The Experts below are selected from a list of 228 Experts worldwide ranked by ideXlab platform
Andre Hoekema - One of the best experts on this subject based on the ideXlab platform.
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new agrobacterium helper Plasmids for gene transfer to plants
Transgenic Research, 1993Co-Authors: Elizabeth E Hood, Stanton B Gelvin, Leo S Melchers, Andre HoekemaAbstract:We describe the construction of new helper Ti Plasmids forAgrobacterium-mediated plant transformation. These Plasmids are derived from three differentAgrobacterium tumefaciens Ti Plasmids, the octopine Plasmid pTiB6, the nopaline Plasmid pTiC58, and the L,L-succinamopine Plasmid pTiBo542. The T-DNA regions of these Plasmids were deleted using site-directed mutagenesis to yield replicons carrying thevir genes that will complement binary vectorsin trans. Data are included that demonstrate strain utility. The advantages ofAgrobacterium strains harbouring these ‘disamed’ Ti Plasmids for plant transformation viaAgrobacterium are discussed.
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NewAgrobacterium helper Plasmids for gene transfer to plants
Transgenic Research, 1993Co-Authors: Elizabeth E Hood, Stanton B Gelvin, Leo S Melchers, Andre HoekemaAbstract:We describe the construction of new helper Ti Plasmids for Agrobacterium -mediated plant transformation. These Plasmids are derived from three different Agrobacterium tumefaciens Ti Plasmids, the octopine Plasmid pTiB6, the nopaline Plasmid pTiC58, and the L,L-succinamopine Plasmid pTiBo542. The T-DNA regions of these Plasmids were deleted using site-directed mutagenesis to yield replicons carrying the vir genes that will complement binary vectors in trans . Data are included that demonstrate strain utility. The advantages of Agrobacterium strains harbouring these ‘disamed’ Ti Plasmids for plant transformation via Agrobacterium are discussed.
Kathryn E Holt - One of the best experts on this subject based on the ideXlab platform.
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Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid
PLoS Neglected Tropical Diseases, 2011Co-Authors: Kathryn E Holt, Satheesh Nair, Minh Duy Phan, Stephen Baker, Pham Thanh Duy, Tran Vu Thieu Nga, A.keith Turner, Ciara Walsh, Séamus Fanning, Sinéad Farrell-wardAbstract:Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), remains a serious global health concern. Since their emergence in the mid-1970s multi-drug resistant (MDR) S. Typhi now dominate drug sensitive equivalents in many regions. MDR in S. Typhi is almost exclusively conferred by self-transmissible IncHI1 Plasmids carrying a suite of antimicrobial resistance genes. We identified over 300 single nucleotide polymorphisms (SNPs) within conserved regions of the IncHI1 Plasmid, and genotyped both Plasmid and chromosomal SNPs in over 450 S. Typhi dating back to 1958. Prior to 1995, a variety of IncHI1 Plasmid types were detected in distinct S. Typhi haplotypes. Highly similar Plasmids were detected in co-circulating S. Typhi haplotypes, indicative of Plasmid transfer. In contrast, from 1995 onwards, 98% of MDR S. Typhi were Plasmid sequence type 6 (PST6) and S. Typhi haplotype H58, indicating recent global spread of a dominant MDR clone. To investigate whether PST6 conferred a selective advantage compared to other IncHI1 Plasmids, we used a phenotyping array to compare the impact of IncHI1 PST6 and PST1 Plasmids in a common S. Typhi host. The PST6 Plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU.
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variation in salmonella enterica serovar typhi inchi1 Plasmids during the global spread of resistant typhoid fever
Antimicrobial Agents and Chemotherapy, 2009Co-Authors: Minhduy Phan, Claire Kidgell, Satheesh Nair, Kathryn E Holt, Arthur K Turner, Jason Hinds, Philip D Butcher, Fiona J Cooke, Nicholas R Thomson, Richard W TitballAbstract: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. Plasmid multilocus sequence typing, a molecular typing method for IncHI1 Plasmids, was developed using variation in six conserved loci to trace the spread of these Plasmids and to elucidate their evolutionary relationships. The application of this method to a collection of 36 IncHI1 Plasmids revealed a chronological clustering of Plasmids despite their difference in geographical origins. Our findings suggest that the predominant Plasmid types present after 1993 have not evolved directly from the earlier predominant Plasmid type but have displaced them. We propose that antibiotic selection acts to maintain resistance genes on the Plasmid, but there is also competition between Plasmids encoding the same resistance phenotype.
