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Shafranskaya D, Chori A, Korobeynikov A. Graph-Based Approaches Significantly Improve the Recovery of Antibiotic Resistance Genes From Complex Metagenomic Datasets. Front Microbiol 2021; 12:714836. [PMID: 34690959 PMCID: PMC8528159 DOI: 10.3389/fmicb.2021.714836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/09/2021] [Indexed: 12/03/2022] Open
Abstract
The lack of control over the usage of antibiotics leads to propagation of the microbial strains that are resistant to many antimicrobial substances. This situation is an emerging threat to public health and therefore the development of approaches to infer the presence of resistant strains is a topic of high importance. The resistome construction of an isolate microbial species could be considered a solved task with many state-of-the-art tools available. However, when it comes to the analysis of the resistome of a microbial community (metagenome), then there exist many challenges that influence the accuracy and precision of the predictions. For example, the prediction sensitivity of the existing tools suffer from the fragmented metagenomic assemblies due to interspecies repeats: usually it is impossible to recover conservative parts of antibiotic resistance genes that belong to different species that occur due to e.g., horizontal gene transfer or residing on a plasmid. The recent advances in development of new graph-based methods open a way to recover gene sequences of interest directly from the assembly graph without relying on cumbersome and incomplete metagenomic assembly. We present GraphAMR—a novel computational pipeline for recovery and identification of antibiotic resistance genes from fragmented metagenomic assemblies. The pipeline involves the alignment of profile hidden Markov models of target genes directly to the assembly graph of a metagenome with further dereplication and annotation of the results using state-of-the art tools. We show significant improvement of the quality of the results obtained (both in terms of accuracy and completeness) as compared to the analysis of an output of ordinary metagenomic assembly as well as different read mapping approaches. The pipeline is freely available from https://github.com/ablab/graphamr.
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Affiliation(s)
- Daria Shafranskaya
- Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, Sochi, Russia.,Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander Chori
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,ITMO University, Saint Petersburg, Russia
| | - Anton Korobeynikov
- Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, Sochi, Russia.,Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
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Molecular Detection of Carbapenemase-Encoding Genes in Multidrug-Resistant Acinetobacter baumannii Clinical Isolates in South Africa. Int J Microbiol 2020; 2020:7380740. [PMID: 32612659 PMCID: PMC7306865 DOI: 10.1155/2020/7380740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/17/2020] [Accepted: 03/13/2020] [Indexed: 01/03/2023] Open
Abstract
Introduction Carbapenem-resistant Acinetobacter baumannii has been responsible for an increasing number of hospital-acquired infections globally. The study investigated the prevalence of carbapenemase-encoding genes in clinical multidrug-resistant A. baumannii strains. Materials and Methods A total of 100 nonduplicate multidrug-resistant A. baumannii strains were cultured from clinical samples obtained from healthcare facilities in the O. R. Tambo district. The strains were confirmed by detecting the intrinsic blaOXA-51-like gene. Antimicrobial susceptibility testing was performed by VITEK® 2 and autoSCAN-4 systems. The MIC of imipenem and meropenem was rechecked by E-test. Colistin MIC was confirmed by the broth microdilution method. Real-time PCR was performed to investigate the presence of carbapenemase-encoding genes. Results Most strains showed high resistance rates (>80%) to the antibiotics tested. Resistance to amikacin, tetracycline, and tigecycline were 50%, 64%, and 48%, respectively. All strains were fully susceptible to colistin. The blaOXA-51-like was detected in all strains whilst blaOXA-23-like, blaOXA-58-like, blaOXA-24-like, blaIMP-1, blaVIM, and blaNDM-1 were found in 70%, 8%, 5%, 4%, 3%, and 2% of strains, respectively. None of the tested strains harboured the genes blaSIM and blaAmpC. The coexistence of blaOXA-23-like, and blaIMP-1 or blaOXA-58-like was detected in 1% and 2% strains, respectively. A distinct feature of our findings was the coharbouring of the genes blaOXA-23-like, blaOXA-58-like, and blaIMP-1 in 2% strains, and this is the first report in the Eastern Cape Province, South Africa. The intI1 was carried in 80% of tested strains whilst ISAba1/blaOXA-51-like and ISAba1/blaOXA-23-like were detected in 15% and 40% of the strains, respectively. The detection of blaOXA-23-like, ISAba1/blaOXA-51-like, ISAba1/blaOXA-23-like, and blaOXA-23-like, blaOXA-58-like, and blaIMP-1 carbapenemases in strains had a significant effect on both imipenem and meropenem MICs. Conclusions Results showed a high level of oxacillinases producing A. baumannii circulating in our study setting, highlighting the need for local molecular surveillance to inform appropriate management and prevention strategies.
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Ramirez MS, Bonomo RA, Tolmasky ME. Carbapenemases: Transforming Acinetobacter baumannii into a Yet More Dangerous Menace. Biomolecules 2020; 10:biom10050720. [PMID: 32384624 PMCID: PMC7277208 DOI: 10.3390/biom10050720] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii is a common cause of serious nosocomial infections. Although community-acquired infections are observed, the vast majority occur in people with preexisting comorbidities. A. baumannii emerged as a problematic pathogen in the 1980s when an increase in virulence, difficulty in treatment due to drug resistance, and opportunities for infection turned it into one of the most important threats to human health. Some of the clinical manifestations of A. baumannii nosocomial infection are pneumonia; bloodstream infections; lower respiratory tract, urinary tract, and wound infections; burn infections; skin and soft tissue infections (including necrotizing fasciitis); meningitis; osteomyelitis; and endocarditis. A. baumannii has an extraordinary genetic plasticity that results in a high capacity to acquire antimicrobial resistance traits. In particular, acquisition of resistance to carbapenems, which are among the antimicrobials of last resort for treatment of multidrug infections, is increasing among A. baumannii strains compounding the problem of nosocomial infections caused by this pathogen. It is not uncommon to find multidrug-resistant (MDR, resistance to at least three classes of antimicrobials), extensively drug-resistant (XDR, MDR plus resistance to carbapenems), and pan-drug-resistant (PDR, XDR plus resistance to polymyxins) nosocomial isolates that are hard to treat with the currently available drugs. In this article we review the acquired resistance to carbapenems by A. baumannii. We describe the enzymes within the OXA, NDM, VIM, IMP, and KPC groups of carbapenemases and the coding genes found in A. baumannii clinical isolates.
