Biology subjects

Kolokotronis, S.-O.

Publications and source records attributed to Kolokotronis, S.-O..

8 recordsLinked to original sources

bioRxiv2023

The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity.

We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.

genomics↗

bioRxiv2022

Structural evolution of an immune evasion determinant shapes Lyme borreliae host tropism

The preferential adaptation of pathogens to specific hosts, known as host tropism, evolves through host-pathogen interactions. Transmitted by ticks and maintained primarily in rodents and birds, the Lyme disease-causing bacterium Borrelia burgdorferi (Bb) is an ideal model to investigate the mechanisms of host tropism. In order to survive in hosts and escape complement-mediated clearance, a first-line host immune defense, Bb produces the outer surface protein CspZ that binds to the complement inhibitor factor H (FH) to facilitate bacterial dissemination in vertebrates. Despite high sequence conservation, CspZ variants vary in human FH-binding ability. Together with the FH polymorphisms found amongst vertebrate hosts, these findings raise a hypothesis that minor sequence variation in a bacterial outer surface protein confers dramatic differences in host- specific, FH-binding-mediated infectivity. We tested this hypothesis by determining the crystal structure of the CspZ-human FH complex, identifying a minor change localized in the FH-binding interface, and uncovered that the bird and rodent FH-specific binding activity of different CspZ variants directly impacts infectivity. Swapping the divergent loop region in the FH-binding interface between rodent- and bird-associated CspZ variants alters the ability to promote rodent- and bird-specific early-onset dissemination. By employing phylogenetic tree thinking, we correlated these loops and respective host-specific, complement-dependent phenotypes with distinct CspZ lineages and elucidated evolutionary mechanisms driving CspZ emergence. Our multidisciplinary work provides mechanistic insights into how a single, short pathogen protein motif could greatly impact host tropism. AUTHOR SUMMARYLyme disease presents a suitable model for the investigation of host tropism - a pathogens ability to colonize and survive in different host species - since its causative agent, the spirochete Borrelia burgdorferi (Bb) is transmitted by ticks and maintained in rodent and bird reservoir hosts. In order to survive in vertebrates and escape from killing by complement, a first-line host immune defense, Bb produces the outer surface protein CspZ that binds the complement inhibitor factor H (FH) to promote infection. Protein sequence conservation seems to be linked to FH-binding activity divergence, raising the hypothesis that even minor variation can confer host-specific, FH- binding-mediated infectivity. Our work shows that that this minor variation is located in a loop in the CspZ protein localized in the CspZ-FH binding interface. Our functional experiments prove that this loop promotes bird- or rodent-specific FH-binding activity and infectivity. Swapping loops between rodent- and bird-associated CspZ variants alters their capability to confer host- specific dissemination. We further investigated the evolutionary mechanisms driving the emergence of the CspZ loop-mediated, host-dependent complement evasion. This multifaceted work demonstrates how a single, short protein motif can significantly impact host tropism.

microbiology↗

bioRxiv2022

Phylogenomic diversity elucidates mechanistic insights into Lyme borreliae host association

Host association- the selective adaptation of pathogens to specific host species - evolves through constant interactions between host and pathogens, leaving a lot yet to be discovered on immunological mechanisms and genomic determinants. The causative agents of Lyme disease (LD) are spirochete bacteria composed of multiple species of the Borrelia burgdorferi sensu lato complex, including B. burgdorferi (Bb), the main LD pathogen in North America - a useful model for the study of mechanisms underlying host-pathogen association. Host adaptation requires pathogens ability to evade host immune responses, such as complement, the first-line innate immune defense mechanism. We tested the hypothesis that different host adapted phenotypes among Bb strains are linked to polymorphic loci that confer complement evasion traits in a host-specific manner. We first examined the survivability of 20 Bb strains in sera in vitro and/or bloodstream and tissues in vivo from rodent and avian LD models. Three groups of complement-dependent host association phenotypes emerged. We analyzed complement-evasion genes, identified a priori among all strains and sequenced and compared genomes for individual strains representing each phenotype. The evolutionary history of ospC loci is correlated with host-specific complement-evasion phenotypes, while comparative genomics suggests several gene families and loci are potentially involved in host association. This multidisciplinary work provides novel insights into the functional evolution of host adapted phenotypes, building a foundation for further investigation of the immunological and genomic determinants of host association. IMPORTANCEHost association is the phenotype that is commonly found in many pathogens that preferential survive in particular hosts. The Lyme disease (LD) causing agent, B. burgdorferi (Bb), is an ideal model to study host association, as Bb is mainly maintained in nature through rodent and avian hosts. A widespread yet untested concept posits that host association in Bb strains is linked to Bb functional genetic variation conferring evasion to complement, an innate defense mechanism in vertebrate sera. Here, we tested this concept by grouping 20 Bb strains into three complement-dependent host association phenotypes based on their survivability in sera and/or bloodstream and distal tissues in rodent and avian LD models. Phylogenomic analysis of these strains further correlated several gene families and loci, including ospC, with host-specific complement-evasion phenotypes. Such multifaceted studies thus pave the road to further identify the determinants of host association, providing mechanistic insights into host-pathogen interaction.

