Is the distribution of plasmid lengths bimodal? DOI Creative Commons
Ian Dewan, Hildegard Uecker

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 11, 2023

Abstract The length of a plasmid is key property which linked to many aspects plas-mid biology. When distributions lengths are shown in the literature, they usually plotted with on logarithmic scale. However, quantity and its logarithm have distinct may differ considerably shape. Mistaking distribution log-lengths for can therefore lead distorted conclusions about distribution; particular, be bimodal when only unimodal. This particular confusion has arisen literature where often claimed based examination what fact log-length distribution. While indeed within bacterial families, it not across ensemble all plasmids. We suggest that authors should careful show distribution, or distinguish two distributions, avoid misleading inferences. Highlights plasmids different, different shapes. typical practice using scale leads between distributions. In not. families bimodal, but plasmids, Clearly distinguishing will ensure biological drawn from them robust.

Language: Английский

Application of next-generation sequencing to identify different pathogens DOI Creative Commons

Aljuboori M. Nafea,

Yuer Wang,

Duanyang Wang

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 14

Published: Jan. 29, 2024

Early and precise detection identification of various pathogens are essential for epidemiological monitoring, disease management, reducing the prevalence clinical infectious diseases. Traditional pathogen techniques, which include mass spectrometry, biochemical tests, molecular testing, culture-based methods, limited in application time-consuming. Next generation sequencing (NGS) has emerged as an technology identifying pathogens. NGS is a cutting-edge method with high throughput that can create massive volumes sequences broad prospects field diagnosis. In this review, we introduce detail, summarizes different pathogens, including bacteria, fungi, viruses, analyze challenges outlook using to identify Thus, work provides theoretical basis studies evidence support distinguishing

Language: Английский

Citations

25
A mathematician’s guide to plasmids: an introduction to plasmid biology for modellers DOI
Ian Dewan, Hildegard Uecker

Microbiology, Journal Year: 2023, Volume and Issue: 169(7)

Published: July 28, 2023

Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role genetics evolution. Our understanding of plasmid biology has been furthered greatly by the development mathematical models, there are many questions about plasmids that models would be useful answering. In this review, we present introductory, yet comprehensive, overview suitable for modellers unfamiliar with who want to get up speed begin working on plasmid-related models. addition reviewing diversity genes they carry, their key physiological functions, interactions between host, also highlight selected topics may particular interest areas where is a need theoretical development. The world holds great variety subjects will biologists, introducing new subject help expand existing body theory.

Language: Английский

Citations

18
Antimicrobial Resistance: What Lies Beneath This Complex Phenomenon? DOI Creative Commons

Giedrė Valdonė Sakalauskienė,

Aurelija Radzevičienė

Diagnostics, Journal Year: 2024, Volume and Issue: 14(20), P. 2319 - 2319

Published: Oct. 18, 2024

Antimicrobial Resistance (AMR) has evolved from a mere concern into significant global threat, with profound implications for public health, healthcare systems, and the economy. Since introduction of antibiotics between 1945 1963, their widespread often indiscriminate use in human medicine, agriculture, animal husbandry led to emergence rapid spread antibiotic-resistant genes. Bacteria have developed sophisticated mechanisms evade effects antibiotics, including drug uptake limitation, degradation, target modification, efflux pumps, biofilm formation, outer membrane vesicles production. As result, AMR now poses threat comparable climate change COVID-19 pandemic, projections suggest that death rates will be up 10 million deaths annually by 2050, along staggering economic cost exceeding $100 trillion. Addressing requires multifaceted approach, development new alternative therapies, shift antibiotic usage regulation. Enhancing surveillance increasing awareness, prioritizing investments research, diagnostics, vaccines are critical steps. By recognizing gravity committing collaborative action, its impact can mitigated, health protected future generations.

Language: Английский

Citations

4
Global insights into the genome dynamics of Clostridioides difficile associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages DOI Creative Commons

Mohammad Sholeh,

Masoumeh Beig, Ebrahim Kouhsari

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 15, 2025

Clostridioides difficile is a significant cause of healthcare-associated infections, with rising antimicrobial resistance complicating treatment. This study offers genomic analysis C. difficile, focusing on sequence types (STs), global distribution, antibiotic genes, and virulence factors in its chromosomal plasmid DNA. A total 19,711 genomes were retrieved from GenBank. Prokka was used for genome annotation, multi-locus typing (MLST) identified STs. Pan-genome Roary core accessory genes. Antibiotic factors, toxins detected using the CARD VFDB databases, ABRicate software. Statistical analyses visualizations performed R. Among 366 STs, ST1 (1,326 isolates), ST2 (1,141), ST11 (893), ST42 (763) predominant. Trends streamlining included reductions length, gene count, protein-coding pseudogenes. Common genes-cdeA (99.46%), cplR (99.63%), nimB (99.67%)-were nearly ubiquitous. Rare genes like blaCTX-M-2, cfxA3, blaZ appeared only 0.005% genomes. Vancomycin susceptibility-reducing vanG cluster at low frequencies. Virulence showed variability, highly prevalent such as zmp1 (99.62%), groEL (99.60%), rpoB/rpoB2 (99.60%). Moderately distributed cwp66 (54.61%) slpA (79.02%). Toxin tcdE (91.26%), tcdC (89.67%), tcdB (89.06%) widespread, while binary toxin cdtA (26.19%) cdtB (26.26%) less common. prevalence, particularly tcdA tcdB, gradual decline over time, sharper cdtB. Gene presence patterns (GPP-1) resistance, virulence, primarily linked to ST2, ST42, ST8. highlights difficile's adaptability genetic diversity. The reflects fewer toxigenic isolates, but bacterium's increasing preserved enable rapid evolution. ST8 dominate globally, emphasizing need ongoing monitoring.

