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Ridenhour BJ, Metzger GA, France M, Gliniewicz K, Millstein J, Forney LJ, Top EM. Persistence of antibiotic resistance plasmids in bacterial biofilms. Evol Appl 2017; 10:640-647. [PMID: 28616070 PMCID: PMC5469168 DOI: 10.1111/eva.12480] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/20/2017] [Indexed: 11/28/2022] Open
Abstract
The emergence and spread of antibiotic resistance is a crisis in health care today. Antibiotic resistance is often horizontally transferred to susceptible bacteria by means of multidrug resistance plasmids that may or may not persist in the absence of antibiotics. Because bacterial pathogens often grow as biofilms, there is a need to better understand the evolution of plasmid persistence in these environments. Here we compared the evolution of plasmid persistence in the pathogen Acinetobacter baumannii when grown under antibiotic selection in biofilms versus well-mixed liquid cultures. After 4 weeks, clones in which the plasmid was more stably maintained in the absence of antibiotic selection were present in both populations. On average plasmid persistence increased more in liquid batch cultures, but variation in the degree of persistence was greater among biofilm-derived clones. The results of this study show for the first time that the persistence of MDR plasmids improves in biofilms.
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Affiliation(s)
- Benjamin J Ridenhour
- Department of Biological Sciences Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA.,Bioinformatics and Computational Biology Program University of Idaho Moscow ID USA
| | - Genevieve A Metzger
- Department of Biological Sciences Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA.,Bioinformatics and Computational Biology Program University of Idaho Moscow ID USA
| | - Michael France
- Department of Biological Sciences Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA.,Bioinformatics and Computational Biology Program University of Idaho Moscow ID USA
| | - Karol Gliniewicz
- Department of Biological Sciences Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA
| | - Jack Millstein
- Department of Biological Sciences Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA
| | - Larry J Forney
- Department of Biological Sciences Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA.,Bioinformatics and Computational Biology Program University of Idaho Moscow ID USA
| | - Eva M Top
- Department of Biological Sciences Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA.,Bioinformatics and Computational Biology Program University of Idaho Moscow ID USA
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Maslunka C, Gürtler V, Seviour R. Unusual features of the sequences of copies of the 16S-23S rRNA internal transcribed spacer regions of Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi arise from horizontal gene transfer events. MICROBIOLOGY-SGM 2014; 161:322-329. [PMID: 25505188 DOI: 10.1099/mic.0.083600-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The highly variable nature of the internal transcribed spacer region (ITS) has been claimed to represent an ideal target for designing species-specific probes/primers capable of differentiating between closely related Acinetobacter species. However, several Acinetobacter species contain multiple ITS copies of variable lengths, and these include Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi. This study shows these length variations result from inter-genomic insertion/deletion events (indels) involving horizontal transfer of ITS fragments of other Acinetobacter species and possibly unrelated bacteria, as shown previously by us. In some instances, indel incorporation results in the loss of probe target sites in the recipient cell ITS. In other cases, some indel sequences contain target sites for probes designed from a single ITS sequence to target other Acinetobacter species. Hence, these can generate false positives. The largest of the indels that remove probe sites is 683 bp (labelled bay/i1-0), and it derives from the horizontal transfer of a complete ITS between A. bereziniae BCRC15423(T) and A. baylyi strain ADP1. As a consequence, ITS sequencing or fingerprinting cannot be used to distinguish between the 683 bp ITS in these two strains.
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Affiliation(s)
- Christopher Maslunka
- Biotechnology Research Centre, La Trobe University, Bendigo, Victoria 3552, Australia
| | - Volker Gürtler
- School of Applied Science, RMIT University, Bundoora, Victoria 3152, Australia
| | - Robert Seviour
- Department of Microbiology, La Trobe University, Bundoora, Victoria 3152, Australia.,Biotechnology Research Centre, La Trobe University, Bendigo, Victoria 3552, Australia
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Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members. PLoS One 2014; 9:e105390. [PMID: 25141005 PMCID: PMC4139376 DOI: 10.1371/journal.pone.0105390] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 07/17/2014] [Indexed: 11/19/2022] Open
Abstract
To determine whether ITS sequences in the rrn operon are suitable for identifying individual Acinetobacter Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between A. nosocomialis BCRC15417T (615 bp) and other strains (607 bp) can be explained by presence of an insertion (indel 13i/1) in the longer ITS variant. The same Indel 13i/1 was also found in ITS sequences of ten strains of A. calcoaceticus, all 639 bp long, and the 628 bp ITS of Acinetobacter strain BENAB127. Four additional indels (13i/2–13i/5) were detected in Acinetobacter strain c/t13TU 10090 ITS length variants (608, 609, 620, 621 and 630 bp). These ITS variants appear to have resulted from horizontal gene transfer involving other Acinetobacter species or in some cases unrelated bacteria. Although some ITS copies in strain c/t13TU 10090 are of the same length (620 bp) as those in Acinetobacter strains b/n1&3, A. pittii (10 strains), A. calcoaceticus and A. oleivorans (not currently acknowledged as an Acb member), their individual ITS sequences differ. Thus ITS length by itself can not by itself be used to identify Acb complex strains. A shared indel in ITS copies in two separate Acinetobacter species compromises the specificity of ITS targeted probes, as shown with the Aun-3 probe designed to target the ITS in A. pitti. The presence of indel 13i/5 in the ITS of Acinetobacter strain c/t13TU means it too responded positively to this probe. Thus, neither ITS sequencing nor the currently available ITS targeted probes can distinguish reliably between Acb member species.
