A5062645497- Pneumonia and Respiratory Infections
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- Evolution and Genetic Dynamics
- Bacterial Infections and Vaccines
- Antibiotics Pharmacokinetics and Efficacy
- Probiotics and Fermented Foods
- Evolutionary Game Theory and Cooperation
- Plant Virus Research Studies
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Immune Response and Inflammation
- HIV Research and Treatment
- Respiratory viral infections research
- Enterobacteriaceae and Cronobacter Research
- Escherichia coli research studies
- Mathematical and Theoretical Epidemiology and Ecology Models
- Insect symbiosis and bacterial influences
- Cancer therapeutics and mechanisms
- Phagocytosis and Immune Regulation
- Microbial infections and disease research
- Cancer Genomics and Diagnostics
- Gene Regulatory Network Analysis
Jagiellonian University
2019-2025
University of Warsaw
2023
Institut Pasteur
2023
Imperial College London
2012-2022
Open Data Institute
2019-2020
University of Oxford
2019-2020
ETH Zurich
2010-2012
St Mary's Hospital
2012
Invasive pneumococcal disease remains an important health priority owing to increasing incidence caused by pneumococci expressing non-vaccine serotypes. We previously defined 621 Global Pneumococcal Sequence Clusters (GPSCs) analysing 20 027 isolates collected worldwide and from published genomic data. In this study, we aimed investigate the lineages behind predominant serotypes, mechanism of serotype replacement in disease, as well major contributing invasive post-vaccine era their...
Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit acquiring novel DNA, here we argue instead that intragenomic conflict provides coherent framework for understanding origins HDT. To test this hypothesis, developed mathematical model clonally descended bacterial population undergoing HDT through transmission mobile genetic...
Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference an evolutionary tree bacteria thus relies on accurate identification the population structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce novel algorithm called fastGEAR which identifies lineages diverse microbial alignments, between them from external...
The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause morbidity mortality worldwide. pneumococcus also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that major impact on evolution pathogen, including acquisition antibiotic resistance serotype-switching. Nevertheless, mechanism rates in an epidemiological context remain poorly understood. Here, we...
Diversity of the polysaccharide capsule in Streptococcus pneumoniae-main surface antigen and target currently used pneumococcal vaccines-constitutes a major obstacle eliminating disease. Such diversity is genetically encoded by almost 100 variants biosynthesis locus, cps. However, evolutionary dynamics remains not fully understood. Here, using genetic data from 4,519 bacterial isolates, we found cps to be an hotspot with elevated substitution recombination rates. These rates were consequence...
Abstract Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with outside world. While SPs can evolve rapidly, their diversity evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on bacterial order Enterobacteriales (including medically relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps kps, using 27,334...
Environmental factors are known to affect the strength and specificity of interactions between hosts parasites. However, how this shapes patterns coevolutionary dynamics is not clear. Here, we construct a simple mathematical model study effect environmental change on host–parasite outcome when matching-alleles or gene-for-gene type. changes may effectively alter selective pressure level specialism in population. Our results suggest that altering selection antagonistic can produce alternating...
Most organisms live in ever-changing environments, and have to cope with a range of different conditions. Often, the set biological traits that are needed grow, reproduce, survive varies between As consequence, evolved sensory systems detect environmental signals, modify expression response. However, there limits ability such plastic responses changing environments. Sometimes, shifts might occur suddenly, without preceding so not time react. Other times, signals be unreliable, causing...
Biological modularity enhances evolutionary adaptability. This principle is vividly exemplified by bacterial viruses (phages), which display extensive genomic modularity. Phage genomes are composed of independent functional modules that evolve separately and recombine in various configurations. While phages has been extensively studied, less attention paid to protein modularity-proteins consisting distinct building blocks can recombine, enhancing genetic diversity. Here, we use a set 133,574...
ABSTRACT Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of below 80%, particularly large reference data sets, challenging due lack scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline estimating alignment fraction (AF) genomes with divergence around...
ABSTRACT Staphylococcus argenteus is a newly named species previously described as divergent lineage of aureus that has recently been shown to have global distribution. Despite growing evidence the clinical importance this species, knowledge about its population epidemiology and genomic architecture limited. We used whole-genome sequencing evaluate compare S. ( n = 251) 68) isolates from adults with staphylococcal sepsis at several hospitals in northeastern Thailand between 2006 2013. The...
Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition gene cassettes. Both occurred in otherwise contrasting histories antibiotic-resistant S. lineages PMEN3 PMEN9. A single clade spread globally, evading vaccine-induced immunity frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. repeatedly integrated Tn 916 -type 1207.1 elements,...
Shigella flexneri is historically regarded as the primary agent of bacillary dysentery, yet closely-related sonnei replacing S. flexneri, especially in developing countries. The underlying reasons for this dramatic shift are mostly unknown. Using a zebrafish (Danio rerio) model infection, we discover that more virulent than vivo. Whole animal dual-RNAseq and testing bacterial mutants suggest virulence depends on its O-antigen oligosaccharide (which unique among species). We show vivo using...
The evolutionary implications of recombination in HIV remain not fully understood. A plausible effect could be an enhancement immune escape from cytotoxic T lymphocytes (CTLs). In order to test this hypothesis, we constructed a population dynamic model and examined the viral-immune dynamics with without recombination. Our shows that (i) increases genetic diversity viral population, (ii) accelerates emergence mutations compensatory mutations, (iii) acquisition early stage infection. We see...
The extent to which evolution is constrained by the rate at horizontal gene transfer (HGT) allows DNA move between genetic lineages an open question, we address in context of antibiotic resistance
Sex and recombination remain one of the biggest riddles evolutionary biology. One most prominent hypotheses, Red Queen Hypothesis, claims that sex has evolved as a means to efficiently create genotypes are resistant against coevolving parasites. However, previous models have assumed all individuals equally likely engage in sexual reproduction, regardless their infection status, an assumption may not be true reality. Here, we consider population genetic model host with parasite population,...
Antagonistic species interactions can lead to coevolutionary genotype or phenotype frequency oscillations, with important implications for ecological and evolutionary processes. However, direct empirical evidence of such oscillations is rare. The rarity observations generally attributed inherent difficulties long-term studies, weak absent interaction between species, the absence negative frequency-dependence. Here, we show that another factor – non-genetic inheritance, mediated example by...
Abstract Objectives We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread relation to nationwide clinical interventions. Methods whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST antibiotic resistance were inferred genomes. An SNP tree was built using Gubbins. Temporal reconstructed a birth–death model. Results identified 131 none carried other known tet genes. Tetracycline...
Human immunodeficiency virus (HIV-1) is, like most pathogens, under selective pressure to escape the immune system of its host. In particular, HIV-1 can avoid recognition by cytotoxic T lymphocytes (CTLs) altering binding affinity viral peptides human leukocyte antigen (HLA) molecules, role which is present those system. It generally assumed that HLA mutations carry a replicative fitness cost, but these costs have not been quantified. this study, we assess cost are likely presentation...
Host-parasite coevolution has been studied extensively in the context of evolution sex. Although hosts typically coevolve with several parasites, most studies considered one-host/one-parasite interactions. Here, we study population-genetic models which interact two parasites. We find that host/multiple-parasite differ nontrivially from host/single-parasite models. Selection for sex resulting interactions a single parasite is often outweighed by detrimental effects due to interaction between...
Abstract Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference an evolutionary tree bacteria thus relies on accurate identification the population structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce novel algorithm called fastGEAR which identifies lineages diverse microbial alignments, between them from...
Abstract The estimation of Average Nucleotide Identity (ANI) plays a pivotal role in microbial and viral research, facilitating species delineation, taxonomy, genome dereplication metagenomics even detection horizontal gene transfer. Traditional tools, optimised for bacterial genomes, fall short addressing the complexities phage genomics such as high sequence variability, mosaicism or absence universally shared genes. To bridge this gap, we introduce MANIAC (MMseqs2-based ANI Accurate...
As antibiotic resistance creates a significant global health threat, we need not only to accelerate the development of novel antibiotics but also develop better treatment strategies using existing drugs improve their efficacy and prevent selection further resistance. We require new tools rationally design dosing regimens from data collected in early phases development. Mathematical models such as mechanistic pharmacodynamic drug-target binding explain details how given drug concentration...
Abstract Biological modularity enhances evolutionary adaptability by allowing rearrangement of functional components. One striking example are bacterial viruses (phages). They exhibit extensive genomic being built independent modules that evolve separately and combine in various ways, making them astoundingly diverse. While multiple studies have investigated phages, less attention has been given to protein modularity—proteins having distinct building blocks or domains can recombine,...