Biology subjects

Ribeca, P.

Publications and source records attributed to Ribeca, P..

16 recordsLinked to original sources

bioRxiv2026

Emergence of short-lived meningococci causing focal epidemics can be associated with gene transfer from carriage-associated Neisseria

In March 2026, an unusually large outbreak of invasive meningococcal disease (IMD) in Kent, UK, was linked to attendance at one nightclub over a single weekend. The outbreak organism was a Neisseria meningitidis variant belonging to the longstanding hyperinvasive genotype, cc41/44. Using genome analysis of six isolates from patients, alongside >48,000 meningococcal genomes, we investigated whether the outbreak variant had acquired traits potentially contributing to the highly invasive phenotype. The six isolates were capsular group B, sequence type (ST-)485, and essentially indistinguishable, consistent with the focal nature of the outbreak. Compared with their closest available relatives, we found changes mediated by phase variation, nucleotide variation, and horizontal gene transfer (HGT) involving adhesins, iron-acquisition systems (including Transferrin and Lactoferrin binding proteins, and FetA), and Type IV pili (Tfp), factors which affect bacteria-bacteria and bacteria-host interactions. These changes occurred in a ST-485 sub-lineage that expressed capsule at high levels and a PorA porin with a truncated surface-exposed epitope, both of which are predicted to reduce immune recognition. Donors for the HGT events were predominantly carriage-associated N. meningitidis and Neisseria cinerea. We show that meningococcal variants responsible for previous focal outbreaks have not been seen subsequently. We propose that focal outbreaks of IMD are caused by meningococcal variants that may have acquired traits from non- or less invasive organisms, but subsequently these variants disappear, as their highly invasive phenotype is inconsistent with sustained transmission. Ongoing disease surveillance alongside carriage studies are therefore essential to inform public health risk and manage epidemic IMD.

genomics↗

bioRxiv2025

Diagnostics of dated phylogenies in microbial population genetics

Microbial population genetic studies often involve the use of a dated phylogeny to show how the genomes are related over a relevant timescale. Many tools have recently been developed to date the nodes of a standard phylogeny, but all make underlying assumptions that may not be realistic for a given dataset, making the results potentially unreliable. Model comparison is sometimes used to remedy this issue, whereby inference under several models is compared to establish which result can be trusted. Although such comparison is clearly useful to assess the relative merits of several inference attempts, here instead we focus on the problem of evaluating how good an inference is in absolute terms, without comparison. We consider several approaches for diagnosing potential issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking and residual analysis. These methods are well-established diagnostics tools in other areas of statistics, but here we show how they can be applied to the specific inference of dated phylogenies. We illustrate their use on many simulated datasets, with inference being performed either from the correct model to quantify the specificity or from an incorrect model to quantify the sensitivity of the diagnostics methods. We also applied the methods to three real-life datasets to showcase the range of issues that they can detect. We advocate the use of these diagnostics tools for all microbial population genetic studies that involve the reconstruction of a dated phylogeny.

evolutionary biology↗

bioRxiv2025

Large-scale genomic characterisation of phage-plasmids in clinical Enterobacteriaceae isolates

The life cycle of certain bacteriophages involves their maintenance within the bacterial cell as extrachromosomal elements, complete with replication and partitioning systems. These "phage-plasmids" (P-Ps) are distributed widely among bacterial phyla but are not typically included during genomic surveillance studies, and previous reports do not consider the context of their host strain diversity. We recently identified a P1-like P-P carrying the blaCTX-M-15 resistance gene in Salmonella enterica serovar Typhi, prompting a subsequent investigation into the overall frequency of P-Ps among gastrointestinal bacteria under routine genomic surveillance within England. We expanded our study to include P-P groups known to be associated with Enterobacteriaceae (P1, D6, SSU5, N15) and scanned a collection of 66,856 genomes of diarrhoeagenic Escherichia spp., Shigella spp. and S. enterica. All four P-P groups were detected in our dataset, totalling 9% of E. coli and Shigella genomes and 2% of S. enterica genomes. A small subset harboured two distinct P-P groups. P1-like P-Ps, some of which carried a cytotoxic necrotising factor, were predominantly associated with Shiga toxin-producing E. coli strains of public health concern, including clonal complexes CC11 (O157:H7), CC29 (O26:H11) and CC165. In contrast, SSU5 group P-Ps were linked with multidrug-resistant lineages of both S. Typhi and Shigella sonnei. We found multiple antimicrobial resistance genes inserted into P-Ps via transposons, integrons and insertion sequences, and numerous defence/anti-defence systems. There was evidence of vertical transmission but also many links across species, time and geography, indicating that horizontal transfer is occurring regularly. Phage-plasmids are often described only as cryptic elements or not detected during genomic surveillance. We show that P-Ps are associated with clinically relevant lineages of human pathogens and can acquire accessory genes that may impact on disease severity and therefore should play a more prominent role in pathogen surveillance and epidemiology.

