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Journal articles on the topic 'Plasmids'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Lopez, Jaime G., Mohamed S. Donia, and Ned S. Wingreen. "Modeling the ecology of parasitic plasmids." ISME Journal 15, no. 10 (2021): 2843–52. http://dx.doi.org/10.1038/s41396-021-00954-6.

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AbstractPlasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the central role they play in antibiotic resistance and modern biotechnology, our understanding of plasmids’ natural ecology is limited. Recent experiments have shown that plasmids can spread even when they are a burden to the cell, suggesting that natural plasmids may exist as parasites. Here, we use mathematical modeling to explore the ecology of such parasitic plasmids. We first develop models of single plasmids and find that a plasmid’s population dynami

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Lopez-Diaz, Maria, Nicholas Ellaby, Jane Turton, Neil Woodford, Maria Tomas, and Matthew J. Ellington. "NDM-1 carbapenemase resistance gene vehicles emergent on distinct plasmid backbones from the IncL/M family." Journal of Antimicrobial Chemotherapy 77, no. 3 (2022): 620–24. http://dx.doi.org/10.1093/jac/dkab466.

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Abstract Objectives To assess the genetic contexts surrounding blaNDM-1 genes carried on IncM plasmids harboured by six carbapenemase-producing Enterobacterales (CPE) isolates referred to the UK Health Security Agency’s Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit. Methods Between 2014 and 2018, the AMRHAI Reference Unit undertook WGS of CPE isolates using Illumina NGS. Nanopore sequencing was used for selected isolates and publicly available plasmid references were downloaded. Analysis of incRNA, which encodes the antisense RNA regulating plasmidic rep

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Li, Feifeng, Jiong Wang, Ying Jiang, et al. "Adaptive Evolution Compensated for the Plasmid Fitness Costs Brought by Specific Genetic Conflicts." Pathogens 12, no. 1 (2023): 137. http://dx.doi.org/10.3390/pathogens12010137.

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New Delhi metallo-β-lactamase (NDM)-carrying IncX3 plasmids is important in the transmission of carbapenem resistance in Escherichia coli. Fitness costs related to plasmid carriage are expected to limit gene exchange; however, the causes of these fitness costs are poorly understood. Compensatory mutations are believed to ameliorate plasmid fitness costs and enable the plasmid’s wide spread, suggesting that such costs are caused by specific plasmid–host genetic conflicts. By combining conjugation tests and experimental evolution with comparative genetic analysis, we showed here that the fitness

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Bahl, Martin Iain, Lars Hestbjerg Hansen, Tine Rask Licht, and Søren J. Sørensen. "Conjugative Transfer Facilitates Stable Maintenance of IncP-1 Plasmid pKJK5 in Escherichia coli Cells Colonizing the Gastrointestinal Tract of the Germfree Rat." Applied and Environmental Microbiology 73, no. 1 (2006): 341–43. http://dx.doi.org/10.1128/aem.01971-06.

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ABSTRACT Quantitative determination of IncP-1 plasmid loss from Escherichia coli cells colonizing the gastrointestinal tracts of germfree rats was achieved by flow cytometry. Results show that the plasmid's ability to conjugate counteracts plasmid loss and is thus an important mechanism for the stable maintenance of IncP-1 plasmids within the gastrointestinal environment.

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Longtine, M. S., S. Enomoto, S. L. Finstad, and J. Berman. "Yeast telomere repeat sequence (TRS) improves circular plasmid segregation, and TRS plasmid segregation involves the RAP1 gene product." Molecular and Cellular Biology 12, no. 5 (1992): 1997–2009. http://dx.doi.org/10.1128/mcb.12.5.1997-2009.1992.

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Telomere repeat sequences (TRSs) can dramatically improve the segregation of unstable circular autonomously replicating sequence (ARS) plasmids in Saccharomyces cerevisiae. Deletion analysis demonstrated that yeast TRSs, which conform to the general sequence (C(1-3)A)n, are able to stabilize circular ARS plasmids. A number of TRS clones of different primary sequence and C(1-3)A tract length confer the plasmid stabilization phenotype. TRS sequences do not appear to improve plasmid replication efficiency, as determined by plasmid copy number analysis and functional assays for ARS activity. Pedig

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Longtine, M. S., S. Enomoto, S. L. Finstad, and J. Berman. "Yeast telomere repeat sequence (TRS) improves circular plasmid segregation, and TRS plasmid segregation involves the RAP1 gene product." Molecular and Cellular Biology 12, no. 5 (1992): 1997–2009. http://dx.doi.org/10.1128/mcb.12.5.1997.

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Telomere repeat sequences (TRSs) can dramatically improve the segregation of unstable circular autonomously replicating sequence (ARS) plasmids in Saccharomyces cerevisiae. Deletion analysis demonstrated that yeast TRSs, which conform to the general sequence (C(1-3)A)n, are able to stabilize circular ARS plasmids. A number of TRS clones of different primary sequence and C(1-3)A tract length confer the plasmid stabilization phenotype. TRS sequences do not appear to improve plasmid replication efficiency, as determined by plasmid copy number analysis and functional assays for ARS activity. Pedig

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Pollet, Rebecca M., James D. Ingle, Jeff P. Hymes, et al. "Processing of Nonconjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci." Journal of Bacteriology 198, no. 6 (2016): 888–97. http://dx.doi.org/10.1128/jb.00832-15.

