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Sabtcheva S, Stoikov I, Ivanov IN, Donchev D, Lesseva M, Georgieva S, Teneva D, Dobreva E, Christova I. Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria. Antibiotics (Basel) 2024; 13:455. [PMID: 38786183 PMCID: PMC11117914 DOI: 10.3390/antibiotics13050455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.
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Affiliation(s)
- Stefana Sabtcheva
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
| | - Ivan Stoikov
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Ivan N. Ivanov
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Deyan Donchev
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Magdalena Lesseva
- Department of Microbiology, University Multiprofile Hospital for Active Treatment and Emergency Medicine “N. I. Pirogov”, 1606 Sofia, Bulgaria;
| | - Sylvia Georgieva
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
| | - Deana Teneva
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Elina Dobreva
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Iva Christova
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
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Pokrant E, Vargas MB, Navarrete MJ, Yévenes K, Trincado L, Cortés P, Maddaleno A, Lapierre L, Cornejo J. Assessing the Effect of Oxytetracycline on the Selection of Resistant Escherichia coli in Treated and Untreated Broiler Chickens. Antibiotics (Basel) 2023; 12:1652. [PMID: 38136686 PMCID: PMC10740798 DOI: 10.3390/antibiotics12121652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/10/2023] [Accepted: 11/18/2023] [Indexed: 12/24/2023] Open
Abstract
Oxytetracycline (OTC) is administered in the poultry industry for the treatment of digestive and respiratory diseases. The use of OTC may contribute to the selection of resistant bacteria in the gastrointestinal tract of birds or in the environment. To determine the effect of OTC on the selection of resistant Escherichia coli strains post-treatment, bacteria were isolated from droppings and litter sampled from untreated and treated birds. Bacterial susceptibility to tetracyclines was determined by the Kirby-Bauer test. A total of 187 resistant isolates were analyzed for the presence of tet(A), (B), (C), (D), (E), and (M) genes by PCR. Fifty-four strains were analyzed by PFGE for subtyping. The proportion of tetracycline-resistant E. coli strains isolated was 42.88%. The susceptibility of the strains was treatment-dependent. A high clonal diversity was observed, with the tet(A) gene being the most prevalent, followed by tet(C). Even at therapeutic doses, there is selection pressure on resistant E. coli strains. The most prevalent resistance genes were tet(A) and tet(C), which could suggest that one of the main mechanisms of resistance of E. coli to tetracyclines is through active efflux pumps.
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Affiliation(s)
- Ekaterina Pokrant
- Laboratory of Food Safety, Department of Preventive Animal Medicine, Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (E.P.); (M.B.V.); (M.J.N.); (K.Y.)
- Doctorate Program of Forestry, Agriculture, and Veterinary Sciences (DCSAV), University of Chile, Av. Santa Rosa 11315, La Pintana, Santiago 8820808, Chile;
- Laboratory of Veterinary Pharmacology (FARMAVET), Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (P.C.); (A.M.)
| | - María Belén Vargas
- Laboratory of Food Safety, Department of Preventive Animal Medicine, Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (E.P.); (M.B.V.); (M.J.N.); (K.Y.)
- Doctorate Program of Forestry, Agriculture, and Veterinary Sciences (DCSAV), University of Chile, Av. Santa Rosa 11315, La Pintana, Santiago 8820808, Chile;
| | - María José Navarrete
- Laboratory of Food Safety, Department of Preventive Animal Medicine, Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (E.P.); (M.B.V.); (M.J.N.); (K.Y.)
| | - Karina Yévenes
- Laboratory of Food Safety, Department of Preventive Animal Medicine, Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (E.P.); (M.B.V.); (M.J.N.); (K.Y.)
- Doctorate Program of Forestry, Agriculture, and Veterinary Sciences (DCSAV), University of Chile, Av. Santa Rosa 11315, La Pintana, Santiago 8820808, Chile;
| | - Lina Trincado
- Doctorate Program of Forestry, Agriculture, and Veterinary Sciences (DCSAV), University of Chile, Av. Santa Rosa 11315, La Pintana, Santiago 8820808, Chile;
- Laboratory of Veterinary Pharmacology (FARMAVET), Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (P.C.); (A.M.)
| | - Paula Cortés
- Laboratory of Veterinary Pharmacology (FARMAVET), Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (P.C.); (A.M.)
| | - Aldo Maddaleno
- Laboratory of Veterinary Pharmacology (FARMAVET), Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (P.C.); (A.M.)
| | - Lisette Lapierre
- Laboratory of Bacterial Pathogens Diagnostic and Antimicrobial Resistance, Department of Preventive Animal Medicine, Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile
| | - Javiera Cornejo
- Laboratory of Food Safety, Department of Preventive Animal Medicine, Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (E.P.); (M.B.V.); (M.J.N.); (K.Y.)
- Laboratory of Veterinary Pharmacology (FARMAVET), Faculty of Veterinary and Animal Sciences, University of Chile, Santiago 8820808, Chile; (P.C.); (A.M.)
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Barbu IC, Gheorghe-Barbu I, Grigore GA, Vrancianu CO, Chifiriuc MC. Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors. Int J Mol Sci 2023; 24:7892. [PMID: 37175597 PMCID: PMC10178704 DOI: 10.3390/ijms24097892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.
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Affiliation(s)
- Ilda Czobor Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Irina Gheorghe-Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Georgiana Alexandra Grigore
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050044 Bucharest, Romania
- Romanian Academy, 010071 Bucharest, Romania
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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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Pál T, Butt AB, Ghazawi A, Thomsen J, Rizvi TA, Sonnevend Á. Early Years of Carbapenem-Resistant Enterobacterales Epidemic in Abu Dhabi. Antibiotics (Basel) 2022; 11:1435. [PMID: 36290093 PMCID: PMC9598120 DOI: 10.3390/antibiotics11101435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/28/2022] Open
Abstract
Recent studies showed that the current endemic of carbapenem-resistant Enterobacterales (CRE) in the Emirate of Abu Dhabi is dominated by highly resistant Klebsiella pneumoniae clones ST14, ST231, and CC147, respectively. In the absence of continuous, molecular typing-based surveillance, it remained unknown whether they lately emerged and rapidly became dominant, or they had been present from the early years of the endemic. Therefore, antibiotic resistance, the presence of carbapenemase and 16S methylase genes, and the sequence types of CRE strains collected between 2009 and 2015 were compared with those collected between 2018 and 2019. It was found that members of these three clones, particularly those of the most prevalent ST14, started dominating already in the very early years of the CRE outbreak. Furthermore, while severely impacting the overall antibiotic resistance patterns, the effect of these clones was not exclusive: for example, increasing trends of colistin or decreasing rates of tigecycline resistance were also observed among nonclonal isolates. The gradually increasing prevalence of few major, currently dominating clones raises the possibility that timely, systematic, molecular typing-based surveillance could have provided tools to public health authorities for an early interference with the escalation of the local CRE epidemic.
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Affiliation(s)
- Tibor Pál
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Aqdas B. Butt
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
| | - Jens Thomsen
- Abu Dhabi Public Health Center, Abu Dhabi P.O. Box 5674, United Arab Emirates
| | - Tahir A. Rizvi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
| | - Ágnes Sonnevend
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary
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Research Updates of Plasmid-Mediated Aminoglycoside Resistance 16S rRNA Methyltransferase. Antibiotics (Basel) 2022; 11:antibiotics11070906. [PMID: 35884160 PMCID: PMC9311965 DOI: 10.3390/antibiotics11070906] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
With the wide spread of multidrug-resistant bacteria, a variety of aminoglycosides have been used in clinical practice as one of the effective options for antimicrobial combinations. However, in recent years, the emergence of high-level resistance against pan-aminoglycosides has worsened the status of antimicrobial resistance, so the production of 16S rRNA methyltransferase (16S-RMTase) should not be ignored as one of the most important resistance mechanisms. What is more, on account of transferable plasmids, the horizontal transfer of resistance genes between pathogens becomes easier and more widespread, which brings challenges to the treatment of infectious diseases and infection control of drug-resistant bacteria. In this review, we will make a presentation on the prevalence and genetic environment of 16S-RMTase encoding genes that lead to high-level resistance to aminoglycosides.
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Taylor E, Jauneikaite E, Sriskandan S, Woodford N, Hopkins KL. Novel 16S rRNA methyltransferase RmtE3 in Acinetobacter baumannii ST79. J Med Microbiol 2022; 71. [PMID: 35588089 DOI: 10.1099/jmm.0.001531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction. The 16S rRNA methyltransferase (16S RMTase) gene armA is the most common mechanism conferring high-level aminoglycoside resistance in Acinetobacter baumannii, although rmtA, rmtB, rmtC, rmtD and rmtE have also been reported.Hypothesis/Gap statement. The occurrence of 16S RMTase genes in A. baumannii in the UK and Republic of Ireland is currently unknown.Aim. To identify the occurrence of 16S RMTase genes in A. baumannii isolates from the UK and the Republic of Ireland between 2004 and 2015.Methodology. Five hundred and fifty pan-aminoglycoside-resistant A. baumannii isolates isolated from the UK and the Republic of Ireland between 2004 and 2015 were screened by PCR to detect known 16S RMTase genes, and then whole-genome sequencing was conducted to screen for novel 16S RMTase genes.Results. A total of 96.5 % (531/550) of isolates were positive for 16S RMTase genes, with all but 1 harbouring armA (99.8 %, 530/531). The remaining isolates harboured rmtE3, a new rmtE variant. Most (89.2 %, 473/530) armA-positive isolates belonged to international clone II (ST2), and the rmtE3-positive isolate belonged to ST79. rmtE3 shared a similar genetic environment to rmtE2 but lacked an ISCR20 element found upstream of rmtE2.Conclusion. This is the first report of rmtE in A. baumannii in Europe; the potential for transmission of rmtE3 to other bacterial species requires further research.
