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Ambrose SJ, Hall RM. dfrA trimethoprim resistance genes found in Gram-negative bacteria: compilation and unambiguous numbering. J Antimicrob Chemother 2021; 76:2748-2756. [PMID: 34180526 DOI: 10.1093/jac/dkab212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To track the spread of antibiotic resistance genes, accurate identification of individual genes is essential. Acquired trimethoprim resistance genes encoding trimethoprim-insensitive homologues of the sensitive dihydrofolate reductases encoded by the folA genes of bacteria are increasingly found in genome sequences. However, naming and numbering in publicly available records (journal publications or entries in the GenBank non-redundant DNA database) has not always been unambiguous. In addition, the nomenclature has evolved over time. Here, the changes in nomenclature and the most commonly encountered problems and pitfalls affecting dfrA gene identification arising from historically incorrect or inaccurate numbering are explained. The complete set of dfrA genes/DfrA proteins found in Gram-negative bacteria for which readily searchable sequence information is currently available has been compiled using less than 98% identity for both the gene and the derived protein sequence as the criteria for assignment of a new number. In most cases, trimethoprim resistance has been demonstrated. The gene context, predominantly in a gene cassette or near the ori end of CR1 or CR2, is also covered. The RefSeq database that underpins the programs used to automatically identify resistance genes in genome data sets has been curated to assign all sequences listed to the correct number. This led to the assignment of corrected or new gene numbers to several mis-assigned sequences. The unique numbers assigned for the dfrA/DfrA set are now listed in the RefSeq database, which we propose provides a way forward that should end future duplication of numbers and the confusion that causes.
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Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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2
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Jové T, Da Re S, Tabesse A, Gassama-Sow A, Ploy MC. Gene Expression in Class 2 Integrons Is SOS-Independent and Involves Two Pc Promoters. Front Microbiol 2017; 8:1499. [PMID: 28861047 PMCID: PMC5559693 DOI: 10.3389/fmicb.2017.01499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/26/2017] [Indexed: 12/22/2022] Open
Abstract
Integrons are powerful bacterial genetic elements that permit the expression and dissemination of antibiotic-resistance gene cassettes. They contain a promoter Pc that allows the expression of gene cassettes captured through site-specific recombination catalyzed by IntI, the integron-encoded integrase. Class 1 and 2 integrons are found in both clinical and environmental settings. The regulation of intI and of Pc promoters has been extensively studied in class 1 integrons and the regulatory role of the SOS response on intI expression has been shown. Here we investigated class 2 integrons. We characterized the PintI2 promoter and showed that intI2 expression is not regulated via the SOS response. We also showed that, unlike class 1 integrons, class 2 integrons possess not one but two active Pc promoters that are located within the attI2 region that seem to contribute equally to gene cassette expression. Class 2 integrons mostly encode an inactive truncated integrase, but the rare class 2 integrons that encode an active integrase are associated with less efficient Pc2 promoter variants. We propose an evolutionary model for class 2 integrons in which the absence of repression of the integrase gene expression led to mutations resulting in either inactive integrase or Pc variants of weaker activity, thereby reducing the potential fitness cost of these integrons.
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Affiliation(s)
- Thomas Jové
- INSERM, CHU Limoges, UMR 1092, Université LimogesLimoges, France
| | - Sandra Da Re
- INSERM, CHU Limoges, UMR 1092, Université LimogesLimoges, France
| | - Aurore Tabesse
- INSERM, CHU Limoges, UMR 1092, Université LimogesLimoges, France
| | - Amy Gassama-Sow
- Unité de Bactériologie Expérimentale, Institut Pasteur de DakarDakar, Senegal
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3
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Alotaibi M, Reyes BD, Le T, Luong P, Valafar F, Metzger RP, Fogel GB, Hecht D. Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution. J Mol Graph Model 2017; 71:135-153. [PMID: 27914300 PMCID: PMC5203806 DOI: 10.1016/j.jmgm.2016.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/04/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022]
Abstract
Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomal-encoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.
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Affiliation(s)
- Mona Alotaibi
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; King Saud University, P.O. Box 245714, Riyadh 11312, Saudi Arabia.
| | - Ben Delos Reyes
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Tin Le
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Phuong Luong
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Faramarz Valafar
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, CA 92182-7720, USA.
| | - Robert P Metzger
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
| | - Gary B Fogel
- Natural Selection, Inc., 6480 Weathers Place, Suite 350, San Diego, CA 92121, USA.
| | - David Hecht
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; Department of Chemistry, Southwestern College, 900 Otay Lakes Rd., Chula Vista, CA 91910, USA.
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Sumrall ET, Gallo EB, Aboderin AO, Lamikanra A, Okeke IN. Dissemination of the transmissible quinolone-resistance gene qnrS1 by IncX plasmids in Nigeria. PLoS One 2014; 9:e110279. [PMID: 25340787 PMCID: PMC4207749 DOI: 10.1371/journal.pone.0110279] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/16/2014] [Indexed: 11/29/2022] Open
Abstract
The plasmid-encoded quinolone resistance gene qnrS1 was recently found to be commonly associated with ciprofloxacin resistance in Nigeria. We mapped the qnrS1 gene from an Escherichia coli isolate obtained in Nigeria to a 43.5 Kb IncX2 plasmid. The plasmid, pEBG1, was sufficient to confer ciprofloxacin non-susceptibility, as well as tetracycline and trimethoprim resistance, on E. coli K-12. Deletion analysis confirmed that qnrS1 accounted for all the ciprofloxacin non-suceptibility conferred by pEBG1 and tetracycline and trimethoprim resistance could be attributed to tetAR and dfrA14 genes respectively. While it contained a complete IncX conjugation system, pEBG1 was not self-transmissible likely due to an IS3 element inserted between the pilX5 and pilX6 genes. The plasmid was however efficiently mobilizable. pEBG1 was most similar to another qnrS1-bearing IncX2 plasmid from Nigeria, but both plasmids acquired qnrS1 independently and differ in their content of other resistance genes. Screening qnrS1–positive isolates from other individuals in Nigeria revealed that they carried neither pEBG1 nor pNGX2-QnrS1 but that IncX plasmids were prevalent. This study demonstrates that the IncX backbone is a flexible platform that has contributed to qnrS1 dissemination in Nigeria.
