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Animals : An Open Access Journal From... May 2024Avian influenza viruses (AIVs) are highly contagious respiratory viruses of birds, leading to significant morbidity and mortality globally and causing substantial... (Review)
Review
Avian influenza viruses (AIVs) are highly contagious respiratory viruses of birds, leading to significant morbidity and mortality globally and causing substantial economic losses to the poultry industry and agriculture. Since their first isolation in 2013-2014, the Asian-origin H5 highly pathogenic avian influenza viruses (HPAI) of clade 2.3.4.4b have undergone unprecedented evolution and reassortment of internal gene segments. In just a few years, it supplanted other AIV clades, and now it is widespread in the wild migratory waterfowl, spreading to Asia, Europe, Africa, and the Americas. Wild waterfowl, the natural reservoir of LPAIVs and generally more resistant to the disease, also manifested high morbidity and mortality with HPAIV clade 2.3.4.4b. This clade also caused overt clinical signs and mass mortality in a variety of avian and mammalian species never reported before, such as raptors, seabirds, sealions, foxes, and others. Most notably, the recent outbreaks in dairy cattle were associated with the emergence of a few critical mutations related to mammalian adaptation, raising concerns about the possibility of jumping species and acquisition of sustained human-to-human transmission. The main clinical signs and anatomopathological findings associated with clade 2.3.4.4b virus infection in birds and non-human mammals are hereby summarized.
PubMed: 38731377
DOI: 10.3390/ani14091372 -
Nature Communications May 2024Heteroresistance is a medically relevant phenotype where small antibiotic-resistant subpopulations coexist within predominantly susceptible bacterial populations....
Heteroresistance is a medically relevant phenotype where small antibiotic-resistant subpopulations coexist within predominantly susceptible bacterial populations. Heteroresistance reduces treatment efficacy across diverse bacterial species and antibiotic classes, yet its genetic and physiological mechanisms remain poorly understood. Here, we investigated a multi-resistant Klebsiella pneumoniae isolate and identified three primary drivers of gene dosage-dependent heteroresistance for several antibiotic classes: tandem amplification, increased plasmid copy number, and transposition of resistance genes onto cryptic plasmids. All three mechanisms imposed fitness costs and were genetically unstable, leading to fast reversion to susceptibility in the absence of antibiotics. We used a mouse gut colonization model to show that heteroresistance due to elevated resistance-gene dosage can result in antibiotic treatment failures. Importantly, we observed that the three mechanisms are prevalent among Escherichia coli bloodstream isolates. Our findings underscore the necessity for treatment strategies that address the complex interplay between plasmids, resistance cassettes, and transposons in bacterial populations.
Topics: Klebsiella pneumoniae; Animals; Anti-Bacterial Agents; Mice; Plasmids; DNA Copy Number Variations; Escherichia coli; Drug Resistance, Multiple, Bacterial; Microbial Sensitivity Tests; Gene Dosage; Klebsiella Infections; Humans; DNA Transposable Elements; Female
PubMed: 38730266
DOI: 10.1038/s41467-024-48233-0 -
The Science of the Total Environment Jul 2024Staphylococcus aureus is a versatile pathobiont, exhibiting a broad host range, including humans, other mammals, and avian species. Host specificity determinants,...
Staphylococcus aureus is a versatile pathobiont, exhibiting a broad host range, including humans, other mammals, and avian species. Host specificity determinants, virulence, and antimicrobial resistance genes are often shared by strains circulating at the animal-human interface. While transmission dynamics studies have shown strain exchange between humans and livestock, knowledge of the source, genetic diversification, and transmission drivers of S. aureus in wildlife lag behind. In this work, we explore a wide array of S. aureus genomes from different sources in the Iberian Peninsula to understand population structure, gene content and niche adaptation at the human-livestock-wildlife nexus. Through Bayesian inference, we address the hypothesis that S. aureus strains in wildlife originate from humanized landscapes, either from contact with humans or through interactions with livestock. Phylogenetic reconstruction applied to whole genome sequence data was completed with a dataset of 450 isolates featuring multiple clones from the 1990-2022 period and a subset of CC398 strains representing the 2008-2022 period. Phylodynamic signatures of S. aureus from the Iberian Peninsula suggest widespread circulation of most clones among humans before jumping to other hosts. The number of transitions of CC398 strains within each host category (human, livestock, wildlife) was high (88.26 %), while the posterior probability of transitions from livestock to wildlife was remarkably high (0.99). Microbial genome-wide association analysis did not evidence genome rearrangements nor biomarkers suggesting S. aureus niche adaptation to wildlife, thus supporting recent spill overs. Altogether, our findings indicate that S. aureus isolates collected in the past years from wildlife most likely represent multiple introduction events from livestock. The clonal origin of CC398 and its potential to disseminate and evolve through different animal host species are highlighted, calling for management practices at the livestock-wildlife axis to improve biosecurity and thus restrict S. aureus transmission and niche expansion along gradients of human influence.