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Affiliation(s)
- Emma Taylor
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
- Present address: Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Elita Jauneikaite
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- School of Public Health, Imperial College London, London W2 1PG, UK
| | - Shiranee Sriskandan
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2DD, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Katie L Hopkins
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London NW9 5EQ, UK
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A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure. Appl Environ Microbiol 2022; 88:e0255421. [PMID: 35285243 DOI: 10.1128/aem.02554-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The high diversity of bacterial antibiotic resistance genes (ARGs) and the different health risks due to their association with different bacterial hosts require environmental ARG risk assessment to have capabilities of both high throughput and host differentiation. Current whole genome sequencing of cultivated isolates is low in throughput, while direct metagenomic next generation sequencing (mNGS) of environmental samples is nonselective with respect to bacterial hosts. This study introduced a population metagenomic approach that combines isolate library construction and mNGS of the population metagenomic DNA, which enables studying ARGs and their association with mobile genetic elements (MGEs) in a specific bacterial population. The population metagenomic approach was demonstrated with the E. coli population in cattle manure, which detected the co-location of multiple ARGs on the same MGEs and their correspondence to the prevalence of resistance phenotypes of the E. coli isolates. When compared with direct mNGS of the cattle manure samples, the E. coli population metagenomes exhibited a significantly different resistome and an overall higher relative abundance of ARGs and horizontal gene transfer risks. IMPORTANCE Bacterial antibiotic resistance genes in the environment are ubiquitous and can pose different levels of human health risks due to their bacterial host association and subsequent mobility. This study introduced a population metagenomic approach to study ARGs and their mobility in specific bacterial populations through a combination of selective cultivation followed by next generation sequencing and bioinformatic analysis of the combined metagenome of isolates. The utility of this approach was demonstrated with the E. coli population in cattle manure samples, which showed that ARGs detected in the E. coli population corresponded to the observed resistance phenotypes, co-location of multiple ARGs on the same mobile genetic elements.
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Extraintestinal Pathogenic Escherichia coli: Beta-Lactam Antibiotic and Heavy Metal Resistance. Antibiotics (Basel) 2022; 11:antibiotics11030328. [PMID: 35326791 PMCID: PMC8944441 DOI: 10.3390/antibiotics11030328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/10/2022] Open
Abstract
Multiple-antibiotic-resistant (MAR) extra-intestinal pathogenic Escherichia coli (ExPEC) represents one of the most frequent causes of human nosocomial and community-acquired infections, whose eradication is of major concern for clinicians. ExPECs may inhabit indefinitely as commensal the gut of humans and other animals; from the intestine, they may move to colonize other tissues, where they are responsible for a number of diseases, including recurrent and uncomplicated UTIs, sepsis and neonatal meningitis. In the pre-antibiotic era, heavy metals were largely used as chemotherapeutics and/or as antimicrobials in human and animal healthcare. As with antibiotics, the global incidence of heavy metal tolerance in commensal, as well as in ExPEC, has increased following the ban in several countries of antibiotics as promoters of animal growth. Furthermore, it is believed that extensive bacterial exposure to heavy metals present in soil and water might have favored the increase in heavy-metal-tolerant microorganisms. The isolation of ExPEC strains with combined resistance to both antibiotics and heavy metals has become quite common and, remarkably, it has been recently shown that heavy metal resistance genes may co-select antibiotic-resistance genes. Despite their clinical relevance, the mechanisms underlining the development and spread of heavy metal tolerance have not been fully elucidated. The aim of this review is to present data regarding the development and spread of resistance to first-line antibiotics, such as beta-lactams, as well as tolerance to heavy metals in ExPEC strains.
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Wangkheimayum J, Paul D, Chanda DD, Melson Singha K, Bhattacharjee A. Elevated expression of rsmI can act as a reporter of aminoglycoside resistance in Escherichia coli using kanamycin as signal molecule. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105229. [PMID: 35104679 DOI: 10.1016/j.meegid.2022.105229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 11/26/2022]
Abstract
We aimed to design and analyse expressional response of endogenous and exogenous 16S rRNA methyl transferase genes under sub inhibitory concentration stress of different clinically relevant aminoglycoside antibiotics in Escherichia coli to identify an endogenous marker. One hundred twenty nine aminoglycoside resistant E. coli of clinical origin were collected for detection of 16S rRNA methyl transferase genes by PCR assay and each gene type was cloned within E. coli JM107. Parent isolates were subjected to plasmid elimination by SDS treatment. Expression analysis of both acquired and endogenous 16S rRNA methyl transferase genes were performed by quantitative real-time PCR in clones and parent isolates under aminoglycoside stress (4 mg/L). Majority of the isolates were harbouring rmtC (35/129), followed by rmtB (32/129), rmtA (21/129), rmtE (13/129), armA (11/129) rmtF (9/129) and rmtH (8/129). Plasmid was successfully eliminated for all the isolates with 6% of SDS. Expression analysis indicates that kanamycin, tobramycin and netilmicin stress could increase the expression of 16S rRNA methyltransferese genes. In the presence of kanamycin stress the expression of rsmI was consistently elevated for all the wild type isolates and clones tested. Except for isolates harbouring rmtB and rmtC expression of rsmE and rsmF was increased in the presence of all aminoglycosides. For all the cured mutants it was apparently observed that expression of endogenous methyl transferases were marginally increased. Elevated expression of constitutive rsmI can be used as a potential biomarker for detection of acquired 16S rRNA methyl transferase mediated aminoglycoside resistance by using sub inhibitory concentration of kanamycin as signal molecule.
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Affiliation(s)
| | - Deepjyoti Paul
- Department of Microbiology, Assam University Silchar, India
| | | | - K Melson Singha
- Department of Microbiology, Silchar Medical College and Hospital, Silchar, India
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Emergence of rmtD1 gene in clinical isolates of Pseudomonas aeruginosa carrying bla KPC and/or bla VIM-2 genes in Brazil. Braz J Microbiol 2021; 52:1959-1965. [PMID: 34420185 DOI: 10.1007/s42770-021-00576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 07/10/2021] [Indexed: 10/20/2022] Open
Abstract
OBJECTIVES The aim of the present study is to describe clinical aminoglycoside- or carbapenem-resistant Pseudomonas aeruginosa isolates collected between 2018 and 2019 in a hospital in Recife City, Northeastern Brazil. It was done based on phenotypic and molecular markers of antimicrobial resistance, as well as on the clonal diversity of the investigated isolates. METHODS Thirty-four carbapenem- and/or aminoglycoside-resistant P. aeruginosa isolates were collected in a hospital in Recife City-PE, Brazil. Their antimicrobial susceptibility profile was identified based on the automated BD Phoenix ™ system. In addition, broth microdilution was performed to determine the MICs of tobramycin and polymyxin B. Eventually, isolates were subjected to PCR and sequencing in order to detect the carbapenemase enzyme (blaKPC, blaNDM, blaVIM, blaSPM-1, and blaIMP) and 16S rRNA methylase (armA, rmtB, rmtD, rmtF, and rmtG) genes; ERIC-PCR was conducted for clonal profile determination purposes. RESULTS Thirty-four of the 64 isolates evaluated in the present study were selected for complementary molecular phenotypic tests, based on sample inclusion criteria. The blaKPC and blaVIM-2 genes were identified in 32.4% (11/34) and 38.2% (13/34) of tested isolates, respectively. The rmtD1 gene was detected in 32.4% (11/34) of analyzed isolates. Eight isolates carried both the blaKPC and rmtD1 genes, whereas blaVIM-2 and rmtD1 genes co-occurrence was detected in three strains; one isolate had all blaKPC, blaVIM-2, and rmtD1 genes. ERIC-PCR molecular typing has evidenced cross-transmission of three pathogenic clones among patients in the hospital. CONCLUSIONS The present study is a pioneer in describing isolates harboring both blaVIM-2 and rmtD1 genes. Moreover, it emphasizes the need of conducting local molecular epidemiology studies at different time intervals in order to monitor measures adopted to prevent nosocomial infections in different hospital units.
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Functional and Structural Characterization of Acquired Pan-Aminoglycoside Resistance 16S rRNA Methyltransferase NpmB1. Antimicrob Agents Chemother 2021; 65:e0100921. [PMID: 34310216 DOI: 10.1128/aac.01009-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Post-translational methylation of the A site of 16S rRNA at position A1408 leads to pan-aminoglycoside resistance encompassing both 4,5- and 4,6-disubstituted 2-deoxystreptamine (DOS) aminoglycosides. To date, NpmA is the only acquired enzyme with such function. Here, we present function and structure of NpmB1 whose sequence was identified in Escherichia coli genomes registered from the United Kingdom. NpmB1 possesses 40% amino acid identity with NpmA1 and confers resistance to all clinically relevant aminoglycosides including 4,5-DOS agents. Phylogenetic analysis of NpmB1 and NpmB2, its single amino acid variant, revealed that the encoding gene was likely acquired by E. coli from a soil bacterium. The structure of NpmB1 suggests that it requires a structural change of the β6/7 linker in order to bind to 16S rRNA. These findings establish NpmB1 and NpmB2 as the second group of acquired pan-aminoglycoside resistance 16S rRNA methyltransferases.
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13
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Caméléna F, Morel F, Merimèche M, Decousser JW, Jacquier H, Clermont O, Darty M, Mainardis M, Cambau E, Tenaillon O, Denamur E, Berçot B. Genomic characterization of 16S rRNA methyltransferase-producing Escherichia coli isolates from the Parisian area, France. J Antimicrob Chemother 2021; 75:1726-1735. [PMID: 32300786 DOI: 10.1093/jac/dkaa105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/15/2020] [Accepted: 02/27/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The resistance to all aminoglycosides (AGs) conferred by 16S rRNA methyltransferase enzymes (16S-RMTases) is a major public health concern. OBJECTIVES To characterize the resistance genotype, its genetic environment and plasmid support, and the phylogenetic relatedness of 16S-RMTase-producing Escherichia coli from France. METHODS We screened 137 E. coli isolates resistant to all clinically relevant AGs from nine Parisian hospitals for 16S-RMTases. WGS was performed on clinical isolates with high-level AG resistance (MIC ≥256 mg/L) and their transformants. RESULTS Thirty of the 137 AG-resistant E. coli produced 16S-RMTases: 11 ArmA, 18 RmtB and 1 RmtC. The 16S-RMTase producers were also resistant to third-generation cephalosporins (90% due to a blaCTX-M gene), co-trimoxazole, fluoroquinolones and carbapenems (blaNDM and blaVIM genes) in 97%, 83%, 70% and 10% of cases, respectively. Phylogenomic diversity was high in ArmA producers, with 10 different STs, but a similar genetic environment, with the Tn1548 transposon carried by a plasmid closely related to pCTX-M-3 in 6/11 isolates. Conversely, RmtB producers belonged to 12 STs, the most frequent being ST405 and ST complex (STc) 10 (four and four isolates, respectively). The rmtB gene was carried by IncF plasmids in 10 isolates and was found in different genetic environments. The rmtC gene was carried by the pNDM-US plasmid. CONCLUSIONS ArmA and RmtB are the predominant 16S-RMTases in France, but their spread follows two different patterns: (i) dissemination of a conserved genetic support carrying armA in E. coli with high levels of genomic diversity; and (ii) various genetic environments surrounding rmtB in clonally related E. coli.