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Affiliation(s)
- Eric T. Sumrall
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Elizabeth B. Gallo
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Aaron Oladipo Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Adebayo Lamikanra
- Department of Pharmaceutics, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Iruka N. Okeke
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail:
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Dang TND, Zhang L, Zöllner S, Srinivasan U, Abbas K, Marrs CF, Foxman B. Uropathogenic Escherichia coli are less likely than paired fecal E. coli to have CRISPR loci. INFECTION GENETICS AND EVOLUTION 2013; 19:212-8. [DOI: 10.1016/j.meegid.2013.07.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 07/01/2013] [Accepted: 07/16/2013] [Indexed: 11/26/2022]
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Okeke IN, Wallace-Gadsden F, Simons HR, Matthews N, Labar AS, Hwang J, Wain J. Multi-locus sequence typing of enteroaggregative Escherichia coli isolates from Nigerian children uncovers multiple lineages. PLoS One 2010; 5:e14093. [PMID: 21124856 PMCID: PMC2990770 DOI: 10.1371/journal.pone.0014093] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 11/04/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Enteroaggregative Escherichia coli (EAEC) are defined by their stacked-brick adherence pattern to human epithelial cells. There is no all-encompassing genetic marker for EAEC. The category is commonly implicated in diarrhea but research is hampered by perplexing heterogeneity. METHODOLOGY/PRINCIPAL FINDINGS To identify key EAEC lineages, we applied multilocus sequence typing to 126 E. coli isolates from a Nigerian case-control study that showed aggregative adherence in the HEp-2 adherence assay, and 24 other EAEC strains from diverse locations. EAEC largely belonged to the A, B1 and D phylogenetic groups and only 7 (4.6%) isolates were in the B2 cluster. As many as 96 sequence types (STs) were identified but 60 (40%) of the EAEC strains belong to or are double locus variants of STs 10, 31, and 394. The remainder did not belong to predominant complexes. The most common ST complex, with predicted ancestor ST10, included 32 (21.3%) of the isolates. Significant age-related distribution suggests that weaned children in Nigeria are at risk for diarrhea from of ST10-complex EAEC. Phylogenetic group D EAEC strains, predominantly from ST31- and ST394 complexes, represented 38 (25.3%) of all isolates, include genome-sequenced strain 042, and possessed conserved chromosomal loci. CONCLUSIONS/SIGNIFICANCE We have developed a molecular phylogenetic framework, which demonstrates that although grouped by a shared phenotype, the category of 'EAEC' encompasses multiple pathogenic lineages. Principal among isolates from Nigeria were ST10-complex EAEC that were associated with diarrhea in children over one year and ECOR D strains that share horizontally acquired loci.
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Affiliation(s)
- Iruka N Okeke
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA.
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Kim YB. Improved trimethoprim-resistance cassette for prokaryotic selections. J Biosci Bioeng 2010; 108:441-5. [PMID: 19804872 DOI: 10.1016/j.jbiosc.2009.05.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 05/21/2009] [Accepted: 05/22/2009] [Indexed: 11/28/2022]
Abstract
Many of the antibiotic resistance elements used in molecular biology have idiosyncratic limitations. For example, beta-lactam selections rely on antibiotics that are unstable to hydrolysis and allow satellite colonies to form upon extended incubation, and tetracycline selections typically give rise to widely varying colony sizes and lower transformation efficiencies. Although prokaryotic Type II dihydrofolate reductase (dfr) genes have long been considered to have potential utility for the selection of plasmids and mobile elements in bacteria, practical limitations to the quality of those selections, mostly relating to background and inefficiency, have led for the most part to their underuse. I describe here the construction of a Type IIa dfr prokaryotic expression cassette that confers strong resistance against trimethoprim (Tmp), a bactericidal dfr inhibiting antibiotic. The Tmp-resistance cassette provides consistent and efficient selections and plasmid transformation frequencies equivalent to those encountered with beta-lactamases.
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Affiliation(s)
- Young Bae Kim
- Center for Computational and Integrative Biology (CCIB), Massachusetts General Hospital and Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114, USA.
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8
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Abstract
Integrons can insert and excise antibiotic resistance genes on plasmids in bacteria by site-specific recombination. Class 1 integrons code for an integrase, IntI1 (337 amino acids in length), and are generally borne on elements derived from Tn5090, such as that found in the central part of Tn21. A second class of integron is found on transposon Tn7 and its relatives. We have completed the sequence of the Tn7 integrase gene, intI2, which contains an internal stop codon. This codon was found to be conserved among intI2 genes on three other Tn7-like transposons harboring different cassettes. The predicted peptide sequence (IntI2*) is 325 amino acids long and is 46% identical to IntI1. In order to detect recombination activity, the internal stop codon at position 179 in the parental allele was changed to a triplet coding for glutamic acid. The sequences flanking the cassette arrays in the class 1 and 2 integrons are not closely related, but a common pool of mobile cassettes is used by the different integron classes; two of the three antibiotic resistance cassettes on Tn7 and its close relatives are also found in various class 1 integrons. We also observed a fourth excisable cassette downstream of those described previously in Tn7. The fourth cassette encodes a 165-amino-acid protein of unknown function with 6.5 contiguous repeats of a sequence coding for 7 amino acids. IntI2*179E promoted site-specific excision of each of the cassettes in Tn7 at different frequencies. The integrases from Tn21 and Tn7 showed limited cross-specificity in that IntI1 could excise all cassettes from both Tn21 and Tn7. However, we did not observe a corresponding excision of the aadA1 cassette from Tn21 by IntI2*179E.
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Affiliation(s)
- Karin Hansson
- Department of Pharmaceutical Biosciences, Division of Microbiology, Uppsala University, Uppsala, Sweden
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9
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Okeke IN, Steinrück H, Kanack KJ, Elliott SJ, Sundström L, Kaper JB, Lamikanra A. Antibiotic-resistant cell-detaching Escherichia coli strains from Nigerian children. J Clin Microbiol 2002; 40:301-5. [PMID: 11773139 PMCID: PMC120082 DOI: 10.1128/jcm.40.1.301-305.2002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The properties of 23 cell-detaching Escherichia coli strains that were isolated from stool specimens in Nigeria are described. Common properties of the strains included the presence of genes encoding alpha-hemolysin (100%), pyelonephritis-associated pili (100%), and cytotoxic necrotizing factor 1 (70%) as well as lactose negativity (70%) and multiple antibiotic resistance (74%). Antibiotic resistance was shown in most cases to be transferable and associated with the presence of class 1 integrons. Phenotypic properties and pulsed-field gel electrophoresis analysis demonstrated that the majority of the strains, particularly multiply resistant, lactose-negative O4:H40 strains, were closely related. Multiply-resistant cell-detaching E. coli strains may represent an important reservoir for antibiotic resistance genes.
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Affiliation(s)
- Iruka N Okeke
- Department of Microbiology and Immunology and Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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10
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Gibreel A, Sköld O. An integron cassette carrying dfr1 with 90-bp repeat sequences located on the chromosome of trimethoprim-resistant isolates of Campylobacter jejuni. Microb Drug Resist 2001; 6:91-8. [PMID: 10990262 DOI: 10.1089/107662900419384] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The frequent occurrence of high-level trimethoprim resistance in clinical isolates of Campylobacter jejuni was shown to be related to the acquisition of foreign resistance genes (dfrl or dfr9 or both) coding for resistant variants of the enzyme dihydrofolate reductase, the target of trimethoprim. The dfr1 gene detected on the chromosome of 40 different clinical strains of C. jejuni was studied further regarding structure and genetic organization. Most of the dfr1 genes were found as integron cassettes inserted in the chromosome. In 36% of the examined isolated, the dfr1 gene showed identity to that previously characterized in trimethoprim-resistant Escherichia coli. In 40% of the cases, however, a variant of the dfr1 gene containing a 90-bp direct repeat was detected, and in 5% of the isolates, the repeat-containing dfr1 variant was found to occur in the form of two cassettes in tandem in an integron context. The existence of the 90-bp repeat within the coding sequence of the dfr1gene was found to play a role in the adaptation of C. jejuni to ambient concentrations of trimethoprim.