genomics↗

bioRxiv2025

Genome sequence and annotation of ovine herpesvirus-1

Ovine herpesvirus 1 (OvHV-1) was first identified over 50 years ago in sheep with ovine pulmonary adenocarcinoma (OPA). An aetiological role in OPA was later ruled out and OvHV-1 was found to be a common infection in sheep in several countries. Here, we report the sequence and annotation of the complete OvHV-1 genome. The virus has a similar genomic architecture to members of the Macavirus genus of the subfamily Gammaherpesvirinae and is most closely related to bovine gammaherpesvirus 6 (BoGHV6). The OvHV-1 genome comprises a 144,637 base pair unique region predicted to encode at least 74 proteins bounded by multiple copies of a 699 base pair GC-rich repetitive terminal repeat. Predicted genes include 61 ORFs conserved among all gammaherpesviruses, and 12 genes present only in macavirus genomes, including a homologue of ovine interleukin-10, previously reported only in ovine gammaherpesvirus-2, and an ornithine decarboxylase, previously described only in BoGHV6. A further gene appears unique to OvHV-1 among macaviruses, encoding a viral-FLIP (FLICE-like inhibitory protein), similar to those found in some other gammaherpesviruses. Notably, several macavirus genes previously predicted in BoGHV6 are defective in OvHV-1. The availability of the genome sequence of OvHV-1 will facilitate studies on its relationship to other macaviruses and its role, if any, in disease.

microbiology↗

bioRxiv2024

Presence of phage-plasmids in multiple serovars of Salmonella enterica

Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterised a circular P1-like phage-plasmid harbouring a blaCTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47,784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8-98.2kb in size, with an average length of 92.1kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterisation with long-read sequencing. Data SummaryAll of the FASTQ files examined in this study have been uploaded to the Sequence Read Archive under BioProject PRJNA248792. Accessions of individual isolates which were found to contain phage plasmids are listed in Supplementary Table S1. Impact StatementBacteriophage-like plasmids are increasingly being recognised as important mobile elements in many species of bacteria, particularly due to their involvement in the transmission of antimicrobial resistance (AMR); however, few studies of their overall prevalence in clinical datasets have been undertaken to date. In this study we have performed the first large-scale surveillance of human disease-associated Salmonella genomes for the presence of P1-like phage-plasmids, showing that they are more common than previously thought. Furthermore, we highlight how valuable information about the evolution and transmission of phage-plasmids in Salmonella and other Enterobacterales can be revealed by linking phage-plasmid prevalence and genetic diversity to epidemiologically relevant metadata such as S. enterica serovar, outbreak clusters, time, and geography. Our work shows the ability to use sequencing data and scalable bioinformatics workflows for the detection and characterisation of these extrachromosomal elements, highlights the importance of screening for novel mechanisms of AMR transmission, and provides a foundation for further surveillance studies of phage-plasmid prevalence.

microbiology↗

bioRxiv2023

GIN-TONIC: Non-hierarchical full-text indexing for graph-genomes

This paper presents a new data structure, GIN-TONIC, designed to index arbitrary string-labelled directed graphs representing, for instance, pangenomes or transcriptomes. GIN-TONIC provides several capabilities not offered by other graph-indexing methods based on the FM-index. It is non-hierarchical, handling a graph as a single monolithic object; it indexes at nucleotide resolution all possible walks in the graph without the need to explicitly store them; it supports exact substring queries in polynomial time and space for all possible walk roots in the graph, even if there are exponentially many walks corresponding to such roots. Specific ad-hoc optimisations, such as a precomputed cache, allow GIN-TONIC to achieve excellent performance for input graphs of various topologies and sizes. Robust scalability capabilities and a querying performance close to that of a linear FM-Index are demonstrated for two real-world applications, a human pangenome and transcriptome. Source code and associated benchmarks are available on GitHub. Availability and implementationGIN-TONIC and all related programs are available at https://github.com/uensalo/gin.