microbiology↗

bioRxiv2022

Host adaptation drives genetic diversity in a vector-borne disease system

The range of hosts a pathogen can infect is a key trait influencing human disease risk and reservoir host infection dynamics. Borrelia burgdorferi sensu stricto (Bb), an emerging zoonotic pathogen, causes Lyme disease and is widely considered a host generalist, commonly infecting mammals and birds. Yet the extent of intraspecific variation in Bb host breadth, its role in determining host competence and potential implications to human infection remain unclear. We conducted a long-term study of Bb diversity, defined by the polymorphic ospC locus, across white-footed mice, passerine birds, and tick vectors leveraging long-read amplicon sequencing. Our results reveal strong variation in host breadth across Bb genotypes, exposing a spectrum of genotype-specific host-adapted phenotypes. We found support for multiple niche polymorphism maintaining Bb diversity in nature and little evidence of temporal shifts in genotype dominance, as would be expected under negative frequency-dependent selection. Passerine birds support the circulation of several human invasive strains in the local tick population and harbor greater Bb genotypic diversity compared to white-footed mice. Mouse-adapted Bb genotypes exhibited longer persistence in individual mice compared to non-adapted genotypes and infection communities infecting individual mice preferentially became dominated by mouse-adapted genotypes over time. We posit that intraspecific variation in Bb host breadth and specificity helps maintain overall species fitness in response to transmission by a generalist vector. Because pathogen genotypes vary in host breadth and result in diverse human disease manifestations, our findings indicate that a more nuanced definition of host competence incorporating local genotype frequency is warranted. SignificanceLyme disease is the most common vector-borne disease in the US with a causative agent (Borrelia burgdorferi) exhibiting high genetic diversity that partially correlates with human disease manifestations. Understanding the extent of host specificity in pathogens is critical for evaluating disease risk, but host specificity and mechanisms maintaining genetic diversity in Bb are unknown. We show that Bb genotypes exhibit variable host adaptation to white-footed mice and passerine birds, two common reservoir hosts, which appears to promote high intraspecific pathogen diversity. Conversely, we find limited evidence of negative frequency-dependent selection, an alternative mechanism for diversity maintenance. Our results reveal cryptic intraspecies host breadth variation and suggest that evaluating host competence depends on the frequency of host-adapted genotypes in local environments.

microbiology↗

bioRxiv2021

Host tropism determination by convergent evolution of immunological evasion in the Lyme disease system

Microparasites selectively adapt in some hosts, known as host tropism. Transmitted through ticks and carried mainly by mammals and birds, the Lyme disease (LD) bacterium is a well-suited model to study such tropism. LD bacteria species vary in host ranges through mechanisms eluding characterization. By feeding ticks infected with different LD bacteria species, utilizing feeding chambers and live mice and quail, we found species-level differences of bacterial transmission. These differences localize on the tick blood meal, and complement, a defense in vertebrate blood, and a bacterial polymorphic protein, CspA, which inactivates complement by binding to a host complement inhibitor, FH. CspA selectively confers bacterial transmission to vertebrates that produce FH capable of allele-specific recognition. Phylogenetic analyses revealed convergent evolution as the driver of such findings, which likely emerged during the last glacial maximum. Our results identify LD bacterial determinants of host tropism, defining an evolutionary mechanism that shapes host-microparasite associations.