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Affiliation(s)
- A Gibreel
- Department of Pharmaceutical Biosciences, Biomedical Center, Uppsala University, Sweden
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11
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Navia MM, Capitano L, Ruiz J, Vargas M, Urassa H, Schellemberg D, Gascon J, Vila J. Typing and characterization of mechanisms of resistance of Shigella spp. isolated from feces of children under 5 years of age from Ifakara, Tanzania. J Clin Microbiol 1999; 37:3113-7. [PMID: 10488163 PMCID: PMC85506 DOI: 10.1128/jcm.37.10.3113-3117.1999] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eighty-six strains of Shigella spp. were isolated during the dry season from stool samples of children under 5 years of age in Ifakara, Tanzania. The epidemiological relationship as well as the antimicrobial susceptibility and mechanisms of resistance to ampicillin, chloramphenicol, and co-trimoxazole were investigated. Four different epidemiological tools, pulsed-field gel electrophoresis (PFGE), repetitive extragenic palindromic (REP)-PCR, plasmid analysis, and antibiogram, were compared for typing Shigella strains. Seventy-eight (90%) strains were Shigella flexneri and were distributed into four groups, by either PFGE or REP-PCR, with 51, 17, 7, and 3 strains. The four strains of Shigella dysenteriae belonged to the same group, and the four strains of Shigella sonnei were distributed in two groups with three and one strain each. Plasmid analysis showed a high level of heterogeneity among strains belonging to the same PFGE group, while the antibiogram was less discriminative. REP-PCR provided an alternative, rapid, powerful genotyping method for Shigella spp. Overall, antimicrobial susceptibility testing showed a high level of resistance to ampicillin (81.8%), chloramphenicol (72.7%), tetracycline (96.9%), and co-trimoxazole (87.9%). Ampicillin resistance was related to an integron-borne OXA-1-type beta-lactamase in 85.1% of the cases and to a TEM-1-type beta-lactamase in the remaining 14.8%. Resistance to co-trimoxazole was due to the presence of a dhfr Ia gene in all groups except one of S. flexneri, where a dhfr VII gene was found within an integron. Chloramphenicol resistance was associated in every case with positive chloramphenicol acetyltransferase activity. All strains were susceptible to nalidixic acid, ciprofloxacin, ceftazidime, cefotaxime, and cefoxitin. Therefore, these antimicrobial agents may be good alternatives for the treatment of diarrhea caused by Shigella in Tanzania.
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Affiliation(s)
- M M Navia
- Departament de Microbiologia, Hospital Clinic, Institut d'Investigacions Biomèdiques August Pí i Sunyer, Villarroel 170, Barcelona 08036, Spain
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Seward RJ. Detection of integrons in worldwide nosocomial isolates of Acinetobacter spp. Clin Microbiol Infect 1999; 5:308-318. [PMID: 11856275 DOI: 10.1111/j.1469-0691.1999.tb00149.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE: To examine the distribution of integrons in genotypically unrelated worldwide multiresistant clinical isolates of Acinetobacter spp. METHODS: The presence and genetic location of class 1, 2 and 3 integrons were examined in a genotypically heterogeneous collection of 25 nosocomial isolates of Acinetobacter spp., from 15 locations in 11 different countries worldwide, by hybridization and PCR-based methods. Class 1 integron structures were characterized genetically by a PCR mapping technique. RESULTS: Class 1 integrons were detected in 17 of the 25 Acinetobacter isolates examined. Only one isolate contained a class 2 integron. No class 3 integrons were detected. The integrons varied in size and in the number of inserted cassettes, but similar integrons were found in genotypically distinct isolates from different locations worldwide. These structures were integrated into the chromosome in all isolates where they were detected, although some integrons were capable of subsequent transfer or mobilization. Genes coding for aminoglycoside-modifying enzymes formed the predominant cassettes identified within the integrons. CONCLUSIONS: Clinical isolates of Acinetobacter spp. from diverse locations seem to share resistance mechanisms acquired from other genera by a variety of mechanisms, including dissemination of integrons. Once integrons are incorporated into the bacterial genome, Acinetobacter spp. are potentially able to act as a reservoir of resistance genes for other species and genera.
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Affiliation(s)
- Rebecca J. Seward
- Department of Microbiology and PHLS Laboratory, University Hospital, Queen's Medical Centre, Nottingham, UK
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Falbo V, Carattoli A, Tosini F, Pezzella C, Dionisi AM, Luzzi I. Antibiotic resistance conferred by a conjugative plasmid and a class I integron in Vibrio cholerae O1 El Tor strains isolated in Albania and Italy. Antimicrob Agents Chemother 1999; 43:693-6. [PMID: 10049292 PMCID: PMC89185 DOI: 10.1128/aac.43.3.693] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/1998] [Accepted: 12/30/1998] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant Vibrio cholerae O1 El Tor strains isolated during the 1994 outbreak of cholera in Albania and Italy were characterized for the molecular basis of antibiotic resistance. All strains were found to be resistant to tetracycline, streptomycin, spectinomycin, trimethoprim, sulfathiazole, and the vibriostatic compound O/129 (2,4-diamino-6,7-diisopropylteridine). Resistance genes were self-transferable by a conjugative plasmid of about 60 MDa, with the exception of spectinomycin resistance, which was conferred by the aadA1 gene cassette located in the bacterial chromosome within a class 1 integron. The resistance to trimethoprim and O/129 was conferred by the dfrA1 gene, which was present on the plasmid. Although the dfrA1 gene is known to be borne on an integron cassette, class 1, 2, or 3 intI genes were not detected as part of the plasmid DNA from the strains studied.
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Affiliation(s)
- V Falbo
- Laboratory of Ultrastructures, Istituto Superiore di Sanità, Rome, Italy
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14
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Gibreel A, Sköld O. High-level resistance to trimethoprim in clinical isolates of Campylobacter jejuni by acquisition of foreign genes (dfr1 and dfr9) expressing drug-insensitive dihydrofolate reductases. Antimicrob Agents Chemother 1998; 42:3059-64. [PMID: 9835491 PMCID: PMC105999 DOI: 10.1128/aac.42.12.3059] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pathogenic bacterium Campylobacter jejuni has been regarded as endogenously resistant to trimethoprim. The genetic basis of this resistance was characterized in two collections of clinical isolates of C. jejuni obtained from two different parts of Sweden. The majority of these isolates were found to carry foreign dfr genes coding for resistant variants of the dihydrofolate reductase enzyme, the target of trimethoprim. The resistance genes, found on the chromosome, were dfr1 and dfr9. In about 10% of the strains, the dfr1 and dfr9 genes occurred simultaneously. About 10% of the examined isolates were found to be negative for these dfr genes and showed a markedly lower trimethoprim resistance level than the other isolates. The dfr9 and dfr1 genes were located in the context of remnants of a transposon and an integron, respectively. Two different surroundings for the dfr9 gene were characterized. One was identical to the right-hand end of the transposon Tn5393, and in the other, the dfr9 gene was flanked by only a few nucleotides of a Tn5393 sequence. The insertion of the dfr9 gene into the C. jejuni chromosome could have been mediated by Tn5393. The frequent occurrence of high-level trimethoprim resistance in clinical isolates of C. jejuni could be related to the heavy exposure of food animals to antibacterial drugs, which could lead to the acquisition of foreign resistance genes in naturally transformable strains of C. jejuni.