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Affiliation(s)
- François Caméléna
- AP-HP, Service de Microbiologie, Hôpital Saint-Louis, Paris, France.,Université de Paris, INSERM, IAME, Paris, France
| | - Florence Morel
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Service de Bactériologie-Virologie, Hôpital Lariboisière, Paris, France
| | - Manel Merimèche
- AP-HP, Service de Microbiologie, Hôpital Saint-Louis, Paris, France.,Université de Paris, INSERM, IAME, Paris, France
| | - Jean-Winoc Decousser
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Service de Bactériologie et d'Hygiène Hospitalière, Hôpital Henri Mondor, Créteil, France
| | - Hervé Jacquier
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Service de Bactériologie-Virologie, Hôpital Lariboisière, Paris, France
| | | | - Mélanie Darty
- AP-HP, Service de Bactériologie et d'Hygiène Hospitalière, Hôpital Henri Mondor, Créteil, France
| | - Mary Mainardis
- AP-HP, Service de Microbiologie, Hôpital Saint-Louis, Paris, France
| | - Emmanuelle Cambau
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Service de Bactériologie-Virologie, Hôpital Lariboisière, Paris, France
| | | | - Erick Denamur
- Université de Paris, INSERM, IAME, Paris, France.,AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Béatrice Berçot
- AP-HP, Service de Microbiologie, Hôpital Saint-Louis, Paris, France.,Université de Paris, INSERM, IAME, Paris, France
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14
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Rashvand P, Peymani A, Mohammadi M, Karami A, Samimi R, Hajian S, Porasgari D, Habibollah-Pourzereshki N. Molecular survey of aminoglycoside-resistant Acinetobacter baumannii isolated from tertiary hospitals in Qazvin, Iran. New Microbes New Infect 2021; 42:100883. [PMID: 34094583 PMCID: PMC8165567 DOI: 10.1016/j.nmni.2021.100883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/10/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
Aminoglycoside-modifying enzymes (AMEs) and 16S rRNA methylases (16S RMTase) are two main resistance mechanisms against aminoglycosides. This study aimed to evaluate the frequency of AMEs and 16S rRNA methylase genes among aminoglycoside non-susceptible Acinetobacter baumannii isolates and to assess their clonal relationship using repetitive extragenic palindromic-PCR (rep-PCR). In this cross-sectional study, a total of 192 A. baumannii isolates were collected from the patients hospitalized in Qazvin, Iran (January 2016 to January 2018). Identification of isolates was performed by standard laboratory methods and API 20E strips. Antimicrobial susceptibility was determined by Kirby–Bauer method followed by examination of the genes encoding the AMEs and 16S RMTase by PCR and sequencing methods. The clonal relationship of isolates was carried out by rep-PCR. In total, 98.4% of isolates were non-susceptible to aminoglycosides, 98.4%, 97.9% and 83.9% of isolates were found to be non-susceptible against gentamicin, tobramycin and amikacin, respectively. The frequencies of aph(3′)-VI, aac(6′)-Ib, aac(3)-II, aph(3′)-Ia and armA genes were 59.3%, 39.2%, 39.2%, 31.7% and 69.8%, respectively, either alone or in combination. Rep-PCR results showed that the aminoglycoside non-susceptible isolates belonged to three distinct clones: A (79.4%), B (17.5%) and C (3.2%). The findings of this study showed a high frequency for AMEs with the emergence of armA genes among the aminoglycoside non-susceptible A. baumannii isolates. Rational administration of aminoglycosides as well as using an appropriate infection control policy may reduce the presence of resistance to antibiotics in medical centres. Little is known regarding carbapenem resistance mechanisms in A. baumannii in our region. More than 85% of our isolates were non-susceptible to carbapenems in Qazvin hospitals, Iran. blaOXA-23, blaOXA-24, blaIMP-1, and blaVIM-1 genes is established in carbapenem resistant A. baumannii isolates. Clonal distribution of carbapenem resistant A. baumannii was demonstrated in investigated hospital settings.
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Affiliation(s)
- P. Rashvand
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - A. Peymani
- Medical Microbiology Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
- Corresponding author: A. Peymani, Medical Microbiology Research Centre, Qazvin University of Medical Sciences, Minoodar, Velayat Hospital, Qazvin, Iran.
| | - M. Mohammadi
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - A.A. Karami
- Department of Urology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - R. Samimi
- Medical Microbiology Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
| | - S. Hajian
- Department of Nephrology, Velayat Hospital, Qazvin University of Medical Sciences, Qazvin, Iran
| | - D. Porasgari
- Medical Microbiology Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
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Hobson C, Chan AN, Wright GD. The Antibiotic Resistome: A Guide for the Discovery of Natural Products as Antimicrobial Agents. Chem Rev 2021; 121:3464-3494. [PMID: 33606500 DOI: 10.1021/acs.chemrev.0c01214] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of life-saving antibiotics has long been plagued by the ability of pathogenic bacteria to acquire and develop an array of antibiotic resistance mechanisms. The sum of these resistance mechanisms, the antibiotic resistome, is a formidable threat to antibiotic discovery, development, and use. The study and understanding of the molecular mechanisms in the resistome provide the basis for traditional approaches to combat resistance, including semisynthetic modification of naturally occurring antibiotic scaffolds, the development of adjuvant therapies that overcome resistance mechanisms, and the total synthesis of new antibiotics and their analogues. Using two major classes of antibiotics, the aminoglycosides and tetracyclines as case studies, we review the success and limitations of these strategies when used to combat the many forms of resistance that have emerged toward natural product-based antibiotics specifically. Furthermore, we discuss the use of the resistome as a guide for the genomics-driven discovery of novel antimicrobials, which are essential to combat the growing number of emerging pathogens that are resistant to even the newest approved therapies.
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Affiliation(s)
- Christian Hobson
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Andrew N Chan
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
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Wachino JI, Doi Y, Arakawa Y. Aminoglycoside Resistance: Updates with a Focus on Acquired 16S Ribosomal RNA Methyltransferases. Infect Dis Clin North Am 2020; 34:887-902. [PMID: 33011054 PMCID: PMC10927307 DOI: 10.1016/j.idc.2020.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The clinical usefulness of aminoglycosides has been revisited as an effective choice against β-lactam-resistant and fluoroquinolone-resistant gram-negative bacterial infections. Plazomicin, a next-generation aminoglycoside, was introduced for the treatment of complicated urinary tract infections and acute pyelonephritis. In contrast, bacteria have resisted aminoglycosides, including plazomicin, by producing 16S ribosomal RNA (rRNA) methyltransferases (MTases) that confer high-level and broad-range aminoglycoside resistance. Aminoglycoside-resistant 16S rRNA MTase-producing gram-negative pathogens are widespread in various settings and are becoming a grave concern. This article provides up-to-date information with a focus on aminoglycoside-resistant 16S rRNA MTases.
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Affiliation(s)
- Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan.
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, S829 Scaife Hall, 3350 Terrace Street, Pittsburgh, PA 15261, USA; Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Japan; Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan; Department of Medical Technology, Shubun University, Japan
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17
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Lee IM, Tu IF, Yang FL, Wu SH. Bacteriophage Tail-Spike Proteins Enable Detection of Pseudaminic-Acid-Coated Pathogenic Bacteria and Guide the Development of Antiglycan Antibodies with Cross-Species Antibacterial Activity. J Am Chem Soc 2020; 142:19446-19450. [PMID: 33166120 DOI: 10.1021/jacs.0c07314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pseudaminic acid (Pse), a unique carbohydrate in surface-associated glycans of pathogenic bacteria, has pivotal roles in virulence. Owing to its significant antigenicity and absence in mammals, Pse is considered an attractive target for vaccination or antibody-based therapies against bacterial infections. However, a specific and universal probe for Pse, which could also be used in immunotherapy, has not been reported. In a prior study, we used a tail spike protein from a bacteriophage (ΦAB6TSP) that digests Pse-containing exopolysaccharide (EPS) from Acinetobacter baumannii strain 54149 (Ab-54149) to form a glycoconjugate for preparing anti-Ab-54149 EPS serum. We report here that a catalytically inactive ΦAB6TSP (I-ΦAB6TSP) retains binding ability toward Pse. In addition, an I-ΦAB6TSP-DyLight-650 conjugate (Dy-I-ΦAB6TSP) was more sensitive in detecting Ab-54149 than an antibody purified from anti- Ab-54149 EPS serum. Dy-I-ΦAB6TSP also cross-reacted with other pathogenic bacteria containing Pse on their surface polysaccharides (e.g., Helicobacter pylori and Enterobacter cloacae), revealing it to be a promising probe for detecting Pse across bacterial species. We also developed a detection method that employs I-ΦAB6TSP immobilized on microtiter plate. These results suggested that the anti-Ab-54149 EPS serum would exhibit cross-reactivity to Pse on other organisms. When this was tested, this serum facilitated complement-mediated killing of H. pylori and E. cloacae, indicating its potential as a cross-species antibacterial agent. This work opens new avenues for diagnosis and treatment of multidrug resistant (MDR) bacterial infections.
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Affiliation(s)
- I-Ming Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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18
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van Duijkeren E, Schwarz C, Bouchard D, Catry B, Pomba C, Baptiste KE, Moreno MA, Rantala M, Ružauskas M, Sanders P, Teale C, Wester AL, Ignate K, Kunsagi Z, Jukes H. The use of aminoglycosides in animals within the EU: development of resistance in animals and possible impact on human and animal health: a review. J Antimicrob Chemother 2020; 74:2480-2496. [PMID: 31002332 DOI: 10.1093/jac/dkz161] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aminoglycosides (AGs) are important antibacterial agents for the treatment of various infections in humans and animals. Following extensive use of AGs in humans, food-producing animals and companion animals, acquired resistance among human and animal pathogens and commensal bacteria has emerged. Acquired resistance occurs through several mechanisms, but enzymatic inactivation of AGs is the most common one. Resistance genes are often located on mobile genetic elements, facilitating their spread between different bacterial species and between animals and humans. AG resistance has been found in many different bacterial species, including those with zoonotic potential such as Salmonella spp., Campylobacter spp. and livestock-associated MRSA. The highest risk is anticipated from transfer of resistant enterococci or coliforms (Escherichia coli) since infections with these pathogens in humans would potentially be treated with AGs. There is evidence that the use of AGs in human and veterinary medicine is associated with the increased prevalence of resistance. The same resistance genes have been found in isolates from humans and animals. Evaluation of risk factors indicates that the probability of transmission of AG resistance from animals to humans through transfer of zoonotic or commensal foodborne bacteria and/or their mobile genetic elements can be regarded as high, although there are no quantitative data on the actual contribution of animals to AG resistance in human pathogens. Responsible use of AGs is of great importance in order to safeguard their clinical efficacy for human and veterinary medicine.