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ABSTRACTAntimicrobial resistance inStaphylococcus aureuspresents an increasing threat to human health. This resistance is often encoded on mobile plasmids, such as pSK41; however, the mechanism of transfer of these plasmids is not well understood. In this study, we first examine key protein-DNA interactions formed by the relaxase enzyme, NES, which initiates and terminates the transfer of the multidrug resistance plasmid pSK41. Two loops on the NES protein, hairpin loops 1 and 2, form extensive contacts with the DNA hairpin formed at theoriTregion of pSK41, and here we establish that these con

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Brown, Celeste J., Diya Sen, Hirokazu Yano, et al. "Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes." Applied and Environmental Microbiology 79, no. 24 (2013): 7684–95. http://dx.doi.org/10.1128/aem.02252-13.

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ABSTRACTBroad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. T

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Wu, Shang Wei, Kathrine Dornbusch, Göran Kronvall та Mari Norgren. "Characterization and Nucleotide Sequence of a Klebsiella oxytoca Cryptic Plasmid Encoding a CMY-Type β-Lactamase: Confirmation that the Plasmid-Mediated Cephamycinase Originated from the Citrobacter freundii AmpC β-Lactamase". Antimicrobial Agents and Chemotherapy 43, № 6 (1999): 1350–57. http://dx.doi.org/10.1128/aac.43.6.1350.

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ABSTRACT Plasmid pTKH11, originally obtained by electroporation of aKlebsiella oxytoca plasmid preparation intoEscherichia coli XAC, expressed a high level of an AmpC-like β-lactamase. The enzyme, designated CMY-5, conferred resistance to extended-spectrum β-lactams in E. coli; nevertheless, the phenotype was cryptic in the K. oxytocadonor. Determination of the complete nucleotide sequence of pTKH11 revealed that the 8,193-bp plasmid encoded seven open reading frames, including that for the CMY-5 β-lactamase (bla CMY-5). Thebla CMY-5 product was similar to the plasmidic CMY-2 β-lactamase of K.

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Paganini, Julian A., Nienke L. Plantinga, Sergio Arredondo-Alonso, Rob J. L. Willems, and Anita C. Schürch. "Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data." Microorganisms 9, no. 8 (2021): 1613. http://dx.doi.org/10.3390/microorganisms9081613.

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The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-su

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Carroll, Amanda C., and Alex Wong. "Plasmid persistence: costs, benefits, and the plasmid paradox." Canadian Journal of Microbiology 64, no. 5 (2018): 293–304. http://dx.doi.org/10.1139/cjm-2017-0609.

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Plasmids are extrachromosomal DNA elements that can be found throughout bacteria, as well as in other domains of life. Nonetheless, the evolutionary processes underlying the persistence of plasmids are incompletely understood. Bacterial plasmids may encode genes for traits that are sometimes beneficial to their hosts, such as antimicrobial resistance, virulence, heavy metal tolerance, and the catabolism of unique nutrient sources. In the absence of selection for these traits, however, plasmids generally impose a fitness cost on their hosts. As such, plasmid persistence presents a conundrum: mo

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Smith, Hilde, Alex Bossers, Frank Harders та ін. "Characterization of Epidemic IncI1-Iγ Plasmids Harboring Ambler Class A and C Genes in Escherichia coli and Salmonella enterica from Animals and Humans". Antimicrobial Agents and Chemotherapy 59, № 9 (2015): 5357–65. http://dx.doi.org/10.1128/aac.05006-14.

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ABSTRACTThe aim of the study was to identify the plasmid-encoded factors contributing to the emergence and spread of epidemic IncI1-Iγ plasmids obtained fromEscherichia coliandSalmonella entericaisolates from animal and human reservoirs. For this, 251 IncI1-Iγ plasmids carrying various extended-spectrum β-lactamase (ESBL) or AmpC β-lactamase genes were compared using plasmid multilocus sequence typing (pMLST). Thirty-two of these plasmids belonging to different pMLST types were sequenced using Roche 454 and Illumina platforms. Epidemic IncI1-Iγ plasmids could be assigned to various dominant cl

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Rebelo, João S., Célia P. F. Domingues, and Francisco Dionisio. "Plasmid Costs Explain Plasmid Maintenance, Irrespective of the Nature of Compensatory Mutations." Antibiotics 12, no. 5 (2023): 841. http://dx.doi.org/10.3390/antibiotics12050841.

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Conjugative plasmids often carry virulence and antibiotic-resistant genes. Therefore, understanding the behavior of these extra-chromosomal DNA elements gives insights into their spread. Bacteria frequently replicate slower after plasmids’ entry, an observation inconsistent with the plasmids’ ubiquity in nature. Several hypotheses explain the maintenance of plasmids among bacterial communities. However, the numerous combinations of bacterial species and strains, plasmids, and environments claim a robust elucidatory mechanism of plasmid maintenance. Previous works have shown that donor cells al

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Wilt, G. R., G. Wu, and R. Curtis Bird. "Characterization of the plasmids of Moraxella bovis." American Journal of Veterinary Research 50, no. 10 (1989): 1678–83. https://doi.org/10.2460/ajvr.1989.50.10.1678.