Topics: Animals; Livestock; Staphylococcus aureus; Staphylococcal Infections; Animals, Wild; Spain; Humans; Phylogeny; Portugal
PubMed: 38729368
DOI: 10.1016/j.scitotenv.2024.173027 -
Nature Genetics Jun 2024Concurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing...
Concurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90-99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000-50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.
Topics: Humans; DNA Methylation; Animals; Male; Prostatic Neoplasms; Mice; Sequence Analysis, DNA; Chromatin; DNA; DNA Transposable Elements; High-Throughput Nucleotide Sequencing; CpG Islands; Cell Line, Tumor; CCCTC-Binding Factor; Transposases
PubMed: 38724748
DOI: 10.1038/s41588-024-01748-0 -
MBio Jun 2024Bacteria are highly adaptable and grow in diverse niches, where they often interact with eukaryotic organisms. These interactions with different hosts span the entire... (Review)
Review
Bacteria are highly adaptable and grow in diverse niches, where they often interact with eukaryotic organisms. These interactions with different hosts span the entire spectrum from symbiosis to pathogenicity and thus determine the lifestyle of the bacterium. Knowledge of the genetic determinants involved in animal and plant host colonization by pathogenic and mutualistic bacteria is not only crucial to discover new drug targets for disease management but also for developing novel biostimulant strategies. In the last decades, significant progress in genome-wide high-throughput technologies such as transposon insertion sequencing has led to the identification of pathways that enable efficient host colonization. However, the extent to which similar genes play a role in this process in different bacteria is yet unclear. This review highlights the commonalities and specificities of bacterial determinants important for bacteria-host interaction.
Topics: Bacteria; DNA Transposable Elements; Animals; Host Microbial Interactions; Symbiosis; Plants; Host-Pathogen Interactions; Humans
PubMed: 38722161
DOI: 10.1128/mbio.00390-24 -
BMC Genomics May 2024Standard ChIP-seq and RNA-seq processing pipelines typically disregard sequencing reads whose origin is ambiguous ("multimappers"). This usual practice has potentially...
BACKGROUND
Standard ChIP-seq and RNA-seq processing pipelines typically disregard sequencing reads whose origin is ambiguous ("multimappers"). This usual practice has potentially important consequences for the functional interpretation of the data: genomic elements belonging to clusters composed of highly similar members are left unexplored.
RESULTS
In particular, disregarding multimappers leads to the underrepresentation in epigenetic studies of recently active transposable elements, such as AluYa5, L1HS and SVAs. Furthermore, this common strategy also has implications for transcriptomic analysis: members of repetitive gene families, such the ones including major histocompatibility complex (MHC) class I and II genes, are under-quantified.
CONCLUSION
Revealing inherent biases that permeate routine tasks such as functional enrichment analysis, our results underscore the urgency of broadly adopting multimapper-aware bioinformatic pipelines -currently restricted to specific contexts or communities- to ensure the reliability of genomic and transcriptomic studies.
Topics: Humans; High-Throughput Nucleotide Sequencing; DNA Transposable Elements; Computational Biology; Gene Expression Profiling; Genomics; Sequence Analysis, RNA
PubMed: 38720252
DOI: 10.1186/s12864-024-10344-9 -
Nature Communications May 2024The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell...