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Affiliation(s)
- A Gibreel
- Division of Microbiology, Department of Pharmaceutical Biosciences, Biomedical Center, Uppsala University, S-751 23 Uppsala, Sweden
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15
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Tosini F, Visca P, Luzzi I, Dionisi AM, Pezzella C, Petrucca A, Carattoli A. Class 1 integron-borne multiple-antibiotic resistance carried by IncFI and IncL/M plasmids in Salmonella enterica serotype typhimurium. Antimicrob Agents Chemother 1998; 42:3053-8. [PMID: 9835490 PMCID: PMC105998 DOI: 10.1128/aac.42.12.3053] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The presence and genetic content of integrons were investigated for 37 epidemiologically unrelated multiple-drug-resistant strains of Salmonella enterica serotype Typhimurium from humans. All isolates were resistant to ampicillin, chloramphenicol, kanamycin, streptomycin, sulfonamides, and trimethoprim, as well as to tetracycline and/or nalidixic acid; 20% of them were also resistant to gentamicin and amikacin. Three different class 1 integrons (In-t1, In-t2, and In-t3) were identified by Southern blot hybridization, PCR, and DNA sequencing, and these integrons were found to carry the aadB, catB3, oxa1, aadA1a, aacA4, and aacC1 gene cassettes. Integrons In-t1 (aadB and catB3) and In-t2 (oxa1 and aadA1a) were both located on a conjugative IncFI plasmid of 140 kb. In-t3 (aacA4, aacC1, and aadAIa) was located on an IncL/M plasmid of 100 kb which was present, in association with the IncFI plasmid, in gentamicin- and amikacin-resistant isolates. Despite the extensive similarity at the level of the antibiotic resistance phenotype, integrons were not found on the prototypic IncFI plasmids carried by epidemic Salmonella strains isolated during the late 1970s. The recent appearance and the coexistence of multiple integrons on two conjugative plasmids in the same Salmonella isolate are examples of how mobile gene cassettes may contribute to the acquisition and dissemination of antibiotic resistance.
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Affiliation(s)
- F Tosini
- Laboratory of Cellular Biology, and Institute of Microbiology, University of Rome, "La Sapienza," Rome, Italy
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16
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Preston KE, Kacica MA, Limberger RJ, Archinal WA, Venezia RA. The resistance and integrase genes of pACM1, a conjugative multiple-resistance plasmid, from Klebsiella oxytoca. Plasmid 1997; 37:105-18. [PMID: 9169202 DOI: 10.1006/plas.1997.1284] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
pACM1 is an 85-kb conjugative plasmid from a clinical isolate of Klebsiella oxytoca that encodes resistance to beta-lactams (mediated by SHV-5 extended spectrum beta-lactamase), trimethoprim, sulfonamides, tetracycline, aminoglycosides, and mercuric chloride. The expression of the aminoglycoside resistance is difficult to detect, which could have clinical implications. A region of pACM1 containing five resistance genes and two putative integrons was characterized by restriction mapping and partial DNA sequencing. One integron appears to be class I (sull type); the second lacks a recognizable 3' conserved segment. Neither integron has the BamHI site predicted for the 5' conserved segment. Plasmids encoding SHV-5 from other bacterial strains appear to be closely related to pACM1 by restriction enzyme analysis, but have resistance/ integron regions that vary in size and content from that of pACM1. Integrase-mediated recombination might be responsible for genetic divergence in a widely distributed family of pACM1-like plasmids.
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Affiliation(s)
- K E Preston
- Department of Pathology and Laboratory Medicine, Albany Medical College, New York 12208, USA
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17
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Affiliation(s)
- N L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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18
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Huovinen P, Sundström L, Swedberg G, Sköld O. Trimethoprim and sulfonamide resistance. Antimicrob Agents Chemother 1995; 39:279-89. [PMID: 7726483 PMCID: PMC162528 DOI: 10.1128/aac.39.2.279] [Citation(s) in RCA: 300] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- P Huovinen
- Antimicrobial Research Laboratory, National Public Health Institute, Turku, Finland
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19
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Lévesque C, Piché L, Larose C, Roy PH. PCR mapping of integrons reveals several novel combinations of resistance genes. Antimicrob Agents Chemother 1995; 39:185-91. [PMID: 7695304 PMCID: PMC162507 DOI: 10.1128/aac.39.1.185] [Citation(s) in RCA: 744] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The integron is a new type of mobile element which has evolved by a site-specific recombinational mechanism. Integrons consist of two conserved segments of DNA separated by a variable region containing one or more genes integrated as cassettes. Oligonucleotide probes specific for the conserved segments have revealed that integrons are widespread in recently isolated clinical bacteria. Also, by using oligonucleotide probes for several antibiotic resistance genes, we have found novel combinations of resistance genes in these strains. By using PCR, we have determined the content and order of the resistance genes inserted between the conserved segments in the integrons of these clinical isolates. PCR mapping of integrons can be a useful epidemiological tool to study the evolution of multiresistance plasmids and transposons and dissemination of antibiotic resistance genes.
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Affiliation(s)
- C Lévesque
- Département de Biochimie, Faculté des Sciences et de Génie, Université Laval, Ste-Foy, Quebec, Canada
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20
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Hall RM, Stokes HW. Integrons: novel DNA elements which capture genes by site-specific recombination. Genetica 1993; 90:115-32. [PMID: 8119588 DOI: 10.1007/bf01435034] [Citation(s) in RCA: 143] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Integrons are unusual DNA elements which include a gene encoding a site-specific DNA recombinase, a DNA integrase, and an adjacent site at which a wide variety of antibiotic resistance and other genes are found as inserts. One or more genes can be found in the insert region, but each gene is part of an independent gene cassette. The inserted genes are expressed from a promoter in the conserved sequences located 5' to the genes, and integrons are thus natural expression vectors. A model for gene insertion in which circular gene cassettes are inserted individually via a single site-specific recombination event has been proposed and verified experimentally. The gene cassettes include a gene coding region and, at the 3' end of the gene an imperfect inverted repeat, a 59-base element. The 59-base elements are a diverse family of elements which function as sites recognized by the DNA integrase. Site-specific insertion of individual genes thus represents a further mechanism which contributes to the evolution of the genomes of Gram-negative bacteria and their plasmids and transposons. Members of the most studied class of integrons, which include the sulI gene in the conserved sequences, are believed to be mobile DNA elements on the basis that they are found in many independent locations, and a discrete boundary is found at the outer end of the 5'-conserved segment. However, the length of the 3'-conserved segment is variable in the integrons examined to date, and it is likely that this variability has arisen as the result of insertion and deletion events. Though the true extent of the 3'-conserved segment remains to be determined, it seems likely that these integrons are mobile DNA elements. The second known class of integrons comprises members of the Tn7 transposon family.
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Affiliation(s)
- R M Hall
- CSIRO Division of Biomolecular Engineering, North Ryde NSW, Australia
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21
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Heikkilä E, Skurnik M, Sundström L, Huovinen P. A novel dihydrofolate reductase cassette inserted in an integron borne on a Tn21-like element. Antimicrob Agents Chemother 1993; 37:1297-304. [PMID: 8392309 PMCID: PMC187956 DOI: 10.1128/aac.37.6.1297] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In this study, a 498-bp dhfrXII gene coding for trimethoprim resistance was found inserted in a cassette-like manner in the recombinationally active locus, the integron, borne on a transposon Tn21-like element. The dhfrXII cassette is distinct from those cassettes earlier observed in integrons and was found here upstream of two similarly inserted cassettes. The second one carried the new unidentified orfF, which is 85% identical to the orfD cassette in R46. The third cassette contained the aadA2 gene mediating spectinomycin resistance. The plasmid carrying this Tn21-like element was originally isolated from a trimethoprim-resistant urinary tract pathogen, Escherichia coli, from Turku City Hospital, Turku, Finland. By colony hybridization and polymerase chain reaction, this group of three cassettes, including dhfrXII, was detected in four additional E. coli strains of similar origin and in four Shigella strains isolated in Finland but originating from Asia. The dihydrofolate reductase produced from dhfrXII showed an unusual drug resistance in that 50% of the enzymatic activity remained at a trimethoprim concentration of 1 mM.