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SUMMARY Restriction endonuclease digestions were performed on plasmids purified from Moraxella bovis isolates GRS, Newport, and IBH64. It was determined from single and double digestions of plasmid dna that GRS and Newport isolates carried 3 large plasmids having molecular sizes of 43.8, 41.3, and 32.8 kilobases (kb). Digestion of the 3 large plasmids and restriction endonucleases Hae III, HindIII, Nde I, and Ava I strongly indicated that these isolates shared structurally identical large plasmids. Timed single digestions with Ava I revealed that the IBH64 isolate carried 2 large plasmids havi

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Dimitriu, Tatiana, Andrew C. Matthews, and Angus Buckling. "Increased copy number couples the evolution of plasmid horizontal transmission and plasmid-encoded antibiotic resistance." Proceedings of the National Academy of Sciences 118, no. 31 (2021): e2107818118. http://dx.doi.org/10.1073/pnas.2107818118.

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Conjugative plasmids are mobile elements that spread horizontally between bacterial hosts and often confer adaptive phenotypes, including antimicrobial resistance (AMR). Theory suggests that opportunities for horizontal transmission favor plasmids with higher transfer rates, whereas selection for plasmid carriage favors less-mobile plasmids. However, little is known about the mechanisms leading to variation in transmission rates in natural plasmids or the resultant effects on their bacterial host. We investigated the evolution of AMR plasmids confronted with different immigration rates of susc

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McMillan, Elizabeth A., Ly-Huong T. Nguyen, Lari M. Hiott, et al. "Genomic Comparison of Conjugative Plasmids from Salmonella enterica and Escherichia coli Encoding Beta-Lactamases and Capable of Mobilizing Kanamycin Resistance Col-like Plasmids." Microorganisms 9, no. 11 (2021): 2205. http://dx.doi.org/10.3390/microorganisms9112205.

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Salmonella enterica and Escherichia coli are important human pathogens that frequently contain plasmids, both large and small, carrying antibiotic resistance genes. Large conjugative plasmids are known to mobilize small Col plasmids, but less is known about the specificity of mobilization. In the current study, six S. enterica and four E. coli strains containing large plasmids were tested for their ability to mobilize three different kanamycin resistance Col plasmids (KanR plasmids). Large conjugative plasmids from five isolates, four S. enterica and one E. coli, were able to mobilize KanR pla

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Pedersen, K., T. Tiainen, and J. L. Larsen. "Plasmid profiles, restriction fragment length polymorphisms and O-serotypes amongVibrio anguillarumisolates." Epidemiology and Infection 117, no. 3 (1996): 471–78. http://dx.doi.org/10.1017/s0950268800059136.

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SummaryA total of 279Vibrio anguillarumstrains were serotyped and examined for plasmid content. Plasmids were subjected to digestion with restriction enzymes. Most strains belonged to serogroup O1 (39%) and O2 (16%). In total 164 strains (53%) carried plasmids. Of the O1 and O2 isolates, 92% and 30%, respectively, carried one or more plasmids. Restriction fragment length polymorphism (RFLP) analysis of plasmid DNA indicated that plasmids belonged to several groups. Each group seemed to be restricted to a single O-serovar. The largest group was the pJM1-like plasmids among most serovar O1 strai

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Rasko, David A., M. J. Rosovitz, Ole Andreas Økstad, et al. "Complete Sequence Analysis of Novel Plasmids from Emetic and Periodontal Bacillus cereus Isolates Reveals a Common Evolutionary History among the B. cereus-Group Plasmids, Including Bacillus anthracis pXO1." Journal of Bacteriology 189, no. 1 (2006): 52–64. http://dx.doi.org/10.1128/jb.01313-06.

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ABSTRACTThe plasmids of the members of theBacillus cereussensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example,Bacillus anthraciscontains two plasmids, pXO1 and pXO2, encoding toxin production and encapsulation, respectively, that define this species pathogenic potential, whereas the presence of a Bt toxin-encoding plasmid definesBacillus thuringiensisisolates. In this study the plasmids fromB. cereusisolates that produce emetic toxin or are linked to periodontal disease were sequenced and analyzed. Two periodontal i

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Sengupta, Manjistha, and Stuart Austin. "Prevalence and Significance of Plasmid Maintenance Functions in the Virulence Plasmids of Pathogenic Bacteria." Infection and Immunity 79, no. 7 (2011): 2502–9. http://dx.doi.org/10.1128/iai.00127-11.

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ABSTRACTVirulence functions of pathogenic bacteria are often encoded on large extrachromosomal plasmids. These plasmids are maintained at low copy number to reduce the metabolic burden on their host. Low-copy-number plasmids risk loss during cell division. This is countered by plasmid-encoded systems that ensure that each cell receives at least one plasmid copy. Plasmid replication and recombination can produce plasmid multimers that hinder plasmid segregation. These are removed by multimer resolution systems. Equitable distribution of the resulting monomers to daughter cells is ensured by pla

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van Passel, Mark W. J., Arie van der Ende, and Aldert Bart. "Plasmid Diversity in Neisseriae." Infection and Immunity 74, no. 8 (2006): 4892–99. http://dx.doi.org/10.1128/iai.02087-05.

