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Sordo M, Grilo T, Freire S, Rodrigues B, Bouvier M, Poirel L, Aires-de-Sousa M. Rapid culture-based LNZ test for detection of linezolid susceptibility/resistance in staphylococci and enterococci. Diagn Microbiol Infect Dis 2023; 107:116058. [PMID: 37657232 DOI: 10.1016/j.diagmicrobio.2023.116058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
A rapid, easy-to-handle, cost-effective and universal culture-based test was developed for the identification of linezolid resistance among the most clinically relevant enterococcal and staphylococcal species. Our technique was tested using linezolid-resistant (n = 50) and linezolid-susceptible (n = 67) Gram-positive isolates: 34 Enterococcus faecium, 20 Enterococcus faecalis, 20 Staphylococcus aureus, 38 Staphylococcus epidermidis, and 5 Staphylococcus capitis. The susceptibility/resistance phenotype of E. faecium, E. faecalis, S. aureus, and S. epidermidis to linezolid was detected within 4.5 hours, while an extended timeframe was actually required for S. capitis (6.5 hours). The Rapid LNZ test showed a full agreement with the standard broth microdilution method, independently of the molecular resistance mechanism and MIC values, with sensitivities and specificities of 100% for all species.
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Affiliation(s)
- Miguel Sordo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Teresa Grilo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Samanta Freire
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal; Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Bruna Rodrigues
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Maxime Bouvier
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Marta Aires-de-Sousa
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisboa, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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2
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Singh NV, Singh KV, Dinh AQ, Arias CA, Shropshire WC, Hanson BM, Murray BE. Colocalization of Linezolid Resistance ( cfr) and Virulence Factors Cytolysin and Hemolysin ( cln and hln) on a Plasmid in Enterococcus faecalis. Antimicrob Agents Chemother 2023; 67:e0025923. [PMID: 37162332 PMCID: PMC10269126 DOI: 10.1128/aac.00259-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Affiliation(s)
- Nikita V. Singh
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Kavindra V. Singh
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medicine (WCMC), New York, New York, USA
| | - An Q. Dinh
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Center for Infectious Diseases, University of Texas Health Science Center School of Public Health, Houston, Texas, USA
| | - Cesar A. Arias
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medicine (WCMC), New York, New York, USA
| | - William C. Shropshire
- Center for Infectious Diseases, University of Texas Health Science Center School of Public Health, Houston, Texas, USA
| | - Blake M. Hanson
- Center for Infectious Diseases, University of Texas Health Science Center School of Public Health, Houston, Texas, USA
| | - Barbara E. Murray
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
- Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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3
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Martínez JR, Alcalde-Rico M, Jara-Videla E, Rios R, Moustafa AM, Hanson B, Rivas L, Carvajal LP, Rincon S, Diaz L, Reyes J, Quesille-Villalobos A, Riquelme-Neira R, Undurraga EA, Olivares-Pacheco J, García P, Araos R, Planet PJ, Arias CA, Munita JM. Heavy Metal Pollution From a Major Earthquake and Tsunami in Chile Is Associated With Geographic Divergence of Clinical Isolates of Methicillin-Resistant Staphylococcus aureus in Latin America. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541300. [PMID: 37293062 PMCID: PMC10245734 DOI: 10.1101/2023.05.18.541300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a priority pathogen listed by the World Health Organization. The global spread of MRSA is characterized by successive waves of epidemic clones that predominate in specific geographical regions. The acquisition of genes encoding resistance to heavy-metals is thought to be a key feature in the divergence and geographical spread of MRSA. Increasing evidence suggests that extreme natural events, such as earthquakes and tsunamis, could release heavy-metals into the environment. However, the impact of environmental exposition to heavy-metals on the divergence and spread of MRSA clones has been insufficiently explored. We assess the association between a major earthquake and tsunami in an industrialized port in southern Chile and MRSA clone divergence in Latin America. We performed a phylogenomic reconstruction of 113 MRSA clinical isolates from seven Latin American healthcare centers, including 25 isolates collected in a geographic area affected by an earthquake and tsunami that led to high levels of heavy-metal environmental contamination. We found a divergence event strongly associated with the presence of a plasmid harboring heavy-metal resistance genes in the isolates obtained in the area where the earthquake and tsunami occurred. Moreover, clinical isolates carrying this plasmid showed increased tolerance to mercury, arsenic, and cadmium. We also observed a physiological burden in the plasmid-carrying isolates in absence of heavy-metals. Our results are the first evidence that suggests that heavy-metal contamination, in the aftermath of an environmental disaster, appears to be a key evolutionary event for the spread and dissemination of MRSA in Latin America.
