Publications by authors named "Sion Bayliss"

28 Publications

  • Page 1 of 1

Genome evolution and the emergence of pathogenicity in avian Escherichia coli.

Nat Commun 2021 02 3;12(1):765. Epub 2021 Feb 3.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK.

Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.
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http://dx.doi.org/10.1038/s41467-021-20988-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7858641PMC
February 2021

Determining the prevalence, identity and possible origin of bacterial pathogens in soil.

Environ Microbiol 2020 12 8;22(12):5327-5340. Epub 2020 Oct 8.

European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter Medical School, Exeter, UK.

Soil biomes are vast, exceptionally diverse and crucial to the health of ecosystems and societies. Soils also contain an appreciable, but understudied, diversity of opportunistic human pathogens. With climate change and other forms of environmental degradation potentially increasing exposure risks to soilborne pathogens, it is necessary to gain a better understanding of their ecological drivers. Here we use the Galleria mellonella insect virulence model to selectively isolate pathogenic bacteria from soils in Cornwall (UK). We find a high prevalence of pathogenic soil bacteria with two genera, Providencia and Serratia, being especially common. Providencia alcalifaciens, P. rustigianii, Serratia liquefaciens and S. plymuthica strains were studied in more detail using phenotypic virulence and antibiotic resistance assays and whole-genome sequencing. Both genera displayed low levels of antibiotic resistance and antibiotic resistance gene carriage. However, Serratia isolates were found to carry the recently characterized metallo-β-lactamase blaSPR-1 that, although not conferring high levels of resistance in these strains, poses a potential risk of horizontal transfer to other pathogens where it could be fully functional. The Galleria assay can be a useful approach to uncover the distribution and identity of pathogenic bacteria in the environment, as well as uncover resistance genes with an environmental origin.
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http://dx.doi.org/10.1111/1462-2920.15243DOI Listing
December 2020

Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon.

PLoS Negl Trop Dis 2020 08 10;14(8):e0008533. Epub 2020 Aug 10.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.
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http://dx.doi.org/10.1371/journal.pntd.0008533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7440661PMC
August 2020

A Hopeful Sea-Monster: A Very Large Homologous Recombination Event Impacting the Core Genome of the Marine Pathogen .

Front Microbiol 2020 29;11:1430. Epub 2020 Jun 29.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.

is the causative agent of vibriosis in many species important to aquaculture. We generated whole genome sequence (WGS) data on a diverse collection of 64 strains, which we supplemented with 41 publicly available genomes to produce a combined dataset of 105 strains. These WGS data resolved six major lineages (L1-L6), and the additional use of multilocus sequence analysis (MLSA) clarified the association of L1 with serotype O1 and hosts (salmon/trout), and L2 with serotypes O2a/O2b/O2c and hosts (cod). Our analysis also revealed a large-scale homologous replacement of 526-kb of core genome in an L2 strain from a con-specific donor. Although the strains affected by this recombination event are exclusively associated with , we find no clear genetic evidence that it has played a causal role in host specialism. Whilst it is established that species freely recombine, to our knowledge this is the first report of a contiguous recombinational replacement of this magnitude in any genome. We also note a smaller accessory region of high single nucleotide polymorphism (SNP) density and gene content variation that contains lipopolysaccharide biosynthesis genes which may play a role in determining serotype.
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http://dx.doi.org/10.3389/fmicb.2020.01430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336808PMC
June 2020

Agricultural intensification and the evolution of host specialism in the enteric pathogen .

Proc Natl Acad Sci U S A 2020 05 4;117(20):11018-11028. Epub 2020 May 4.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7AY Bath, United Kingdom;

Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen () in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.
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http://dx.doi.org/10.1073/pnas.1917168117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245135PMC
May 2020

Gene Composition as a Potential Barrier to Large Recombinations in the Bacterial Pathogen Klebsiella pneumoniae.

Genome Biol Evol 2019 11;11(11):3240-3251

Sky Net UNIMI Platform - Pediatric Clinical Research Center Romeo ed Enrica Invernizzi, Dipartimento di Bioscienze, Università degli Studi di Milano, Italy.