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ABSTRACT Horizontal gene transfer constitutes an important force in prokaryotic genome evolution, and it is well-known that plasmids are vehicles for DNA transfer. Chromosomal DNA is frequently exchanged between pathogenic and commensal neisseriae, but relatively little is known about plasmid diversity and prevalence among these nasopharyngeal inhabitants. We investigated the plasmid contents of 18 Neisseria lactamica isolates and 20 nasopharyngeal Neisseria meningitidis isolates. Of 18 N. lactamica strains, 9 harbored one or more plasmids, whereas only one N. meningitidis isolate contained a

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Berg, Tracey, Neville Firth, Sumalee Apisiridej, Anusha Hettiaratchi, Amornrut Leelaporn, and Ronald A. Skurray. "Complete Nucleotide Sequence of pSK41: Evolution of Staphylococcal Conjugative Multiresistance Plasmids." Journal of Bacteriology 180, no. 17 (1998): 4350–59. http://dx.doi.org/10.1128/jb.180.17.4350-4359.1998.

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ABSTRACT The 46.4-kb nucleotide sequence of pSK41, a prototypical multiresistance plasmid from Staphylococcus aureus, has been determined, representing the first completely sequenced conjugative plasmid from a gram-positive organism. Analysis of the sequence has enabled the identification of the probable replication, maintenance, and transfer functions of the plasmid and has provided insights into the evolution of a clinically significant group of plasmids. The basis of deletions commonly associated with pSK41 family plasmids has been investigated, as has the observed insertion site specificit

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Chen, Liang, Kalyan D. Chavda, Roberto G. Melano, et al. "Molecular Survey of the Dissemination of TwoblaKPC-Harboring IncFIA Plasmids in New Jersey and New York Hospitals." Antimicrobial Agents and Chemotherapy 58, no. 4 (2014): 2289–94. http://dx.doi.org/10.1128/aac.02749-13.

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ABSTRACTKlebsiella pneumoniaecarbapenemase (KPC)-producingK. pneumoniaestrains have spread worldwide and become a major threat in health care facilities. Transmission ofblaKPC, the plasmid-borne KPC gene, can be mediated by clonal spread and horizontal transfer. Here, we report the complete nucleotide sequences of two novelblaKPC-3-harboring IncFIA plasmids, pBK30661 and pBK30683. pBK30661 is 74 kb in length, with a mosaic plasmid structure; it exhibits homologies to several other plasmids but lacks the plasmid transfer operon (tra) and the origin of transfer (oriT) that are required for plasm

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Ogbolu, David Olusoga, Oluwole Adebayo Daini, Afolabi Ogunledun, Oyebode Armstrong Terry Alli, and Mark Alexander Webber. "Dissemination of IncF plasmids carrying beta-lactamase genes in Gram-negative bacteria from Nigerian hospitals." Journal of Infection in Developing Countries 7, no. 05 (2013): 382–90. http://dx.doi.org/10.3855/jidc.2613.

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Introduction: Production of beta-lactamases is the predominant cause of resistance to beta-lactam antibiotics in Gram-negative bacteria. We investigated the diversity of plasmid-borne beta-lactamase genes and replicon type of the plasmids carrying the respective genes in Gram-negative bacteria recovered from clinical infection in Nigerian hospitals. Methodology: A total of 134 Gram-negative bacteria of 13 species were analyzed for antimicrobial susceptibility, phenotypic and genotypic detection of various beta-lactamases, and plasmid analysis, including replicon typing. Results: Of the 134 iso

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Wang, Pengxia, Dongmei He, Baiyuan Li, et al. "Eliminating mcr-1-harbouring plasmids in clinical isolates using the CRISPR/Cas9 system." Journal of Antimicrobial Chemotherapy 74, no. 9 (2019): 2559–65. http://dx.doi.org/10.1093/jac/dkz246.

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Abstract Objectives To eliminate mcr-1-harbouring plasmids and MDR plasmids in clinical Escherichia coli isolates. Methods Plasmid pMBLcas9 expressing Cas9 was constructed and used to clone target single-guide RNAs (sgRNAs) for plasmid curing. The recombinant plasmid pMBLcas9-sgRNA was transferred by conjugation into two clinical E. coli isolates. The curing efficiency of different sgRNAs targeting conserved genes was tested. The elimination of targeted plasmids and the generation of transposase-mediated recombination of p14EC033a variants were characterized by PCR and DNA sequencing. Results

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Guillard, Thomas, Emmanuelle Cambau, Catherine Neuwirth, et al. "Description of a 2,683-Base-Pair Plasmid ContainingqnrDin Two Providencia rettgeri Isolates." Antimicrobial Agents and Chemotherapy 56, no. 1 (2011): 565–68. http://dx.doi.org/10.1128/aac.00081-11.

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ABSTRACTqnrgenes are plasmid-mediated quinolone resistance genes mainly harbored on large conjugative multiresistant plasmids. TheqnrDgene was recently observed inSalmonella entericaon a small nonconjugative plasmid (p2007057). We describe two strains ofProvidencia rettgeriharboringqnrDon nonconjugative plasmids. The plasmids were 99% identical, with 2,683 bp and four open reading frames, includingqnrD, but exhibited only 53% identity with the plasmid found inS. enterica.

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Rosenshine, Ilan, and Moshe Mevarech. "Isolation and partial characterization of plasmids found in three Halobacterium volcanii isolates." Canadian Journal of Microbiology 35, no. 1 (1989): 92–95. http://dx.doi.org/10.1139/m89-014.