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Affiliation(s)
- Jose Rw Martínez
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Manuel Alcalde-Rico
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Grupo de Resistencia a los Antibióticos en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Chile
| | - Estefanía Jara-Videla
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Rafael Rios
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
| | - Lina Rivas
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Lina P Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Sandra Rincon
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Lorena Diaz
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Ana Quesille-Villalobos
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Roberto Riquelme-Neira
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Santiago, Chile
| | - Eduardo A Undurraga
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago, RM, Chile
- Research Center for Integrated Disaster Risk Management (CIGIDEN), Santiago, Chile
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Grupo de Resistencia a los Antibióticos en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Chile
| | - Patricia García
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Departamento de Enfermedades Infecciosas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael Araos
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- American Museum of Natural History, New York, NY 10024, USA
| | - César A Arias
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institution, Houston, TX, USA
| | - Jose M Munita
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
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4
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AbdAlhafiz AI, Elleboudy NS, Aboshanab KM, Aboulwafa MM, Hassouna NA. Phenotypic and genotypic characterization of linezolid resistance and the effect of antibiotic combinations on methicillin-resistant Staphylococcus aureus clinical isolates. Ann Clin Microbiol Antimicrob 2023; 22:23. [PMID: 37013561 PMCID: PMC10069030 DOI: 10.1186/s12941-023-00574-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 03/12/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Methicillin-Resistant Staphylococcus aureus (MRSA) causes life-threatening infections, with narrow therapeutic options including: vancomycin and linezolid. Accordingly, this study aimed to characterize phenotypically and genotypically, the most relevant means of linezolid resistance among some MRSA clinical isolates. METHODS A total of 159 methicillin-resistant clinical isolates were collected, of which 146 were indentified microscopically and biochemically as MRSA. Both biofilm formation and efflux pump activity were assessed for linezolid-resistant MRSA (LR-MRSA) using the microtiter plate and carbonyl cyanide 3-chlorophenylhydrazone (CCCP) methods, respectively. Linezolid resistance was further characterized by polymerase chain reaction (PCR) amplification and sequencing of domain V of 23 S rRNA; rplC; rplD;and rplV genes. Meanwhile, some resistance genes were investigated: cfr; cfr(B); optrA; msrA;mecA; and vanA genes. To combat LR-MRSA, the effect of combining linezolid with each of 6 different antimicrobials was investigated using the checkerboard assay. RESULTS Out of the collected MRSA isolates (n = 146), 5.48% (n = 8) were LR-MRSA and 18.49% (n = 27) were vancomycin-resistant (VRSA). It is worth noting that all LR-MRSA isolates were also vancomycin-resistant. All LR-MRSA isolates were biofilm producers (r = 0.915, p = 0.001), while efflux pumps upregulation showed no significant contribution to development of resistance (t = 1.374, p = 0.212). Both mecA and vanA genes were detected in 92.45% (n = 147) and 6.92% (n = 11) of methicillin-resistant isolates, respectively. In LR-MRSA isolates, some 23 S rRNA domain V mutations were observed: A2338T and C2610G (in 5 isolates); T2504C and G2528C (in 2 isolates); and G2576T (in 1 isolate). Amino acids substitutions were detected: in L3 protein (rplC gene) of (3 isolates) and in L4 protein (rplD gene) of (4 isolates). In addition, cfr(B) gene was detected (in 3 isolates). In 5 isolates, synergism was recorded when linezolid was combined with chloramphenicol, erythromycin, or ciprofloxacin. Reversal of linezolid resistance was observed in some LR-MRSA isolates when linezolid was combined with gentamicin or vancomycin. CONCLUSIONS LR-MRSA biofilm producers' phenotypes evolved in the clinical settings in Egypt. Various antibiotic combinations with linezolid were evaluated in vitro and showed synergistic effects.
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Affiliation(s)
- Asmaa I AbdAlhafiz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nooran S Elleboudy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Khaled M Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohammad M Aboulwafa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
- Faculty of Pharmacy, King Salman International University, South Sinai, Ras-Sudr, Egypt.
| | - Nadia A Hassouna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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5
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Suzuki K, Saito M, Hanaki H. Increased copy number of 23S ribosomal RNA gene with point mutation in MRSA associated with linezolid resistance in a patient treated with long-term linezolid. J Infect Chemother 2023; 29:481-484. [PMID: 36736701 DOI: 10.1016/j.jiac.2023.01.019] [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: 12/06/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) infection is one of the most difficult infections we have to treat. Linezolid is one of the effective treatment options for refractory MRSA infections. There are cases where we are forced to use long-term linezolid treatment for refractory MRSA infections. OBJECTIVE To discuss the evolution of Linezolid resistance factors in clinical isolates of MRSA. METHODS We investigated 16 MRSA isolated from a patient treated with linezolid for a long period of 75 days. We performed antibiotic susceptibility test, 23S rRNA genes sequencing analysis, Pulsed-field gel electrophoresis. RESULTS MRSA isolates were susceptible to linezolid before the start of treatment, but became less susceptible by prolonged treatment. The 23S rRNA sequencing analysis of linezolid-resistant strains that appeared 17 days after the start of treatment with linezolid revealed that all resistant MRSA had the G2576T substitution (Escherichia coli 23S rRNA gene number). The number of copies of this mutation increased with the use of linezolid. CONCLUSION Long-term use of linezolid in a patient or reuse of linezolid in a patient who has been previously treated with linezolid can lead to the emerging of linezolid-resistant MRSA in the host.