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Affiliation(s)
| | - Christine Schwarz
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Damien Bouchard
- French Agency for Food, Environmental, and Occupational Safety, National Agency for Veterinary Medicinal Products, Fougères, France
| | - Boudewijn Catry
- Sciensano, Brussels, Belgium
- Faculty of Medicine, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Constança Pomba
- Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | | | - Miguel A Moreno
- Faculty of Veterinary Medicine, Complutense University, Madrid, Spain
| | - Merja Rantala
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Pascal Sanders
- French Agency for Food, Environmental, and Occupational Safety, Fougères Laboratory, Fougères, France
| | | | | | | | | | - Helen Jukes
- Veterinary Medicines Directorate, Addlestone, UK
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19
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Wangkheimayum J, Bhattacharjee M, Das BJ, Singha KM, Chanda DD, Bhattacharjee A. Expansion of acquired 16S rRNA methytransferases along with CTX-M-15, NDM and OXA-48 within three sequence types of Escherichia coli from northeast India. BMC Infect Dis 2020; 20:544. [PMID: 32711470 PMCID: PMC7382822 DOI: 10.1186/s12879-020-05264-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/16/2020] [Indexed: 11/25/2022] Open
Abstract
Background This study aimed to identify ten different 16S rRNA methyltransferase genes (rmtA, rmtB, rmtC, rmtD, armA, rmtF, npmA, rmtH, rmtE and rmtG) and their coexisting ESBL and carbapenemase with the emergence of three E.coli clones within a single study centre. Methods A total of 329 non-duplicate E.coli isolates were studied to detect the presence of 16S rRNA methyltransferases along with β-lactamases (TEM, SHV, OXA, VEB, GES, PER,CTX-M types, NDM, OXA-48,VIM, IMP and KPC) using PCR assay. Horizontal transferability were validated by transformation and conjugation analysis. Plasmid incompatibility typing and MLST analysis was also performed. Results A total of 117 isolates were found to be resistant to at least one of the aminoglycoside antibiotics. It was observed that 77 (65.8%) were positive for 16S rRNA methyltransferases. Among them thirty nine isolates were found to harbour only blaCTX-M-15, whereas combination of genes were observed in three isolates (blaVEB+ blaCTX-M-15 in 2 isolates and blaPER + blaCTX-M-15 in 1 isolate). blaNDM and blaOXA-48 like genes were found in 23 and 9 isolates, respectively. All the resistance genes were conjugatively transferable, and incompatibility typing showed multiple 16S rRNA methyltransferase genes were originated from a single Inc. I1 group. MLST analysis detected 3 clones of E.coliST4410, ST1341 and ST3906. Conclusion The present study identified emergence of three clones of E.coli, resistant to aminoglycoside -cephalosporin- carbapenem. This warrants immediate measures to trace their transmission dynamics in order to slow down their spread in clinical setting.
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Affiliation(s)
| | | | - Bhaskar Jyoti Das
- Department of Microbiology, Assam University Silchar, Silchar, India
| | - K Melson Singha
- Department of Microbiology, Silchar Medical College and Hospital, Silchar, India
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Nasiri G, Peymani A, Farivar TN, Hosseini P. Molecular epidemiology of aminoglycoside resistance in clinical isolates of Klebsiella pneumoniae collected from Qazvin and Tehran provinces, Iran. INFECTION GENETICS AND EVOLUTION 2018; 64:219-224. [PMID: 29964191 DOI: 10.1016/j.meegid.2018.06.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 06/02/2018] [Accepted: 06/27/2018] [Indexed: 11/18/2022]
Abstract
Production of aminoglycoside modifying enzymes (AMEs) and 16S rRNA methylases are two main resistance mechanisms against these antibiotics. This study determined the frequency of AMEs and 16 s rRNA methylase genes among aminoglycoside non-susceptible K. pneumoniae isolates and evaluated their clonal relationship by enterobacterial repetitive intergenic consensus (ERIC)-PCR. A total of 177 K. pneumoniae isolates were collected from hospitals of Qazvin and Tehran, Iran. The identification of isolates was done by standard laboratory methods and API 20E strips. Aminoglycosides susceptibility was determined by Kirby-Bauer method and AMEs and 16S rRNA methylase encoding genes were studied by PCR and sequencing methods. Clonal relatedness of isolates was assessed by ERIC-PCR method. In total, 74% of isolates were non-susceptible to the aminoglycosides used in the study among those kanamycin 110 (62.1%), tobramycin 91 (51.4%), and gentamycin 87 (49.2%) showed the highest rates of resistance whereas netilmicin and amikacin revealed high susceptibility rates of 67.8% and 61.0%, respectively. Of 130 aminoglycoside non-susceptible isolates, 91.5% were positive for the presence of aac(6')-Ib as the most dominant gene followed by aac(3)-II (78.5%), aph(3')-IIIa (14.6%), ant(4')-Ia (3.1%), and armA (7.7%) either alone or in combination. ERIC-PCR results showed 67.7% of non-susceptible isolates had different banding patterns followed by three distinct clones including A (16.2%), B (10.8%), and C (5.4%). Among those isolates carrying AMEs genes, 85 (68%) isolates belonged to independent groups and 21 (16.8%), 12 (9.6%), and 7 (5.6%) isolates belonged to groups A, B, and C, respectively, whereas 7 (70%) of 16S rRNA methylase-producing isolates belonged to independent groups. Our results revealed high prevalence of AMEs with the emergence of armA genes among the genetically unrelated resistant isolates of K. pneumonia in Iran, suggesting the need for more effective therapeutic strategies to reduce the selection pressure and better management of the patients infected with these resistant isolates.
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Affiliation(s)
- Gelareh Nasiri
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, IR, Iran
| | - Amir Peymani
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, IR, Iran.
| | - Taghi Naserpour Farivar
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, IR, Iran
| | - Peyman Hosseini
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, IR, Iran
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21
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Bado I, Papa-Ezdra R, Delgado-Blas JF, Gaudio M, Gutiérrez C, Cordeiro NF, García-Fulgueiras V, Araújo Pirez L, Seija V, Medina JC, Rieppi G, Gonzalez-Zorn B, Vignoli R. Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii in the Intensive Care Unit of Uruguay's University Hospital Identifies the First rmtC Gene in the Species. Microb Drug Resist 2018; 24:1012-1019. [PMID: 29920143 PMCID: PMC6154759 DOI: 10.1089/mdr.2017.0300] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) infections are an increasing concern in intensive care units (ICUs) worldwide. The combination of carbapenemases and 16S rRNA-methyltransferases (16S-RMTases) further reduces the therapeutic options. OXA-carbapenemase/A. baumannii clone tandems in Latin America have already been described; however, no information exists in this region regarding the occurrence of 16S-RMTases in this microorganism. In addition, the epidemiology of A. baumannii in ICUs and its associated resistance profiles are poorly understood. Our objectives were as follows: to study the clonal relationship and antibiotic resistance profiles of clinical and digestive colonizing A. baumannii isolates in an ICU, to characterize the circulating carbapenemases, and to detect 16S-RMTases. Patients admitted between August 2010 and July 2011 with a clinically predicted hospital stay > 48 hr were included. Pharyngeal and rectal swabs were obtained during the first fortnight after hospitalization. Resistance profiles were determined with MicroScan® and VITEK2 system. Carbapenemases and 16S-RMTases were identified by PCR and sequencing, and clonality was assessed by pulsed-field gel electrophoresis and multilocus sequence typing. Sixty-nine patients were studied and 63 were diagnosed with bacterial infections. Among these, 29 were CRAB isolates; 49 A. baumannii were isolated as digestive colonizers. These 78 isolates were clustered in 7 pulsetypes, mostly belonging to ST79. The only carbapenemase genes detected were blaOXA-51 (n = 78), blaOXA-23 (n = 62), and blaOXA-58 (n = 3). Interestingly, two clinical isolates harbored the rmtC 16S-RMTase gene. To the best of our knowledge, this is the first description of the presence of rmtC in A. baumannii.
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Affiliation(s)
- Inés Bado
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Romina Papa-Ezdra
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Jose F Delgado-Blas
- 2 Departamento de Salud Animal y VISAVET, Universidad Complutense de Madrid , Madrid, Spain
| | - Micaela Gaudio
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay .,2 Departamento de Salud Animal y VISAVET, Universidad Complutense de Madrid , Madrid, Spain
| | - Claudia Gutiérrez
- 3 Departamento de Laboratorio Clínico, Área Microbiología, Facultad de Medicina, Hospital de Clínicas , Universidad de la República, Montevideo, Uruguay
| | - Nicolás F Cordeiro
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Virginia García-Fulgueiras
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Lucía Araújo Pirez
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Verónica Seija
- 3 Departamento de Laboratorio Clínico, Área Microbiología, Facultad de Medicina, Hospital de Clínicas , Universidad de la República, Montevideo, Uruguay
| | - Julio C Medina
- 4 Cátedra de Enfermedades Infecciosas, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Gloria Rieppi
- 5 Facultad de Medicina, Unidad de Cuidados Intensivos del Hospital de Clínicas , Universidad de la República, Montevideo, Uruguay
| | - Bruno Gonzalez-Zorn
- 2 Departamento de Salud Animal y VISAVET, Universidad Complutense de Madrid , Madrid, Spain
| | - Rafael Vignoli
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
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22
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Liu BT, Zhang XY, Wan SW, Hao JJ, Jiang RD, Song FJ. Characteristics of Carbapenem-Resistant Enterobacteriaceae in Ready-to-Eat Vegetables in China. Front Microbiol 2018; 9:1147. [PMID: 29910786 PMCID: PMC5992273 DOI: 10.3389/fmicb.2018.01147] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/14/2018] [Indexed: 01/22/2023] Open
Abstract
Vegetables harboring bacteria resistant to antibiotics are a growing food safety issue. However, data concerning carbapenem-resistant Enterobacteriaceae (CRE) in ready-to-eat fresh vegetables is still rare. In this study, 411 vegetable samples from 36 supermarkets or farmer's markets in 18 cities in China, were analyzed for CRE. Carbapenemase-encoding genes and other resistance genes were analyzed among the CRE isolates. Plasmids carrying carbapenemase genes were studied by conjugation, replicon typing, S1-PFGE southern blot, restriction fragment length polymorphism (RFLP), and sequencing. CRE isolates were also analyzed by pulsed-field gel electrophoresis (PFGE). Ten vegetable samples yielded one or more CRE isolates. The highest detection rate of CRE (14.3%, 4/28) was found in curly endive. Twelve CRE isolates were obtained and all showed multidrug resistance: Escherichia coli, 5; Citrobacter freundii, 5; and Klebsiella pneumoniae, 2. All E. coli and C. freundii carried blaNDM, while K. pneumoniae harbored blaKPC−2. Notably, E. coli with blaNDM and ST23 hypervirulent Klebsiella pneumoniae (hvKP) carrying blaKPC−2 were found in the same cucumber sample and clonal spread of E. coli, C. freundii, and K. pneumoniae isolates were all observed between vegetable types and/or cities. IncX3 plasmids carrying blaNDM from E. coli and C. freundii showed identical or highly similar RFLP patterns, and the sequenced IncX3 plasmid from cucumber was also identical or highly similar (99%) to the IncX3 plasmids from clinical patients reported in other countries, while blaKPC−2 in K. pneumoniae was mediated by similar F35:A-:B1 plasmids. Our results suggest that both clonal expansion and horizontal transmission of IncX3- or F35:A-:B1-type plasmids may mediate the spread of CRE in ready-to-eat vegetables in China. The presence of CRE in ready-to-eat vegetables is alarming and constitutes a food safety issue. To our knowledge, this is the first report of either the C. freundii carrying blaNDM, or K. pneumoniae harboring blaKPC−2 in vegetables. This is also the first report of ST23 carbapenem-resistant hvKP strain in vegetables.