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Three new isolates of Halobacterium volcanii were screened for the presence of plasmids. Each of the different isolates was found to contain one plasmid. These plasmids do not show any homology to each other, nor to the previously isolated plasmid pHV2. Partial restriction maps of these plasmids were determined. One of the plasmids contains chromosomal repetitive sequences as judged by the existence of homologous sequences in the chromosomal DNA of the three isolates. Using the protoplast fusion technique, we showed that at least one of the newly isolated plasmids is compatible with pHV2.Key w

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Guo, Rui, Gen Li, Leilei Lu, et al. "The Plasmid pEX18Gm Indirectly Increases Caenorhabditis elegans Fecundity by Accelerating Bacterial Methionine Synthesis." International Journal of Molecular Sciences 23, no. 9 (2022): 5003. http://dx.doi.org/10.3390/ijms23095003.

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Plasmids are mostly found in bacteria as extrachromosomal genetic elements and are widely used in genetic engineering. Exploring the mechanisms of plasmid–host interaction can provide crucial information for the application of plasmids in genetic engineering. However, many studies have generally focused on the influence of plasmids on their bacterial hosts, and the effects of plasmids on bacteria-feeding animals have not been explored in detail. Here, we use a “plasmid–bacteria–Caenorhabditis elegans” model to explore the impact of plasmids on their host bacteria and bacterivorous nematodes. F

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Qin, Zhongjun, Meijuan Shen, and Stanley N. Cohen. "Identification and Characterization of a pSLA2 Plasmid Locus Required for Linear DNA Replication and Circular Plasmid Stable Inheritance in Streptomyces lividans." Journal of Bacteriology 185, no. 22 (2003): 6575–82. http://dx.doi.org/10.1128/jb.185.22.6575-6582.2003.

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ABSTRACT Streptomyces linear plasmids and linear chromosomes can replicate also in a circular form when their telomeres are deleted. The 17-kb linear plasmid pSLA2 has been a useful model in studies of such replicons. Here we report that the minimal origin initiating replication of pSLA2-derived plasmids as circular molecules cannot propagate these plasmids in a linear mode unless they also contain a novel plasmid-encoded locus, here named rlrA (required for linear replication). In contrast with the need for rlrA to accomplish replication of telomere-containing linear plasmids, expression of r

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Chen, Chin-Yi, Ly-Huong T. Nguyen, and Terence P. Strobaugh. "Sequence analysis and plasmid mobilization of a 6.6-kb kanamycin resistance plasmid, pSNC3-Kan, from a Salmonella enterica serotype Newport isolate." PLOS ONE 17, no. 7 (2022): e0268502. http://dx.doi.org/10.1371/journal.pone.0268502.

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Research on the transfer of antibiotic resistance plasmids has been mainly focused on the large multi-drug resistance conjugative plasmids, while the transmission of small mobilizable plasmids remains under-investigated. A series of diverse ColE-like kanamycin resistance plasmids (“KanR plasmids”) from Salmonella enterica were characterized previously. In this study, the 6.6-kb pSNC3-Kan from a Salmonella enterica serotype Newport isolate was investigated. It possessed highly conserved RNA I/II and Tn602 (IS903-aph-IS903) regions to two other KanR plasmids pSe-Kan and pSBardo-Kan, but carried

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Zhang, Ran, Ana Zeng, Ping Fang, and Zhongjun Qin. "Characterization of Replication and Conjugation of Streptomyces Circular Plasmids pFP1 and pFP11 and Their Ability To Propagate in Linear Mode with Artificially Attached Telomeres." Applied and Environmental Microbiology 74, no. 11 (2008): 3368–76. http://dx.doi.org/10.1128/aem.00402-08.

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ABSTRACT Many Streptomyces species harbor circular plasmids (8 to 31 kb) as well as linear plasmids (12 to 1,700 kb). We report the characterization of two newly detected circular plasmids, pFP11 (35,139 bp) and pFP1 (39,360 bp). As on linear plasmids, their replication loci comprise repA genes and adjacent iterons, to which RepA proteins bind specifically in vitro. Plasmids containing the minimal iterons plus the repA locus of pFP11 were inherited extremely unstably; par and additional loci were required for stable inheritance. Surprisingly, plasmids containing replication loci from pFP11 or

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Dahlberg, Cecilia, and Lin Chao. "Amelioration of the Cost of Conjugative Plasmid Carriage in Eschericha coli K12." Genetics 165, no. 4 (2003): 1641–49. http://dx.doi.org/10.1093/genetics/165.4.1641.

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Abstract Although plasmids can provide beneficial functions to their host bacteria, they might confer a physiological or energetic cost. This study examines how natural selection may reduce the cost of carrying conjugative plasmids with drug-resistance markers in the absence of antibiotic selection. We studied two plasmids, R1 and RP4, both of which carry multiple drug resistance genes and were shown to impose an initial fitness cost on Escherichia coli. To determine if and how the cost could be reduced, we subjected plasmid-containing bacteria to 1100 generations of evolution in batch culture

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Galen, James E., Jay Nair, Jin Yuang Wang, et al. "Optimization of Plasmid Maintenance in the Attenuated Live Vector Vaccine Strain Salmonella typhiCVD 908-htrA." Infection and Immunity 67, no. 12 (1999): 6424–33. http://dx.doi.org/10.1128/iai.67.12.6424-6433.1999.