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Affiliation(s)
- E Heikkilä
- Department of Medical Microbiology, Turku University, Finland
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22
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Jansson C, Franklin A, Sköld O. Spread of a newly found trimethoprim resistance gene, dhfrIX, among porcine isolates and human pathogens. Antimicrob Agents Chemother 1992; 36:2704-8. [PMID: 1482138 PMCID: PMC245532 DOI: 10.1128/aac.36.12.2704] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A plasmid-borne gene mediating trimethoprim resistance, dhfrIX, newly found among porcine strains of Escherichia coli, was observed at a frequency of 11% among trimethoprim-resistant veterinary isolates. This rather high frequency of dhfrIX could be due to the extensive use of trimethoprim in veterinary practice in Sweden. After searching several hundred clinical isolates, one human E. coli strain was also found to harbor the dhfrIX gene. Thus, the dhfrIX gene seems to have spread from porcine bacteria to human pathogens. Furthermore, the occurrence of other genes coding for resistant dihydrofolate reductase enzymes (dhfrI, dhfrII, dhfrV, dhfrVII, and dhfrVIII) among the porcine isolates was investigated. In addition, association of dhfr genes with the integraselike open reading frames of transposons Tn7 and Tn21 was studied. In colony hybridization experiments, both dhfrI and dhfrII were found associated with these integrase genes. The most common combination was dhfrI and int-Tn7, indicating a high prevalence of Tn7.
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Affiliation(s)
- C Jansson
- Department of Pharmaceutical Microbiology, Uppsala University, Sweden
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23
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Parsons Y, Hall RM, Stokes HW. A new trimethoprim resistance gene, dhfrX, in the In7 integron of plasmid pDGO100. Antimicrob Agents Chemother 1991; 35:2436-9. [PMID: 1804022 PMCID: PMC245401 DOI: 10.1128/aac.35.11.2436] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A new trimethoprim resistance determinant, designated dhfrX, was identified in the In7 integron of pDGO100. The sequence of the dhfrX dihydrofolate reductase is up to 28% identical to the sequences of several known dihydrofolate reductase proteins. The dhfrX gene is adjacent to the second 3'-conserved segment of the In7 integron, but the first 77 bases of this segment are not present.
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Affiliation(s)
- Y Parsons
- School of Biological Sciences, Macquarie University, Sydney, NSW, Australia
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24
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Abstract
The bacterial transposon Tn7 is an unusual mobile DNA segment. Most transposable elements move at low-frequency and display little target site-selectivity. By contrast, Tn7 inserts at high-frequency into a single specific site in the chromosomes of many bacteria. In the absence of this specific site, called attTn7 in Escherichia coli where Tn7 has been most extensively studied, Tn7 transposes at low-frequency and inserts into many different sites. Much has recently been learned about Tn7 transposition from both genetic and biochemical studies. The Tn7 recombination machinery is elaborate and includes a large number of Tn7-encoded proteins, probably host-encoded proteins and also rather large cis-acting transposition sequences at the transposon termini and at the target site. Dissection of the Tn7 transposition mechanism has revealed that the DNA strand breakage and joining reactions that underlie the translocation of Tn7 have several unusual features.
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Affiliation(s)
- N L Craig
- Department of Microbiology and Immunology, George W. Hooper Foundation, University of California, San Francisco 94143
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25
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Jansson C, Sköld O. Appearance of a new trimethoprim resistance gene, dhfrIX, in Escherichia coli from swine. Antimicrob Agents Chemother 1991; 35:1891-9. [PMID: 1659308 PMCID: PMC245287 DOI: 10.1128/aac.35.9.1891] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A new gene, dhfrIX, coding for a trimethoprim-resistant dihydrofolate reductase (DHFR), was found in porcine isolates of Escherichia coli. The new enzyme, DHFR IX, containing 178 amino acids, showed an amino acid similarity of about 26% with DHFR I and the chromosomal DHFR of E. coli K-12. The dhfrIX gene was observed to occur on two distinctly different transferable plasmids, although a fragment of about 2.9 kb, including dhfrIX, had an identical restriction enzyme digestion map in each case. The new plasmid-borne dhfrIX gene mediates resistance to a drug level of only about 250 micrograms/ml, as compared with more than 1,000 micrograms/ml for the more frequently encountered dhfrI gene. The new plasmid-borne trimethoprim resistance gene could have been selected and spread as a consequence of the extensive use of trimethoprim in veterinary practice in Sweden. It will be important to try to follow its possible occurrence in human pathogens as well.
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Affiliation(s)
- C Jansson
- Department of Pharmaceutical Microbiology, Uppsala University, Sweden
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26
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Heikkilä E, Sundström L, Skurnik M, Huovinen P. Analysis of genetic localization of the type I trimethoprim resistance gene from Escherichia coli isolated in Finland. Antimicrob Agents Chemother 1991; 35:1562-9. [PMID: 1656867 PMCID: PMC245219 DOI: 10.1128/aac.35.8.1562] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Among a collection of clinical Escherichia coli isolates, the type I dihydrofolate reductase (DHFR) mediating trimethoprim resistance was generally observed to be chromosomally determined. Only a minority of isolates carried the type I DHFR gene simultaneously on a plasmid. The majority of E. coli isolates studied also hybridized with a probe specific for the transposition gene tnsC of transposon Tn7; and in most of these isolates, Tn7 was found to be inserted into a preferred site in the E. coli chromosome. A minority of isolates that harbored the type I DHFR gene in the chromosome lacked a complete Tn7. Some of these harbored the type I DHFR gene inserted in a structure similar to that containing the gene for streptomycin resistance in Tn21. In the other isolates that were negative for a complete Tn7, the sequences upstream of the type I DHFR gene were demonstrated to be homologous to those flanking the type I DHFR gene in Tn7. This could indicate that the antibiotic resistance region of Tn7 may occur independently of this transposon. In two isolates, no sequences resembling Tn7 or Tn21 were found adjacent to the type I DHFR gene.
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Affiliation(s)
- E Heikkilä
- Department of Medical Microbiology, Turku University, Finland
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27
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Hall RM, Brookes DE, Stokes HW. Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point. Mol Microbiol 1991; 5:1941-59. [PMID: 1662753 DOI: 10.1111/j.1365-2958.1991.tb00817.x] [Citation(s) in RCA: 221] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
From examination of published DNA sequences of genes found inserted at a specific site in integrons, all genes are shown to be associated, at their 3' ends, with a short imperfect inverted repeat sequence, a 59-base element or relative of this element. The similarity of the arrangement of gene inserts in the integron and in the Tn7 transposon family is described. A refined consensus for the 59-base element is reported. Members of this family are highly diverged and the relationship of a group of longer elements to the 59-base elements is demonstrated. The ability of 59-base elements of different length and sequence to act as sites for recombination catalysed by the integron-encoded DNA integrase is demonstrated, confirming that elements of this family have a common function. The ability of elements located between gene pairs to act as recombination sites has also been demonstrated. The recombination cross-over point has been localized to the GTT triplet which is conserved in the core sites, GTTRRRY, found at the 3' end of 59-base elements. Recombination at the core site found in inverse orientation at the 5' end of the 59-base elements was not detected, and the sequences responsible for orientation of the recombination event appear to reside within the 59-base element. A model for site-specific insertion of genes into integrons and Tn7-like transposons is proposed. Circular units consisting of a gene associated with a 59-base element are inserted into an ancestral element which contains neither a gene nor a 59-base element.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- R M Hall
- CSIRO Division of Biomolecular Engineering, Laboratory for Molecular Biology, North Ryde, New South Wales, Australia
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28
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Abstract
The bacterial transposon, Tn7, encodes an elaborate array of transposition genes, tnsABCDE. We report here the direct identification of the TnsA, TnsB, TnsC and TnsD polypeptides by immunoblotting. Our results demonstrate that the complexity of the protein information devoted to Tn7 transposition is considerable: the aggregate molecular size of the five Tns polypeptides is about 300 kDa. We also report the sequence of the tnsA gene and of the 5' ends of tnsB and tnsD. This analysis reveals that all five tns genes are oriented in the same direction within Tn7.