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Affiliation(s)
- Bao-Tao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiao-Yan Zhang
- Institute of Plant Protection, Qingdao Academy of Agricultural Sciences, Qingdao, China
| | - Shu-Wei Wan
- Institute of Plant Protection, Qingdao Academy of Agricultural Sciences, Qingdao, China
| | - Jun-Jie Hao
- Institute of Plant Protection, Qingdao Academy of Agricultural Sciences, Qingdao, China
| | - Rui-De Jiang
- Institute of Plant Protection, Qingdao Academy of Agricultural Sciences, Qingdao, China
| | - Feng-Jing Song
- Institute of Plant Protection, Qingdao Academy of Agricultural Sciences, Qingdao, China
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23
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Belaynehe KM, Shin SW, Hong-Tae P, Yoo HS. Occurrence of aminoglycoside-modifying enzymes among isolates of Escherichia coli exhibiting high levels of aminoglycoside resistance isolated from Korean cattle farms. FEMS Microbiol Lett 2018. [PMID: 28637330 DOI: 10.1093/femsle/fnx129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
This study investigated 247 Escherichia coli isolates collected from four cattle farms to characterize aminoglycoside-modifying enzyme (AME) genes, their plasmid replicons and transferability. Out of 247 isolates a high number of isolates (total 202; 81.78%) were found to be resistant to various antibiotics by disc diffusion. Of the 247 strains, 139 (56.3%) were resistant to streptomycin, and other antibiotic resistances followed as tetracycline (12.15%), ampicillin (7%), chloramphenicol (5.7%) and trimethoprim-sulfamethoxazole (0.8%). Among 247 isolates B1 was the predominant phylogenetic group identified comprising 151 isolates (61.1%), followed by groups A (27.9%), D (7%) and B2 (4%). Out of 139 isolates investigated for AME, 130 (93.5%) isolates carried at least one AME gene. aph3″-1a and aph3″-1b (46%) were the principal genes detected, followed by aac3-IVa (34.5%). ant2″-1a was the least detected gene (2.2%). Nine (6.5%) strains carried no AME genes. Twelve (63.2%) among 19 isolates transferred an AME gene to a recipient and aph3΄-1a was the dominant transferred gene. Transferability mainly occurred via the IncFIB replicon type (52.6%). Pulsed-field gel electrophoresis typing demonstrated a higher degree of diversity with 14 distinct cluster types. This result suggests that commensal microflora from food-producing animals has a tremendous ability to harbor and transfer AME genes, and poses a potential risk by dissemination of resistance to humans through the food chain.
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Affiliation(s)
- Kuastros Mekonnen Belaynehe
- Department of infectious diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Won Shin
- Department of infectious diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | | | - Han Sang Yoo
- Department of infectious diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
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24
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Takahashi Y, Igarashi M. Destination of aminoglycoside antibiotics in the 'post-antibiotic era'. J Antibiot (Tokyo) 2017; 71:ja2017117. [PMID: 29066797 DOI: 10.1038/ja.2017.117] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 12/17/2022]
Abstract
Aminoglycoside antibiotics (AGAs) were developed at the dawn of the antibiotics era and have significantly aided in the treatment of infectious diseases. Aminoglycosides have become one of the four major types of antibiotics in use today and, fortunately, still have an important role in the clinical treatment of severe bacterial infections. In this review, the current usage, modes of action and side effects of AGAs, along with the most common bacterial resistance mechanisms, are outlined. Finally, the recent development situation and possibility of new AGAs in the 'post-antibiotic era' are considered.The Journal of Antibiotics advance online publication, 25 October 2017; doi:10.1038/ja.2017.117.
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25
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Doi Y, Wachino JI, Arakawa Y. Aminoglycoside Resistance: The Emergence of Acquired 16S Ribosomal RNA Methyltransferases. Infect Dis Clin North Am 2017; 30:523-537. [PMID: 27208771 DOI: 10.1016/j.idc.2016.02.011] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aminoglycoside-producing Actinobacteria are known to protect themselves from their own aminoglycoside metabolites by producing 16S ribosomal RNA methyltransferase (16S-RMTase), which prevents them from binding to the 16S rRNA targets. Ten acquired 16S-RMTases have been reported from gram-negative pathogens. Most of them posttranscriptionally methylate residue G1405 of 16S rRNA resulting in high-level resistance to gentamicin, tobramycin, amikacin, and plazomicin. Strains that produce 16S-RMTase are frequently multidrug-resistant or even extensively drug-resistant. Although the direct clinical impact of high-level aminoglycoside resistance resulting from production of 16S-RMTase is yet to be determined, ongoing spread of this mechanism will further limit treatment options for multidrug-resistant and extensively drug-resistant gram-negative infections.
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Affiliation(s)
- Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, S829 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA.
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
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26
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Kashef MT, Helmy OM. Genetic Characterization of a Novel Composite Transposon Carrying armA and aac(6)-Ib Genes in an Escherichia coli Isolate from Egypt. Pol J Microbiol 2017; 66:163-169. [PMID: 28735317 DOI: 10.5604/01.3001.0010.7835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aminoglycosides are used in treating a wide range of infections caused by Gram-positive and Gram-negative bacteria; however, aminoglycoside resistance is common and occurs by several mechanisms. Among these mechanisms is bacterial rRNA methylation by the 16S rRNA methyl transferase (16S-RMTase) enzymes; but data about the spread of this mechanism in Egypt are scarce. Cephalosporins are the most commonly used antimicrobial agents in Egypt; therefore, this study was conducted to determine the frequency of 16S-RMTase among third generation cephalosporin-resistant clinical isolates in Egypt. One hundred and twenty three cephalosporin resistant Gram-negative clinical isolates were screened for aminoglycosides resistance by the Kirby Bauer disk diffusion method and tested for possible production of 16S-RMTase. PCR testing and sequencing were used to confirm the presence of 16S-RMTase and the associated antimicrobial resistance determinants, as well as the genetic region surrounding the armA gene. Out of 123 isolates, 66 (53.66%) were resistant to at least one aminoglycoside antibiotic. Only one Escherichia coli isolate (E9ECMO) which was totally resistant to all tested aminoglycosides, was confirmed to have the armA gene in association with blaTEM-1, blaCTX-M-15, blaCTX-M-14 and aac(6)-Ib genes. The armA gene was found to be carried on a large A/C plasmid. Genetic mapping of the armA surrounding region revealed, for the first time, the association of armA with aac(6)-Ib on the same transposon. In conclusion, the isolation frequency of 16S-RMTase was low among the tested aminoglycoside-resistant clinical samples. However, a novel composite transposon has been detected conferring high-level aminoglycosides resistance.
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Affiliation(s)
- Mona T Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Omneya M Helmy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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27
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Głuszek S, Sas-Paszt L, Sumorok B, Kozera R. Biochar-Rhizosphere Interactions – a Review. Pol J Microbiol 2017; 66:151-161. [DOI: 10.5604/01.3001.0010.6288] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biochar is a solid material of biological origin obtained from biomass carbonization, designed as a mean to reduce greenhouse gases emission and carbon sequestration in soils for a long time. Biochar has a wide spectrum of practical utilization and is applied as a promising soil improver or fertilizer in agriculture, or as a medium for soil or water remediation. Preparations of biochar increase plant growth and yielding when applied into soil and also improve plant growth conditions, mainly bio, physical and chemical properties of soil. Its physical and chemical properties have an influence on bacteria, fungi and invertebrates, both in field and laboratory conditions. Such effects on rhizosphere organisms are positive or negative depending on biochar raw material origin, charring conditions, frequency of applications, applications method and doses, but long term effects are generally positive and are associated mainly with increased soil biota activity. However, a risk assessment of biochar applications is necessary to protect food production and the soil environment. This should be accomplished by biochar production and characterization, land use implementation, economic analysis, including life cycle assessment, and environmental impact assessment.
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Affiliation(s)
| | | | - Beata Sumorok
- Research Institute of Horticulture, Skierniewice, Poland
| | - Ryszard Kozera
- Warsaw University of Life Sciences – SGGW, Warsaw, Poland
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28
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Li B, Pacey MP, Doi Y. Chromosomal 16S Ribosomal RNA Methyltransferase RmtE1 in Escherichia coli Sequence Type 448. Emerg Infect Dis 2017; 23:876-878. [PMID: 28418308 PMCID: PMC5403052 DOI: 10.3201/eid2305.162000] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We identified rmtE1, an uncommon 16S ribosomal methyltransferase gene, in an aminoglycoside- and cephalosporin-resistant Escherichia coli sequence type 448 clinical strain co-harboring blaCMY-2. Long-read sequencing revealed insertion of a 101,257-bp fragment carrying both resistance genes to the chromosome. Our findings underscore E. coli sequence type 448 as a potential high-risk multidrug-resistant clone.