Klebsiella pneumoniae (Kp) is one of the most important nosocomial pathogens worldwide, able to cause multiorgan infections and hospital outbreaks. One of the most widely disseminated lineage of Kp is the clonal group 258 (CG258), which includes the highly resistant "high-risk" sequence types ST258 and ST11. Genomic investigations revealed that very large recombination events have occurred during the emergence of Kp lineages. A striking example is provided by ST258, which has undergone a recombination event that replaced over 1 Mb of the genome with DNA from an unrelated Kp donor. Although several examples of this phenomenon have been documented in Kp and other bacterial species, the significance of these very large recombination events for the emergence of either hypervirulent or resistant clones remains unclear. Here, we present an analysis of 834 Kp genomes that provides data on the frequency of these very large recombination events (defined as those involving >100 kb), their distribution within the genome, and the dynamics of gene flow within the Kp population. We note that very large recombination events occur frequently, and in multiple lineages, and that the majority of recombinational exchanges are clustered within two overlapping genomic regions, which have been involved by recombination events with different frequencies. Our results also indicate that certain lineages are more likely to act as donors to CG258. Furthermore, comparison of gene content in CG258 and non-CG258 strains agrees with this pattern, suggesting that the success of a large recombination depends on gene composition in the exchanged genomic portion.
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http://dx.doi.org/10.1093/gbe/evz236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6865855PMC
November 2019

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.

Gigascience 2019 10;8(10)

The Milner Centre for Evolution, Department of Biology and Biochemistry, Claverton Down, University of Bath, Bath BA2 7AY, UK.

Background: Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets.

Results: Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation, and estimates sequence divergence for each gene family.

Conclusions: We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.
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http://dx.doi.org/10.1093/gigascience/giz119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6785682PMC
October 2019

First isolation of Flavobacterium psychrophilum associated with reports of moribund wild European eel (Anguilla anguilla) in Scotland.

J Fish Dis 2019 Nov 27;42(11):1509-1521. Epub 2019 Aug 27.

Marine Laboratory, Marine Scotland Science, Aberdeen, UK.

In late April 2015, the River Dee Trust informed Marine Scotland Science, Fish Health Inspectorate (FHI), that there had been observations of dead and moribund European eels on the River Dee. Later in May, the Spey Fishery Board also reported a number of moribund European eels in a rotary screw smolt trap on the River Spey. In total, 10 cases involving moribund eels were investigated in 2015 and one case in 2016. In addition, a health screen was conducted to investigate the potential presence of Flavobacterium psychrophilum in healthy eels and Atlantic salmon from the River Dee in 2015. Externally, the diseased eels demonstrated white patches in different locations of the body. In all cases, F. psychrophilum was detected by bacterial isolation and/or molecular methods. Three isolates were further characterized by whole-genome sequencing (WGS) as belonging to sequence type 15 (ST15). Histological examination of diseased European eels revealed lesions at the level of the integument. The pathogen screen for F. psychrophilum in wild healthy fish tested negative by PCR. Further investigation is required to understand the pathogenicity of this bacterium on the health of eels and the potential impact on the wild salmonid population.
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http://dx.doi.org/10.1111/jfd.13069DOI Listing
November 2019

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease.

Environ Microbiol 2019 12 27;21(12):4597-4613. Epub 2019 Aug 27.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA27AY, Bath, UK.

The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food-borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink populations. In particular, questions remain about how Campylobacter resistomes interact between species and hosts, and the potential role of sewage as a conduit for the spread of AMR. Here, we investigate the genomic variation associated with AMR in 168 C. jejuni and 92 C. coli strains isolated from humans, livestock and urban effluents in Spain. AMR was tested in vitro and isolate genomes were sequenced and screened for putative AMR genes and alleles. Genes associated with resistance to multiple drug classes were observed in both species and were commonly present in multidrug-resistant genomic islands (GIs), often located on plasmids or mobile elements. In many cases, these loci had alleles that were shared among C. jejuni and C. coli consistent with horizontal transfer. Our results suggest that specific antibiotic resistance genes have spread among Campylobacter isolated from humans, animals and the environment.
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http://dx.doi.org/10.1111/1462-2920.14760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6916351PMC
December 2019

Patterns of cross-resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials.

Evol Appl 2019 Jun 28;12(5):878-887. Epub 2019 Jan 28.

European Centre for Environment and Human Health University of Exeter Medical School Cornwall UK.