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Affiliation(s)
- Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
| | - Robert A. Bonomo
- Medical Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA;
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics; Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- WRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
- Correspondence: ; Tel.: +657-278-5263
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Willms IM, Yuan J, Penone C, Goldmann K, Vogt J, Wubet T, Schöning I, Schrumpf M, Buscot F, Nacke H. Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use. Genes (Basel) 2020; 11:E150. [PMID: 32019196 PMCID: PMC7073645 DOI: 10.3390/genes11020150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 12/28/2022] Open
Abstract
Antibiotic-resistant pathogens claim the lives of thousands of people each year and are currently considered as one of the most serious threats to public health. Apart from clinical environments, soil ecosystems also represent a major source of antibiotic resistance determinants, which can potentially disseminate across distinct microbial habitats and be acquired by human pathogens via horizontal gene transfer. Therefore, it is of global importance to retrieve comprehensive information on environmental factors, contributing to an accumulation of antibiotic resistance genes and mobile genetic elements in these ecosystems. Here, medically relevant antibiotic resistance genes, class 1 integrons and IncP-1 plasmids were quantified via real time quantitative PCR in soils derived from temperate grasslands and forests, varying in land use over a large spatial scale. The generated dataset allowed an analysis, decoupled from regional influences, and enabled the identification of land use practices and soil characteristics elevating the abundance of antibiotic resistance genes and mobile genetic elements. In grassland soils, the abundance of the macrolide resistance gene mefA as well as the sulfonamide resistance gene sul2 was positively correlated with organic fertilization and the abundance of aac(6')-lb, conferring resistance to different aminoglycosides, increased with mowing frequency. With respect to forest soils, the beta-lactam resistance gene blaIMP-12 was significantly correlated with fungal diversity which might be due to the fact that different fungal species can produce beta-lactams. Furthermore, except blaIMP-5 and blaIMP-12, the analyzed antibiotic resistance genes as well as IncP-1 plasmids and class-1 integrons were detected less frequently in forest soils than in soils derived from grassland that are commonly in closer proximity to human activities.
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Affiliation(s)
- Inka M. Willms
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany; (I.M.W.); (J.Y.)
| | - Jingyue Yuan
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany; (I.M.W.); (J.Y.)
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, CH-3013 Bern, Switzerland;
| | - Kezia Goldmann
- Department of Soil Ecology, UFZ—Helmholtz Centre for Environmental Research, D-06120 Halle-Saale, Germany; (K.G.); (F.B.)
| | - Juliane Vogt
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, Technical University of Munich, D-85354 Freising, Germany;
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ—Helmholtz Centre for Environmental Research, D-06120 Halle-Saale, Germany;
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103 Leipzig, Germany
| | - Ingo Schöning
- Max Planck Institute for Biogeochemistry, D-07745 Jena, Germany; (I.S.); (M.S.)
| | - Marion Schrumpf
- Max Planck Institute for Biogeochemistry, D-07745 Jena, Germany; (I.S.); (M.S.)
| | - François Buscot
- Department of Soil Ecology, UFZ—Helmholtz Centre for Environmental Research, D-06120 Halle-Saale, Germany; (K.G.); (F.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103 Leipzig, Germany
| | - Heiko Nacke
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany; (I.M.W.); (J.Y.)
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Wang S, Zhou K, Xiao S, Xie L, Gu F, Li X, Ni Y, Sun J, Han L. A Multidrug Resistance Plasmid pIMP26, Carrying bla IMP-26, fosA5, bla DHA-1, and qnrB4 in Enterobacter cloacae. Sci Rep 2019; 9:10212. [PMID: 31308469 PMCID: PMC6629617 DOI: 10.1038/s41598-019-46777-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/04/2019] [Indexed: 11/20/2022] Open
Abstract
IMP-26 was a rare IMP variant with more carbapenem-hydrolyzing activities, which was increasingly reported now in China. This study characterized a transferable multidrug resistance plasmid harboring blaIMP-26 from one Enterobacter cloacae bloodstream isolate in Shanghai and investigated the genetic environment of resistance genes. The isolate was subjected to antimicrobial susceptibility testing and multilocus sequence typing using broth microdilution method, Etest and PCR. The plasmid was analyzed through conjugation experiments, S1-nuclease pulsed-field gel electrophoresis and hybridization. Whole genome sequencing and sequence analysis was conducted for further investigation of the plasmid. E. cloacae RJ702, belonging to ST528 and carrying blaIMP-26, blaDHA-1, qnrB4 and fosA5, was resistant to almost all β-lactams, but susceptible to quinolones and tigecycline. The transconjugant inherited the multidrug resistance. The resistance genes were located on a 329,420-bp IncHI2 conjugative plasmid pIMP26 (ST1 subtype), which contained trhK/trhV, tra, parA and stbA family operon. The blaIMP-26 was arranged following intI1. The blaDHA-1 and qnrB4 cluster was the downstream of ISCR1, same as that in p505108-MDR. The fosA5 cassette was mediated by IS4. This was the first report on complete nucleotide of a blaIMP-26-carrying plasmid in E. cloacae in China. Plasmid pIMP26 hosted high phylogenetic mosaicism, transferability and plasticity.
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Affiliation(s)
- Su Wang
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaixin Zhou
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuzhen Xiao
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lianyan Xie
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feifei Gu
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinxin Li
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuxing Ni
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Lizhong Han
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Cheikh HB, Domingues S, Silveira E, Kadri Y, Rosário N, Mastouri M, Da Silva GJ. Molecular characterization of carbapenemases of clinical Acinetobacter baumannii- calcoaceticus complex isolates from a University Hospital in Tunisia. 3 Biotech 2018; 8:297. [PMID: 29963357 DOI: 10.1007/s13205-018-1310-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/15/2018] [Indexed: 02/07/2023] Open
Abstract
The aim of this study was to identify the carbapenemases from clinical carbapenem-resistant Acinetobacter baumannii-calcoaceticus complex (CRABC) isolates and to assess their potential dissemination by conjugation and natural transformation. CRABC (n = 101) were collected consecutively from inpatients of the University Hospital of Monastir, Tunisia, from 2013 to 2016. Antimicrobial susceptibility was determined by the disk diffusion method and E-test. Carbapenemase-encoding genes were screened by PCR. Genotyping was performed by Pasteur MLST scheme. Isolates were resistant to all beta-lactams, fluoroquinolones and aminoglycosides while 80 and 90% were susceptible to tigecycline and colistin, respectively. Resistance and intermediate resistance to imipenem were 87 and 13%, respectively. The genes blaOXA-24-like, blaOXA-58-like, blaOXA-143-like, blaOXA-48-like, blaVIM, blaIMP, and blaKPC were not found. The blaOXA-51-like and blaOXA-23-like genes were present in 100 and 82.17% isolates, respectively. One isolate (< 1%) carried blaNDM-1 and blaOXA-51-like and belonged to Sequence Type 85 (ST85). Absence of transconjugants suggests a chromosomal location of NDM-1 determinant. The blaNDM-1 gene was inserted in a truncated form of Tn125, which may explain the absence of blaNDM-1 carrier-transformants. To our knowledge, this is the first report of the finding of NDM-positive A. baumannii in Tunisian territory. The study shows that despite the low prevalence and potential spread of NDM-1 enzyme among CRABC, continuous regional antimicrobial resistance surveillance and improved infection control measures are required in Tunisia to prevent further dissemination.