microbiology↗

bioRxiv2020

A previously uncharacterized gene in SARS-CoV-2 illuminates the functional dynamics and evolutionary origins of the COVID-19 pandemic

Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics, but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.

evolutionary biology↗

bioRxiv2019

Genomic epidemiology of vancomycin 1 resistant Enterococcus faecium (VREfm) in Latin America: Revisiting the global VRE population structure

The prevalence of vancomycin-resistant Enterococcus faecium varies across geographical regions yet little is known about its population structure in Latin America. Here, we provide a complete genomic characterization of 55 representative Latin American VREfm recovered from 1998-2015 in 5 countries. We found that VREfm population in the region is structured into two main clinical clades without geographical clustering. To place our regional findings in context, we reconstructed the global population structure of VREfm by including 285 genomes from 36 countries from 1946-2017. Our results differ from previous studies showing an early branching of animal related isolates and a further split of clinical isolates into two sub-clades, all within clade A. The overall phylogenomic structure was highly dependent on recombination (54% of the genome) and the split between clades A and B is estimated to have occurred more than 3585 years BP. Furthermore, while the branching of animal isolates and clinical clades was predicted to have occur [~]894 years BP, our molecular clock calculations suggest that the split within the clinical clade occurred around [~]371 years BP. By including isolates from Latin America, we present novel insights into the population structure of VREfm and revisit the evolution of this pathogen.

microbiology↗

bioRxiv2018

Genotypic clustering does not imply recent tuberculosis transmission in a high prevalence setting: A genomic epidemiology study in Lima, Peru

BackgroundWhole genome sequencing (WGS) can elucidate Mycobacterium tuberculosis (Mtb) transmission patterns but more data is needed to guide its use in high-burden settings. In a household-based transmissibility study of 4,000 TB patients in Lima, Peru, we identified a large MIRU-VNTR Mtb cluster with a range of resistance phenotypes and studied host and bacterial factors contributing to its spread.\n\nMethodsWGS was performed on 61 of 148 isolates in the cluster. We compared transmission link inference using epidemiological or genomic data with and without the inclusion of controversial variants, and estimated the dates of emergence of the cluster and antimicrobial drug resistance acquisition events by generating a time-calibrated phylogeny. We validated our findings in genomic data from an outbreak of 325 TB cases in London. Using a larger set of 12,032 public Mtb genomes, we determined bacterial factors characterizing this cluster and under positive selection in other Mtb lineages.\n\nFindingsFour isolates were distantly related and the remaining 57 isolates diverged ca. 1968 (95% HPD: 1945-1985). Isoniazid resistance arose once, whereas rifampicin resistance emerged subsequently at least three times. Amplification of other drug resistance occurred as recently as within the last year of sampling. High quality PE/PPE variants and indels added information for transmission inference. We identified five cluster-defining SNPs, including esxV S23L to be potentially contributing to transmissibility.\n\nInterpretationClusters defined by MIRU-VNTR typing, could be circulating for decades in a high-burden setting. WGS allows for an improved understanding of transmission, as well as bacterial resistance and fitness factors.\n\nFundingThe study was funded by the National Institutes of Health (Peru Epi study U19-AI076217 and K01-ES026835 to MRF). The funding sources had no role in any aspect of the study, manuscript or decision to submit it for publication.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSUse of whole genome sequencing (WGS) to study tuberculosis (TB) transmission has proven to have higher resolution that traditional typing methods in low-burden settings. The implications of its use in high-burden settings are not well understood.\n\nAdded value of this studyUsing WGS, we found that TB clusters defined by traditional typing methods may be circulating for several decades. Genomic regions typically excluded from WGS analysis contain large amount of genetic variation that may affect interpretation of transmission events. We also identified five bacterial mutations that may contribute to transmission fitness.\n\nImplications of all the available evidenceAdded value of WGS for understanding TB transmission may be even higher in high-burden vs. low-burden settings. Methods integrating variants found in polymorphic sites and insertions and deletions are likely to have higher resolution. Several host and bacterial factors may be responsible for higher transmissibility that can be targets of intervention to interrupt TB transmission in communities.

microbiology↗