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ABSTRACT The broad objective of the research presented here is to develop a noncatalytic plasmid maintenance system for the stabilization of multicopy expression plasmids encoding foreign antigens in aSalmonella typhi live-vector vaccine strain such as CVD 908-htrA. We have enhanced the maintenance of expression plasmids at two independent levels. First, we removed dependence upon balanced-lethal maintenance systems that involve catalytic enzymes expressed from multicopy plasmids; we accomplished this through incorporation into expression plasmids of a postsegregational killing system based on

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Ding, Pengyun, Qianqian Wang, Liangliang Wang, et al. "Mechanisms of Transmission and Adaptation of tet(X4)-Positive IncHI1 Plasmids in XDR Escherichia coli from Pet Dogs: The Role of trhC, rsp, and the Tra1 Region." Veterinary Sciences 12, no. 5 (2025): 418. https://doi.org/10.3390/vetsci12050418.

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tet(X4)-positive IncHI1 plasmids are widely prevalent in various bacteria. To understand their transmission characteristics, we analyzed two extensively drug-resistant (XDR) Escherichia coli strains isolated from pet dog feces in Henan Province, China. Strain T28R harbored tet(X4)-positive IncHI1, IncF18:A-:B-, and mcr-1-positive IncI2 plasmids, while T16R carried tet(X4)-positive IncHI1, F16:A-:B-, and mcr-1-positive IncX4 plasmids. Four representative fusion plasmids, pT28R-F1, pT28R-F2, pT28R-F3, and pT16R-F1, in transconjugants were analyzed using WGS and PCR mapping. The results showed th

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Gregorova, Daniela, Jitka Matiasovicova, Alena Sebkova, Marcela Faldynova, and Ivan Rychlik. "Salmonella entericasubsp.entericaserovar Enteritidis harbours ColE1, ColE2, and rolling-circle-like replicating plasmids." Canadian Journal of Microbiology 50, no. 2 (2004): 107–12. http://dx.doi.org/10.1139/w03-113.

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Using DNA hybridization, at least three distinct groups of low molecular mass plasmids were identified in Salmonella enterica subsp. enterica serovar Enteritidis. After sequencing representative plasmids from each group, we concluded that they belonged to ColE1, ColE2, and rolling-circle-like replicating plasmids. Plasmid pK (4245 bp) is a representative of widely distributed ColE1 plasmids. Plasmid pP (4301 bp) is homologous to ColE2 plasmids and was present predominantly in single-stranded DNA form. The smallest plasmids pJ (2096 bp) and pB (1983 bp) were classified as rolling-circle-like re

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Nishida, Hiromi. "Comparative Analyses of Base Compositions, DNA Sizes, and Dinucleotide Frequency Profiles in Archaeal and Bacterial Chromosomes and Plasmids." International Journal of Evolutionary Biology 2012 (March 26, 2012): 1–5. http://dx.doi.org/10.1155/2012/342482.

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In the present paper, I compared guanine-cytosine (GC) contents, DNA sizes, and dinucleotide frequency profiles in 109 archaeal chromosomes, 59 archaeal plasmids, 1379 bacterial chromosomes, and 854 bacterial plasmids. In more than 80% of archaeal and bacterial plasmids, the GC content was lower than that of the host chromosome. Furthermore, most of the differences in GC content found between a plasmid and its host chromosome were less than 10%, and the GC content in plasmids and host chromosomes was highly correlated (Pearson’s correlation coefficient in bacteria and 0.917 in archaea). These

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Ishii, Hiroshi, Fujio Hayashi, Shizuko Iyobe, and Hajime Hashimoto. "Characterization and classification of Actinobacillus (Haemophilus) pleuropneumoniae plasmids." American Journal of Veterinary Research 52, no. 11 (1991): 1816–20. http://dx.doi.org/10.2460/ajvr.1991.52.11.1816.

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SUMMARY Actinobacillus (Haemophilus) pleuropneumoniae plasmids were characterized and classified. They were isolated from A pleuropneumoniae strains different in serotype, year isolated, or location from which isolated. Six of 8 plasmids encoded streptomycin (Sm) and sulfonamide (Su) resistance (SmSu). One of the other plasmids, pVM105, encoded ampicillin (Ap) resistance and another, pHM0, encoded no drug resistance. All SmSu plasmids were transferred to Escherichia coli strains by transformation. Among them, pABO and pMS260 were 8.1 kb and incompatible with each other; they were stable in E c

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Ishii, Hiroshi, Tsuguaki Fukuyasu, Shizuko Iyobe, and Hajime Hashimoto. "Characterization of newly isolated plasmids from Actinobacillus pleuropneumoniae." American Journal of Veterinary Research 54, no. 5 (1993): 701–8. http://dx.doi.org/10.2460/ajvr.1993.54.05.701.