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Affiliation(s)
- Hadhemi Ben Cheikh
- 1Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- 2Faculty of Science, Bizerta Carthage University, Bizerta, Tunisia
- Laboratory of Contagious Disease and Biologically Active Substances LR99-ES27, Monastir's Pharmacy Faculty, Monastir, Tunisia
| | - Sara Domingues
- 1Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- 4Laboratory of Microbiology, Center for Neuroscience and Cell Biology (CNC), Faculty of Pharmacy, Health Sciences Campus, University of Coimbra, Azinhaga de Sta Comba, 3000-548 Coimbra, Portugal
| | | | - Yosr Kadri
- Laboratory of Contagious Disease and Biologically Active Substances LR99-ES27, Monastir's Pharmacy Faculty, Monastir, Tunisia
- 5Laboratory of Microbiology, Fattouma Bourguiba University Hospital, Monastir, Tunisia
| | - Natasha Rosário
- 1Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Maha Mastouri
- Laboratory of Contagious Disease and Biologically Active Substances LR99-ES27, Monastir's Pharmacy Faculty, Monastir, Tunisia
- 5Laboratory of Microbiology, Fattouma Bourguiba University Hospital, Monastir, Tunisia
| | - Gabriela Jorge Da Silva
- 1Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- 4Laboratory of Microbiology, Center for Neuroscience and Cell Biology (CNC), Faculty of Pharmacy, Health Sciences Campus, University of Coimbra, Azinhaga de Sta Comba, 3000-548 Coimbra, Portugal
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Mojica MF, Bonomo RA, Fast W. B1-Metallo-β-Lactamases: Where Do We Stand? Curr Drug Targets 2017; 17:1029-50. [PMID: 26424398 DOI: 10.2174/1389450116666151001105622] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 12/31/1969] [Accepted: 09/14/2015] [Indexed: 11/22/2022]
Abstract
Metallo-β-Lactamases (MBLs) are class Bβ-lactamases that hydrolyze almost all clinically-availableβ-lactam antibiotics. MBLs feature the distinctive αβ/βα sandwich fold of the metallo-hydrolase/oxidoreductase superfamily and possess a shallow active-site groove containing one or two divalent zinc ions, flanked by flexible loops. According to sequence identity and zinc ion dependence, MBLs are classified into three subclasses (B1, B2 and B3), of which the B1 subclass enzymes have emerged as the most clinically significant. Differences among the active site architectures, the nature of zinc ligands, and the catalytic mechanisms have limited the development of a common inhibitor. In this review, we will describe the molecular epidemiology and structural studies of the most prominent representatives of class B1 MBLs (NDM-1, IMP-1 and VIM-2) and describe the implications for inhibitor design to counter this growing clinical threat.
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Affiliation(s)
| | - Robert A Bonomo
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Blvd., Cleveland, OH 44106, USA.
| | - Walter Fast
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin TX, 78712, USA.
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Insights on the Horizontal Gene Transfer of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter baumannii. Microorganisms 2016; 4:microorganisms4030029. [PMID: 27681923 PMCID: PMC5039589 DOI: 10.3390/microorganisms4030029] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/21/2016] [Accepted: 08/09/2016] [Indexed: 12/23/2022] Open
Abstract
Horizontal gene transfer (HGT) is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen.
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Domingues S, Nielsen KM, da Silva GJ. Various pathways leading to the acquisition of antibiotic resistance by natural transformation. Mob Genet Elements 2014; 2:257-260. [PMID: 23482877 PMCID: PMC3575418 DOI: 10.4161/mge.23089] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Natural transformation can lead to exchange of DNA between taxonomically diverse bacteria. In the case of chromosomal DNA, homology-based recombination with the recipient genome is usually necessary for heritable stability. In our recent study, we have shown that natural transformation can promote the transfer of transposons, IS elements, and integrons and gene cassettes, largely independent of the genetic relationship between the donor and recipient bacteria. Additional results from our study suggest that natural transformation with species-foreign DNA might result in the uptake of a wide range of DNA fragments; leading to changes in the antimicrobial susceptibility profile and contributing to the generation of antimicrobial resistance in bacteria.
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Affiliation(s)
- Sara Domingues
- Centre of Pharmaceutical Studies; Faculty of Pharmacy; University of Coimbra; Coimbra, Portugal ; Department of Pharmacy; Faculty of Health Sciences; University of Tromsø; Tromsø, Norway
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Domingues S, da Silva GJ, Nielsen KM. Integrons: Vehicles and pathways for horizontal dissemination in bacteria. Mob Genet Elements 2014; 2:211-223. [PMID: 23550063 PMCID: PMC3575428 DOI: 10.4161/mge.22967] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Integrons are genetic elements first described at the end of the 1980s. Although most integrons were initially described in human clinical isolates, they have now been identified in many non-clinical environments, such as water and soil. Integrons are present in ≈10% of the sequenced bacterial genomes and are frequently linked to mobile genetic elements (MGEs); particularly the class 1 integrons. Genetic linkage to a diverse set of MGEs facilitates horizontal transfer of class 1 integrons within and between bacterial populations and species. The mechanistic aspects limiting transfer of MGEs will therefore limit the transfer of class 1 integrons. However, horizontal movement due to genes provided in trans and homologous recombination can result in class 1 integron dynamics independent of MGEs. A key determinant for continued dissemination of class 1 integrons is the probability that transferred MGEs will be vertically inherited in the recipient bacterial population. Heritability depends both on genetic stability as well as the fitness costs conferred to the host. Here we review the factors known to govern the dissemination of class 1 integrons in bacteria.