Alessandra Carattoli - One of the best experts on this subject based on the ideXlab platform.
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Evolution of Plasmids and evolution of virulence and antibiotic-resistance Plasmids.
Evolutionary Biology of Bacterial and Fungal Pathogens, 2014Co-Authors: Alessandra CarattoliAbstract:This chapter discusses the characteristics and features of Plasmids, providing limited but significant and often cited examples of the evolution of natural Plasmids. The evolution of Plasmid-mediated antibiotic resistance is illustrated through the description of the IncFIme Plasmid, a well-studied virulence and resistance Plasmid, and of other broad-host-range resistance Plasmids. Many natural Plasmids are stably maintained at their characteristic copy number within the growing bacterial population. The study of how the evolution of virulence Plasmids happens may allow a more complete understanding of how pathogens evolve, and the analysis of those sequences offers the opportunity to compare virulence Plasmids from closely related or distant species to better understand the origin of the pathogenic traits. Furthermore, the virulence Plasmid might occasionally be replaced or driven away by incoming Plasmids of the same Inc group. A model developed to describe the evolution of the iteron-based replication system is that of the IncQ Plasmids. Bacterial conjugation is an essential property for Plasmid dissemination. Conjugative systems (Tra systems) in gram-negative bacteria support transfer between different genera and kingdoms, regardless of their replication mechanisms. They consist of three components: the transferosome, the relaxosome, and the coupling protein. The presence of multiple physically linked resistance genes on the same Plasmid, conferring resistance to different classes of antibiotics, may confer a selective advantage to the bacterial host when several antimicrobials are simultaneously administered. Such synergy between different coexpressed resistance genes would allow the recipient host to be positively selected by each individual class of antibiotics.
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expansion of the incx Plasmid family for improved identification and typing of novel Plasmids in drug resistant enterobacteriaceae
Plasmid, 2012Co-Authors: Timothy J. Johnson, Eliza Maria Bielak, Daniela Fortini, Lars Hestbjerg Hansen, Henrik Hasman, Chitrita Debroy, Lisa K Nolan, Alessandra CarattoliAbstract:Abstract IncX Plasmids are narrow host range Plasmids of Enterobactericeae that have been isolated for over 50 years. They are known to encode type IV fimbriae enabling their own conjugative transfer, and to provide accessory functions to their host bacteria such as resistance towards antimicrobial agents and biofilm formation. Previous Plasmid-based replicon typing procedures have indicated that the prevalence of IncX Plasmids is low among members of the Enterobacteriaceae. However, examination of a number of IncX-like Plasmid sequences and their occurrence in various organisms suggests that IncX Plasmid diversity and prevalence is underappreciated. To address these possible shortcomings, we generated additional Plasmid sequences of IncX Plasmids of interest and compared them to the genomes of all sequenced IncX-like Plasmids. These comparisons revealed that IncX Plasmids possess a highly syntenic Plasmid backbone, but that they are quite divergent with respect to nucleotide and amino acid similarity. Based on phylogenetic comparisons of the sequenced IncX Plasmids, the IncX Plasmid group has been expanded to include at least four subtypes, IncX1-IncX4. A revised IncX Plasmid replicon typing procedure, based upon these sequences and subtypes, was then developed. Use of this revised typing procedure revealed that IncX Plasmid occurrence among bacterial populations is much more common than had previously been acknowledged. Thus, this revised procedure can be used to better discern the occurrence of IncX type Plasmids among enterobacterial populations.