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Affiliation(s)
- Katsunori Suzuki
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Japan.
| | - Mitsumasa Saito
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Japan
| | - Hideaki Hanaki
- Infection Control Research Center, Kitasato University, Tokyo, Japan
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6
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Lade H, Joo HS, Kim JS. Molecular Basis of Non-β-Lactam Antibiotics Resistance in Staphylococcus aureus. Antibiotics (Basel) 2022; 11:1378. [PMID: 36290036 PMCID: PMC9598170 DOI: 10.3390/antibiotics11101378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most successful human pathogens with the potential to cause significant morbidity and mortality. MRSA has acquired resistance to almost all β-lactam antibiotics, including the new-generation cephalosporins, and is often also resistant to multiple other antibiotic classes. The expression of penicillin-binding protein 2a (PBP2a) is the primary basis for β-lactams resistance by MRSA, but it is coupled with other resistance mechanisms, conferring resistance to non-β-lactam antibiotics. The multiplicity of resistance mechanisms includes target modification, enzymatic drug inactivation, and decreased antibiotic uptake or efflux. This review highlights the molecular basis of resistance to non-β-lactam antibiotics recommended to treat MRSA infections such as macrolides, lincosamides, aminoglycosides, glycopeptides, oxazolidinones, lipopeptides, and others. A thorough understanding of the molecular and biochemical basis of antibiotic resistance in clinical isolates could help in developing promising therapies and molecular detection methods of antibiotic resistance.
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Affiliation(s)
- Harshad Lade
- Department of Laboratory Medicine, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul 05355, Korea
| | - Hwang-Soo Joo
- Department of Biotechnology, College of Engineering, Duksung Women’s University, Seoul 01369, Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul 05355, Korea
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7
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Tsai K, Stojković V, Noda-Garcia L, Young ID, Myasnikov AG, Kleinman J, Palla A, Floor SN, Frost A, Fraser JS, Tawfik DS, Fujimori DG. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. eLife 2022; 11:e70017. [PMID: 35015630 PMCID: PMC8752094 DOI: 10.7554/elife.70017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022] Open
Abstract
Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition of cfr results in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant that achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-electron microscopy structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr.
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Affiliation(s)
- Kaitlyn Tsai
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
| | - Vanja Stojković
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
| | - Lianet Noda-Garcia
- Department of Biomolecular Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Iris D Young
- Department of Bioengineering and Therapeutic Sciences, University of California San FranciscoSan FranciscoUnited States
| | - Alexander G Myasnikov
- Department of Biochemistry and Biophysics, University of California San FranciscoSan FranciscoUnited States
| | - Jordan Kleinman
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
| | - Ali Palla
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
| | - Stephen N Floor
- Helen Diller Family Comprehensive Cancer Center, University of California San FranciscoSan FranciscoUnited States
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute, University of California San FranciscoSan FranciscoUnited States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute, University of California San FranciscoSan FranciscoUnited States
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute, University of California San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, University of California San FranciscoSan FranciscoUnited States
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8
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Fernández-Cuenca F, López-Hernández I, Cercenado E, Conejo C, Tormo N, Gimeno C, Pascual A. Reporting antimicrobial susceptibilities and resistance phenotypes in Staphylococcus spp.: a nationwide proficiency study. J Antimicrob Chemother 2021; 76:1187-1196. [PMID: 33555012 PMCID: PMC8784165 DOI: 10.1093/jac/dkab017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/05/2021] [Indexed: 11/24/2022] Open
Abstract
Objectives To evaluate the proficiency of microbiology laboratories in Spain in antimicrobial susceptibility testing (AST) of Staphylococcus spp. Materials and methods Eight Staphylococcus spp. with different resistance mechanisms were selected: six Staphylococcus aureus (CC-01/mecA, CC-02/mecC, CC-03/BORSA, CC-04/MLSBi, CC-06/blaZ and CC-07/linezolid resistant, cfr); one Staphylococcus epidermidis (CC-05/linezolid resistant, 23S rRNA mutation); and one Staphylococcus capitis (CC-08/daptomycin non-susceptible). Fifty-one laboratories were asked to report: (i) AST system used; (ii) antimicrobial MICs; (iii) breakpoints used (CLSI or EUCAST); and (iv) clinical category. Minor, major and very major errors (mEs, MEs and VMEs, respectively) were determined. Results The greatest MIC discrepancies found were: (i) by AST method: 19.4% (gradient diffusion); (ii) by antimicrobial agent: daptomycin (21.3%) and oxacillin (20.6%); and (iii) by isolate: CC-07/cfr (48.0%). The greatest error rates were: (i) by AST method: gradient diffusion (4.3% and 5.1% VMEs, using EUCAST and CLSI, respectively); (ii) by breakpoint: 3.8% EUCAST and 2.3% CLSI; (iii) by error type: mEs (0.8% EUCAST and 1.0% CLSI), MEs (1.8% EUCAST and 0.7% CLSI) and VMEs (1.2% EUCAST and 0.6% CLSI); (iii) by antimicrobial agent: VMEs (4.7% linezolid and 4.3% oxacillin using EUCAST); MEs (14.3% fosfomycin, 9.1% tobramycin and 5.7% gentamicin using EUCAST); and mEs (22.6% amikacin using EUCAST). Conclusions Clinical microbiology laboratories should improve their ability to determine the susceptibility of Staphylococcus spp. to some antimicrobial agents to avoid reporting false-susceptible or false-resistant results. The greatest discrepancies and errors were associated with gradient diffusion, EUCAST breakpoints and some antimicrobials (mEs for aminoglycosides; MEs for fosfomycin, aminoglycosides and oxacillin; and VMEs for linezolid and oxacillin).