bioinformatics↗

bioRxiv2023

Inference of infectious disease transmission using multiple genomes per host

In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However, transmission analysis cannot rely solely on a phylogeny of the genomes but must account for the within-host evolution of the pathogen, which blurs the relationship between phylogenetic and transmission trees. When only a single genome is sampled for each host, the uncertainty about who infected whom can be quite high. Consequently, transmission analysis based on multiple genomes of the same pathogen per host has a clear potential for delivering more precise results, even though it is more laborious to achieve. Here we present a new methodology that can use any number of genomes sampled from a set of individuals to reconstruct their transmission network. We use simulated data to show that our method becomes more accurate as more genomes per host are provided, and that it can infer key infectious disease parameters such as the size of the transmission bottleneck, within-host growth rate, basic reproduction number and sampling fraction. We demonstrate the usefulness of our method in applications to real datasets from an outbreak of Pseudomonas aeruginosa amongst cystic fibrosis patients and a nosocomial outbreak of Klebsiella pneumoniae.

microbiology↗

bioRxiv2023

Different Coexisting Mpox Lineages Were Continuously Circulating in Humans Prior to 2022

The origin and hazardous potential of human mpox is obscured by a lack of genomic data between the 2018, when exportations from Nigeria were recorded, and 2022 when the global outbreak started. Here, 18 genomes from patients across southern Nigeria in 2019/20 reveal multiple lineages of Monkeypox virus have achieved sustained human-to-human transmission, co-existing in humans for several years and accumulating mutations consistent with APOBEC3 activity suggesting the virus in humans is now segregated from its natural reservoir. Remarkably, three genomes have disruptions in the A46R gene, which contributes to innate immune modulation. The data demonstrates that the A.2 lineage, multiply exported to North America since 2021 independently of the global outbreak, has persisted in Nigeria for more than two years prior to its latest exportation. One-Sentence SummaryMpox is now a human diseae evolving in humans with multiple variants taking separate paths towards adaptation, some analogous to those of Variola

microbiology↗

bioRxiv2022

A Binary RNA and DNA Self-Amplifying Platform for Next Generation Vaccines and Therapeutics

Conventional mRNA-based vaccines were instrumental in lowering the burden of the pandemic on healthcare systems and in reducing mortality. However, such first-generation vaccines have significant weaknesses. Here, we describe a high-performance binary recombinant vectoral platform offering the flexibility to be used as a self-amplifying mRNA or a self-amplifying DNA. Both formats drive long-lasting expression and actuate robust antibody responses against SAR-CoV-2 spike, and neither format require encapsulation with lipid nanoparticles (LNP) in the generation immune responses. The platform combines the power of conventional mRNA with the low-dosage of self-amplifying vectors together with the simplicity, rapid creation, ease of storage, and convenience of distribution of plasmid DNA vectors. This platform promises to pave the way for more effective, less expensive, and truly democratized vaccines and therapeutics. One-Sentence SummaryGemini: a versatile platform that improves on existing vaccine formats in terms of effectiveness, manufacturing, distribution, and cost.

immunology↗

bioRxiv2022

Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease

The ability to distinguish imported cases from locally acquired cases has important consequences for the selection of public health control strategies. Genomic data can be useful for this, for example using a phylogeographic analysis in which genomic data from multiple locations is compared to determine likely migration events between locations. However, these methods typically require good samples of genomes from all locations, which is rarely available. Here we propose an alternative approach that only uses genomic data from a location of interest. By comparing each new case with previous cases from the same location we are able to detect imported cases, as they have a different genealogical distribution than that of locally acquired cases. We show that, when variations in the size of the local population are accounted for, our method has good sensitivity and excellent specificity for the detection of imports. We applied our method to data simulated under the structured coalescent model and demonstrate relatively good performance even when the local population has the same size as the external population. Finally, we applied our method to several recent genomic datasets from both bacterial and viral pathogens, and show that it can, in a matter of seconds or minutes, deliver important insights on the number of imports to a geographically limited sample of a pathogen population.

evolutionary biology↗

bioRxiv2022

KPop: An assembly-free and scalable method for the comparative analysis of microbial genomes

The recent explosion in the amount of available sequencing data challenges existing analysis techniques. Here we introduce KPop, a novel versatile method based on full k-mer spectra and dataset-specific transformations, through which thousands of assembled or unassembled microbial genomes can be quickly compared. Unlike minimizer-based methods that produce distances and have lower resolution, KPop is able to accurately map sequences onto a low-dimensional space. Extensive validation on simulated and real-life viral and bacterial datasets shows that KPop can correctly separate sequences at both species and sub-species levels even when the overall genomic diversity is low. KPop also rapidly identifies related sequences and systematically outperforms minimizer-based methods. KPops code is open-source and available on GitHub at https://github.com/PaoloRibeca/KPop.

bioinformatics↗

bioRxiv2021

Mutagenesis Mapping of RNA Structures within the Foot-and-Mouth Disease Virus Genome Reveals Functional Elements Localised in the Polymerase (3Dpol) Encoding Region.

