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Li G, Long TF, Zhou SY, Xia LJ, Gao A, Wan L, Diao XY, He YZ, Sun RY, Yang JT, Tang SQ, Ren H, Fang LX, Liao XP, Liu YH, Chen L, Sun J. CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota. Drug Resist Updat 2024; 77:101142. [PMID: 39214042 DOI: 10.1016/j.drup.2024.101142] [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: 11/04/2023] [Revised: 08/04/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.
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Affiliation(s)
- Gong Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Teng-Fei Long
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Shi-Ying Zhou
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Li-Juan Xia
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Ang Gao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Lei Wan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Xiao-Yuan Diao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Yu-Zhang He
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Ruan-Yang Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Jin-Tao Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Sheng-Qiu Tang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, PR China
| | - Hao Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Liang-Xing Fang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Xiao-Ping Liao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Ya-Hong Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China
| | - Liang Chen
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, United States.
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, PR China.
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Marí-Almirall M, Cosgaya C, Pitart C, Viñes J, Muñoz L, Campo I, Cuscó A, Rodríguez-Serna L, Santana G, Del Río A, Francino O, Ciruela P, Pujol I, Ballester F, Marco F, Martínez JA, Soriano Á, Vila J, Roca I. Dissemination of NDM-producing Klebsiella pneumoniae and Escherichia coli high-risk clones in Catalan healthcare institutions. J Antimicrob Chemother 2021; 76:345-354. [PMID: 33200193 DOI: 10.1093/jac/dkaa459] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To characterize the clonal spread of carbapenem-resistant Klebsiella pneumoniae and Escherichia coli isolates between different healthcare institutions in Catalonia, Spain. METHODS Antimicrobial susceptibility was tested by disc diffusion. MICs were determined by gradient diffusion or broth microdilution. Carbapenemase production was confirmed by lateral flow. PCR and Sanger sequencing were used to identify the allelic variants of resistance genes. Clonality studies were performed by PFGE and MLST. Plasmid typing, conjugation assays, S1-PFGE plus Southern blotting and MinION Oxford Nanopore sequencing were used to characterize resistance plasmids. RESULTS Twenty-nine carbapenem-resistant isolates recovered from three healthcare institutions between January and November 2016 were included: 14 K. pneumoniae isolates from a tertiary hospital in the south of Catalonia (hospital A); 2 K. pneumoniae isolates from a nearby healthcare centre; and 12 K. pneumoniae isolates and 1 E. coli isolate from a tertiary hospital in Barcelona (hospital B). The majority of isolates were resistant to all antimicrobial agents, except colistin, and all were NDM producers. PFGE identified a major K. pneumoniae clone (n = 27) belonging to ST147 and co-producing NDM-1 and CTX-M-15, with a few isolates also harbouring blaOXA-48. Two sporadic isolates of K. pneumoniae ST307 and E. coli ST167 producing NDM-7 were also identified. blaNDM-1 was carried in two related IncR plasmid populations and blaNDM-7 in a conjugative 50 kb IncX3 plasmid. CONCLUSIONS We report the inter-hospital dissemination of XDR high-risk clones of K. pneumoniae and E. coli associated with the carriage of small, transferable plasmids harbouring blaNDM genes.