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Affiliation(s)
- Sara Domingues
- Centre of Pharmaceutical Studies; Faculty of Pharmacy; University of Coimbra; Coimbra, Portugal ; Department of Pharmacy; Faculty of Health Sciences; University of Tromsø; Tromsø, Norway
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Sung JY, Koo SH, Kim S, Kwon KC. Epidemiological characterizations of class 1 integrons from multidrug-resistant acinetobacter isolates in Daejeon, Korea. Ann Lab Med 2014; 34:293-9. [PMID: 24982834 PMCID: PMC4071186 DOI: 10.3343/alm.2014.34.4.293] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/09/2013] [Accepted: 05/01/2014] [Indexed: 01/19/2023] Open
Abstract
Background Multidrug-resistant (MDR) Acinetobacter spp. acquire antimicrobial agent-resistance genes via class 1 integrons. In this study, integrons were characterized to investigate the antimicrobial resistance mechanisms of MDR Acinetobacter isolates. In addition, the relationship between the integron type and integron-harboring bacterial species was analyzed by using epidemiological typing methods. Methods Fifty-six MDR Acinetobacter spp.-A. baumannii (N=30), A. bereziniae (N=4), A. nosocomialis (N=5), and A. pittii (N=17)-were isolated. The minimum inhibitory concentrations (MICs) were determined on the basis of the results of the Epsilometer test (Etest). PCR and DNA sequencing was performed to characterize the gene cassette arrays of class 1 integrons. Multilocus sequence typing (MLST) and repetitive extragenic palindromic sequence (REP)-PCR were performed for epidemiological typing. Results Class 1 integrons were detected in 50 (89.3%) of the 56 isolates, but no class 2 or 3 integron was found within the cohorts. The class 1 integrons were classified into 4 types: 2.3-kb type A (aacA4-catB8-aadA1), 3.0-kb type B (aacA4-blaIMP-1-blaOXA-2), 3.0-kb type C (blaVIM-2-aacA7-aadA1), and 1.8-kb type D (aac3-1-blaOXA-2-orfD). Type A was most prevalent and was detected only in A. baumannii isolates, except for one A. bereziniae isolate; however, type B was amplified in all Acinetobacter isolates except for A. baumannii isolates, regardless of clone and separation time of the bacteria. Conclusions Although class 1 integron can be transferred horizontally between unrelated isolates belonging to different species, certain types of class 1 integrons tend to transfer horizontally and vertically among A. baumannii or non-baumannii Acinetobacter isolates.
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Affiliation(s)
- Ji Youn Sung
- Department of Biomedical Laboratory Science, Far East University, Eumseong, Korea
| | - Sun Hoe Koo
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Semi Kim
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Kye Chul Kwon
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
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Blue-carba, an easy biochemical test for detection of diverse carbapenemase producers directly from bacterial cultures. J Clin Microbiol 2013; 51:4281-3. [PMID: 24108615 DOI: 10.1128/jcm.01634-13] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Identical miniature inverted repeat transposable elements flank class 1 integrons in clinical isolates of Acinetobacter spp. J Clin Microbiol 2013; 51:2382-4. [PMID: 23596242 DOI: 10.1128/jcm.00692-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Miniature inverted repeat transposable elements (MITEs) have been identified flanking class 1 integrons. We have identified and characterized a 439-bp MITE-like structure in seven Acinetobacter species isolates from Portugal and Brazil. The complete sequence similarity of the elements and flanking regions suggests that MITEs may act as mobilizable vectors for the dissemination of integrons.
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Domingues S, Harms K, Fricke WF, Johnsen PJ, da Silva GJ, Nielsen KM. Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species. PLoS Pathog 2012; 8:e1002837. [PMID: 22876180 PMCID: PMC3410848 DOI: 10.1371/journal.ppat.1002837] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/19/2012] [Indexed: 12/24/2022] Open
Abstract
We have investigated to what extent natural transformation acting on free DNA substrates can facilitate transfer of mobile elements including transposons, integrons and/or gene cassettes between bacterial species. Naturally transformable cells of Acinetobacter baylyi were exposed to DNA from integron-carrying strains of the genera Acinetobacter, Citrobacter, Enterobacter, Escherichia, Pseudomonas, and Salmonella to determine the nature and frequency of transfer. Exposure to the various DNA sources resulted in acquisition of antibiotic resistance traits as well as entire integrons and transposons, over a 24 h exposure period. DNA incorporation was not solely dependent on integrase functions or the genetic relatedness between species. DNA sequence analyses revealed that several mechanisms facilitated stable integration in the recipient genome depending on the nature of the donor DNA; homologous or heterologous recombination and various types of transposition (Tn21-like and IS26-like). Both donor strains and transformed isolates were extensively characterized by antimicrobial susceptibility testing, integron- and cassette-specific PCRs, DNA sequencing, pulsed field gel electrophoreses (PFGE), Southern blot hybridizations, and by re-transformation assays. Two transformant strains were also genome-sequenced. Our data demonstrate that natural transformation facilitates interspecies transfer of genetic elements, suggesting that the transient presence of DNA in the cytoplasm may be sufficient for genomic integration to occur. Our study provides a plausible explanation for why sequence-conserved transposons, IS elements and integrons can be found disseminated among bacterial species. Moreover, natural transformation of integron harboring populations of competent bacteria revealed that interspecies exchange of gene cassettes can be highly efficient, and independent on genetic relatedness between donor and recipient. In conclusion, natural transformation provides a much broader capacity for horizontal acquisitions of genetic elements and hence, resistance traits from divergent species than previously assumed. Genetic elements, such as transposons and integrons, frequently carry antimicrobial resistance determinants and can be found widely disseminated among pathogenic bacteria. Their distribution pattern suggests dissemination through horizontal gene transfer. The role of natural transformation in horizontal transfer of genetic elements other than those that are self-replicative (plasmids) has remained largely unexplored. We have tested if natural transformation can facilitate transfer of transposons and class 1 integrons between bacterial species. We here provide experimental evidence showing that natural transformation can be a general mechanism for dissemination of genetic elements that by themselves do not encode interspecies transfer functions (e.g. transposons, insertion sequences). We demonstrate that antibiotic resistance determinants present in such genetic elements can spread by natural transformation between species of clinical interest. We show by quantitative data that interspecies exchange of resistance gene cassettes is highly efficient among integron-containing strains and species. Our study also provides a plausible explanation for how sequence-conserved integrons can become distributed among bacterial species.