Bacteria interact with a multitude of other organisms, many of which produce antimicrobials. Selection for resistance to these antimicrobials has the potential to result in resistance to clinical antibiotics when active compounds target the same bacterial pathways. The possibility of such cross-resistance between natural antimicrobials and antibiotics has to our knowledge received very little attention. The antimicrobial activity of extracts from seaweeds, known to be prolific producers of antimicrobials, is here tested against isolates with varied clinical antibiotic resistance profiles. An overall effect consistent with cross-resistance is demonstrated, with multidrug-resistant strains being on average more resistant to seaweed extracts. This pattern could potentially indicate that evolution of resistance to antimicrobials in the natural environment could lead to resistance against clinical antibiotics. However, patterns of antimicrobial activity of individual seaweed extracts vary considerably and include collateral sensitivity, where increased resistance to a particular antibiotic is associated with decreased resistance to a particular seaweed extract. Our correlation-based methods allow the identification of antimicrobial extracts bearing most promise for downstream active compound identification and pharmacological testing.
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http://dx.doi.org/10.1111/eva.12762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503891PMC
June 2019

Biogeography of the fish pathogen Aeromonas salmonicida inferred by vapA genotyping.

FEMS Microbiol Lett 2019 04;366(7)

Fish Health Research Group, Norwegian Veterinary Institute, Oslo, Norway.

A recently described typing system based on sequence variation in the virulence array protein (vapA) gene, encoding the A-layer surface protein array, allows unambiguous subtyping of Aeromonas salmonicida. In the present study, we compile A-layer typing results from a total of 675 A. salmonicida isolates, recovered over a 59-year period from 50 different fish species in 26 countries. Nine novel A-layer types (15-23) are identified, several of which display a strong predilection towards certain fish hosts, including e.g. Cyprinidae and Pleuronectidae species. Moreover, we find indications that anthropogenic transport of live fish may have aided the near global dissemination of two cyprinid-associated A-layer types. Comparison of whole genome phylogeny and A-layer typing for a subset of strains further resulted in compatible tree topologies, indicating the utility of vapA as a phylogenetic as well as an epizootiological marker in A. salmonicida. A Microreact project (microreact.org/project/r1pcOAx9m) has been created, allowing public access to the vapA analyses and relevant metadata. In sum, the results generated provide valuable insights into the global population structure of A. salmonicida, particularly in relation to its piscine host spectrum and the geographic distribution of these hosts.
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http://dx.doi.org/10.1093/femsle/fnz074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6502549PMC
April 2019

WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome.

J Antimicrob Chemother 2019 07;74(7):1776-1785

Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark.

Objectives: From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium (VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized.

Methods: WGS of 1058 E. faecium isolates was carried out on the Illumina platform to perform SNP analysis and to identify the pan-genome. One isolate was also sequenced on the PacBio platform to close the genome. Epidemiological data were collected from laboratory information systems.

Results: Phylogeny of 892 VREfm and 166 VSEfm revealed a polyclonal structure, with a single clonal group (ST80) accounting for 40% of the VREfm isolates. VREfm and VSEfm co-occurred within many clonal groups; however, no VSEfm were related to the dominant VREfm group. A similar vanA plasmid was identified in ≥99% of isolates belonging to the dominant group and 69% of the remaining VREfm. Ten plasmids were identified in the completed genome, and ∼29% of this genome consisted of dispensable accessory genes. The size of the pan-genome among isolates in the dominant group was 5905 genes.

Conclusions: Most probably, VREfm emerged owing to importation of a successful VREfm clone which rapidly transmitted to the majority of hospitals in the region whilst simultaneously disseminating a vanA plasmid to pre-existing VSEfm. Acquisition of a heterogeneous accessory genome may account for the success of this clone by facilitating adaptation to new environmental challenges.
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http://dx.doi.org/10.1093/jac/dkz118DOI Listing
July 2019

Real time monitoring of Aeromonas salmonicida evolution in response to successive antibiotic therapies in a commercial fish farm.

Environ Microbiol 2019 03 22;21(3):1113-1123. Epub 2019 Feb 22.

