azithromycin-resistant S. flexneri as the most commonly isolated species in this setting.

genomics↗

bioRxiv2019

SGI-4 in monophasic Salmonella Typhimurium ST34 is a novel ICE that enhances resistance to copper

A multi drug resistant (MDR) Salmonella enterica 4,[5],12:i-of sequence type 34 (monophasic S. Typhimurium ST34) is a current pandemic clone associated with livestock and numerous outbreaks in the human population. A large genomic island, termed SGI-4, is present in the monophasic Typhimurium ST34 clade and absent from other S. Typhimurium strains. SGI-4 consists of 78 open reading frames including sil and pco genes previously implicated in resistance to copper and silver, and multiple genes predicted to be involved in mobilisation and transfer by conjugation. SGI-4 was excised from the chromosome, circularised and transferred to recipient strains of S. Typhimurium at a frequency influenced by stress and induced by mitomycin C and oxygen tension. The presence of SGI-4 was associated with increased resistance to copper, particularly but not exclusively under anaerobic conditions. The presence of silCBA genes, predicted to encode an RND family efflux pump that transports copper from the periplasm to the external milieu, was sufficient to impart the observed enhanced resistance to copper. The presence of silCBA genes resulted in the absence of copper-dependent induction of a multicopper oxidase system encoded by pco genes, also present on SGI-4, suggesting that the system effectively limits the copper availability in the periplasm. The presence of silCBA genes did not affect SodCI-dependent macrophage survival.

microbiology↗

bioRxiv2019

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers

Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of typhoid fever, a systemic human infection with a burden exceeding 20 million cases each year that occur disproportionately among children in low and middle income countries. Antimicrobial therapy is the mainstay for treatment, but resistance to multiple agents is common. Here we report genotypes and antimicrobial resistance (AMR) determinants detected from routine whole-genome sequencing (WGS) of 533 S. Typhi isolates referred to Public Health England between April 2014 and April 2017, 488 (92%) of which had accompanying patient travel information obtained via an enhanced surveillance questionnaire. The majority of cases involved S. Typhi 4.3.1 (H58) linked with travel to South Asia (58%). Travel to East and West Africa were associated with genotypes 4.3.1 and 3.3.1, respectively. Point mutations in the quinolone resistance determining region (QRDR), associated with reduced susceptibility to fluoroquinolones, were very common (85% of all cases) but the frequency varied significantly by region of travel: 95% in South Asia, 43% in East Africa, 27% in West Africa. QRDR triple mutants, resistant to ciprofloxacin, were restricted to 4.3.1 lineage II and associated with travel to India, accounting for 23% of cases reporting travel to the country. Overall 24% of isolates were MDR, however the frequency varied significantly by region and country of travel: 27% in West Africa, 52% in East Africa, 55% in Pakistan, 24% in Bangladesh, 3% in India. MDR determinants were plasmid-borne (IncHI1 PST2 plasmids) in S. Typhi 3.1.1 linked to West Africa, but in all other regions MDR was chromosomally integrated in 4.3.1 lineage I. We propose that routine WGS data from travel-associated cases in industrialised countries could serve as informal sentinel AMR genomic surveillance data for countries where WGS is not available or routinely performed.\n\nAuthor SummaryOur data demonstrate how routine WGS data produced by Public Health England can be further mined for informal passive surveillance of Salmonella Typhi circulating in different geographical regions where typhoid is endemic. We have shown the public health utility of a simplified approach to WGS reporting based on the GenoTyphi genotyping framework and nomenclature, which doesnt require the generation of a phylogenetic tree or other phylogenetic analysis. These approaches yielded results consistent with previously reported antimicrobial resistance (AMR) patterns of S. Typhi, including prevalence of multi-drug resistant (MDR) and fluoroquinolone resistance in different regions in association with different pathogen variants. These data provide a rationale and framework for the extraction and reporting of geographically stratified genotype and AMR data from public health labs in non-endemic countries. Prospective analysis and reporting of such data could potentially detect shifts in regional S. Typhi populations, such as replacement or spread of different subclades and the emergence and dissemination of MDR, fluoroquinolone resistant and/or extensively drug resistant S. Typhi, providing valuable data to inform typhoid control measures in low and middle income countries that are still building their genomics capacity.

microbiology↗

bioRxiv2018

Evaluation of whole genome sequencing for the identification and typing of Vibrio cholerae

Epidemiological and microbiological data on Vibrio cholerae isolated between 2004 and 2017 (n=836) and held in the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome derived species identification and serotype for a sub-set of isolates (n=152). Of the 836 isolates, 750 (89.7%) were from faecal specimens, 206 (24.6%) belonged to serogroup O1 and seven (0.8%) were serogroup O139, and 792 (94.7%) isolates from patients reporting recent travel abroad, most commonly to India (n=209) and Pakistan (n=104). Of the 152 isolates of V. cholerae speciated by kmer identification, 149 (98.1%) were concordant with the traditional biochemical approach. Traditional serotyping results were 100% concordant with the whole genome sequencing (WGS) analysis for identification of serogroups O1 and O139 and Classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type (ST) 69, and in V. cholerae O1 Classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from UK travellers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from UK travellers will contribute to global surveillance programs, and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travellers and mitigate the impact of imported infections and the associated risks to public health.

microbiology↗

bioRxiv2017

SnapperDB: A database solution for routine sequencing analysis of bacterial isolates

Real-time surveillance of infectious disease using whole genome sequencing data poses challenges in both result generation and communication. SnapperDB represents a set of tools to store bacterial variant data and facilitate reproducible and scalable analysis of bacterial populations. We also introduce the SNP address nomenclature to describe the relationship between isolates in a population to the single nucleotide resolution.\n\nSummaryWe announce the release of SnapperDB v1.0 a program for scalable routine SNP analysis and storage of microbial populations.\n\nAvailabilitySnapperDB is implemented as a python application under the open source BSD license. All code and user guides are available at https://github.com/phe-bioinformatics/snapperdb.\n\nContacttim.dallman@phe.gov.uk\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