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Affiliation(s)
- Felipe Fernández-Cuenca
- Unidad Clínica de Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva, Hospital Universitario Virgen Macarena, Sevilla, Spain.,Instituto de Biomedicina de Sevilla (IBIs), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain.,Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada López-Hernández
- Unidad Clínica de Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva, Hospital Universitario Virgen Macarena, Sevilla, Spain.,Instituto de Biomedicina de Sevilla (IBIs), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain.,Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Emilia Cercenado
- Servicio de Microbiología y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Departamento de Medicina, Facultad de Medicina, Universidad Complutense, Madrid, Spain.,CIBERES, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, CB06/06/0058, Madrid, Spain
| | - Carmen Conejo
- Instituto de Biomedicina de Sevilla (IBIs), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain.,Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Nuria Tormo
- Servicio de Microbiología, Hospital General de Valencia, Valencia, Spain
| | - Concha Gimeno
- Servicio de Microbiología, Hospital General de Valencia, Valencia, Spain
| | - Alvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva, Hospital Universitario Virgen Macarena, Sevilla, Spain.,Instituto de Biomedicina de Sevilla (IBIs), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain.,Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
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Schwarz S, Zhang W, Du XD, Krüger H, Feßler AT, Ma S, Zhu Y, Wu C, Shen J, Wang Y. Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 PMCID: PMC8262807 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.
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Affiliation(s)
- Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Henrike Krüger
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Andrea T. Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Shizhen Ma
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Congming Wu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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Carvalhaes CG, Sader HS, Rhomberg PR, Mendes RE. Tedizolid activity against a multicentre worldwide collection of Staphylococcus aureus and Streptococcus pneumoniae recovered from patients with pneumonia (2017-2019). Int J Infect Dis 2021; 107:92-100. [PMID: 33857605 DOI: 10.1016/j.ijid.2021.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES The antimicrobial activity of tedizolid and comparators was evaluated against a large worldwide collection of Staphylococcus aureus and Streptococcus pneumoniae isolates recovered from patients with pneumonia. METHODS Clinical isolates were collected from patients in 96 medical centres in the Asia-Pacific region, Europe, Latin America and the USA between 2017 and 2019, and tested for susceptibility by reference broth microdilution. RESULTS The most active agents against S. aureus (n = 4667) were tedizolid (100.0% susceptible), linezolid (100.0% susceptible), ceftaroline (96.2% susceptible) and vancomycin (100.0% susceptible), but only tedizolid, linezolid and vancomycin retained activity against >95% of meticillin-resistant S. aureus isolates from all regions. In general, linezolid, ceftriaxone, ceftaroline, levofloxacin, penicillin and vancomycin showed susceptibility rates >95% against S. pneumoniae (n = 3008). However, only linezolid, ceftaroline, levofloxacin and vancomycin remained active (>95% susceptibility) against isolates displaying penicillin-non-susceptible or multidrug-resistant phenotypes. Penicillin-non-susceptible S. pneumoniae isolates were recovered less frequently from patients aged <5 years compared with other age groups. CONCLUSION The in-vitro data presented here confirm the high potency of tedizolid against S. aureus and S. pneumoniae causing pneumonia worldwide. There is a need for further clinical evaluations of tedizolid for treating pneumonia caused by these pathogens.
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Investigation of SCCmec types I-IV in clinical isolates of methicillin-resistant coagulase-negative staphylococci in Ahvaz, Southwest Iran. Biosci Rep 2021; 40:222874. [PMID: 32347308 PMCID: PMC7214399 DOI: 10.1042/bsr20200847] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 01/05/2023] Open
Abstract
Today methicillin resistant coagulase-negative staphylococci (MR-CoNS) are important in terms of causing significant nosocomial infections. Besides, MR-CoNS are confirmed as the reservoir of SCCmec elements that carry mecA (methicillin-resistant) gene. Hence, the present study was designed to evaluate the susceptibility pattern, prevalence and diversity of SCCmec types I, II, III, and IV in MR-CoNS strains. In this cross-sectional study, 44 clinical isolates of MR-CoNS were identified using the cefoxitin disc method and further confirmation by polymerase chain reaction (PCR) amplification of the mecA gene. Antimicrobial susceptibility of isolates was investigated by disc diffusion. The identification of CoNS was done by amplification and sequencing of the tuf gene. Multiplex PCR method was done for the determination of SCCmec types. In the present study, the Staphylococcus epidermidis and Staphylococcus haemolyticus were the most predominant isolates with a prevalence of 45.4%. The highest resistance rates were observed against erythromycin (84.1%) and clindamycin (75%). Multiplex PCR revealed the SCCmec type I as the predominant type in the present study. Our study showed that there was no significant relationship between the presence of different types of SCCmec elements and resistance to antibiotics. The present study highlighted a frequent prevalence of MR-CoNS harboring SCCmec type genes in Ahvaz, southwest of Iran. Thus, the molecular typing and periodical monitoring of their drug resistance pattern should be considered in national stewardship programs to designing useful antibiotic prescription strategies.
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Turner AM, Lee JYH, Gorrie CL, Howden BP, Carter GP. Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus. Front Microbiol 2021; 12:637656. [PMID: 33796088 PMCID: PMC8007764 DOI: 10.3389/fmicb.2021.637656] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 12/17/2022] Open
Abstract
Multidrug-resistant Staphylococcus and vancomycin-resistant Enterococcus (VRE) are important human pathogens that are resistant to most clinical antibiotics. Treatment options are limited and often require the use of 'last-line' antimicrobials such as linezolid, daptomycin, and in the case of Staphylococcus, also vancomycin. The emergence of resistance to these last-line antimicrobial agents is therefore of considerable clinical concern. This mini-review provides an overview of resistance to last-line antimicrobial agents in Staphylococcus and VRE, with a particular focus on how genomics has provided critical insights into the emergence of resistant clones, the molecular mechanisms of resistance, and the importance of mobile genetic elements in the global spread of resistance to linezolid.