State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Our ability to predict evolutionary trajectories of pathogens in response to antibiotic pressure is one of the promising leverage to fight against the present antibiotic resistance worldwide crisis. Yet, few studies tackled this question in situ at the outbreak level, due to the difficulty to link a given pathogenic clone evolution with its precise antibiotic exposure over time. In this study, we monitored the real-time evolution of an Aeromonas salmonicida clone in response to successive antibiotic and vaccine therapies in a commercial fish farm. The clone was responsible for a four-year outbreak of furunculosis within a Recirculating Aquaculture System Salmo salar farm in China, and we reconstructed the precise tempo of mobile genetic elements (MGEs) acquisition events during this period. The resistance profile provided by the acquired MGEs closely mirrored the antibiotics used to treat the outbreak, and we evidenced that two subclonal groups developed similar resistances although unrelated MGE acquisitions. Finally, we also demonstrated the efficiency of vaccination in outbreak management and its positive effect on antibiotic resistance prevalence. Our study provides unprecedented knowledge critical to understand evolutionary trajectories of resistant pathogens outside the laboratory.
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http://dx.doi.org/10.1111/1462-2920.14531DOI Listing
March 2019

Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry.

Microb Genom 2018 09 24;4(9). Epub 2018 Jul 24.

1​Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.

Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD), which is a commercially important disease of farmed salmonids. Typing by conventional methods provides limited information on the evolution and spread of this pathogen, as there is a low level of standing variation within the R. salmoninarum population. Here, we apply whole-genome sequencing to 42 R. salmoninarum isolates from Chile, primarily from salmon farms, in order to understand the epidemiology of BKD in this country. The patterns of genomic variation are consistent with multiple introductions to Chile, followed by rapid dissemination over a 30 year period. The estimated dates of introduction broadly coincide with major events in the development of the Chilean aquaculture industry. We find evidence for significant barriers to transmission of BKD in the Chilean salmon production chain that may also be explained by previously undescribed signals of host tropism in R. salmoninarum. Understanding the genomic epidemiology of BKD can inform disease intervention and improve sustainability of the economically important salmon industry. This article contains data hosted by Microreact.
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http://dx.doi.org/10.1099/mgen.0.000201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6202448PMC
September 2018

Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA.

Genome Biol 2018 07 18;19(1):94. Epub 2018 Jul 18.

School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.

Background: Fitness costs imposed on bacteria by antibiotic resistance mechanisms are believed to hamper their dissemination. The scale of these costs is highly variable. Some, including resistance of Staphylococcus aureus to the clinically important antibiotic mupirocin, have been reported as being cost-free, which suggests that there are few barriers preventing their global spread. However, this is not supported by surveillance data in healthy communities, which indicate that this resistance mechanism is relatively unsuccessful.

Results: Epistasis analysis on two collections of MRSA provides an explanation for this discord, where the mupirocin resistance-conferring mutation of the ileS gene appears to affect the levels of toxins produced by S. aureus when combined with specific polymorphisms at other loci. Proteomic analysis demonstrates that the activity of the secretory apparatus of the PSM family of toxins is affected by mupirocin resistance. As an energetically costly activity, this reduction in toxicity masks the fitness costs associated with this resistance mutation, a cost that becomes apparent when toxin production becomes necessary. This hidden fitness cost provides a likely explanation for why this mupirocin-resistance mechanism is not more prevalent, given the widespread use of this antibiotic.

Conclusions: With dwindling pools of antibiotics available for use, information on the fitness consequences of the acquisition of resistance may need to be considered when designing antibiotic prescribing policies. However, this study suggests there are levels of depth that we do not understand, and that holistic, surveillance and functional genomics approaches are required to gain this crucial information.
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http://dx.doi.org/10.1186/s13059-018-1469-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6052701PMC
July 2018

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria.

Gigascience 2018 04;7(4):1-11

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY.

Background: The concept of the "pan-genome," which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences.

Findings: To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent ("switched") intergenic regions (IGRs) upstream of genes. We demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli.

Conclusions: For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).
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http://dx.doi.org/10.1093/gigascience/giy015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890482PMC
April 2018

Clonal differences in Staphylococcus aureus bacteraemia-associated mortality.

Nat Microbiol 2017 Oct 7;2(10):1381-1388. Epub 2017 Aug 7.

Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK.