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Affiliation(s)
- K A Orle
- Department of Microbiology and Immunology, University of California, San Francisco 94143
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29
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Sundström L, Roy PH, Sköld O. Site-specific insertion of three structural gene cassettes in transposon Tn7. J Bacteriol 1991; 173:3025-8. [PMID: 1850404 PMCID: PMC207888 DOI: 10.1128/jb.173.9.3025-3028.1991] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transposon Tn7 has been known to carry genes for resistance to trimethoprim and spectinomycin. A poorly expressed streptothricin resistance gene, identical to the sat gene found in transposons Tn1825 and Tn1826, was localized between the two mentioned genes in Tn7. The surroundings of all three resistance genes indicated site-specific insertion of genetic cassettes.
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Affiliation(s)
- L Sundström
- Department of Pharmaceutical Microbiology, Uppsala University, Sweden
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30
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Tietze E, Brevet J. The trimethoprim resistance transposon Tn7 contains a cryptic streptothricin resistance gene. Plasmid 1991; 25:217-20. [PMID: 1656477 DOI: 10.1016/0147-619x(91)90015-o] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The transposon Tn7 codes for a trimethoprim resistance and for a streptomycin/spectinomycin resistance function of the bacterial host cells. Cloning of a restriction fragment of Tn7 into the vector plasmid pUC19 reveals the presence in Tn7 of an additional potential resistance determinant. A streptothricin resistance gene, which appears cryptic in the original Tn7 context becomes activated in the recombinant plasmid upon supplying the promoter function of the lacZ system of pUC19. These results together with previously published sequence data further disclose the modular character in the resistance gene regions of Tn7-like transposons.
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Affiliation(s)
- E Tietze
- Institut des Sciences Végétales, CNRS, Gif-sur-Yvette, France
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31
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McIvor RS, Simonsen CC. Isolation and characterization of a variant dihydrofolate reductase cDNA from methotrexate-resistant murine L5178Y cells. Nucleic Acids Res 1990; 18:7025-32. [PMID: 2263462 PMCID: PMC332765 DOI: 10.1093/nar/18.23.7025] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dihydrofolate reductase (DHFR) cDNA sequences were isolated from a methotrexate-resistant mouse L5178Y cell line previously shown to contain methotrexate-resistant dihydrofolate reductase enzyme activity. Specifically-primed reverse transcription products were amplified using the polymerase chain reaction and then cloned into a mammalian expression plasmid. Candidate clones were identified by restriction analysis and then functionally tested by transfection into mouse 3T3 fibroblasts, selecting for methotrexate-resistant colonies. Sequence analysis of the cDNA clones demonstrated the substitution of tryptophan (TGG) in place of the wild-type phenylalanine (TTC) at codon 31. Sequencing of PCR-amplified genomic DNA extracted from the drug-resistant L5178Y cells confirmed the tryptophan codon at position 31. Transfection of mammalian tissue culture cells with expression plasmids containing the trp31 DHFR sequence resulted in substantial methotrexate-resistant colony formation. Recombinant trp31 DHFR enzyme activity expressed in stably-transfected Chinese hamster ovary cells was approximately 20-fold less sensitive to methotrexate inhibition than wild-type mouse DHFR enzyme activity. We conclude that the cloned Trp31 DHFR sequence encodes an enzyme substantially resistant to methotrexate which confers a drug-resistance phenotype to cells in which it is expressed.
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Affiliation(s)
- R S McIvor
- Institute of Human Genetics, University of Minnesota, Minneapolis 55455
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32
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Lahti R, Kolakowski LF, Heinonen J, Vihinen M, Pohjanoksa K, Cooperman BS. Conservation of functional residues between yeast and E. coli inorganic pyrophosphatases. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1038:338-45. [PMID: 2160278 DOI: 10.1016/0167-4838(90)90246-c] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The alignments of the amino acid sequences of inorganic pyrophosphatase (PPase) from Saccharomyces cerevisiae (Y1-PPase, 286 amino acids) and Escherichia coli (E-PPase, 175 amino acids) are examined in the light of crystallographic and chemical modification results placing specific amino acid residues at the active site of the yeast enzyme. The major results are: (1) the full E-PPase sequence aligns within residues 28-225 of Y1-PPase, raising the possibility that the N-terminal and C-terminal portions of Y1-PPase may not be essential for activity, and (2) that whereas the overall identity between the two sequences is only modest (22-27% depending on the choice of alignment parameters), of some 17 putative active site residues, 14-16 are identical between Y-PPase and E-PPase. PPase thus appears to be an example of enzymes from widely divergent species that conserve common functional elements within the context of substantial overall sequence variation.
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Affiliation(s)
- R Lahti
- Department of Biochemistry, University of Turku, Finland
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33
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Abstract
Sites of transposon Tn7 insertion in the Escherichia coli chromosome were examined, and two distinct classes of target sites differing in nucleotide sequence were identified. The target site choice was found to be determined by Tn7-encoded transposition genes.
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Affiliation(s)
- K M Kubo
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143
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34
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Sundström L, Sköld O. The dhfrI trimethoprim resistance gene of Tn7 can be found at specific sites in other genetic surroundings. Antimicrob Agents Chemother 1990; 34:642-50. [PMID: 2188588 PMCID: PMC171658 DOI: 10.1128/aac.34.4.642] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The dhfrI gene, mediating high-level trimethoprim resistance, was earlier found only on Tn7. Evidence is given here for an alternative location of this gene at a site identical to sites observed earlier for dhfrII on plasmid R388, dhfrV on pLMO20, and aadA on Tn21. All these genes and dhfrI are precisely inserted as discrete GTTA-flanked elements at distinct loci in very conserved surrounding sequences. One of these dhfrI insertions was observed to occur in association with a similarly inserted aadA nucleotidyltransferase gene, which mediates streptomycin and spectinomycin resistance. Close to the insertion site, there is an open reading frame translating into a 337-amino-acid peptide which shows striking similarities to recombinases of the integrase family, sulI, the sulfonamide resistance gene, is very often found close to the insertion point forming a genetic surrounding, originally observed as a part of Tn21-like transposons. The alleged integration mechanism thus provides a recombination pathway for the genetic linkage of sulfonamide and other antibiotic resistance genes, including the most frequently encountered gene for trimethoprim resistance, dhfrI. Furthermore, the newly observed location of dhfrI could shed light on the evolution of the antibiotic resistance region of Tn7, which could be able to take up genes by the same mechanism as that of Tn21-like transposons.