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Affiliation(s)
- Sara Domingues
- Centre of Pharmaceutical Studies, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Klaus Harms
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - W. Florian Fricke
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Pål J. Johnsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Gabriela J. da Silva
- Centre of Pharmaceutical Studies, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Kaare Magne Nielsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- Genøk-Centre for Biosafety, Tromsø, Norway
- * E-mail:
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15
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Roca I, Espinal P, Vila-Farrés X, Vila J. The Acinetobacter baumannii Oxymoron: Commensal Hospital Dweller Turned Pan-Drug-Resistant Menace. Front Microbiol 2012; 3:148. [PMID: 22536199 PMCID: PMC3333477 DOI: 10.3389/fmicb.2012.00148] [Citation(s) in RCA: 243] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 03/28/2012] [Indexed: 12/28/2022] Open
Abstract
During the past few decades Acinetobacter baumannii has evolved from being a commensal dweller of health-care facilities to constitute one of the most annoying pathogens responsible for hospitalary outbreaks and it is currently considered one of the most important nosocomial pathogens. In a prevalence study of infections in intensive care units conducted among 75 countries of the five continents, this microorganism was found to be the fifth most common pathogen. Two main features contribute to the success of A. baumannii: (i) A. baumannii exhibits an outstanding ability to accumulate a great variety of resistance mechanisms acquired by different mechanisms, either mutations or acquisition of genetic elements such as plasmids, integrons, transposons, or resistant islands, making this microorganism multi- or pan-drug-resistant and (ii) The ability to survive in the environment during prolonged periods of time which, combined with its innate resistance to desiccation and disinfectants, makes A. baumannii almost impossible to eradicate from the clinical setting. In addition, its ability to produce biofilm greatly contributes to both persistence and resistance. In this review, the pathogenesis of the infections caused by this microorganism as well as the molecular bases of antibacterial resistance and clinical aspects such as treatment and potential future therapeutic strategies are discussed in depth.
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Affiliation(s)
- Ignasi Roca
- Department of Clinical Microbiology, School of Medicine, IDIBAPS and Barcelona Centre for International Health Research, Hospital Clínic-Universitat de Barcelona Barcelona, Spain
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16
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IMP-29, a novel IMP-type metallo-β-lactamase in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2012; 56:2187-90. [PMID: 22290960 DOI: 10.1128/aac.05838-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of two clonally related multiresistant Pseudomonas aeruginosa isolates led to the identification of a novel IMP-type metallo-β-lactamase. IMP-29 was significantly different from the other IMP variants (the closest variant being IMP-5 with 93% amino acid identity). The bla(IMP-29) gene cassette was carried by a class 1 integron in strain 10.298, while in strain 10.266 it was located in a rearranged DNA region on a 30-kb conjugative plasmid. Biochemical analysis confirmed that IMP-29 efficiently hydrolyzed carbapenems.
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17
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Partridge SR, Tsafnat G, Coiera E, Iredell JR. Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 2009; 33:757-84. [PMID: 19416365 DOI: 10.1111/j.1574-6976.2009.00175.x] [Citation(s) in RCA: 447] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Gene cassettes are small mobile elements, consisting of little more than a single gene and recombination site, which are captured by larger elements called integrons. Several cassettes may be inserted into the same integron forming a tandem array. The discovery of integrons in the chromosome of many species has led to the identification of thousands of gene cassettes, mostly of unknown function, while integrons associated with transposons and plasmids carry mainly antibiotic resistance genes and constitute an important means of spreading resistance. An updated compilation of gene cassettes found in sequences of such 'mobile resistance integrons' in GenBank was facilitated by a specially developed automated annotation system. At least 130 different (<98% identical) cassettes that carry known or predicted antibiotic resistance genes were identified, along with many cassettes of unknown function. We list exemplar GenBank accession numbers for each and address some nomenclature issues. Various modifications to cassettes, some of which may be useful in tracking cassette epidemiology, are also described. Despite potential biases in the GenBank dataset, preliminary analysis of cassette distribution suggests interesting differences between cassettes and may provide useful information to direct more systematic studies.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, University of Sydney, Westmead Hospital, Sydney, NSW, Australia.
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18
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First occurrence of an IMP metallo-beta-lactamase in Aeromonas caviae: IMP-19 in an isolate from France. Antimicrob Agents Chemother 2007; 51:4486-8. [PMID: 17938180 DOI: 10.1128/aac.01462-06] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the first IMP metallo-beta-lactamase in Aeromonas caviae: IMP-19, which differed from IMP-2 by a single amino acid change (Arg to Ala at position 38). bla(IMP-19) was found within a class 1 integron located on a 35-kb plasmid. This is also the first description of an IMP producer in France.
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19
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Abstract
Carbapenemases are beta-lactamases with versatile hydrolytic capacities. They have the ability to hydrolyze penicillins, cephalosporins, monobactams, and carbapenems. Bacteria producing these beta-lactamases may cause serious infections in which the carbapenemase activity renders many beta-lactams ineffective. Carbapenemases are members of the molecular class A, B, and D beta-lactamases. Class A and D enzymes have a serine-based hydrolytic mechanism, while class B enzymes are metallo-beta-lactamases that contain zinc in the active site. The class A carbapenemase group includes members of the SME, IMI, NMC, GES, and KPC families. Of these, the KPC carbapenemases are the most prevalent, found mostly on plasmids in Klebsiella pneumoniae. The class D carbapenemases consist of OXA-type beta-lactamases frequently detected in Acinetobacter baumannii. The metallo-beta-lactamases belong to the IMP, VIM, SPM, GIM, and SIM families and have been detected primarily in Pseudomonas aeruginosa; however, there are increasing numbers of reports worldwide of this group of beta-lactamases in the Enterobacteriaceae. This review updates the characteristics, epidemiology, and detection of the carbapenemases found in pathogenic bacteria.
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Affiliation(s)
- Anne Marie Queenan
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Raritan, NJ 08869, USA.