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Affiliation(s)
- Adrianna M Turner
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - Claire L Gorrie
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Austin Health, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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Abstract
The absence of acquired resistance to antimicrobials has become an important criterion in evaluation of the biosafety of lactobacilli used as industrial starter or probiotic cultures. The aim of this study was to assess antibiotic resistance in starter and non-starter lactobacilli of food origin. Minimal inhibitory concentrations of ampicillin, chloramphenicol, clindamycin, erythromycin, gentamicin, kanamycin, streptomycin, tetracycline and vancomycin were established in 81 strains of lactobacilli (L. acidophilus, L. animalis, L. brevis, L. curvatus, L. delbrueckii, L. fermentum, L. helveticus, L. paracasei, L. plantarum, L. rhamnosus and L. sakei) by the microdilution method. The strains were classified as susceptible or resistant to antimicrobials based on the cut-off values according to the EFSA guideline. Sixty-two strains (77% food isolates, 76% starter or adjunct cultures) were resistant to at least one antimicrobial agent (the most frequently to aminoglycosides). Adjunct cultures showed a higher antibiotic resistance (80%) than starters (60%). Four multiresistant strains (3 food isolates, 1 adjunct culture) were analyzed by whole genome sequencing. One potentially transferable aadE gene (responsible for streptomycin resistance) was detected only in one multi-drug resistant strain of L. animalis originating from an adjunct culture. Thus, there is a risk of horizontal transmission of this gene. It is necessary to eliminate such strains from use in the food industry. This study provides relevant data concerning the use of lactobacilli in safe food production. To ensure food safety, detailed characterization of resistance to antimicrobials is necessary not only in starter strains but also in non-starter lactic acid bacteria isolated from food products.
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Characterization of Clostridioides difficile Isolates Available through the CDC & FDA Antibiotic Resistance Isolate Bank. Microbiol Resour Announc 2021; 10:10/1/e01011-20. [PMID: 33414286 PMCID: PMC8407687 DOI: 10.1128/mra.01011-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Thirty Clostridioides difficile isolates collected in 2016 through the Centers for Disease Control and Prevention Emerging Infections Program were selected for reference antimicrobial susceptibility testing and whole-genome sequencing. Here, we present the genetic characteristics of these isolates and announce their availability in the CDC & FDA Antibiotic Resistance Isolate Bank. Thirty Clostridioides difficile isolates collected in 2016 through the Centers for Disease Control and Prevention Emerging Infections Program were selected for reference antimicrobial susceptibility testing and whole-genome sequencing. Here, we present the genetic characteristics of these isolates and announce their availability in the CDC & FDA Antibiotic Resistance Isolate Bank.
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Prevalence and mechanisms of linezolid resistance among staphylococcal clinical isolates from Egypt. Eur J Clin Microbiol Infect Dis 2020; 40:815-823. [PMID: 33104900 DOI: 10.1007/s10096-020-04045-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
The emergence of methicillin-resistant staphylococci necessitated the search for alternative agents as linezolid, introduced to treat infections due to multidrug-resistant bacteria. Linezolid resistance has since emerged, yet its global prevalence remains low. In Egypt, little is known about the situation. We investigated the prevalence and mechanisms of resistance among Egyptian staphylococcal clinical isolates. Linezolid resistance among 232 staphylococcal isolates obtained from Alexandria Main Hospitals between 2011 and 2016 was assessed using disc diffusion and minimum inhibitory concentration. Resistant isolates were checked for cfr presence using polymerase chain reaction. The V domain of different alleles of 23S rRNA gene was investigated for mutations. Selection for linezolid-resistant mutants was performed in vitro through serial passages in linezolid sub-inhibitory concentrations. Combinations of linezolid with imipenem or anti-inflammatory agents were investigated using time-kill and modified checkerboard assays. Three Staphylococcus haemolyticus isolates (1.3%) from 2015 to 2016 were linezolid-resistant. One isolate carried cfr which was plasmid-borne, and together with another isolate which had a G2603T point mutation in the V domain of 23S rRNA gene. Successive exposure to linezolid sub-inhibitory concentrations was selected for three resistant Staphylococcus aureus mutants out of ten susceptible isolates. These mutants were more resistant towards different antibiotic classes than their susceptible parents. Linezolid combinations with imipenem, ibuprofen, or aspirin were synergistic against the isolates and mutants. Despite unregulated use of linezolid, resistance remains fairly low among the Egyptian isolates. Strict antimicrobial stewardship guidelines are needed in hospitals and the community to guard against further evolution of resistant mutants.