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Affiliation(s)
- L Sundström
- Department of Pharmaceutical Microbiology, Uppsala University, Sweden
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35
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Tietze E, Brevet J. Nucleotide sequence of the streptothricin-acetyl-transferase gene sat-2. Nucleic Acids Res 1990; 18:1283. [PMID: 2157196 PMCID: PMC330445 DOI: 10.1093/nar/18.5.1283] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- E Tietze
- Institut für Experimentelle Epidemiologie, Wernigerode, GDR
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36
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37
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38
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Wohlleben W, Arnold W, Bissonnette L, Pelletier A, Tanguay A, Roy PH, Gamboa GC, Barry GF, Aubert E, Davies J. On the evolution of Tn21-like multiresistance transposons: sequence analysis of the gene (aacC1) for gentamicin acetyltransferase-3-I(AAC(3)-I), another member of the Tn21-based expression cassette. MOLECULAR & GENERAL GENETICS : MGG 1989; 217:202-8. [PMID: 2549372 DOI: 10.1007/bf02464882] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The aminoglycoside-3-O-acetyltransferase-I gene (aacC1) from R plasmids of two incompatibility groups (R1033 [Tn1696], and R135) was cloned and sequenced. In the case of R1033, it was shown that the aacC gene is coded by a precise insertion of 833 bp between the aadA promoter and its structural gene in a Tn21 related transposon (Tn1696). This insertion occurs at the same target sequence as that of the OXA-1 beta-lactamase gene insertion in Tn2603. Upstream of the aacC gene, we found an open reading frame (ORF) which is probably implicated in the site-specific recombinational events involved in the evolution of this family of genetic elements. These results provide additional confirmation of the role of Tn21 elements as naturally occurring interspecific transposition and expression cassettes.
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Affiliation(s)
- W Wohlleben
- Fakultät für Biologie, Universität Bielefeld, Federal Republic of Germany
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39
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Arciszewska LK, Drake D, Craig NL. Transposon Tn7. cis-Acting sequences in transposition and transposition immunity. J Mol Biol 1989; 207:35-52. [PMID: 2544738 DOI: 10.1016/0022-2836(89)90439-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have identified and characterized the cis-acting sequences at the termini of the bacterial transposon Tn7 that are necessary for its transposition. Tn7 participates in two kinds of transposition event: high-frequency transposition to a specific target site (attTn7) and low-frequency transposition to apparently random target sites. Our analyses suggest that the same sequences at the Tn7 ends are required for both transposition events. These sequences differ in length and nucleotide structure: about 150 base-pairs at the left end (Tn7L) and about 70 base-pairs at the right end (Tn7R) are necessary for efficient transposition. We also show that the ends of Tn7 are functionally distinct: a miniTn7 element containing two Tn7R ends is active in transposition but an element containing two Tn7L ends is not. We also report that the presence of Tn7's cis-acting transposition sequences anywhere in a target replicon inhibits subsequent insertion of another copy of Tn7 into either an attTn7 target site or into random target sites. The inhibition to an attTn7 target site is most pronounced when the Tn7 ends are immediately adjacent to attTn7. We also show that the presence of Tn7R's cis-acting transposition sequences in a target replicon is necessary and sufficient to inhibit subsequent Tn7 insertion into the target replicon.
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Affiliation(s)
- L K Arciszewska
- Department of Microbiology and Immunology, University of California, San Francisco 94143
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40
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Rouch DA, Messerotti LJ, Loo LS, Jackson CA, Skurray RA. Trimethoprim resistance transposon Tn4003 from Staphylococcus aureus encodes genes for a dihydrofolate reductase and thymidylate synthetase flanked by three copies of IS257. Mol Microbiol 1989; 3:161-75. [PMID: 2548057 DOI: 10.1111/j.1365-2958.1989.tb01805.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Trimethoprim resistance mediated by the Staphylococcus aureus multi-resistance plasmid pSK1 is encoded by a structure with characteristics of a composite transposon which we have designated Tn4003. Nucleotide sequence analysis of Tn4003 revealed it to be 4717 bp in length and to contain three copies of the insertion element IS257 (789-790 bp), the outside two of which are flanked by directly repeated 8-bp target sequences. IS257 has imperfect terminal inverted repeats of 27-28 bp and encodes for a putative transposase with two potential alpha-helix-turn-alpha-helix DNA recognition motifs. IS257 shares sequence similarities with members of the IS15 family of insertion sequences from Gram-negative bacteria and with ISS1 from Streptococcus lactis. The central region of the transposon contains the dfrA gene that specifies the S1 dihydrofolate reductase (DHFR) responsible for trimethoprim resistance. The S1 enzyme shows sequence homology with type I and V trimethoprim-resistant DHFRs from Gram-negative bacteria and with chromosomally encoded DHFRs from Gram-positive and Gram-negative bacteria. 5' to dfrA is a thymidylate synthetase gene, designated thyE.
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Affiliation(s)
- D A Rouch
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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41
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Sundström L, Rådström P, Swedberg G, Sköld O. Site-specific recombination promotes linkage between trimethoprim- and sulfonamide resistance genes. Sequence characterization of dhfrV and sulI and a recombination active locus of Tn21. MOLECULAR & GENERAL GENETICS : MGG 1988; 213:191-201. [PMID: 3054482 DOI: 10.1007/bf00339581] [Citation(s) in RCA: 192] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A new gene for trimethoprim resistance, dhfrV, found in several plasmid isolates with different characteristics, was sequenced and found to correspond to a peptide of 157 amino acids showing 75% similarity with the previously characterized, drug resistant dihydrofolate reductase of type I. The sequenced surroundings of dhfrV in plasmid pLMO20, were found to be almost identical with genetic areas surrounding resistance genes in transposon Tn21 and in R plasmid R388. The trimethoprim resistance genes of pLMO20 and R388 and the spectinomycin resistance gene of Tn21 could be regarded as having been inserted, by recombination, into an evolutionary older structure containing the sulfonamide resistance gene, sulI. The latter gene was sequenced and found to correspond to a peptide of 279 amino acids and with a molecular weight of 30,126 daltons. The inserted genes were found to be governed by a promoter situated in the highly conserved structure and also controlling expression of sulI. The insertion points of the different resistance genes were precisely defined, and at the 3' ends of the inserted genes inverted repeats allowing the formation of stem and loop structures were found. Similar structures were found at the 3' ends of the antibiotic resistance genes in Tn7, which could indicate similar recombination mechanisms to be effective in the evolutionary construction of all these different resistance elements.
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Affiliation(s)
- L Sundström
- Department of Pharmaceutical Microbiology, Uppsala University, Sweden
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Simonsen CS, Walter M, Levinson AD. Expression of the plasmid-encoded type I dihydrofolate reductase gene in cultured mammalian cells: a novel selectable marker. Nucleic Acids Res 1988; 16:2235-46. [PMID: 3357775 PMCID: PMC338212 DOI: 10.1093/nar/16.5.2235] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A recombinant plasmid has been designed to express the gene encoding a type I methotrexate-resistant dihydrofolate reductase, derived from the bacterial plasmid R483, in DHFR- Chinese hamster ovary cells. Vectors containing the wild type gene, whose coding sequence initiates with a GTG codon, fail to direct the synthesis of detectable levels of protein. Substitution of the GTG codon by an AG codon using in vitro mutagenesis overcomes this block; cells transfected with the modified vector synthesize a functional prokaryotic protein that sustains the growth of these cells in the presence of dihydrofolic acid in the culture media. This property is consistent with the inability of the type I enzyme to reduce folate to dihydrofolate, and enabled the development of a selection strategy whereby prokaryotic and mammalian DHFRs genes could be used sequentially as independently selectable markers.