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29
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Inventory of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae in France as Assessed by a Multicenter Study. Antimicrob Agents Chemother 2017; 61:AAC.01911-16. [PMID: 27956424 DOI: 10.1128/aac.01911-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/02/2016] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to perform an inventory of the extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae isolates responsible for infections in French hospitals and to assess the mechanisms associated with ESBL diffusion. A total of 200 nonredundant ESBL-producing Enterobacteriaceae strains isolated from clinical samples were collected during a multicenter study performed in 18 representative French hospitals. Antibiotic resistance genes were identified by PCR and sequencing experiments. The clonal relatedness between isolates was investigated by the use of the DiversiLab system. ESBL-encoding plasmids were compared by PCR-based replicon typing and plasmid multilocus sequence typing. CTX-M-15, CTX-M-1, CTX-M-14, and SHV-12 were the most prevalent ESBLs (8% to 46.5%). The three CTX-M-type EBSLs were significantly observed in Escherichia coli (37.1%, 24.2%, and 21.8%, respectively), and CTX-M-15 was the predominant ESBL in Klebsiella pneumoniae (81.1%). SHV-12 was associated with ESBL-encoding Enterobacter cloacae strains (37.9%). qnrB, aac(6')-Ib-cr, and aac(3)-II genes were the main plasmid-mediated resistance genes, with prevalences ranging between 19.5% and 45% according to the ESBL results. Molecular typing did not identify wide clonal diffusion. Plasmid analysis suggested the diffusion of low numbers of ESBL-encoding plasmids, especially in K. pneumoniae and E. cloacae However, the ESBL-encoding genes were observed in different plasmid replicons according to the bacterial species. The prevalences of ESBL subtypes differ according to the Enterobacteriaceae species. Plasmid spread is a key determinant of this epidemiology, and the link observed between the ESBL-encoding plasmids and the bacterial host explains the differences observed in the Enterobacteriaceae species.
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30
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Adler A, Sturlesi N, Fallach N, Zilberman-Barzilai D, Hussein O, Blum SE, Klement E, Schwaber MJ, Carmeli Y. Gentamicin- and Ciprofloxacin-Resistant Enterobacteriaceae in Cattle Farms in Israel: Risk Factors for Carriage and the Effect of Microbiological Methodology on the Measured Prevalence. Microb Drug Resist 2016; 23:660-665. [PMID: 27828758 DOI: 10.1089/mdr.2016.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Our objectives were to establish a methodology for surveillance of ciprofloxacin-resistant Enterobacteriaceae and gentamicin-resistant Enterobacteriaceae (CPRE and GNRE, respectively) in cattle and to study the prevalence and risk factors for carriage of these bacteria in a national survey. This was a point prevalence study conducted from July to October 2013 in Israel. Stool samples were collected from 1,226 cows in 123 sections of 40 farms of all production types. The number of CPRE- and GNRE-positive cows was highest in quarantine stations and fattening farms and was lowest in pasture farms (p < 0.01). The number of CPRE- and GNRE-positive cows was lowest in dairy farm sections containing adult cows (>25 months) and highest in calves (<4 months) (p < 0.001). In bivariate analysis, other variables that were significant risk factors for CPRE and GNRE carriage included fewer troughs, crowding, lack of manure cleaning, and recent arrival of new calves. Antimicrobial prophylaxis was given almost exclusively to calves and was associated with a higher prevalence of carriers (p < 0.001). Compared to the use of nonselective media (MacConkey agar alone), the use of selective media (MacConkey agar with 10 μg/ml of ciprofloxacin or 5 μg/ml of gentamicin) increased the sensitivity of screening for CPRE and GNRE by 6.6- and 13.5-fold, respectively. CPRE and GNRE were identified in 609 (49.7%) and 840 (68.5%) samples, respectively. This study provides novel data regarding both the epidemiology of CPRE and GNRE carriage in livestock and the microbiological methodology for their surveillance.
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Affiliation(s)
- Amos Adler
- 1 National Center for Infection Control , Ministry of Health, Tel-Aviv, Israel .,2 Tel-Aviv Sourasky Medical Center, Affiliated with the Sackler Faculty of Medicine, Tel-Aviv University , Tel-Aviv, Israel
| | - Na'ama Sturlesi
- 3 Koret School of Veterinary Medicine, Hebrew University , Rehovot, Israel
| | - Noga Fallach
- 1 National Center for Infection Control , Ministry of Health, Tel-Aviv, Israel
| | | | - Omar Hussein
- 1 National Center for Infection Control , Ministry of Health, Tel-Aviv, Israel
| | | | - Eyal Klement
- 3 Koret School of Veterinary Medicine, Hebrew University , Rehovot, Israel
| | - Mitchell J Schwaber
- 1 National Center for Infection Control , Ministry of Health, Tel-Aviv, Israel
| | - Yehuda Carmeli
- 1 National Center for Infection Control , Ministry of Health, Tel-Aviv, Israel
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31
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Beyrouthy R, Robin F, Hamze M, Bonnet R. IncFIIk plasmid harbouring an amplification of 16S rRNA methyltransferase-encoding gene rmtH associated with mobile element ISCR2. J Antimicrob Chemother 2016; 72:402-406. [PMID: 27793962 DOI: 10.1093/jac/dkw435] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/02/2016] [Accepted: 09/17/2016] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To investigate the resistance mechanisms and genetic support underlying the high resistance level of the Klebsiella pneumoniae strain CMUL78 to aminoglycoside and β-lactam antibiotics. METHODS Antibiotic susceptibility was assessed by the disc diffusion method and MICs were determined by the microdilution method. Antibiotic resistance genes and their genetic environment were characterized by PCR and Sanger sequencing. Plasmid contents were analysed in the clinical strain and transconjugants obtained by mating-out assays. Complete plasmid sequencing was performed with PacBio and Illumina technology. RESULTS Strain CMUL78 co-produced the 16S rRNA methyltransferase (RMTase) RmtH, carbapenemase OXA-48 and ESBL SHV-12. The rmtH- and blaSHV-12-encoding genes were harboured by a novel ∼115 kb IncFIIk plasmid designated pRmtH, and blaOXA-48 by a ∼62 kb IncL/M plasmid related to pOXA-48a. pRmtH plasmid possessed seven different stability modules, one of which is a novel hybrid toxin-antitoxin system. Interestingly, pRmtH plasmid harboured a 4-fold amplification of an rmtH-ISCR2 unit arranged in tandem and inserted within a novel IS26-based composite transposon designated Tn6329. CONCLUSIONS This is the first known report of the 16S RMTase-encoding gene rmtH in a plasmid. The rmtH-ISCR2 unit was inserted in a composite transposon as a 4-fold tandem repeat, a scarcely reported organization.
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Affiliation(s)
- Racha Beyrouthy
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France.,Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France.,Clermont Université, Université d'Auvergne, M2iSH, Clermont-Ferrand, France.,UMR INSERM 1071, Clermont-Ferrand, France.,USC INRA2018, Clermont-Ferrand, France
| | - Frederic Robin
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France.,Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France.,Clermont Université, Université d'Auvergne, M2iSH, Clermont-Ferrand, France.,UMR INSERM 1071, Clermont-Ferrand, France.,USC INRA2018, Clermont-Ferrand, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale en Sciences et Technologies et Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Richard Bonnet
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France .,Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France.,Clermont Université, Université d'Auvergne, M2iSH, Clermont-Ferrand, France.,UMR INSERM 1071, Clermont-Ferrand, France.,USC INRA2018, Clermont-Ferrand, France
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32
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Ou B, Chen L, Song Y, Yang Y, Zhang Q, Yang Y, Li L, Tham WL, Francis DH, Zhu G. Impact of acquisition of 16S rRNA methylase RmtB on the fitness of Escherichia coli. J Glob Antimicrob Resist 2016; 6:32-38. [PMID: 27530836 DOI: 10.1016/j.jgar.2016.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 02/21/2016] [Accepted: 02/23/2016] [Indexed: 10/22/2022] Open
Abstract
The aim of this study was to elucidate the biological phenotypes of 16S rRNA methylase RmtB in Escherichia coli and the impact of RmtB acquisition on the fitness of the target bacterium. An rmtB in-frame deletion mutant in E. coli was constructed using a suicide vector (pDMS197)-based double crossover allelic exchange, and its corresponding complemented strain was established. Combined studies of microdilution susceptibility testing, conjugation experiments, growth kinetics assays, competitive experiments, biofilm formation tests and motility assays were performed to study the rmtB-mediated fitness among the prototype E. coli strain, its isogenic mutant and the corresponding complemented strain. The minimum inhibitory concentrations (MICs) of 4,6-disubstituted 2-deoxystreptamines for the rmtB wild-type strain, its isogenic mutant and the complemented strain were ≥1024, ≤2 and ≥1024mg/L, respectively. Both the growth rates and the competitive abilities of the wild-type and complemented strains were relatively inferior to the ΔrmtB mutant. There was no significant difference in biofilm formation and motility among the three strains. In conclusion, the data presented here suggest that acquisition of the 16S rRNA methylase gene rmtB in E. coli can exact a fitness cost on the bacteria, subsequently reducing the growth rate slightly and decreasing the competitive capacity of the bacterium, whereas it does not affect biofilm formation or motility.
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Affiliation(s)
- Bingming Ou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Lin Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China
| | - Yujie Song
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Ying Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Qian Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Yi Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Luan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Wai Liang Tham
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - David H Francis
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China.
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33
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Complete Sequences of Multidrug Resistance Plasmids Bearing rmtD1 and rmtD2 16S rRNA Methyltransferase Genes. Antimicrob Agents Chemother 2016; 60:1928-31. [PMID: 26729503 DOI: 10.1128/aac.02562-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/27/2015] [Indexed: 11/20/2022] Open
Abstract
Complete nucleotide sequences were determined for two plasmids bearing rmtD group 16S rRNA methyltransferase genes. pKp64/11 was 78 kb in size, belonged to the IncL/M group, and harbored blaTEM-1b, sul1, qacEΔ1, dfrA22, and rmtD1 across two multidrug resistance regions (MRRs). pKp368/10 was 170 kb in size, belonged to the IncA/C group, and harbored acrB, sul1, qacEΔ1, ant(3″)-Ia, aac(6')-Ib, cat, rmtD2, and blaCTX-M-8 across three MRRs. The rmtD-containing regions shared a conserved motif, suggesting a common origin for the two rmtD alleles.