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Kerschner H, Rosel AC, Hartl R, Hyden P, Stoeger A, Ruppitsch W, Allerberger F, Apfalter P. Oxazolidinone Resistance Mediated by optrA in Clinical Enterococcus faecalis Isolates in Upper Austria: First Report and Characterization by Whole Genome Sequencing. Microb Drug Resist 2020; 27:685-690. [PMID: 33090061 DOI: 10.1089/mdr.2020.0098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genetic mechanisms associated with acquisition of linezolid (LZD) resistance are diverse, including point mutations in the V domain of the 23S rRNA and the 50S ribosomal proteins as well as cfr, optrA, and/or poxtA genes, which may be plasmid- or chromosomally encoded. The aim of this study was to investigate through Whole Genome Sequencing (WGS)-based typing the presence and location of genes and point mutations associated with LZD resistance in two Enterococcus faecalis isolates from Upper Austrian patients. The isolates were retrieved during screening by LZD disk diffusion test of a total of 911 clinical E. faecalis isolates in 2017. The two E. faecalis isolates had LZD minimum inhibitory concentrations of 8 and 32 mg/L and were optrA-positive (ST476 and ST585). Bioinformatic analysis revealed the presence of optrA located in the chromosome of both isolates. One isolate carried the optrA gene in the transposon 6674, previously reported as chromosomally encoded, and the second isolate in fragments originating from the integrative plasmid pEF10748. Additional mechanisms of LZD resistance on the 23S rRNA and the 50S ribosomal proteins were detected. None of the patients reported travels to geographical areas with high LZD resistance or previous LZD treatments. This is the first report of optrA carrying E. faecalis, including characterization by WGS from Austria. LZD resistance in a low-prevalence setting is of concern and should be further monitored.
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Affiliation(s)
- Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Adriana Cabal Rosel
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Patrick Hyden
- CUBE, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Stoeger
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Werner Ruppitsch
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Franz Allerberger
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
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Guerin F, Sassi M, Dejoies L, Zouari A, Schutz S, Potrel S, Auzou M, Collet A, Lecointe D, Auger G, Cattoir V. Molecular and functional analysis of the novel cfr(D) linezolid resistance gene identified in Enterococcus faecium. J Antimicrob Chemother 2020; 75:1699-1703. [DOI: 10.1093/jac/dkaa125] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/08/2020] [Accepted: 03/10/2020] [Indexed: 12/17/2022] Open
Abstract
Abstract
Objectives
To characterize the novel cfr(D) gene identified in an Enterococcus faecium clinical isolate (15-307.1) collected from France.
Methods
The genome of 15-307.1 was entirely sequenced using a hybrid approach combining short-read (MiSeq, Illumina) and long-read (GridION, Oxford Nanopore Technologies) technologies in order to analyse in detail the genetic support and environment of cfr(D). Transfer of linezolid resistance from 15-307.1 to E. faecium BM4107 was attempted by filter-mating experiments. The recombinant plasmid pAT29Ωcfr(D), containing cfr(D) and its own promoter, was transferred to E. faecium HM1070, Enterococcus faecalis JH2-2 and Escherichia coli AG100A.
Results
As previously reported, 15-307.1 belonged to ST17 and was phenotypically resistant to linezolid (MIC, 16 mg/L), vancomycin and teicoplanin. A hybrid sequencing approach confirmed the presence of several resistance genes including vanA, optrA and cfr(D). Located on a 103 kb plasmid, cfr(D) encoded a 357 amino acid protein, which shared 64%, 64%, 48% and 51% amino acid identity with Cfr, Cfr(B), Cfr(C) and Cfr(E), respectively. Both optrA and cfr(D) were successfully co-transferred to E. faecium BM4107. When expressed in E. faecium HM1070 and E. faecalis JH2-2, pAT29Ωcfr(D) did not confer any resistance, whereas it was responsible for an expected PhLOPSA resistance phenotype in E. coli AG100A. Analysis of the genetic environment of cfr(D) showed multiple IS1216 elements, putatively involved in its mobilization.
Conclusions
Cfr(D) is a novel member of the family of 23S rRNA methyltransferases. While only conferring a PhLOPSA resistance phenotype when expressed in E. coli, enterococci could constitute an unknown reservoir of cfr(D).
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Affiliation(s)
- François Guerin
- CHU de Caen, Service de Microbiologie, Caen, France
- Université de Caen Normandie, EA4655 Caen, France
| | - Mohamed Sassi
- Université de Rennes 1, Inserm U1230, Rennes, France
| | - Loren Dejoies
- Université de Rennes 1, Inserm U1230, Rennes, France
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
| | - Asma Zouari
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
| | - Sacha Schutz
- CHU de Rennes, Service de Génétique moléculaire et Génomique médicale, Rennes, France
| | - Sophie Potrel
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
| | - Michel Auzou
- CHU de Caen, Service de Microbiologie, Caen, France
| | - Anaïs Collet
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
| | - Didier Lecointe
- Unité Fonctionnelle d’Hygiène Hospitalière et de Lutte contre les Infections Nosocomiales, Centre Hospitalier Sud Francilien, Corbeil-Essonnes, France
| | - Gabriel Auger
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
| | - Vincent Cattoir
- Université de Rennes 1, Inserm U1230, Rennes, France
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
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Comparative genomics analysis of Raoultella planticola S25 isolated from duck in China, with florfenicol resistance. Comp Immunol Microbiol Infect Dis 2019; 68:101398. [PMID: 31775114 DOI: 10.1016/j.cimid.2019.101398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 12/29/2022]
Abstract
To characterize the florfenicol resistance gene and analyze the structure of the resistance gene-related sequence of an Raoultella planticola strain S25 isolated from a duck fecal sample from a farm in South China. Molecular cloning was performed to clone the resistance genes such as mdfA, floR and so on, and the minimum inhibitory concentrations (MICs) were quantified to determine the resistance levels generated by the cloned genes and the related strains. Sequencing and comparative genomics methods were used to analyze the structure of the resistance gene-related sequence. The result showed that the genome of R. planticola S25 consists of a 5.47 Mb chromosome encoding 4962 predicted coding sequence (CDS) and a 68,566 bp plasmid, pS25-68, encoding 84 ORFs. The plasmid sharing the greatest sequence identity with the floR-carrying plasmid pS25-68 is plasmid1 in Klebsiella pneumoniae strain blaNDM-1, which was isolated from a patient in Canada. The mdfA1 gene encoded on the chromosome generated resistance to florfenicol in addition to chloramphenicol. Comparative genomic analysis of the floR-related transposon-like fragment of pS25-68 showed that an approximately 3 kb sequence encoding IS91-virD2-floR-lysR was conserved and presented in the majority of the sequences (84.5 %, 169/200) collected from the database. The results of this work demonstrated that horizontal transfer of the florfenicol resistance gene floR occurred widely between the bacteria of different species and with different origins and that additional florfenicol resistance genes may be present in the bacterial population.