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Affiliation(s)
- C S Simonsen
- Department of Molecular Biology, Genentech, Inc., San Francisco, CA 94080
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Tietze E, Brevet J, Tschäpe H. Relationships among the streptothricin resistance transposons Tn1825 and Tn1826 and the trimethoprim resistance transposon Tn7. Plasmid 1987; 18:246-9. [PMID: 2832865 DOI: 10.1016/0147-619x(87)90067-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The streptothricin resistance transposons Tn1825 and Tn1826 are closely related, based on physical and genetic characteristics, to the trimethoprim resistance transposon Tn7. These transposons may be considered to be members of a transposon family sharing in common the transposition functions and a basic streptomycin/spectinomycin resistance determinant but differing from one another with respect to particular additional resistance genes inserted to the left of the aadA gene.
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Affiliation(s)
- E Tietze
- Institut für Experimentelle Epidemiologie, Wernigerode, German Democratic Republic
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44
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Affiliation(s)
- P Huovinen
- Department of Medical Microbiology, University of Turku, Finland
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Hall RM, Vockler C. The region of the IncN plasmid R46 coding for resistance to beta-lactam antibiotics, streptomycin/spectinomycin and sulphonamides is closely related to antibiotic resistance segments found in IncW plasmids and in Tn21-like transposons. Nucleic Acids Res 1987; 15:7491-501. [PMID: 2821509 PMCID: PMC306263 DOI: 10.1093/nar/15.18.7491] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The nucleotide sequence of a 2.5 kb segment of the pKM101 (R46) genome has been determined. The 1.3 kb from a BamHI site at 153 to base 1440 differs by only 2 bases from a part of the published sequence of the aadB (gentamicin resistance) gene region including the coding region for the N-terminal 70 amino acids of the predicted aadB product. The same sequence has been found 5'-to the dhfrII gene of R388 and to the aadA gene of Tn21 (R538-1). Three open reading frames are located in this region, two on the same strand as the resistance genes and one on the complementary strand. The latter predicts a polypeptide of 337 amino acids, whose N-terminal segment is 40% homologous to the predicted product of an open reading frame of 179 amino acids located next to the dhfrI gene of Tn7. The oxa2 (oxacillin resistance) gene predicts a long polypeptide commencing with (the N-terminal) 70 amino acids of the aadB product. A similar arrangement is found in the aadA gene of R538-1. The N-terminal segment of an aadA gene is located 3'- to oxa2, separated by 36 bases. Sequences surrounding the BamHI site are identical to sequences 5'- to the tnpM gene of Tn21 and homology ceases where homology between Tn21 and Tn501 commences. The possibility that this antibiotic resistance segment is a discrete mobile DNA element is discussed.
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Affiliation(s)
- R M Hall
- CSIRO Division of Molecular Biology, North Ryde, NSW, Australia
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Sundström L, Vinayagamoorthy T, Sköld O. Novel type of plasmid-borne resistance to trimethoprim. Antimicrob Agents Chemother 1987; 31:60-6. [PMID: 3566240 PMCID: PMC174652 DOI: 10.1128/aac.31.1.60] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A novel trait for transferable resistance to high concentrations of trimethoprim was found to dominate among enterobacteria collected from different parts of Sri Lanka. Drug resistance was a result of the production of dihydrofolate reductase with a decreased sensitivity to antifolates. By characterization of the partially purified enzyme and by restriction enzyme digestion analysis, the newly found gene was shown to be distinct from the earlier known plasmid-borne resistance genes which express dihydrofolate reductases of types I, II, and III. Cloning of fragments containing the resistance gene and further restriction enzyme digestion analysis showed that this gene was inserted very close to a sulfonamide resistance gene. Evolution of trimethoprim resistance in Sri Lanka thus seems to have taken a different route from that taken in the industrialized world, where transposon Tn7 seems to dominate. The close combination of the new trimethoprim resistance gene with sulfonamide resistance on the plasmids studied would effect an efficient spread of these genes, since trimethoprim has most often been used in combination with a sulfonamide.
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Chinault AC, Blakesley VA, Roessler E, Willis DG, Smith CA, Cook RG, Fenwick RG. Characterization of transferable plasmids from Shigella flexneri 2a that confer resistance to trimethoprim, streptomycin, and sulfonamides. Plasmid 1986; 15:119-31. [PMID: 3517903 DOI: 10.1016/0147-619x(86)90048-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A set of plasmids conferring resistance to several antibiotics, including the combination of trimethoprim and sulfamethoxazole, has been isolated from Escherichia coli following conjugative cotransfer from a clinical isolate of Shigella flexneri 2a. One of the plasmids, pCN1, was shown by subcloning and DNA sequencing to carry a gene encoding a trimethoprim-insensitive dihydrofolate reductase identical to that found in E. coli transposon 7. This plasmid was also shown to confer resistance to both streptomycin and spectinomycin by production of an adenylyltransferase that inactivated the drugs and the gene encoding this enzyme has also been sequenced. A second plasmid from the set, pCN2, was shown to inactivate streptomycin by a phosphotransferase mechanism and also to confer resistance to sulfonamides. The third plasmid from the set could not be correlated with a drug-resistance phenotype, but does appear to play a crucial role in plasmid mobilization.
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Caras IW, Levinson BB, Fabry M, Williams SR, Martin DW. Cloned mouse ribonucleotide reductase subunit M1 cDNA reveals amino acid sequence homology with Escherichia coli and herpesvirus ribonucleotide reductases. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)88881-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Pulkkinen L, Huovinen P, Vuorio E, Toivanen P. Characterization of trimethoprim resistance by use of probes specific for transposon Tn7. Antimicrob Agents Chemother 1984; 26:82-6. [PMID: 6089656 PMCID: PMC179922 DOI: 10.1128/aac.26.1.82] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Transposon Tn7 codes for resistance to trimethoprim and streptomycin. For detection of Tn7 by DNA-DNA hybridization, two recombinant plasmids were constructed. The former contained a 1-kilobase BamHI fragment and the latter contained a 4.3-kilobase EcoRI-BamHI fragment of Tn7. These DNA fragments, which did not include the drug resistance genes, were used as probes for detecting Tn7-like sequences in bacterial strains by colony hybridization. They hybridized strongly to bacterial DNA known to carry Tn7 but not to DNA known to carry transposons other than Tn7. These probes were used to study the occurrence of Tn7 in bacterial strains isolated in the Turku City Hospital in Finland. Transposon Tn7 was present in 47.2% of 199 trimethoprim-resistant enterobacteria (MIC greater than or equal to 8 micrograms/ml). Among the 69 Proteus mirabilis strains studied, 75% contained Tn7, although none of these strains transferred trimethoprim resistance in conjugation tests. The reliability of colony hybridization was further confirmed by Southern hybridization to detect the Tn7-specific 2.6-kilobase HindIII restriction fragment. Colony hybridization proved to be a sensitive and rapid method for detecting Tn7-determined sequences.
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Purohit S, Mathews CK. Nucleotide sequence reveals overlap between T4 phage genes encoding dihydrofolate reductase and thymidylate synthase. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(20)82135-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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