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Affiliation(s)
- Marta Marí-Almirall
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Clara Cosgaya
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Cristina Pitart
- Department of Clinical Microbiology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Joaquim Viñes
- SVGM, Molecular Genetics Veterinary Service, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,Vetgenomics, PRUAB, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Laura Muñoz
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Irene Campo
- Department of Clinical Microbiology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Anna Cuscó
- Vetgenomics, PRUAB, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Laura Rodríguez-Serna
- Department of Epidemiology and Preventive Medicine, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Gemina Santana
- Department of Epidemiology and Preventive Medicine, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ana Del Río
- Department of Infectious Diseases, Hospital Clínic - Institut d'investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Olga Francino
- SVGM, Molecular Genetics Veterinary Service, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Pilar Ciruela
- Public Health Agency of Catalonia (ASPCAT), Generalitat de Catalunya, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Pujol
- Laboratori de Microbiologia, Hospital Universitari Sant Joan de Reus, Reus, Spain.,Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Frederic Ballester
- Hospital Universitari Sant Joan de Reus-Laboratori de Referència del Camp de Tarragona i de les Terres de l'Ebre, Reus, Spain
| | - Francesc Marco
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Department of Clinical Microbiology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - José Antonio Martínez
- Department of Infectious Diseases, Hospital Clínic - Institut d'investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Álex Soriano
- Department of Infectious Diseases, Hospital Clínic - Institut d'investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Department of Clinical Microbiology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ignasi Roca
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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Spill-Over from Public Health? First Detection of an OXA-48-Producing Escherichia coli in a German Pig Farm. Microorganisms 2020; 8:microorganisms8060855. [PMID: 32517147 PMCID: PMC7356166 DOI: 10.3390/microorganisms8060855] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 12/21/2022] Open
Abstract
Resistance to carbapenems is a severe threat to human health. These last resort antimicrobials are indispensable for the treatment of severe human infections with multidrug-resistant Gram-negative bacteria. In accordance with their increasing medical impact, carbapenemase-producing Enterobacteriaceae (CPE) might be disseminated from colonized humans to non-human reservoirs (i.e., environment, animals, food). In Germany, the occurrence of CPE in livestock and food has been systematically monitored since 2016. In the 2019 monitoring, an OXA-48-producing E. coli (19-AB01443) was recovered from a fecal sample of a fattening pig. Phenotypic resistance was confirmed by broth microdilution and further characterized by PFGE, conjugation, and combined short-/long-read whole genome sequencing. This is the first detection of this resistance determinant in samples from German meat production. Molecular characterization and whole-genome sequencing revealed that the blaOXA-48 gene was located on a common pOXA-48 plasmid-prototype. This plasmid-type seems to be globally distributed among various bacterial species, but it was frequently associated with clinical Klebsiella spp. isolates. Currently, the route of introduction of this plasmid/isolate combination into the German pig production is unknown. We speculate that due to its strong correlation with human isolates a transmission from humans to livestock has occurred.
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4
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Mairi A, Pantel A, Ousalem F, Sotto A, Touati A, Lavigne JP. OXA-48-producing Enterobacterales in different ecological niches in Algeria: clonal expansion, plasmid characteristics and virulence traits. J Antimicrob Chemother 2019; 74:1848-1855. [DOI: 10.1093/jac/dkz146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Assia Mairi
- Laboratoire d’Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algeria
- Institut National de la Santé et de la Recherche Médicale, U1047, Université Montpellier, UFR de Médecine, Nîmes, France
| | - Alix Pantel
- Institut National de la Santé et de la Recherche Médicale, U1047, Université Montpellier, UFR de Médecine, Nîmes, France
- Department of Microbiology, University Hospital Nîmes, Nîmes, France
| | - Farès Ousalem
- Institut de Biologie et de Physico-chimie, UMR826, Université de Paris Diderot, Paris, France
| | - Albert Sotto
- Institut National de la Santé et de la Recherche Médicale, U1047, Université Montpellier, UFR de Médecine, Nîmes, France
- Department of Infectious Diseases, University Hospital Nîmes, Nîmes, France
| | - Abdelaziz Touati
- Laboratoire d’Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algeria
| | - Jean-Philippe Lavigne
- Institut National de la Santé et de la Recherche Médicale, U1047, Université Montpellier, UFR de Médecine, Nîmes, France
- Department of Microbiology, University Hospital Nîmes, Nîmes, France
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5
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Corel E, Méheust R, Watson AK, McInerney JO, Lopez P, Bapteste E. Bipartite Network Analysis of Gene Sharings in the Microbial World. Mol Biol Evol 2019; 35:899-913. [PMID: 29346651 PMCID: PMC5888944 DOI: 10.1093/molbev/msy001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8,217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny. Homologous genes are recycled by lateral gene transfer, and multiple copies of homologous genes are carried by otherwise completely unrelated (and possibly nested) genomes, that is, viruses, plasmids and prokaryotes. When a homologous gene is present on at least one plasmid or virus and at least one chromosome, a process of "gene externalization," affected by a postprocessed selected functional bias, takes place, especially in Bacteria. Bipartite graphs give us a view of vertical and horizontal gene flow beyond classic taxonomy on a single very large, analytically tractable, graph that goes beyond the cellular Web of Life.