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Resistance Plasmid families in Enterobacteriaceae
Antimicrobial Agents and Chemotherapy, 2009Co-Authors: Alessandra CarattoliAbstract:Bacteria carry extrachromosomal, self-replicating genetic el- ements called Plasmids. A Plasmid is defined as a double- stranded, circular DNA molecule capable of autonomous rep- lication. By definition, Plasmids do not carry genes essential for the growth of host cells under nonstressed conditions (109). Plasmids have systems which guarantee their autonomous rep- lication but also have mechanisms controlling their copy num- ber and ensuring stable inheritance during cell division. They can promote lateral transfer among bacteria of different gen- era and kingdoms through the conjugation process. Many plas- mids encode addiction systems generally based on toxin-anti- toxin factors, which are able to kill daughter cells that do not inherit the Plasmid during cell division (46). These systems efficiently promote Plasmid maintenance in the bacterial pop- ulation, regardless of other selective pressure, and do not pro- vide any apparent benefit to the bacterium hosting the Plasmid. However, most of the Plasmids confer positively selectable phenotypes with the presence of antimicrobial resistance genes. We consider Plasmids to be living organisms in spite of their simple structure, since they are unit elements of a con- tinuous lineage with individual evolutionary history. Conjuga- tive Plasmids resemble lambdoid phages, which are capable of theta replication during vegetative growth and rolling-circle replication during “packaging” of the DNA into a recipient cell (62). The ability to recognize and categorize Plasmids in homo- geneous groups on the basis of their phylogenetic relatedness is helpful to analyze their distribution in nature and their relationship to host cells and to discover their evolutionary origins (34). Identification and classification of Plasmids should be based on genetic traits that are present and constant. These criteria are best met by traits concerned with Plasmid maintenance, especially replication controls (28). In 1971, Hedges and Datta proposed a Plasmid classification scheme based on the stability of Plasmids during conjugation, a phenomenon called Plasmid incompatibility (27, 47). Incompatibility is a manifestation of the relatedness of Plasmids that share common replication controls (27, 78). Incompatibility was defined as the inability of two related Plasmids to be propagated stably in the same cell line; thus, only compatible Plasmids can be rescued in transconjugants. The first incompatibility (Inc) groups were * Mailing address: Department of Infectious, Parasitic and Immune- Mediated Diseases, Istituto Superiore di Sanita `, Viale Regina Elena 299, 00161 Rome, Italy. Phone: 39-06-4990-3128. Fax: 39-06-4938- 7112. E-mail: alecara@iss.it. ? Published ahead of print on 23 March 2009. defined as follows: IncI, Plasmids producing type I pili suscep- tible to phage Ifl; IncN, N3-related Plasmids susceptible to phage IKe; IncF, Plasmids producing type F pili susceptible to phage Ff; and IncP, RP4-related Plasmids susceptible to the PRR1 phage (27, 47). Currently, 27 Inc groups are recognized in Enterobacteriaceae by the Plasmid Section of the National Collection of Type Cultures (London, United Kingdom), in- cluding six IncF (FII to VII) and three IncI (I1, I?, I2) variants. In 1988, Couturier and colleagues proposed a genetic Plasmid typing scheme based on Southern blot hybridization, using cloned replication regions (replicons) as probes (26). This ap- proach successfully provided classification for both conjugative and nonconjugative Plasmids, but the low specificity of the hybridization method underestimated Plasmid diversity be- cause of the cross-hybridization reaction among highly related replicons (repI, repB/O, repFII, repFIC). Since 2005, a PCR- based replicon typing (PBRT) scheme has been available, tar- geting the replicons of the major Plasmid families occurring in Enterobacteriaceae (HI2, HI1, I1-?, X, L/M, N, FIA, FIB, FIC, W, Y, P, A/C, T, K, B/O) and also including PCR assays (FrepB and FIIAs PCRs), detecting the FII, FIII, FIV, and FIV variants and the FII replicon of the Salmonella virulence Plasmids, respectively (12). However, the PBRT scheme still has several limitations, since the classification is currently based on Plasmids belonging to the classic Inc groups and can fail to identify divergent or novel replicons. The most accurate method to characterize a Plasmid is based on the determina- tion of the full-length DNA sequence, and to date, more than 800 Plasmids from Gammaproteobacteria have been fully se- quenced (http://www.ncbi.nlm.nih.gov/genome/), contributing to the identification of novel Plasmid families. Furthermore, more than 1,000 resistance Plasmids have been typed and as- signed to specific Plasmid families by PBRT and hybridization/ conjugation methods. This review aims to provide an overview of the major Plasmid families that are currently emerging in multidrug-resistant Enterobacteriaceae strains isolated world- wide among those conferring resistance to clinically relevant antibiotics, such as extended-spectrum cephalosporins, fluoro- quinolones, and aminoglycosides
Satheesh Nair - One of the best experts on this subject based on the ideXlab platform.