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Yang Y, Zhang A, Lei C, Wang H, Guan Z, Xu C, Liu B, Zhang D, Li Q, Jiang W, Pan Y, Yang C. Characteristics of Plasmids Coharboring 16S rRNA Methylases, CTX-M, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Isolates from Chickens in China. Foodborne Pathog Dis 2015; 12:873-80. [DOI: 10.1089/fpd.2015.2025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yongqiang Yang
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Anyun Zhang
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Changwei Lei
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Hongning Wang
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
- “985 Project” Science Innovative Platform for Resource and Environment Protection of Southwestern China, Chengdu, China
| | - Zhongbin Guan
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Changwen Xu
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Bihui Liu
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Dongdong Zhang
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Qingzhou Li
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Wei Jiang
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Yun Pan
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Chunmei Yang
- College of Life Science, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
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First Report of the IncI1/ST898 Conjugative Plasmid Carrying rmtE2 16S rRNA Methyltransferase Gene in Escherichia coli. Antimicrob Agents Chemother 2015; 59:7921-2. [PMID: 26392485 DOI: 10.1128/aac.01235-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Garneau-Tsodikova S, Labby KJ. Mechanisms of Resistance to Aminoglycoside Antibiotics: Overview and Perspectives. MEDCHEMCOMM 2015; 7:11-27. [PMID: 26877861 DOI: 10.1039/c5md00344j] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aminoglycoside (AG) antibiotics are used to treat many Gram-negative and some Gram-positive infections and, importantly, multidrug-resistant tuberculosis. Among various bacterial species, resistance to AGs arises through a variety of intrinsic and acquired mechanisms. The bacterial cell wall serves as a natural barrier for small molecules such as AGs and may be further fortified via acquired mutations. Efflux pumps work to expel AGs from bacterial cells, and modifications here too may cause further resistance to AGs. Mutations in the ribosomal target of AGs, while rare, also contribute to resistance. Of growing clinical prominence is resistance caused by ribosome methyltransferases. By far the most widespread mechanism of resistance to AGs is the inactivation of these antibiotics by AG-modifying enzymes. We provide here an overview of these mechanisms by which bacteria become resistant to AGs and discuss their prevalence and potential for clinical relevance.
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Affiliation(s)
- Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, USA. ; Tel: 859-218-1686
| | - Kristin J Labby
- Beloit College, Department of Chemistry, 700 College Street, Beloit, WI, USA. ; Tel: 608-363-2273
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Development and evaluation of immunochromatography to detect Gram-negative bacteria producing ArmA 16S rRNA methylase responsible for aminoglycoside resistance. J Microbiol Methods 2015; 118:159-63. [PMID: 26381663 DOI: 10.1016/j.mimet.2015.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 11/23/2022]
Abstract
Rapid and reliable detection of aminoglycoside-resistant bacteria is an important infection-control measure and a crucial aspect of antimicrobial chemotherapy. The enzyme 16S rRNA methylase has been shown to mediate aminoglycoside resistance in bacteria. This study describes a newly developed immunochromatographic assay using novel monoclonal antibodies (mAbs) that recognize ArmA 16S rRNA methylase. Epitope mapping showed that these mAbs recognized amino acids 1-93 of ArmA, which consists of 257 amino acids. Evaluation of the assay using ArmA producing and non-producing bacterial species, as well as bacteria producing other types of 16S rRNA methylases, indicated that immunochromatographic detection of the ArmA-type 16S rRNA methylase was fully consistent with PCR analysis for armA genes, with all immunochromatographically positive strains being resistant to aminoglycosides (MIC≥128μg/mL). The detection limit of the assay was 12ng ArmA. These findings indicate that this assay can be used for the rapid and reliable detection of the production of ArmA 16S rRNA methylase by Gram-negative bacteria, including Acinetobacter baumannii and Escherichia coli.
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Yu T, He T, Yao H, Zhang JB, Li XN, Zhang RM, Wang GQ. Prevalence of 16S rRNA Methylase Gene rmtB Among Escherichia coli Isolated from Bovine Mastitis in Ningxia, China. Foodborne Pathog Dis 2015. [DOI: 10.1089/fpd.2015.1983] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Ting Yu
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Tao He
- Key Laboratory of Development and Evaluation of Chemical and Herbal Drugs for Animal Use, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hong Yao
- Key Laboratory of Development and Evaluation of Chemical and Herbal Drugs for Animal Use, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jin-Bao Zhang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Xiao-Na Li
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Rong-Ming Zhang
- Key Laboratory of Development and Evaluation of Chemical and Herbal Drugs for Animal Use, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Gui-Qin Wang
- College of Agriculture, Ningxia University, Yinchuan, China
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Batah R, Loucif L, Olaitan AO, Boutefnouchet N, Allag H, Rolain JM. Outbreak of Serratia marcescens Coproducing ArmA and CTX-M-15 Mediated High Levels of Resistance to Aminoglycoside and Extended-Spectrum Beta-Lactamases, Algeria. Microb Drug Resist 2015; 21:470-6. [DOI: 10.1089/mdr.2014.0240] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Rima Batah
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
- Laboratoire de Biochimie et de Microbiologie Appliquée, Département de Biochimie, Université Badji Mokhtar Annaba, Annaba, Algerie
| | - Lotfi Loucif
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
- Laboratoire de Biotechnologie des Molecules Bioactives et de la Physiopathologie Cellulaire, Université El Hadj Lakhdar, Batna, Algerie
| | - Abiola Olumuyiwa Olaitan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Nafissa Boutefnouchet
- Laboratoire de Biochimie et de Microbiologie Appliquée, Département de Biochimie, Université Badji Mokhtar Annaba, Annaba, Algerie
| | - Hamoudi Allag
- Laboratoire de Bactériologie, Clinique Rénale Daksi Constantine, Constantine, Algerie
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
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Chidamba L, Korsten L. Antibiotic resistance in Escherichia coli isolates from roof-harvested rainwater tanks and urban pigeon faeces as the likely source of contamination. ENVIRONMENTAL MONITORING AND ASSESSMENT 2015; 187:405. [PMID: 26045040 DOI: 10.1007/s10661-015-4636-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 05/21/2015] [Indexed: 06/04/2023]
Abstract
The objective of this study was to investigate the risks associated with the use of roof-harvested rainwater (RHRW) and the implication of pigeons as the most likely source of contamination by testing for antibiotic resistance profiles of Escherichia coli. A total of 239 E. coli were isolated from thirty fresh pigeon faecal samples (130 isolates), 11 RHRW tanks from three sites in Pretoria (78) and two in Johannesburg (31). E. coli isolates were tested against a panel of 12 antibiotics which included ampicillin, amoxicillin, amikacin, cefoxitin, ceftriaxone, chloramphenicol, ciprofloxacin, cotrimoxazole, enrofloxacin, gentamicin, nalidixic acid and tetracycline. In all samples, resistance to ampicillin (22.7.9%), gentamicin (23.6%), amikacin (24%), tetracycline (17.4) and amoxicillin (16.9%) were the most frequently encountered form of resistance. However, a relatively higher proportion of isolates from pigeon faeces (67.3%) were antibiotic resistant than those from RHRW (53.3%). The highest number of phenotypes was observed for single antibiotics, and no single antibiotic resistance was observed for chloramphenicol, ceftriaxone, gentamicin, cefoxitin, cotrimoxazole, although they were detected in multiple antibiotic resistance (MAR) phenotypes. The highest multiple antibiotic resistance (MAR) phenotypes were observed for a combination of four antibiotics, on isolates from JHB (18.8%), pigeon faeces (15.2%) and Pretoria (5.1%). The most abundant resistance phenotype to four antibiotics, Ak-Gm-Cip-T was dominated by isolates from pigeon faeces (6.8%) with Pretoria and Johannesburg isolates having low proportions of 1.3 and 3.1%, respectively. Future studies should target isolates from various environmental settings in which rainwater harvesting is practiced and the characterisation of the antibiotic resistance determinant genes among the isolates.
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Affiliation(s)
- Lizyben Chidamba
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, 0002, South Africa,
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Complete sequence of conjugative IncA/C plasmid encoding CMY-2 β-lactamase and RmtE 16S rRNA methyltransferase. Antimicrob Agents Chemother 2015; 59:4360-1. [PMID: 25896689 DOI: 10.1128/aac.00852-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Ma XJ, Yang HF, Liu YY, Mei Q, Ye Y, Li HR, Cheng J, Li JB. The emergence of the 16S rRNA methyltransferase RmtB in a multidrug-resistant Serratia marcescens isolate in China. Ann Lab Med 2014; 35:172-4. [PMID: 25553305 PMCID: PMC4272956 DOI: 10.3343/alm.2015.35.1.172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/12/2014] [Accepted: 09/10/2014] [Indexed: 11/19/2022] Open
Affiliation(s)
- Xue-Jiao Ma
- Department of Infectious Diseases1, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hai-Fei Yang
- Department of Infectious Diseases1, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yan-Yan Liu
- Institute of Bacterium Resistance, Anhui Medical University, Hefei, China. ; Anhui Center for Surveillance of Bacterial Resistance, Hefei, China
| | - Qing Mei
- Department of Infectious Diseases1, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ying Ye
- Department of Infectious Diseases1, The First Affiliated Hospital of Anhui Medical University, Hefei, China. ; Institute of Bacterium Resistance, Anhui Medical University, Hefei, China. ; Anhui Center for Surveillance of Bacterial Resistance, Hefei, China
| | - Hong-Ru Li
- Department of Clinical Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jun Cheng
- Department of Infectious Diseases1, The First Affiliated Hospital of Anhui Medical University, Hefei, China. ; Institute of Bacterium Resistance, Anhui Medical University, Hefei, China. ; Anhui Center for Surveillance of Bacterial Resistance, Hefei, China
| | - Jia-Bin Li
- Department of Infectious Diseases1, The First Affiliated Hospital of Anhui Medical University, Hefei, China. ; Institute of Bacterium Resistance, Anhui Medical University, Hefei, China. ; Anhui Center for Surveillance of Bacterial Resistance, Hefei, China. ; Department of Infectious Diseases, Chaohu Hospital of Anhui Medical University, Hefei, China, China
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Nagasawa M, Kaku M, Kamachi K, Shibayama K, Arakawa Y, Yamaguchi K, Ishii Y. Loop-mediated isothermal amplification assay for 16S rRNA methylase genes in Gram-negative bacteria. J Infect Chemother 2014; 20:635-8. [PMID: 25179393 DOI: 10.1016/j.jiac.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/01/2014] [Accepted: 08/09/2014] [Indexed: 11/27/2022]
Abstract
Using the loop-mediated isothermal amplification (LAMP) method, we developed a rapid assay for detection of 16S rRNA methylase genes (rmtA, rmtB, and armA), and investigated 16S rRNA methylase-producing strains among clinical isolates. Primer Explorer V3 software was used to design the LAMP primers. LAMP primers were prepared for each gene, including two outer primers (F3 and B3), two inner primers (FIP and BIP), and two loop primers (LF and LB). Detection was performed with the Loopamp DNA amplification kit. For all three genes (rmtA, rmtB, and armA), 10(2) copies/tube could be detected with a reaction time of 60 min. When nine bacterial species (65 strains saved in National Institute of Infectious Diseases) were tested, which had been confirmed to possess rmtA, rmtB, or armA by PCR and DNA sequencing, the genes were detected correctly in these bacteria with no false negative or false positive results. Among 8447 clinical isolates isolated at 36 medical institutions, the LAMP method was conducted for 191 strains that were resistant to aminoglycosides based on the results of antimicrobial susceptibility tests. Eight strains were found to produce 16S rRNA methylase (0.09%), with rmtB being identified in three strains (0.06%) of 4929 isolates of Enterobacteriaceae, rmtA in three strains (0.10%) of 3284 isolates of Pseudomonas aeruginosa, and armA in two strains (0.85%) of 234 isolates of Acinetobacter spp. At present, the incidence of strains possessing 16S rRNA methylase genes is very low in Japan. However, when Gram-negative bacteria showing high resistance to aminoglycosides are isolated by clinical laboratories, it seems very important to investigate the status of 16S rRNA methylase gene-harboring bacilli and monitor their trends among Japanese clinical settings.