AbstractRNA structure plays a crucial role in the replication of positive sense RNA viruses and can form functional elements within the untranslated regions (UTRs) and the protein coding sequences (or open reading frames (ORFs)). While RNA structures in the UTRs of several picornaviruses have been functionally characterised, the roles of putative RNA structures predicted for the ORF remain largely undefined. Here we have undertaken a bioinformatic analysis of the foot-and-mouth disease virus (FMDV) genome and predicted the existence of 53 evolutionarily conserved RNA structures within the ORF. Forty-five (45) of these structures were located in the regions encoding the non-structural proteins (nsps). To investigate if the structures in the regions encoding the nsps are required for FMDV replication we used a mutagenesis method, CDLR mapping, where sequential coding segments were shuffled to minimise RNA secondary structures while preserving protein coding, native dinucleotide frequencies and codon usage. To examine the impact of these changes on replicative fitness, mutated sequences were inserted into an FMDV sub-genomic replicon. We found that three of the RNA structures, all at the 3 termini of the FMDV ORF, were critical for replicon replication. Contrastingly, disruption of the other 42 conserved RNA structures that lie within the regions encoding the nsps had no effect on replicon replication, suggesting that these structures are not required for initiating translation or replication of viral RNA. Conserved RNA structures that are not essential for virus replication could provide ideal targets for the rational attenuation of a wide range of FMDV strains. ImportanceSome RNA structures formed by the genomes of RNA viruses are critical for viral replication. Our study shows that of 45 conserved RNA structures located within the regions of the foot-and-mouth disease virus (FMDV) genome that encode the non-structural proteins, only three are essential for replication of an FMDV sub-genomic replicon. Replicons replication is dependent on RNA translation and synthesis; thus, our results suggest that the three RNA structures are critical for either initiation of viral RNA translation and/or viral RNA synthesis. Although further studies are required to identify if the remaining 42 RNA structures have other roles in virus replication, they may provide targets for the rational large-scale attenuation of a wide range of FMDV strains. FMDV causes a highly contagious disease posing a constant threat to global livestock industries. Such weakened FMDV strains could be investigated as live-attenuated vaccines or could enhance biosecurity of conventional inactivated vaccine production.

evolutionary biology↗

bioRxiv2019

Pervasive differential splicing in Marek’s Disease Virus can discriminate CVI-988 vaccine strain from RB-1B virulent strain in chicken embryonic fibroblasts

Mareks disease is a major scourge challenging poultry health worldwide. It is caused by the highly contagious Mareks disease virus (MDV), an alphaherpesvirus. Here we show that, similar to other members of its Herpesviridae family, MDV also presents a complex landscape of splicing events, most of which are uncharacterised and/or not annotated. Quite strikingly, and although the biological relevance of this fact is unknown, we found that a number of viral splicing isoforms are strain-specific despite the close sequence similarity of the strains considered, virulent RB-1B and vaccine CVI-988. We validated our findings by devising an assay that discriminates infections caused by the two strains in chicken embryonic fibroblasts based on the presence of some RNA species. To our knowledge, this study is the first ever to accomplish such a result, emphasizing how important a comprehensive knowledge of the viral transcriptome can be to understand viral pathogenesis.\n\nImportanceMareks disease virus (MDV) causes an agro-economically important disease of chickens worldwide. Although commercial poultry are vaccinated against MDV, it is not possible to achieve sterilising immunity, and available vaccines can only protect chickens against the symptoms of the disease. Vaccinated chicken often become superinfected with virulent strains, shedding virus into the environment. The most effective MDV vaccine strain, CVI-988, shares >99% sequence identity with the prototype virulent virus strain RB-1B. Interestingly, our work shows that despite their almost identical sequences MDV strains CVI-988 and RB-1B have significantly different splicing profiles, and hence transcriptomes. We independently validated this discovery by detecting with real-time PCR some splicing isoforms expressed by MDV strain CVI-988 and absent in the transcriptome of the RB-1B strain. These results indicate that the coding potential of MDV might be much larger than previously thought, and suggest a likely underestimation of the role of the viral transcriptome in the pathogenesis and prevention of MDV.