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Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid
PLoS Neglected Tropical Diseases, 2011Co-Authors: Kathryn E Holt, Satheesh Nair, Minh Duy Phan, Stephen Baker, Pham Thanh Duy, Tran Vu Thieu Nga, A.keith Turner, Ciara Walsh, Séamus Fanning, Sinéad Farrell-wardAbstract:Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), remains a serious global health concern. Since their emergence in the mid-1970s multi-drug resistant (MDR) S. Typhi now dominate drug sensitive equivalents in many regions. MDR in S. Typhi is almost exclusively conferred by self-transmissible IncHI1 Plasmids carrying a suite of antimicrobial resistance genes. We identified over 300 single nucleotide polymorphisms (SNPs) within conserved regions of the IncHI1 Plasmid, and genotyped both Plasmid and chromosomal SNPs in over 450 S. Typhi dating back to 1958. Prior to 1995, a variety of IncHI1 Plasmid types were detected in distinct S. Typhi haplotypes. Highly similar Plasmids were detected in co-circulating S. Typhi haplotypes, indicative of Plasmid transfer. In contrast, from 1995 onwards, 98% of MDR S. Typhi were Plasmid sequence type 6 (PST6) and S. Typhi haplotype H58, indicating recent global spread of a dominant MDR clone. To investigate whether PST6 conferred a selective advantage compared to other IncHI1 Plasmids, we used a phenotyping array to compare the impact of IncHI1 PST6 and PST1 Plasmids in a common S. Typhi host. The PST6 Plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU.
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variation in salmonella enterica serovar typhi inchi1 Plasmids during the global spread of resistant typhoid fever
Antimicrobial Agents and Chemotherapy, 2009Co-Authors: Minhduy Phan, Claire Kidgell, Satheesh Nair, Kathryn E Holt, Arthur K Turner, Jason Hinds, Philip D Butcher, Fiona J Cooke, Nicholas R Thomson, Richard W TitballAbstract: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. Plasmid multilocus sequence typing, a molecular typing method for IncHI1 Plasmids, was developed using variation in six conserved loci to trace the spread of these Plasmids and to elucidate their evolutionary relationships. The application of this method to a collection of 36 IncHI1 Plasmids revealed a chronological clustering of Plasmids despite their difference in geographical origins. Our findings suggest that the predominant Plasmid types present after 1993 have not evolved directly from the earlier predominant Plasmid type but have displaced them. We propose that antibiotic selection acts to maintain resistance genes on the Plasmid, but there is also competition between Plasmids encoding the same resistance phenotype.
Richard W Titball - One of the best experts on this subject based on the ideXlab platform.
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variation in salmonella enterica serovar typhi inchi1 Plasmids during the global spread of resistant typhoid fever
Antimicrobial Agents and Chemotherapy, 2009Co-Authors: Minhduy Phan, Claire Kidgell, Satheesh Nair, Kathryn E Holt, Arthur K Turner, Jason Hinds, Philip D Butcher, Fiona J Cooke, Nicholas R Thomson, Richard W TitballAbstract: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. Plasmid multilocus sequence typing, a molecular typing method for IncHI1 Plasmids, was developed using variation in six conserved loci to trace the spread of these Plasmids and to elucidate their evolutionary relationships. The application of this method to a collection of 36 IncHI1 Plasmids revealed a chronological clustering of Plasmids despite their difference in geographical origins. Our findings suggest that the predominant Plasmid types present after 1993 have not evolved directly from the earlier predominant Plasmid type but have displaced them. We propose that antibiotic selection acts to maintain resistance genes on the Plasmid, but there is also competition between Plasmids encoding the same resistance phenotype.