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Mendes RE, Kiyota KA, Monteiro J, Castanheira M, Andrade SS, Gales AC, Pignatari ACC, Tufik S. Rapid detection and identification of metallo-beta-lactamase-encoding genes by multiplex real-time PCR assay and melt curve analysis. J Clin Microbiol 2006; 45:544-7. [PMID: 17093019 PMCID: PMC1829038 DOI: 10.1128/jcm.01728-06] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Metallo-beta-lactamase enzymes (MbetaL) are encoded by transferable genes, which appear to spread rapidly among gram-negative bacteria. The objective of this study was to develop a multiplex real-time PCR assay followed by a melt curve step for rapid detection and identification of genes encoding MbetaL-type enzymes based on the amplicon melting peak. The reference sequences of all genes encoding IMP and VIM types, SPM-1, GIM-1, and SIM-1 were downloaded from GenBank, and primers were designed to obtain amplicons showing different sizes and melting peak temperatures (Tm). The real-time PCR assay was able to detect all MbetaL-harboring clinical isolates, and the Tm-assigned genotypes were 100% coincident with previous sequencing results. This assay could be suitable for identification of MbetaL-producing gram-negative bacteria by molecular diagnostic laboratories.
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Affiliation(s)
- Rodrigo E Mendes
- Division of Infectious Diseases, Federal University of São Paulo, Rua Leandro Dupret, 188, São Paulo, SP, Brazil CEP 04025-010.
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21
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Quinteira S, Peixe L. Multiniche screening reveals the clinically relevant metallo-beta-lactamase VIM-2 in Pseudomonas aeruginosa far from the hospital setting: an ongoing dispersion process? Appl Environ Microbiol 2006; 72:3743-5. [PMID: 16672526 PMCID: PMC1472372 DOI: 10.1128/aem.72.5.3743-3745.2006] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A screening study of the presence of metallo-beta-lactamases (IMP and VIM types and SPM-1) in isolates from different nonhospital sources was conducted, and it revealed the presence of bla(VIM-2), associated with the In58 class 1 integron, in two unrelated Pseudomonas aeruginosa strains from aquatic habitats. The results suggest that the hospital setting was the possible origin of these bla(VIM-2)-carrying strains.
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Affiliation(s)
- Sandra Quinteira
- Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Aníbal Cunha 164, 4050-047 Porto, Portugal
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22
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Pagani L, Colinon C, Migliavacca R, Labonia M, Docquier JD, Nucleo E, Spalla M, Li Bergoli M, Rossolini GM. Nosocomial outbreak caused by multidrug-resistant Pseudomonas aeruginosa producing IMP-13 metallo-beta-lactamase. J Clin Microbiol 2005; 43:3824-8. [PMID: 16081918 PMCID: PMC1233900 DOI: 10.1128/jcm.43.8.3824-3828.2005] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An outbreak of Pseudomonas aeruginosa showing a multidrug-resistant (MDR) phenotype (including carbapenems, ceftazidime, cefepime, gentamicin, tobramycin, and fluoroquinolones) was observed, during a 5-month period, in a general intensive care unit of a large tertiary care and clinical research hospital in southern Italy. The outbreak involved 15 patients, with a total of 87 isolates, mostly from lower respiratory tract specimens. Analysis of isolates involved in the outbreak revealed production of metallo-beta-lactamase (MBL) activity, and genotyping by pulsed-field gel electrophoresis of genomic DNA digested by SpeI revealed clonal relatedness among isolates. Molecular analysis of the MBL determinant showed the presence of a bla(IMP-13) gene carried on a gene cassette inserted in a class 1 integron which also contained an aacA4 aminoglycoside resistance cassette encoding an AAC(6')-Ib enzyme. The bla(IMP-13)-containing integron and its genetic environment appeared to be similar to those found in P. aeruginosa isolates producing IMP-13 from a hospital in Rome. The bla(IMP-13) gene was not transferable by conjugation and was apparently carried on the chromosome. The outbreak was coincidental with a shortage of nursing personnel, and resolution was apparently associated with reinstatement of nursing personnel and reinforcement of general infection control practices within the intensive care unit. To our best knowledge this is the first description of a nosocomial outbreak of relatively large size caused by an IMP-producing gram-negative pathogen in Europe.
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Affiliation(s)
- Laura Pagani
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
| | - Céline Colinon
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
| | - Roberta Migliavacca
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
| | - Maria Labonia
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
| | - Jean-Denis Docquier
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
| | - Elisabetta Nucleo
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
| | - Melissa Spalla
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
| | - Michele Li Bergoli
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
| | - Gian Maria Rossolini
- Dipartimento di Scienze Morfologiche, Eidologiche e Cliniche, Sezione di Microbiologia, Università di Pavia, Servizio di Analisi Microbiologiche IRCCS S. Matteo, Pavia, Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, Siena, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy, Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium
- Corresponding author. Mailing address: Dipartimento di Biologia Molecolare, Università di Siena, Policlinico Santa Maria alle Scotte, I-53100 Siena, Italy. Phone: 39-0577-233455. Fax: 39-0577-233334. E-mail:
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23
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Walsh TR, Toleman MA, Poirel L, Nordmann P. Metallo-beta-lactamases: the quiet before the storm? Clin Microbiol Rev 2005; 18:306-25. [PMID: 15831827 PMCID: PMC1082798 DOI: 10.1128/cmr.18.2.306-325.2005] [Citation(s) in RCA: 997] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ascendancy of metallo-beta-lactamases within the clinical sector, while not ubiquitous, has nonetheless been dramatic; some reports indicate that nearly 30% of imipenem-resistant Pseudomonas aeruginosa strains possess a metallo-beta-lactamase. Acquisition of a metallo-beta-lactamase gene will invariably mediate broad-spectrum beta-lactam resistance in P. aeruginosa, but the level of in vitro resistance in Acinetobacter spp. and Enterobacteriaceae is less dependable. Their clinical significance is further embellished by their ability to hydrolyze all beta-lactams and by the fact that there is currently no clinical inhibitor, nor is there likely to be for the foreseeable future. The genes encoding metallo-beta-lactamases are often procured by class 1 (sometimes class 3) integrons, which, in turn, are embedded in transposons, resulting in a highly transmissible genetic apparatus. Moreover, other gene cassettes within the integrons often confer resistance to aminoglycosides, precluding their use as an alternative treatment. Thus far, the metallo-beta-lactamases encoded on transferable genes include IMP, VIM, SPM, and GIM and have been reported from 28 countries. Their rapid dissemination is worrisome and necessitates the implementation of not just surveillance studies but also metallo-beta-lactamase inhibitor studies securing the longevity of important anti-infectives.