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Bassetti M, Carnelutti A, Castaldo N, Peghin M. Important new therapies for methicillin-resistant Staphylococcus aureus. Expert Opin Pharmacother 2019; 20:2317-2334. [PMID: 31622115 DOI: 10.1080/14656566.2019.1675637] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) infections represent a leading cause of infection-related morbidity and mortality worldwide. There has been a welcome increase in the number of agents available for the treatment of MRSA infection over the last decade and several clinical trials are currently investigating the role of new experimental strategies.Areas covered: The purpose of this manuscript is to review the efficacy and safety of recently approved anti-MRSA molecules as well as some newer agents currently under investigation with a specific focus on the potential role of these drugs in everyday clinical practice.Expert opinion: Many new drugs with an activity against MRSA have been recently approved or are in an advanced stage of development. All these compounds represent promising options to enhance our antibiotic armamentarium. However, data regarding the use of these new compounds in real-life terms are limited and their best placement in therapy and in terms of optimization of medical resources and balance of cost-effectiveness requires further investigation.
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Affiliation(s)
- Matteo Bassetti
- Department of Health Sciences, Infectious Disease Clinic, University of Genoa and Hospital Policlinico San Martino-IRCCS, Genoa, Italy
| | - Alessia Carnelutti
- Department of Medicine, Infectious Disease Clinic, University of Udine and Azienda Sanitaria Universitaria Integrata di Udine, Udine, Italy
| | - Nadia Castaldo
- Department of Medicine, Infectious Disease Clinic, University of Udine and Azienda Sanitaria Universitaria Integrata di Udine, Udine, Italy
| | - Maddalena Peghin
- Department of Medicine, Infectious Disease Clinic, University of Udine and Azienda Sanitaria Universitaria Integrata di Udine, Udine, Italy
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Molecules that Inhibit Bacterial Resistance Enzymes. Molecules 2018; 24:molecules24010043. [PMID: 30583527 PMCID: PMC6337270 DOI: 10.3390/molecules24010043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/14/2022] Open
Abstract
Antibiotic resistance mediated by bacterial enzymes constitutes an unmet clinical challenge for public health, particularly for those currently used antibiotics that are recognized as "last-resort" defense against multidrug-resistant (MDR) bacteria. Inhibitors of resistance enzymes offer an alternative strategy to counter this threat. The combination of inhibitors and antibiotics could effectively prolong the lifespan of clinically relevant antibiotics and minimize the impact and emergence of resistance. In this review, we first provide a brief overview of antibiotic resistance mechanism by bacterial secreted enzymes. Furthermore, we summarize the potential inhibitors that sabotage these resistance pathways and restore the bactericidal activity of inactive antibiotics. Finally, the faced challenges and an outlook for the development of more effective and safer resistance enzyme inhibitors are discussed.
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21
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Staphylococcus and Linezolid Resistance in Iran. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2018. [DOI: 10.5812/pedinfect.12236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lee SM, Huh HJ, Song DJ, Shim HJ, Park KS, Kang CI, Ki CS, Lee NY. Resistance mechanisms of linezolid-nonsusceptible enterococci in Korea: low rate of 23S rRNA mutations in Enterococcus faecium. J Med Microbiol 2017; 66:1730-1735. [PMID: 29111969 DOI: 10.1099/jmm.0.000637] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To investigate linezolid-resistance mechanisms in linezolid-nonsusceptible enterococci (LNSE) isolated from a tertiary hospital in Korea. METHODOLOGY Enterococcal isolates exhibiting linezolid MICs ≥4 mg l-1 that were isolated between December 2011 and May 2016 were investigated by PCR and sequencing for mutations in 23S rRNA or ribosomal proteins (L3, L4 and L22) and for the presence of cfr, cfr(B) and optrA genes.Results/Key findings. Among 135 LNSE (87 Enterococcus faecium and 48 Enterococcus faecalis isolates), 39.1 % (34/87) of E. faecium and 18.8 % (9/48) of E. faecalis isolates were linezolid-resistant. The optrA carriage was the dominant mechanism in E. faecalis: 13 isolates, including 10 E. faecalis [70 % (7/10) linezolid-resistant and 30 % (3/10) linezolid-intermediate] and three E. faecium [33.3 % (1/3) linezolid-resistant and 66.7 % (2/3) linezolid-intermediate], contained the optrA gene. G2576T mutations in the 23S rRNA gene were detected only in E. faecium [14 isolates; 71.4 % (10/14) linezolid-resistant and 28.6 % (4/14) linezolid-intermediate]. One linezolid-intermediate E. faecium harboured a L22 protein alteration (Ser77Thr). No isolates contained cfr or cfr(B) genes and any L3 or L4 protein alterations. No genetic mechanism of resistance was identified for 67.6 % (23/34) of linezolid-resistant E. faecium. CONCLUSION A low rate of 23S rRNA mutations and the absence of known linezolid-resistance mechanisms in the majority of E. faecium isolates suggest regional differences in the mechanisms of linezolid resistance and the possibility of additional mechanisms.