Language: Английский

Citations

0
Current state and future prospects of Horizontal Gene Transfer detection DOI Creative Commons
Andika Aji Wijaya, Aleksandar Anžel, Hugues Richard

et al.

NAR Genomics and Bioinformatics, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 7, 2025

Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is driving force evolutionary changes prokaryotes. It widely recognized that it contributes the emergence antimicrobial resistance (AMR), which poses particularly serious threat public health. Many computational approaches have developed study and detect HGT. However, application AI this field not investigated. In work, we conducted review provide information on current trend existing for detecting HGT decipher use field. Here, show growing interest detection, characterized by surge number approaches, including AI-based recent years. We organize into hierarchical structure groups based their methods how each group evolved. make recommendations discuss challenges detection general adoption particular. Moreover, future directions detection.

Language: Английский

Citations

0
Genes for cooperation are not more likely to be carried by plasmids DOI Creative Commons
Anna E. Dewar, Laurence J. Belcher, Thomas W. Scott

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2017)

Published: Feb. 28, 2024

Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis that genes which are more likely be transferred, such those on should code for cooperative traits. Testing requires identifying all cooperation in bacterial genomes. However, previous studies used method misses some these To solve this, we new genomics tool, SOCfinder, uses three distinct modules identify kinds We compared where were located 4648 genomes from 146 species. In contrast the hypothesis, found no evidence plasmid Instead, opposite—that carried chromosomes. Overall, vast majority not suggesting general kin selection sufficient explain prevalence bacteria.

Language: Английский

Citations

3
On qualitative properties of replication and transfer of conjugative plasmids encoding antibiotic resistance genes DOI Creative Commons
Eduardo Ibargüen-Mondragón, L. Esteva, Victoria Otero–Espinar

et al.

Computational and Applied Mathematics, Journal Year: 2025, Volume and Issue: 44(5)

Published: May 7, 2025

Language: Английский

Citations

0
Role of plasmids in antibiotic resistance in clinical infections and implications for epidemiological surveillance: a review DOI Creative Commons

Ayodele Oluwaseun Ajayi,

Olajide Joseph Akinjogunla, Adebowale Odeyemi

et al.

All Life, Journal Year: 2024, Volume and Issue: 17(1)

Published: June 6, 2024

The global upsurge in antibiotic resistant bacteria (ARB) is putting immense pressure on healthcare. spreading of antimicrobial resistance facilitated by mobile genetic elements, most especially plasmids. widespread use antibiotics clinical and veterinary environments creates selective that drives the evolution ARB. Plasmids contribute to propagation AR different types infections. role plasmids play this necessitates their utilization molecular surveillance detect emergence ARB track spread Recent technologies like replicon typing whole genome sequencing (WGS) have become gold standard for epidemiology detection control epidemics settings. Unfortunately, access such limited low- middle-income countries (LMICs). major aim review examine specific contributions settings elucidate various been attributed antibiotic-resistant infections healthcare Healthcare LMICs should be supported build capacity WGS effectively prevent bacterial

Language: Английский

Citations

2
Torsional Mechanics of Circular DNA DOI Creative Commons
Gundeep Singh, Yifeng Hong, James T. Inman

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 10, 2024

Circular DNA found in the cell is actively regulated to an underwound state, with their superhelical density close σ ∼ - 0.06. While this state essential life, how it impacts torsional mechanical properties of not fully understood. In work, we performed simulations understand mechanics circular and validated our results single-molecule measurements analytical theory. We that torque generated at 0.06 near but slightly below required melt DNA, significantly decreasing energy barrier for proteins interact melted DNA. Furthermore, supercoiled experiences force (tension) are equally distributed through contour. have also extended a previous framework show plectonemic twist persistence length depends on intrinsic bending length. Our work establishes understanding supercoiling dynamics

Language: Английский

Citations

2
The many dimensions of combination therapy: How to combine antibiotics to limit resistance evolution DOI Creative Commons
Christin Nyhoegen, Sebastian Bonhoeffer, Hildegard Uecker

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(8)

Published: Aug. 1, 2024

In combination therapy, bacteria are challenged with two or more antibiotics simultaneously. Ideally, separate mutations required to adapt each of them, which is a priori expected hinder the evolution full resistance. Yet, success this strategy ultimately depends on how well controls growth and without resistance mutations. To design treatment, we need choose drugs their doses decide many get mixed. Which combinations good? answer question, set up stochastic pharmacodynamic model determine probability successfully eradicate bacterial population. We consider bacteriostatic types bactericidal drugs-those that kill independent replication those during replication. establish results for null model, non-interacting implement most common models drug independence-Loewe additivity Bliss independence. Our show therapy almost always better in limiting than administering just one drug, even though keep total dose constant 'fair' comparison. exceptions exist steep dose-response curves. Combining can non-replicating cells particularly beneficial. suggest 50:50 ratio-even if not optimal-is usually good safe choice. Applying three four beneficial treatment strains large mutation rates but adding otherwise only provides marginal benefit disadvantage. By systematically addressing key elements design, our study basis future take further factors into account. It also highlights conceptual challenges translating traditional concepts independence single-cell level.

Language: Английский

Citations

1