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Affiliation(s)
- Timothy R Walsh
- Department of Pathology and Microbiology, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom.
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24
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Poirel L, Marqué S, Héritier C, Segonds C, Chabanon G, Nordmann P. OXA-58, a novel class D {beta}-lactamase involved in resistance to carbapenems in Acinetobacter baumannii. Antimicrob Agents Chemother 2005; 49:202-8. [PMID: 15616297 PMCID: PMC538857 DOI: 10.1128/aac.49.1.202-208.2005] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A carbapenem-resistant Acinetobacter baumannii strain was isolated in Toulouse, France, in 2003. Cloning and expression in Escherichia coli identified the carbapenem-hydrolyzing beta-lactamase OXA-58, which is weakly related (less than 50% amino acid identity) to other oxacillinases. It hydrolyzed penicillins, oxacillin, and imipenem but not expanded-spectrum cephalosporins. The bla(OXA-58) gene was located on a ca. 30-kb non-self-transferable plasmid. After electrotransformation in the A. baumannii CIP7010(T) reference strain, it conferred reduced susceptibility to carbapenems. The bla(OXA-58) gene was bracketed by two novel ISAba3-like insertion elements. This study describes a newly characterized beta-lactamase that may contribute to carbapenem resistance in A. baumannii.
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Affiliation(s)
- Laurent Poirel
- Service de Bactériologie-Virologie, Hôpital de Bicêtre, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre Cedex, France
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25
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Mendes RE, Toleman MA, Ribeiro J, Sader HS, Jones RN, Walsh TR. Integron carrying a novel metallo-beta-lactamase gene, blaIMP-16, and a fused form of aminoglycoside-resistant gene aac(6')-30/aac(6')-Ib': report from the SENTRY Antimicrobial Surveillance Program. Antimicrob Agents Chemother 2005; 48:4693-702. [PMID: 15561846 PMCID: PMC529210 DOI: 10.1128/aac.48.12.4693-4702.2004] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since January 2002 Pseudomonas sp. strains resistant to carbapenems and ceftazidime have been routinely screened as part of the SENTRY Antimicrobial Surveillance Program for metallo-beta-lactamase production, and their resistance determinants have been analyzed. Pseudomonas aeruginosa index strain 101-4704, which harbors a novel bla(IMP) variant, bla(IMP-16), was isolated in April 2002 from a 60-year-old man in Brasilia, Brazil. bla(IMP-16) was found on the chromosome of the P. aeruginosa index strain, and the deduced amino acid sequence (IMP-16) showed the greatest identities to IMP-11 (90.3%) and IMP-8 (89.5%). Sequence analysis revealed that bla(IMP-16) was associated with a class 1 integron, which also encoded aminoglycoside-modifying enzymes. Downstream of bla(IMP-16) resided an open reading frame, which consisted of a new aminoglycoside-modifying gene, namely, aac(6')-30, which was fused with aac(6')-Ib'. The amino acid sequence of the aac(6')-30 putative protein showed the most identity (52.7%) to the sequence of AAC(6')-29b described previously. The fourth gene cassette constituted aadA1. The steady-state kinetics of IMP-16 demonstrated that the enzyme preferred cephalosporins and carbapenems to penicillins. The main functional difference observed among the kinetic values for IMP-16 compared to those for other IMPs was a lack of cefoxitin hydrolysis and a lower kcat/Km value for imipenem (0.36 microM(-1) . s(-1)). This report further emphasizes the spread of metallo-beta-lactamase genes and their close association with various aminoglycoside resistance genes.
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Affiliation(s)
- Rodrigo E Mendes
- Disciplina de Doenças Infecciosas e Parasitárias, Universidade Federal de São Paulo, São Paulo, Brazil.
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26
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Castanheira M, Toleman MA, Jones RN, Schmidt FJ, Walsh TR. Molecular characterization of a beta-lactamase gene, blaGIM-1, encoding a new subclass of metallo-beta-lactamase. Antimicrob Agents Chemother 2005; 48:4654-61. [PMID: 15561840 PMCID: PMC529189 DOI: 10.1128/aac.48.12.4654-4661.2004] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As part of the SENTRY Antimicrobial Surveillance Program in 2002, five multidrug-resistant Pseudomonas aeruginosa clinical isolates were detected with metallo-beta-lactamase (MbetaL) activity. The isolates were recovered from different patients in a medical center located in Dusseldorf, Germany. The resistant determinant was isolated amplifying the region between the integrase and the aacA4 gene cassette. Sequencing revealed a novel MbetaL gene, designated bla(GIM-1). Additional analysis showed that GIM-1, comprising 250 amino acids and with a pI value of 5.4, differs in its primary sequence from that described for IMP, VIM, and SPM-1 enzymes by 39 to 43%, 28 to 31%, and 28%, respectively. The enzyme possesses unique amino acids within the major consensus sequence (HXHXD) of the MbetaL family. Kinetics analysis revealed that GIM-1 has no clear preference for any substrate and did not hydrolyze azlocillin, aztreonam, and the serine-beta-lactamase inhibitors. bla(GIM-1) was found on a 22-kb nontransferable plasmid. The new MbetaL gene was embedded in the first position of a 6-kb class 1 integron, In77, with distinct features, including an aacA4 cassette downstream of the MbetaL gene that appeared to be truncated with bla(GIM-1). The aacA4 was followed by an aadA1 gene cassette that was interrupted by a copy of the IS1394. This integron also carried an oxacillinase gene, bla(OXA-2), before the 3'-CS region. GIM-1 appears to be a unique MbetaL, which is located in a distinct integron structure, and represents the fourth subclass of mobile MbetaL enzymes to be characterized.
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Affiliation(s)
- Mariana Castanheira
- Disciplina de Doencas Infecciosas e Parasitarias, Universidade FEderal de Sao Paulo, Brazil.