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Affiliation(s)
- Mitsuaki Nagasawa
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan; Department of Laboratory Medicine, Tohoku University Hospital, Miyagi, Japan; Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Mitsuo Kaku
- Department of Infection Control and Laboratory Diagnostics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology/Drug Resistance and Pathogenesis, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keizo Yamaguchi
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
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Simple multiplex real-time PCR for rapid detection of common 16S rRNA methyltransferase genes. Diagn Microbiol Infect Dis 2014; 80:29-31. [PMID: 25012151 DOI: 10.1016/j.diagmicrobio.2014.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/16/2014] [Accepted: 05/26/2014] [Indexed: 11/20/2022]
Abstract
We have developed a real-time multiplex PCR assay to detect the three most common 16S rRNA methyltransferase genes (armA, rmtB and rmtC), which encode problematic high-level resistance to all clinically-relevant aminoglycoside antibiotics. All results were consistent with published conventional PCR assays and these genes still appear rare in Australia.
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Liu Z, Ling B, Zhou L. Prevalence of 16S rRNA methylase, modifying enzyme, and extended-spectrum beta-lactamase genes among Acinetobacter baumannii isolates. J Chemother 2014; 27:207-12. [PMID: 24766153 DOI: 10.1179/1973947814y.0000000190] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Multidrug-resistant Acinetobacter baumannii has become a worldwide problem, and methylation of 16S rRNA has recently emerged as a new mechanism of resistance to aminoglycosides, which is mediated by a newly recognized group of 16S rRNA methylases. 16S rRNA methylase confers a high-level resistance to all 4,6-substituted deoxystreptamine aminoglycosides that are currently used in clinical practice. Some of the A. baumannii isolates have been found to coproduce extended-spectrum beta-lactamases (ESBLs), contributing to their multidrug resistance. The aim of this study was to detect the determinants of the 16S rRNA methylase genes armA, rmtA, rmtB, rmtC, rmtD, rmtE, and npmA, the modifying enzyme genes aac(6')-Ib, ant(3″)-Ia, aph(3')-I, and the extended-spectrum beta-lactamase genes bla(TEM), bla(SHV), and bla(CTX-M-3) among A. baumannii isolates in northeastern Sichuan, China. Minimum inhibitory concentrations (MICs) of 21 different antimicrobial agents against the A. baumannii isolates were determined. The clinical isolates showed a high level of resistance (MIC≧256 μg/ml) to aminoglycosides, which ranged from 50·1 to 83·8%. The resistances to meropenem and imipenem, two of the beta-lactam antibiotics and the most active antibiotics against A. baumannii, were 9·1 and 8·2%, respectively. Among 60 amikacin-resistant isolates, only the 16S rRNA methylase gene armA was found to be prevalent (66·7%), but the other 16S rRNA methylase genes rmtA, rmtB, rmtC, rmtD, rmtE, and npmA were not detected. The prevalences of the modifying enzyme genes aac (6')-Ib, ant (3″)-Ia, and aph (3')-I were 51·7, 81·7, and 58·3%, respectively, which are different from a previous study in which the occurrences of these genes were 3, 64, and 72%, respectively. Among the 40 isolates that were armA-positive, the prevalences of bla(TEM), bla(SHV), and bla(CTX-M-3) genes were detected for the first time in China, and their occurrences were 45, 65, and 52·5%, respectively. In all, A. baumannii with all the 16S rRNA methylase, modifying enzyme, and ESBL genes is extremely prevalent in northeastern Sichuan, China, posing a serious clinical concern with a major therapeutic threat in the future.
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Escherichia coli sequence type 354 coproducing CMY-2 cephalosporinase and RmtE 16S rRNA methyltransferase. Antimicrob Agents Chemother 2014; 58:4246-7. [PMID: 24752254 DOI: 10.1128/aac.02627-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Cummings KJ, Aprea VA, Altier C. Antimicrobial Resistance Trends Among Escherichia coli Isolates Obtained from Dairy Cattle in the Northeastern United States, 2004–2011. Foodborne Pathog Dis 2014; 11:61-7. [DOI: 10.1089/fpd.2013.1605] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Kevin J. Cummings
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas
| | | | - Craig Altier
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
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Increased prevalence of aminoglycoside resistance in clinical isolates of Escherichia coli and Klebsiella spp. in Norway is associated with the acquisition of AAC(3)-II and AAC(6′)-Ib. Diagn Microbiol Infect Dis 2014; 78:66-9. [DOI: 10.1016/j.diagmicrobio.2013.10.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 09/17/2013] [Accepted: 10/02/2013] [Indexed: 11/19/2022]
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49
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Liao XP, Liu BT, Yang QE, Sun J, Li L, Fang LX, Liu YH. Comparison of plasmids coharboring 16s rrna methylase and extended-spectrum β-lactamase genes among Escherichia coli isolates from pets and poultry. J Food Prot 2013; 76:2018-23. [PMID: 24290675 DOI: 10.4315/0362-028x.jfp-13-200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A total of 247 Escherichia coli isolates (148 from diseased or dead poultry and 99 from diseased pets in the People's Republic of China) were screened for extended-spectrum β-lactamase (ESBL) determinants by PCR and sequencing. Then, 16S rRNA methylase genes were detected among ESBL-producing isolates. Clonal relatedness of the E. coli isolates was examined by pulsed-field gel electrophoresis. Conjugation experiments were performed to investigate the association of 16S rRNA methylases and ESBLs, and plasmid contents were also characterized. Among 247 E. coli isolates, 74 (29.96%) isolates were positive for blaCTX-M genes, 42 from pets (12 from cats and 30 from dogs) and 32 from poultry (12 from chickens and 20 from ducks). The most common CTX-M type in isolates from pets was blaCTX-M-14, whereas blaCTX-M-27 was the most common for poultry. rmtB was dectected in 39 of the 74 blaCTX-M-positive isolates, 18 from pets and 21 from poultry. One strain from a pet was found to harbor blaCTX-M-14, blaCTX-M-15, and rmtB. blaCTX-M and rmtB were found to be colocated on the same transferable plasmid in 16 isolates. These genes were on the same or similar plasmids (eight F2:A-:B- and two IncN) in isolates from ducks, whereas they were colocated on the similar F2:A-:B- or similar F33:A-:B- plasmids in isolates of pets origin. In conclusion, similar F2:A-:B- plasmids and similar F33:A-:B- plasmids are responsible for the dissemination of both rmtB and blaCTX-Mgenes in E. coli isolates from poultry and pets, respectively.
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Affiliation(s)
- Xiao-Ping Liao
- College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues (SCAU), South China Agricultural University, Guangzhou 510642, People's Republic of China
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Shoma S, Kamruzzaman M, Ginn AN, Iredell JR, Partridge SR. Characterization of multidrug-resistant Klebsiella pneumoniae from Australia carrying blaNDM-1. Diagn Microbiol Infect Dis 2013; 78:93-7. [PMID: 24157059 DOI: 10.1016/j.diagmicrobio.2013.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/04/2013] [Accepted: 08/06/2013] [Indexed: 12/23/2022]
Abstract
blaNDM genes, encoding metallo-β-lactamases providing resistance to carbapenems, have been reported in many locations since the initial report in 2008, including in several Enterobacteriaceae isolates in Australia/New Zealand. Here, we compare 4 additional carbapenem-resistant Klebsiella pneumoniae carrying blaNDM-1 isolated in Australia. Two are sequence type ST147, previously associated with blaNDM in Australia and elsewhere. They carry blaNDM-1 and different 16S rRNA methylase genes (armA or rmtC) on different conjugative plasmids, in 1 case with an IncFIIY replicon. One isolate belongs to the globally important ST11 but did not transfer a plasmid to Escherichia coli. The fourth isolate belongs to the novel ST1068 and transferred blaNDM-1, armA, and an IncA/C plasmid. Amplification and sequencing of ompK porin genes suggest that, unlike the case for other carbapenemase genes, ompK36 defects may not be required for NDM to cause clinically relevant levels of carbapenem resistance.
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Affiliation(s)
- Shereen Shoma
- Centre for Research Excellence in Critical Infection and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW 2145, Australia; Westmead Millennium Institute, Westmead, NSW 2145, Australia; International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka 1212, Bangladesh
| | - Muhammad Kamruzzaman
- Centre for Research Excellence in Critical Infection and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW 2145, Australia; Westmead Millennium Institute, Westmead, NSW 2145, Australia; International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka 1212, Bangladesh
| | - Andrew N Ginn
- Centre for Research Excellence in Critical Infection and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW 2145, Australia; Westmead Millennium Institute, Westmead, NSW 2145, Australia; Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmeadx, NSW 2145, Australia
| | - Jonathan R Iredell
- Centre for Research Excellence in Critical Infection and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW 2145, Australia; Westmead Millennium Institute, Westmead, NSW 2145, Australia; Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmeadx, NSW 2145, Australia
| | - Sally R Partridge
- Centre for Research Excellence in Critical Infection and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW 2145, Australia; Westmead Millennium Institute, Westmead, NSW 2145, Australia; Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmeadx, NSW 2145, Australia.
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