The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell by inserting new copies, generating DNA damage, and triggering inflammation. Therefore, L1 inhibition could be used to treat many diseases associated with these processes. Previous research has focused on inhibition of the L1 reverse transcriptase due to the prevalence of well-characterized inhibitors of related viral enzymes. Here we present the L1 endonuclease as another target for reducing L1 activity. We characterize structurally diverse small molecule endonuclease inhibitors using computational, biochemical, and biophysical methods. We also show that these inhibitors reduce L1 retrotransposition, L1-induced DNA damage, and inflammation reinforced by L1 in senescent cells. These inhibitors could be used for further pharmacological development and as tools to better understand the life cycle of this element and its impact on disease processes.
Topics: Humans; Long Interspersed Nucleotide Elements; Endonucleases; Enzyme Inhibitors; DNA Damage; Small Molecule Libraries; Cellular Senescence; Deoxyribonuclease I
PubMed: 38719805
DOI: 10.1038/s41467-024-48066-x -
FEMS Microbiology Letters Jan 2024Acinetobacter baumannii is one of the most prevalent causes of nosocomial infections worldwide. However, a paucity of information exists regarding the connection between...
Acinetobacter baumannii is one of the most prevalent causes of nosocomial infections worldwide. However, a paucity of information exists regarding the connection between metabolic capacity and in vivo bacterial fitness. Elevated lactate is a key marker of severe sepsis. We have previously shown that the putative A. baumannii lactate permease gene, lldP, is upregulated during in vivo infection. Here, we confirm that lldP expression is upregulated in three A. baumannii strains during a mammalian systemic infection. Utilising a transposon mutant disrupted for lldP in the contemporary clinical strain AB5075-UW, and a complemented strain, we confirmed its role in the in vitro utilisation of l-(+)-lactate. Furthermore, disruption of the lactate metabolism pathway resulted in reduced bacterial fitness during an in vivo systemic murine competition assay. The disruption of lldP had no impact on the susceptibility of this strain to complement mediated killing by healthy human serum. However, growth in biologically relevant concentrations of lactate observed during severe sepsis, led to bacterial tolerance to killing by healthy human blood, a phenotype that was abolished in the lldP mutant. This study highlights the importance of the lactate metabolism pathway for survival and growth of A. baumannii during infection.
Topics: Acinetobacter baumannii; Animals; Acinetobacter Infections; Lactic Acid; Mice; Humans; Bacterial Proteins; Female; Sepsis; DNA Transposable Elements; Gene Expression Regulation, Bacterial
PubMed: 38719540
DOI: 10.1093/femsle/fnae032 -
Microbiome May 2024After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering...
BACKGROUND
After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom.
RESULTS
To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots.
CONCLUSIONS
DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
Topics: Microbiota; DNA Transposable Elements; Rhizosphere; Plasmids; Plant Roots; Proteobacteria; Flow Cytometry; Luminescent Proteins; Soil Microbiology
PubMed: 38715147
DOI: 10.1186/s40168-024-01792-2 -
Nature Communications May 2024Unlike coding genes, the number of lncRNA genes in organism genomes is relatively proportional to organism complexity. From plants to humans, the tissues with highest...
Unlike coding genes, the number of lncRNA genes in organism genomes is relatively proportional to organism complexity. From plants to humans, the tissues with highest numbers and levels of lncRNA gene expression are the male reproductive organs. To learn why, we initiated a genome-wide analysis of Drosophila lncRNA spatial expression patterns in these tissues. The numbers of genes and levels of expression observed greatly exceed those previously reported, due largely to a preponderance of non-polyadenylated transcripts. In stark contrast to coding genes, the highest numbers of lncRNAs expressed are in post-meiotic spermatids. Correlations between expression levels, localization and previously performed genetic analyses indicate high levels of function and requirement. More focused analyses indicate that lncRNAs play major roles in evolution by controlling transposable element activities, Y chromosome gene expression and sperm construction. A new type of lncRNA-based particle found in seminal fluid may also contribute to reproductive outcomes.
Topics: Animals; Male; Spermatogenesis; RNA, Long Noncoding; Y Chromosome; Drosophila melanogaster; Evolution, Molecular; DNA Transposable Elements; Drosophila; Spermatids
PubMed: 38714658
DOI: 10.1038/s41467-024-47346-w