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Correia M, Boavida F, Grosso F, Salgado MJ, Lito LM, Cristino JM, Mendo S, Duarte A. Molecular characterization of a new class 3 integron in Klebsiella pneumoniae. Antimicrob Agents Chemother 2003; 47:2838-43. [PMID: 12936982 PMCID: PMC182612 DOI: 10.1128/aac.47.9.2838-2843.2003] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae FFUL 22K was isolated in April 1999 from the urine of an intensive care unit patient in Portugal. The strain showed an extended-spectrum cephalosporin resistance profile. A typical synergistic effect between cefotaxime or cefepime and clavulanic acid was observed. An Escherichia coli transformant displayed a similar resistance phenotype and harbored a ca. 9.4-kb plasmid (p22K9). Cloning experiments revealed that the extended-spectrum beta-lactamase was encoded by bla(GES-1), previously described in class 1 integrons from K. pneumoniae ORI-1 and Pseudomonas aeruginosa Pa695. Further sequence analysis demonstrated that the bla(GES-1) gene cassette was located on a new class 3 integron. The integron was 2863 bp long and consisted of an intI3 integrase gene, an attI3 recombination site, two promoter regions, and two gene cassettes. The IntI3 integrase was 98.8% identical to that of Serratia marcescens AK9373. The bla(GES-1) gene cassette was inserted at the attI3 site. The second gene cassette was the result of a fusion event between bla(OXA-10)-type and aac(6')-Ib gene cassettes and conferred resistance to kanamycin. This is the second class 3 integron reported and the first time that the bla(GES-1) gene cassette has been found on an integron belonging to this class, highlighting the considerable heterogeneity of their genetic environment and the spread of gene cassettes among different classes of integrons.
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Affiliation(s)
- Mário Correia
- Laboratory of Microbiology, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
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Docquier JD, Riccio ML, Mugnaioli C, Luzzaro F, Endimiani A, Toniolo A, Amicosante G, Rossolini GM. IMP-12, a new plasmid-encoded metallo-beta-lactamase from a Pseudomonas putida clinical isolate. Antimicrob Agents Chemother 2003; 47:1522-8. [PMID: 12709317 PMCID: PMC153319 DOI: 10.1128/aac.47.5.1522-1528.2003] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Pseudomonas putida strain showing broad-spectrum resistance to beta-lactams, including expanded-spectrum cephalosporins and carbapenems, was isolated from a patient with a urinary tract infection at the University Hospital of Varese in northern Italy. The isolate was found to produce metallo-beta-lactamase activity and to harbor a 50-kb plasmid, named pVA758, carrying a new bla(IMP) determinant, named bla(IMP-12). Plasmid pVA758 was not self-transferable by conjugation to either Escherichia coli or Pseudomonas aeruginosa but could be introduced by electroporation and maintained in the latter host, where it conferred resistance or decreased susceptibility to various beta-lactams. The IMP-12 enzyme is quite divergent from other IMP variants: its closest relatives are IMP-8 and IMP-2 (89 and 88% sequence identity, respectively), and IMP-1 is 85% identical to IMP-12. The bla(IMP-12) determinant is carried on an integron-borne gene cassette whose attC recombination site is related to those present in cassettes containing bla(IMP-1), bla(IMP-6), bla(IMP-7), bla(IMP-10), and bla(IMP-11) and unrelated to that present in cassettes containing bla(IMP-2) and bla(IMP-8). IMP-12 was overproduced in E. coli by using a T7-based expression system and was purified by cation-exchange chromatography followed by gel filtration. Kinetic analysis revealed that, like other IMP variants, IMP-12 exhibits an overall preference for cephalosporins and carbapenems rather than for penicillins and does not hydrolyze temocillin and aztreonam. However, IMP-12 also exhibits some notable functional differences from other IMP variants, including uniformly poor activity toward penicillins (k(cat)/K(m) values, around 10(4) M(-1). s(-1)) and a remarkably high K(m) (around 900 micro M) for imipenem.
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Affiliation(s)
- Jean-Denis Docquier
- Dipartimento di Biologia Molecolare, Sezione di Microbiologia Università di Siena, I-53100 Siena, Italy
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Houang ETS, Chu YW, Lo WS, Chu KY, Cheng AFB. Epidemiology of rifampin ADP-ribosyltransferase (arr-2) and metallo-beta-lactamase (blaIMP-4) gene cassettes in class 1 integrons in Acinetobacter strains isolated from blood cultures in 1997 to 2000. Antimicrob Agents Chemother 2003; 47:1382-90. [PMID: 12654674 PMCID: PMC152494 DOI: 10.1128/aac.47.4.1382-1390.2003] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized two new gene cassettes in an Acinetobacter isolate: one harbored the metallo-beta-lactamase (IMP-4) gene bla(IMP-4), the other harbored the rifampin ADP-ribosyltransferase (ARR-2) gene arr-2, and both arrayed with the aminoglycoside acetyltransferase [AAC(6')-Ib(7)] gene cassette aacA4 in two separate class 1 integrons. The epidemiology of these gene cassettes in isolates from blood cultures obtained from 1997 to 2000 was studied. Isolates bearing either the bla(IMP-4) or the arr-2 gene cassette or both represented 17.5% (10 of 57) of isolates in 1997, 16.1% (10 of 62) in 1998, 2.5% (1 of 40) in 1999, and 0% (0 of 58) in 2000. These two gene cassettes, probably borne on two separate integrons, were found in at least three genomic DNA groups, with evidence of clonal dissemination in the intensive care unit during 1997 to 1998. Seventeen of the 52 Acinetobacter baumannii (genomic DNA group 2) isolates from 1997 to 2000 harbored intI1, but only one was positive for these gene cassettes, whereas 20 of the 21 intI1-positive isolates of all other genomic DNA groups were positive for either or both of them. Reduced susceptibility to imipenem and rifampin was seen only in isolates harboring the bla(IMP-4) and arr-2 cassettes, respectively. The aminoglycoside phosphotransferase [APH(3')-VIa] gene aph(3')-VIa was detected in all 21 isolates for which the MIC of amikacin was >/=8 micro g/ml, with or without aacA4, whereas aacA4 alone was found in isolates for which the MIC of amikacin was 0.5 to 2 micro g/ml. Significant differences between the 17 intI1-positive and 47 intI1-negative isolates belonging to genomic DNA group 3 from 1997 to 1998 in the MICs of amikacin, gentamicin, imipenem, sulfamethoxazole, and ceftazidime were observed (Mann-Whitney test, P < 0.001 to 0.01).
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Affiliation(s)
- Elizabeth T S Houang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, China.
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