The bacterium Staphylococcus aureus is a major human pathogen for which the emergence of antibiotic resistance is a global public health concern. Infection severity, and in particular bacteraemia-associated mortality, has been attributed to several host-related factors, such as age and the presence of comorbidities. The role of the bacterium in infection severity is less well understood, as it is complicated by the multifaceted nature of bacterial virulence, which has so far prevented a robust mapping between genotype, phenotype and infection outcome. To investigate the role of bacterial factors in contributing to bacteraemia-associated mortality, we phenotyped a collection of sequenced clinical S. aureus isolates from patients with bloodstream infections, representing two globally important clonal types, CC22 and CC30. By adopting a genome-wide association study approach we identified and functionally verified several genetic loci that affect the expression of cytolytic toxicity and biofilm formation. By analysing the pooled data comprising bacterial genotype and phenotype together with clinical metadata within a machine-learning framework, we found significant clonal differences in the determinants most predictive of poor infection outcome. Whereas elevated cytolytic toxicity in combination with low levels of biofilm formation was predictive of an increased risk of mortality in infections by strains of a CC22 background, these virulence-specific factors had little influence on mortality rates associated with CC30 infections. Our results therefore suggest that different clones may have adopted different strategies to overcome host responses and cause severe pathology. Our study further demonstrates the use of a combined genomics and data analytic approach to enhance our understanding of bacterial pathogenesis at the individual level, which will be an important step towards personalized medicine and infectious disease management.
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http://dx.doi.org/10.1038/s41564-017-0001-xDOI Listing
October 2017

Draft Genome Sequences of , , , subsp. , subsp. , and 29 New Isolates Belonging to the Genus .

Genome Announc 2017 Jul 6;5(27). Epub 2017 Jul 6.

Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain

The draft genome sequences of 5 type strains of species of the halophilic genus and 29 new isolates from different hypersaline habitats belonging to the genus have been determined. The genomes have 3,123,148 to 3,641,359 bp, a G+C content of 49.2 to 50.9%, and 2,898 to 3,404 open reading frames (ORFs).
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http://dx.doi.org/10.1128/genomeA.00244-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502842PMC
July 2017

Bayesian identification of bacterial strains from sequencing data.

Microb Genom 2016 08 25;2(8):e000075. Epub 2016 Aug 25.

1​Helsinki Institute for Information Technology, Department of Computer Science, University of Helsinki, Helsinki, Finland.

Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an environmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of the target organisms from short sequence reads obtained from a sample. This task is particularly challenging when the set of interest includes very closely related organisms, such as different strains of pathogenic bacteria, which can vary considerably in terms of virulence, resistance and spread. Using advanced Bayesian statistical modelling and computation techniques we introduce a novel pipeline for bacterial identification that is shown to outperform the currently leading pipeline for this purpose. Our approach enables fast and accurate sequence-based identification of bacterial strains while using only modest computational resources. Hence it provides a useful tool for a wide spectrum of applications, including rapid clinical diagnostics to distinguish among closely related strains causing nosocomial infections. The software implementation is available at https://github.com/PROBIC/BIB.
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http://dx.doi.org/10.1099/mgen.0.000075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320594PMC
August 2016

The use of Oxford Nanopore native barcoding for complete genome assembly.

Gigascience 2017 03;6(3):1-6

Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short read data. The strain we used, MHO_001, represents the important community-acquired methicillin-resistant Staphylococcus aureus lineage USA300.

Findings: Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long read data represented only ∼5% to 10% of an average MinION(TM) run (∼7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss, and gain of mobile genetic elements.

Conclusion: Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short read data to fully complete a bacterial genome. The ability to complete multiple genomes, for which short read data is already available, from a single MinION(TM) run is set to impact our understanding of accessory genome content, plasmid diversity, and genome rearrangements.
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http://dx.doi.org/10.1093/gigascience/gix001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467021PMC
March 2017

Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species.

Genetics 2017 05 9;206(1):363-376. Epub 2017 Mar 9.

Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, BA2 7AY, United Kingdom

Nontranslated intergenic regions (IGRs) compose 10-15% of bacterial genomes, and contain many regulatory elements with key functions. Despite this, there are few systematic studies on the strength and direction of selection operating on IGRs in bacteria using whole-genome sequence data sets. Here we exploit representative whole-genome data sets from six diverse bacterial species: , , , , , and We compare patterns of selection operating on IGRs using two independent methods: the proportion of singleton mutations and the / ratio, where is the number of intergenic SNPs per intergenic site. We find that the strength of purifying selection operating over all intergenic sites is consistently intermediate between that operating on synonymous and nonsynonymous sites. Ribosome binding sites and noncoding RNAs tend to be under stronger selective constraint than promoters and Rho-independent terminators. Strikingly, a clear signal of purifying selection remains even when all these major categories of regulatory elements are excluded, and this constraint is highest immediately upstream of genes. While a paucity of variation means that the data for are more equivocal than for the other species, we find strong evidence for positive selection within promoters of this species. This points to a key adaptive role for regulatory changes in this important pathogen. Our study underlines the feasibility and utility of gauging the selective forces operating on bacterial IGRs from whole-genome sequence data, and suggests that our current understanding of the functionality of these sequences is far from complete.
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http://dx.doi.org/10.1534/genetics.116.195784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5419481PMC
May 2017

The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens.

Front Microbiol 2017 3;8:121. Epub 2017 Feb 3.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK.

Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools.
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http://dx.doi.org/10.3389/fmicb.2017.00121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5290457PMC
February 2017

Genomic analysis of 495 vancomycin-resistant Enterococcus faecium reveals broad dissemination of a vanA plasmid in more than 19 clones from Copenhagen, Denmark.

J Antimicrob Chemother 2017 01 7;72(1):40-47. Epub 2016 Sep 7.

Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.

Objectives: From 2012 to 2014, there has been a huge increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) in Copenhagen, Denmark, with 602 patients infected or colonized with VREfm in 2014 compared with just 22 in 2012. The objective of this study was to describe the genetic epidemiology of VREfm to assess the contribution of clonal spread and horizontal transfer of the vanA transposon (Tn1546) and plasmid in the dissemination of VREfm in hospitals.

Methods: VREfm from Copenhagen, Denmark (2012-14) were whole-genome sequenced. The clonal structure was determined and the structure of Tn1546-like transposons was characterized. One VREfm isolate belonging to the largest clonal group was sequenced using long-read technology to close a 37 kb vanA plasmid.

Results: Phylogeny revealed a polyclonal structure where 495 VREfm isolates were divided into 13 main groups and 7 small groups. The majority of the isolates were located in three groups (n = 44, 100 and 218) and clonal spread of VREfm between wards and hospitals was identified. Five Tn1546-like transposon types were identified. A dominant truncated transposon (type 4, 92%) was spread across all but one VREfm group. The closed vanA plasmid was highly covered by reads from isolates containing the type 4 transposon.

Conclusions: This study suggests that it was the dissemination of the type 4 Tn1546-like transposon and plasmid via horizontal transfer to multiple populations of E. faecium, followed by clonal spread of new VREfm clones, that contributed to the increase in and diversity of VREfm in Danish hospitals.
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http://dx.doi.org/10.1093/jac/dkw360DOI Listing
January 2017

Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.

Appl Environ Microbiol 2016 10 16;82(19):5910-7. Epub 2016 Sep 16.

Medical Research Council Unit, Fajara, The Gambia University of Warwick, Coventry, United Kingdom London School of Hygiene and Tropical Medicine, London, United Kingdom.

Unlabelled: Staphylococcus aureus is an important pathogen of humans and animals. We genome sequenced 90 S. aureus isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of S. aureus from humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade of S. aureus that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of S. aureus from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens.

Importance: The population structures of Staphylococcus aureus in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of S. aureus between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5038045PMC
http://dx.doi.org/10.1128/AEM.01496-16DOI Listing
October 2016

Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species.

Mol Ecol 2015 Jan 31;24(1):208-21. Epub 2014 Dec 31.

Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, UK; SeaMammal Research Unit, University of St Andrews, Fife, KY16 8LB, UK.