genomics↗

bioRxiv2019

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Combining both short and long-read sequencing, we have estimated the almond Prunus dulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.

genomics↗

bioRxiv2018

A role for differential gene regulation in the rapid diversification of melanic plumage coloration in the dark-eyed junco (Junco hyemalis)

Color plays a prominent role in reproductive isolation, therefore understanding the proximal basis of pigmentation can provide insight into speciation. Subspecies of the dark-eyed junco (Junco hyemalis) have evolved marked differences in plumage coloration since the Last Glacial Maximum, yet whether color differences are caused by mutations in coding regions of expressed genes or are instead the result of regulatory differences remains unknown. To address this question, we studied the pigment composition and the genetic basis of coloration in two divergent subspecies, the slate-colored and Oregon juncos. We used HPLC and light microscopy to investigate pigment composition and deposition in feathers from four body areas. We then used RNAseq to compare the relative roles of differential gene expression in developing feathers and sequence divergence in transcribed loci under common garden conditions. Junco feathers differed in eumelanin and pheomelanin content and distribution. Within subspecies, in lighter feathers melanin synthesis genes were downregulated (including PMEL, TYR, TYRP1, OCA2, MLANA), ASIP was upregulated. Feathers from different body regions also showed differential expression of HOX and Wnt genes. Feathers from the same body regions that differed in color between the two subspecies showed differential expression of ASIP and three other genes (MFSD12, KCNJ13, HAND2) associated with pigmentation in other taxa. Sequence variation in the expressed genes was not related to color differences. Our findings support the hypothesis that differential regulation of a few genes can account for marked differences in coloration, a mechanism that may underlie the rapid diversification of juncos.

evolutionary biology↗

bioRxiv2018

Within-host recombination in structural proteins of the Foot-and-Mouth Disease Virus

Although recombination is known to occur in FMDV, it is considered only a minor determinant of virus sequence diversity. This is because recombination appears to be highly suppressed at phylogenetic scales; inter-serotypic recombination events are rare; and in those a mosaic structure is present whereby recombination only occurs almost exclusively in non-structural proteins. Here we show that co-inoculation of closely related strains in buffaloes results over time in extensive within-host recombination in the genomic region coding for structural proteins. This enables us to directly estimate recombination rates for the first time. Quite surprisingly, the effective recombination rate in VP1 during the acute infection phase turns out to be about 0.1 per base per year, i.e. comparable to the mutation/substitution rate. Thanks to the features of our experimental setup, we are also able to build a high-resolution map of effective within-host recombination in the capsid-coding region. We find that the linkage disequilibrium pattern inside VP1 points to a mosaic structure with two main genetic blocks. Positive epistatic interactions between co-evolved variants appear to be present both within and between blocks. These interactions are due to intra-host selection both at the RNA and protein level. Overall our findings show that during FMDV co-infections by closely related strains, capsid-coding genes recombine within the host at a much higher rate than expected, despite the presence of strong constraints dictated by the capsid structure. Although those intra-host results are not immediately transportable to a phylogenetic setting, they force us to reconsider the relevance of recombination and epistasis, suggesting that they must play a major and so far underappreciated role in the molecular evolution of the virus at all time scales.\n\nAuthor summaryRecombination in the capsid-coding region of the Foot-and-Mouth Disease virus genome is highly suppressed at phylogenetic scales. However, the role of recombination in the intra-host dynamics of the virus is not known. In our experiment, a co-infection of African buffaloes with closely related FMDV strains results in a population structure of the intra-host viral swarm, allowing us to detect recombination events. For structural protein-coding sequences, the swarm dynamics is driven by extensive within-host recombination. During the acute infection phase, we infer intra-host recombination rates of 0.1 per base per year, comparable to the typical mutation rate of the virus. The recombination map reveals two linkage blocks within the VP1 protein-coding sequence. Epistatic interactions between co-evolved mutations in VP1 are caused by intra-host selection at the RNA and protein level and are present both within and between blocks. Our findings support a major role for recombination and epistasis in the intra-host evolution of FMDV.

microbiology↗