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Lee CM, Sieo CC, Abdullah N, Ho YW. Estimation of 16S rRNA gene copy number in several probiotic Lactobacillus strains isolated from the gastrointestinal tract of chicken. FEMS Microbiol Lett 2008; 287:136-41. [PMID: 18707622 PMCID: PMC2613232 DOI: 10.1111/j.1574-6968.2008.01305.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Accepted: 07/16/2008] [Indexed: 11/28/2022] Open
Abstract
The copy numbers of 16S rRNA genes in 12 probiotic Lactobacillus strains of poultry origin were analyzed. Genomic DNA of the strains was digested with restriction endonucleases that do not cut within the 16S rRNA gene of the strains. This was followed by Southern hybridization with a biotinylated probe complementary to the 16S rRNA gene. The copy number of the 16S rRNA gene within a Lactobacillus species was found to be conserved. From the hybridization results, Lactobacillus salivarius I 24 was estimated to have seven copies of the 16S rRNA gene, Lactobacillus panis C 17 to have five copies and Lactobacillus gallinarum strains I 16 and I 26 four copies. The 16S rRNA gene copy numbers of L. gallinarum and L. panis reported in the present study are the first record. Lactobacillus brevis strains I 12, I 23, I 25, I 211, I 218 and Lactobacillus reuteri strains C 1, C 10, C 16 were estimated to have at least four copies of the 16S rRNA gene. In addition, distinct rRNA restriction patterns which could discriminate the strains of L. reuteri and L. gallinarum were also detected. Information on 16S rRNA gene copy number is important for physiological, evolutionary and population studies of the bacteria.
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Affiliation(s)
- Chin Mei Lee
- Microbial Biotechnology Unit, Laboratory of Industrial Biotechnology, Institute of Bioscience, Universiti Putra MalaysiaSelangor, Malaysia
| | - Chin Chin Sieo
- Microbial Biotechnology Unit, Laboratory of Industrial Biotechnology, Institute of Bioscience, Universiti Putra MalaysiaSelangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra MalaysiaSelangor, Malaysia
| | - Norhani Abdullah
- Microbial Biotechnology Unit, Laboratory of Industrial Biotechnology, Institute of Bioscience, Universiti Putra MalaysiaSelangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra MalaysiaSelangor, Malaysia
| | - Yin Wan Ho
- Microbial Biotechnology Unit, Laboratory of Industrial Biotechnology, Institute of Bioscience, Universiti Putra MalaysiaSelangor, Malaysia
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Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, Bataille E, Dossat C, Gas S, Kreimeyer A, Lenoble P, Oztas S, Poulain J, Segurens B, Robert C, Abergel C, Claverie JM, Raoult D, Médigue C, Weissenbach J, Cruveiller S. Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS One 2008; 3:e1805. [PMID: 18350144 PMCID: PMC2265553 DOI: 10.1371/journal.pone.0001805] [Citation(s) in RCA: 262] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 02/09/2008] [Indexed: 02/06/2023] Open
Abstract
Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.
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Affiliation(s)
- David Vallenet
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
- * E-mail: (DV); (SC)
| | - Patrice Nordmann
- Service de Bactériologie-Virologie, Hôpital de Bicêtre, Assistance Publique/Hôpitaux de Paris, Faculté de Médecine Paris-Sud, Université Paris XI, Kremlin-Bicêtre, France
| | - Valérie Barbe
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Laurent Poirel
- Service de Bactériologie-Virologie, Hôpital de Bicêtre, Assistance Publique/Hôpitaux de Paris, Faculté de Médecine Paris-Sud, Université Paris XI, Kremlin-Bicêtre, France
| | - Sophie Mangenot
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Elodie Bataille
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Carole Dossat
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Shahinaz Gas
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Annett Kreimeyer
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Patricia Lenoble
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Sophie Oztas
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Julie Poulain
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Béatrice Segurens
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Catherine Robert
- Unité des Rickettsies, CNRS UMR6020, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Chantal Abergel
- Information Génomique et Structurale, CNRS UPR2589, IBSM, Marseille, France
| | | | - Didier Raoult
- Unité des Rickettsies, CNRS UMR6020, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Claudine Médigue
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Jean Weissenbach
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
| | - Stéphane Cruveiller
- Génomique Métabolique, CNRS UMR8030, CEA–Institut de Génomique-Genoscope, Evry, France
- * E-mail: (DV); (SC)
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Unique organization of the 16S-23S intergenic spacer regions of strains of Acinetobacter baylyi provides a means for its identification from other Acinetobacter species. J Microbiol Methods 2008; 73:227-36. [PMID: 18436316 DOI: 10.1016/j.mimet.2008.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 02/29/2008] [Accepted: 03/05/2008] [Indexed: 11/23/2022]
Abstract
This paper extends an earlier report on rrn operon characteristics in members of the genus Acinetobacter. It describes a systematic approach towards developing and validating a protocol for elucidating how the intergenic spacer regions (ISR) in Acinetobacter baylyi strains are organized and allows the numbers of long and short ISRs to be determined. Experimental data confirmed the in silico predictions based on available A. baylyi rrn sequence data. All were shown to possess three long ISRs and 4 short ISRs, differing in most cases in length by about 90nt. However, the ISR arrangement in A. baylyi strain 93A2 was different. Although it also possessed 4 SISRs and three LISRs, their length difference was less (39nt) which was confirmed from its ISR sequence data. Primer sets for PCR identification of A. baylyi could then be determined. Applying the same approach to other species of Acinetobacter showed none shared the same ISR organization as A. baylyi. Its value in typing members of this genus is discussed.
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