Environmental pollution often accompanies the expansion and urbanization of human populations where sewage and wastewaters commonly have an impact on the marine environments. Here, we explored the potential for faecal bacterial pathogens, of anthropic origin, to spread to marine wildlife in coastal areas. The common zoonotic bacterium Campylobacter was isolated from grey seals (Halichoerus grypus), an important sentinel species for environmental pollution, and compared to isolates from wild birds, agricultural sources and clinical samples to characterize possible transmission routes. Campylobacter jejuni was present in half of all grey seal pups sampled (24/50 dead and 46/90 live pups) in the breeding colony on the Isle of May (Scotland), where it was frequently associated with histological evidence of disease. Returning yearling animals (19/19) were negative for C. jejuni suggesting clearance of infection while away from the localized colony infection source. The genomes of 90 isolates from seals were sequenced and characterized using a whole-genome multilocus sequence typing (MLST) approach and compared to 192 published genomes from multiple sources using population genetic approaches and a probabilistic genetic attribution model to infer the source of infection from MLST data. The strong genotype-host association has enabled the application of source attribution models in epidemiological studies of human campylobacteriosis, and here assignment analyses consistently grouped seal isolates with those from human clinical samples. These findings are consistent with either a common infection source or direct transmission of human campylobacter to grey seals, raising concerns about the spread of human pathogens to wildlife marine sentinel species in coastal areas.
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http://dx.doi.org/10.1111/mec.13001DOI Listing
January 2015

A novel bifunctional histone protein in Streptomyces: a candidate for structural coupling between DNA conformation and transcription during development and stress?

Nucleic Acids Res 2013 May 21;41(9):4813-24. Epub 2013 Mar 21.

Institute of Life Science, College of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, UK.

Antibiotic-producing Streptomyces are complex bacteria that remodel global transcription patterns and their nucleoids during development. Here, we describe a novel developmentally regulated nucleoid-associated protein, DdbA, of the genus that consists of an N-terminal DNA-binding histone H1-like domain and a C-terminal DksA-like domain that can potentially modulate RNA polymerase activity in conjunction with ppGpp. Owing to its N-terminal domain, the protein can efficiently bind and condense DNA in vitro. Loss of function of this DNA-binding protein results in changes in both DNA condensation during development and the ability to adjust DNA supercoiling in response to osmotic stress. Initial analysis of the DksA-like activity of DdbA indicates that overexpression of the protein suppresses a conditional deficiency in antibiotic production of relA mutants that are unable to synthesise ppGpp, just as DksA overexpression in Escherichia coli can suppress ppGpp(0) phenotypes. The null mutant is also sensitive to oxidative stress owing to impaired upregulation of transcription of sigR, encoding an alternative sigma factor. Consequently, we propose this bifunctional histone-like protein as a candidate that could structurally couple changes in DNA conformation and transcription during the streptomycete life-cycle and in response to stress.
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http://dx.doi.org/10.1093/nar/gkt180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643593PMC
May 2013

Evaluation of FTIR spectroscopy as a diagnostic tool for lung cancer using sputum.

BMC Cancer 2010 Nov 23;10:640. Epub 2010 Nov 23.

Swansea University, UK.

Background: Survival time for lung cancer is poor with over 90% of patients dying within five years of diagnosis primarily due to detection at late stage. The main objective of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) as a high throughput and cost effective method for identifying biochemical changes in sputum as biomarkers for detection of lung cancer.

Methods: Sputum was collected from 25 lung cancer patients in the Medlung observational study and 25 healthy controls. FTIR spectra were generated from sputum cell pellets using infrared wavenumbers within the 1800 to 950 cm-1 "fingerprint" region.

Results: A panel of 92 infrared wavenumbers had absorbances significantly different between cancer and normal sputum spectra and were associated with putative changes in protein, nucleic acid and glycogen levels in tumours. Five prominent significant wavenumbers at 964 cm-1, 1024 cm-1, 1411 cm-1, 1577 cm-1 and 1656 cm-1 separated cancer spectra from normal spectra into two distinct groups using multivariate analysis (group 1: 100% cancer cases; group 2: 92% normal cases). Principal components analysis revealed that these wavenumbers were also able to distinguish lung cancer patients who had previously been diagnosed with breast cancer. No patterns of spectra groupings were associated with inflammation or other diseases of the airways.

Conclusions: Our results suggest that FTIR applied to sputum might have high sensitivity and specificity in diagnosing lung cancer with potential as a non-invasive, cost-effective and high-throughput method for screening.

Trial Registration: ClinicalTrials.gov: NCT00899262.
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http://dx.doi.org/10.1186/1471-2407-10-640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000851PMC
November 2010