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Summary The genetic basis of drug-resistant strains of Actinobacillus pleuropneumoniae in Japan was studied. The A pleuropneumoniae strains AV277 and AV281 that belong to serotype 2 were resistant to streptomycin (sm) and sulfonamide (sa). Both strains had an 8.1-kilobase (kb) sm-sa plasmid that was previously classified in the H1 group. The AV177 (serotype 1) strain was resistant to sm, sa, ampicillin, and kanamycin (km), but did not have any plasmids. The AV319 and AV324 (serotype 1) strains were resistant to sm, sa, tetracycline (tc), and chloramphenicol (cp). The AV318 (serotype 12) strain

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Tonin, Patricia N., and Robert B. Grant. "Genetic and physical characterization of trimethoprim resistance plasmids from Shigella sonnei and Shigella flexneri." Canadian Journal of Microbiology 33, no. 10 (1987): 905–13. http://dx.doi.org/10.1139/m87-157.

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Analysis of six Shigella flexneri and four S. sonnei isolates with trimethoprim (Tp) resistance from clinical cases in Ontario has shown that, in all isolates, the Tp resistance is mediated by gene(s) on conjugative, multiple antibiotic-resistance plasmids. The physical and genetic characterization of these plasmids revealed that there are three different Tp resistance plasmids. One group, composed of all six S. flexneri plasmids, consists of plasmids which are about 70 megadaltons (MDa) and inhibit the fertility of an Escherichia coli Hfr strain (Fi+). A representative member of this group, p

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Loftie-Eaton, Wesley, and Douglas E. Rawlings. "Comparative Biology of Two Natural Variants of the IncQ-2 Family Plasmids, pRAS3.1 and pRAS3.2." Journal of Bacteriology 191, no. 20 (2009): 6436–46. http://dx.doi.org/10.1128/jb.00864-09.

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ABSTRACT Plasmids pRAS3.1 and pRAS3.2 are two closely related, natural variants of the IncQ-2 plasmid family that have identical plasmid backbones except for two differences. Plasmid pRAS3.1 has five 6-bp repeat sequences in the promoter region of the mobB gene and four 22-bp iterons in its oriV region, whereas pRAS3.2 has only four 6-bp repeats and three 22-bp iterons. Plasmid pRAS3.1 was found to have a higher copy number than pRAS3.2, and we show that the extra 6-bp repeat results in an increase in mobB and downstream mobA/repB expression. Placement of repB (primase) behind an arabinose-ind

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Phan, Minh-Duy, Claire Kidgell, Satheesh Nair, et al. "Variation in Salmonella enterica Serovar Typhi IncHI1 Plasmids during the Global Spread of Resistant Typhoid Fever." Antimicrobial Agents and Chemotherapy 53, no. 2 (2008): 716–27. http://dx.doi.org/10.1128/aac.00645-08.

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ABSTRACT A global collection of plasmids of the IncHI1 incompatibility group from Salmonella enterica serovar Typhi were analyzed by using a combination of DNA sequencing, DNA sequence analysis, PCR, and microarrays. The IncHI1 resistance plasmids of serovar Typhi display a backbone of conserved gene content and arrangement, within which are embedded preferred acquisition sites for horizontal DNA transfer events. The variable regions appear to be preferred acquisition sites for DNA, most likely through composite transposition, which is presumably driven by the acquisition of resistance genes.

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Feizabadi, Mohammad Mehdi, Sorour Asadi, Maryam Zohari, Sara Gharavi, and Gelavizh Etemadi. "Genetic characterization of high-level gentamicin-resistant strains of Enterococcus faecalis in Iran." Canadian Journal of Microbiology 50, no. 10 (2004): 869–72. http://dx.doi.org/10.1139/w04-069.

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The prevalence of resistance to high levels of gentamicin among 182 isolates of Enterococcus faecalis from 2 Iranian hospitals was 42%. Gentamicin resistance was associated with conjugative plasmids (>70 kb) in most strains. Fingerprinting using EcoRI and HindIII showed genetic variation among these plasmids and gave evidence of nosocomial outbreaks and persistence of infection in different wards of the study hospitals, as well as transfer of plasmids between genetically diverse isolates. Using EcoRI, hospital-based specific plasmid fingerprints were detected for the isolates that had previ

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Taylor, Diane E., and Elisa C. Brose. "Characterization of incompatibility group HI1 plasmids from Salmonella typhi by restriction endonuclease digestion and hybridization of DNA probes for Tn3, Tn9, and Tn10." Canadian Journal of Microbiology 31, no. 8 (1985): 721–29. http://dx.doi.org/10.1139/m85-136.

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Chloramphenicol resistance in Salmonella typhi is mediated by plasmids of the incompatibility group H, subgroup 1 (IncHI1). Eight IncHI1 plasmids from S. typhi strains originating in Mexico, Vietnam, Thailand, and India were examined by restriction enzyme digestion. The restriction enzymes, ApaI, XbaI, and PstI were found to be most useful for comparison of plasmid DNAs. Four plasmids from S. typhi isolated in Mexico, Vietnam, and Thailand between 1972 and 1974 had identical restriction patterns with all three enzymes. The other IncHI1 plasmids showed only minor differences. However, some sign

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Colgan, D. J., and D. A. Willcocks. "Host–parasite genome relationships in Acridid grasshoppers. II. Patterns of variation in the plasmids of gut bacteria of Caledia captiva and Locusta migratoria." Genome 29, no. 2 (1987): 264–71. http://dx.doi.org/10.1139/g87-046.