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Affiliation(s)
- Eduardo Corel
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
| | - Raphaël Méheust
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
| | - Andrew K Watson
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
| | - James O McInerney
- Chair in Evolutionary Biology, The University of Manchester, United Kingdom
| | - Philippe Lopez
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
| | - Eric Bapteste
- Unité Mixte de Recherche 7138 Evolution Paris-Seine, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Sorbonne Université, Université Pierre et Marie Curie, Paris, France
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Ludden C, Reuter S, Judge K, Gouliouris T, Blane B, Coll F, Naydenova P, Hunt M, Tracey A, Hopkins KL, Brown NM, Woodford N, Parkhill J, Peacock SJ. Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. Microb Genom 2017; 3:e000114. [PMID: 29026655 PMCID: PMC5605956 DOI: 10.1099/mgen.0.000114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
Abstract
Dissemination of carbapenem resistance among pathogenic Gram-negative bacteria is a looming medical emergency. Efficient spread of resistance within and between bacterial species is facilitated by mobile genetic elements. We hypothesized that wastewater contributes to the dissemination of carbapenemase-producing Enterobacteriaceae (CPE), and studied this through a cross-sectional observational study of wastewater in the East of England. We isolated clinically relevant species of CPE in untreated and treated wastewater, confirming that waste treatment does not prevent release of CPE into the environment. We observed that CPE-positive plants were restricted to those in direct receipt of hospital waste, suggesting that hospital effluent may play a role in disseminating carbapenem resistance. We postulated that plasmids carrying carbapenemase genes were exchanged between bacterial hosts in sewage, and used short-read (Illumina) and long-read (MinION) technologies to characterize plasmids encoding resistance to antimicrobials and heavy metals. We demonstrated that different CPE species (Enterobacter kobei and Raoultella ornithinolytica) isolated from wastewater from the same treatment plant shared two plasmids of 63 and 280 kb. The former plasmid conferred resistance to carbapenems (blaOXA-48), and the latter to numerous drug classes and heavy metals. We also report the complete genome sequence for Enterobacter kobei. Small, portable sequencing instruments such as the MinION have the potential to improve the quality of information gathered on antimicrobial resistance in the environment.
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Affiliation(s)
- Catherine Ludden
- 1London School of Hygiene and Tropical Medicine, London, UK.,2Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sandra Reuter
- 3Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kim Judge
- 2Wellcome Trust Sanger Institute, Cambridge, UK.,3Department of Medicine, University of Cambridge, Cambridge, UK
| | - Theodore Gouliouris
- 3Department of Medicine, University of Cambridge, Cambridge, UK.,4Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Beth Blane
- 3Department of Medicine, University of Cambridge, Cambridge, UK
| | - Francesc Coll
- 1London School of Hygiene and Tropical Medicine, London, UK.,2Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - Martin Hunt
- 2Wellcome Trust Sanger Institute, Cambridge, UK
| | - Alan Tracey
- 2Wellcome Trust Sanger Institute, Cambridge, UK
| | - Katie L Hopkins
- 5Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Nicholas M Brown
- 4Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Neil Woodford
- 5Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
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Potter RF, D'Souza AW, Dantas G. The rapid spread of carbapenem-resistant Enterobacteriaceae. Drug Resist Updat 2016; 29:30-46. [PMID: 27912842 DOI: 10.1016/j.drup.2016.09.002] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/23/2016] [Accepted: 09/07/2016] [Indexed: 02/07/2023]
Abstract
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids. Improved characterization helps detail the co-occurrence of other antibiotic resistance genes in CRE isolates and helps identify pan-drug resistance mechanisms. The novel β-lactamase inhibitor, avibactam, combined with ceftazidime or aztreonam, is a promising CRE treatment compared to current colistin or tigecycline regimens. To halt increasing CRE-associated morbidity and mortality, we must continue quality, cooperative monitoring and urgently investigate novel treatments.
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Affiliation(s)
- Robert F Potter
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA
| | - Alaric W D'Souza
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in Saint Louis, 1 Brookings Drive, St. Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110, USA.
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