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Plasmid preparations were made from 110 isolates of Enterobacter cloacae taken from the guts of members of the Caledia captiva complex of grasshoppers to ascertain whether a relationship exists between these extrachromosomal elements and taxonomic variation in the grasshoppers themselves. Fifty-two plasmids, distinguishable by mobility or restriction fragment pattern differences, were identified. Thirty-seven of these were similar in size. Five plasmids were nick translated and used to probe Southern blots. Only three instances of cross homology with another plasmid were found, implying a very

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Sayeed, Sameera, Jihong Li, and Bruce A. McClane. "Virulence Plasmid Diversity in Clostridium perfringens Type D Isolates." Infection and Immunity 75, no. 5 (2007): 2391–98. http://dx.doi.org/10.1128/iai.02014-06.

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ABSTRACT Clostridium perfringens type D isolates are important in biodefense and also cause natural enterotoxemias in sheep, goats, and occasionally cattle. In these isolates, the gene (etx) encoding ε-toxin is thought to reside on poorly characterized large plasmids. Type D isolates sometimes also produce other potentially plasmid-encoded toxins, including C. perfringens enterotoxin and beta2 toxin, encoded by the cpe and cbp2 genes, respectively. In the current study we demonstrated that the etx, cpe, and cpb2 genes are carried on plasmids in type D isolates and characterized the toxin-encod

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Mayer, L. W. "Use of plasmid profiles in epidemiologic surveillance of disease outbreaks and in tracing the transmission of antibiotic resistance." Clinical Microbiology Reviews 1, no. 2 (1988): 228–43. http://dx.doi.org/10.1128/cmr.1.2.228.

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Plasmids are circular deoxyribonucleic acid molecules that exist in bacteria, usually independent of the chromosome. The study of plasmids is important to medical microbiology because plasmids can encode genes for antibiotic resistance or virulence factors. Plasmids can also serve as markers of various bacterial strains when a typing system referred to as plasmid profiling, or plasmid fingerprinting is used. In these methods partially purified plasma deoxyribonucleic acid species are separated according to molecular size by agarose gel electrophoresis. In a second procedure, plasmid deoxyribon

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Paganini, Julian A., Jesse J. Kerkvliet, Lisa Vader, et al. "PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli." Microbial Genomics 10, no. 2 (2024). http://dx.doi.org/10.1099/mgen.0.001193.

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Accurate reconstruction of Escherichia coli antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct E. coli plasmids using short reads. We developed plasmidEC, an ensemble classifier that identifies plasmid-derived contigs by combining the output of three different binary classification tools. We showed that plasmidEC is especially suited to classify contigs derived from ARG plasmids with a high recall of 0.941. Additionally, we optimized gplas, a graph-base

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Kottara, Anastasia, James P. J. Hall, and Michael A. Brockhurst. "The proficiency of the original host species determines community-level plasmid dynamics." FEMS Microbiology Ecology 97, no. 4 (2021). http://dx.doi.org/10.1093/femsec/fiab026.

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ABSTRACTPlasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency affects plasmid persistence in communities. Here, we test this using multispecies bacterial soil communities comprising species varying in their proficiency to host a large conjugativ

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Androsiuk, Lucy, Sivan Maane, and Shay Tal. "CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range." Microbiology Spectrum, November 7, 2024. http://dx.doi.org/10.1128/spectrum.00104-24.

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ABSTRACT In recent years, there has been a surge in metagenomic studies focused on identifying plasmids in environmental samples. Although these studies have unearthed numerous novel plasmids, enriching our understanding of their environmental roles, a significant gap remains: the scarcity of information regarding the bacterial hosts of these newly discovered plasmids. Furthermore, even when plasmids are identified within bacterial isolates, the reported host is typically limited to the original isolate, with no insights into alternative hosts or the plasmid’s potential host range. Given that

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Wang, Teng, and Lingchong You. "The persistence potential of transferable plasmids." Nature Communications 11, no. 1 (2020). http://dx.doi.org/10.1038/s41467-020-19368-7.

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Abstract Conjugative plasmids can mediate the spread and maintenance of diverse traits and functions in microbial communities. This role depends on the plasmid’s ability to persist in a population. However, for a community consisting of multiple populations transferring multiple plasmids, the conditions underlying plasmid persistence are poorly understood. Here, we describe a plasmid-centric framework that makes it computationally feasible to analyze gene flow in complex communities. Using this framework, we derive the ‘persistence potential’: a general, heuristic metric that predicts the pers

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He, Kun, Jiayu Lin, Yulei Liang, et al. "Coexistence of a nonresistance-conferring IncI1 plasmid favors persistence of the bla _CTX-M -bearing IncFII plasmid in Escherichia coli." Microbiology Spectrum, April 30, 2024. http://dx.doi.org/10.1128/spectrum.04240-23.

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ABSTRACT The interaction between coexisting plasmids can affect plasmid-carried resistance gene persistence and spread. However, whether the persistence of the bla CTX-M gene in clinical Enterobacteriaceae is related to the interaction of coresident nonresistance-conferring plasmids has not been reported. This study was initiated to elucidate how a nonresistance-conferring IncI1 plasmid affected the bla CTX-M -bearing IncFII plasmid colocated on the same cell. Herein, we constructed three isogenic derivatives of E. coli C600, designated as C600 FII , C600 I1 , and C600 FII+I1 , which harbored

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