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Affiliation(s)
- Sae-Mi Lee
- Departments of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Departments of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dong Joon Song
- Departments of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | | | - Cheol-In Kang
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chang-Seok Ki
- Departments of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nam Yong Lee
- Departments of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Inkster T, Coia J, Meunier D, Doumith M, Martin K, Pike R, Imrie L, Kane H, Hay M, Wiuff C, Wilson J, Deighan C, Hopkins KL, Woodford N, Hill R. First outbreak of colonization by linezolid- and glycopeptide-resistant Enterococcus faecium harbouring the cfr gene in a UK nephrology unit. J Hosp Infect 2017; 97:397-402. [PMID: 28698020 DOI: 10.1016/j.jhin.2017.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/04/2017] [Indexed: 01/06/2023]
Abstract
AIM To describe an outbreak of colonization by linezolid- and glycopeptide-resistant Enterococcus faecium harbouring the cfr gene in a UK nephrology unit. METHODS Isolates of linezolid-resistant E. faecium were typed by pulsed-field gel electrophoresis (PFGE), and examined by polymerase chain reaction (PCR) and sequencing for the transmissible cfr gene that confers resistance to linezolid. Enhanced environmental cleaning, initial and weekly screening of all patients, and monitoring of adherence to standard infection control precautions were implemented. FINDINGS Five patients with pre-existing renal disease were found to have rectal colonization with linezolid-resistant E. faecium over a two-week period. The index case was a 57-year-old male from India who had travelled to the UK. One patient also had a linezolid-resistant E. faecium of a different PFGE profile isolated from a heel wound. All isolates were confirmed to harbour the cfr gene by PCR and Sanger sequencing, and all were resistant to glycopeptides (VanA phenotype). CONCLUSIONS This article describes the first UK outbreak with a single strain of linezolid- and glycopeptide-resistant E. faecium harbouring the cfr gene, affecting five patients in a nephrology unit. Following the implementation of aggressive infection control measures, no further cases were detected beyond a two-week period.
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Affiliation(s)
- T Inkster
- Queen Elizabeth University Hospital, Glasgow, UK.
| | - J Coia
- Glasgow Royal Infirmary, Glasgow, UK
| | - D Meunier
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - M Doumith
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - K Martin
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - R Pike
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - L Imrie
- Health Protection Scotland, Glasgow, UK
| | - H Kane
- Health Protection Scotland, Glasgow, UK
| | - M Hay
- Glasgow Royal Infirmary, Glasgow, UK
| | - C Wiuff
- Health Protection Scotland, Glasgow, UK
| | - J Wilson
- Health Protection Scotland, Glasgow, UK
| | - C Deighan
- Glasgow Royal Infirmary, Glasgow, UK
| | - K L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - N Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - R Hill
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
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Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol 2017; 43:263-293. [PMID: 28129707 DOI: 10.3109/1040841x.2016.1169990] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.
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Affiliation(s)
- Hagen Frickmann
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | - Andreas Erich Zautner
- b Department of Medical Microbiology, University Medical Center Göttingen , Göttingen , Germany
| | - Annette Moter
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Judith Kikhney
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Ralf Matthias Hagen
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | | | - Sven Poppert
- e Institute for Medical Microbiology, Justus-Liebig-University Giessen , Giessen , Germany
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25
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Investigation of Linezolid Resistance in Staphylococci and Enterococci. J Clin Microbiol 2016; 54:1289-94. [PMID: 26935728 DOI: 10.1128/jcm.01929-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 01/27/2016] [Indexed: 12/23/2022] Open
Abstract
The objective of this study was to investigate an apparent increase in linezolid-nonsusceptible staphylococci and enterococci following a laboratory change in antimicrobial susceptibility testing from disk diffusion to an automated susceptibility testing system. Isolates with nonsusceptible results (n = 27) from Vitek2 were subjected to a battery of confirmatory testing which included disk diffusion, Microscan broth microdilution, Clinical and Laboratory Standards Institute (CLSI) reference broth microdilution, gradient diffusion (Etest), 23S rRNA gene sequencing, and cfr PCR. Our results show that there is poor correlation between methods and that only 70 to 75% of isolates were confirmed as linezolid resistant with alternative phenotypic testing methods (disk diffusion, Microscan broth microdilution, CLSI broth microdilution, and Etest). 23S rRNA gene sequencing identified mutations previously associated with linezolid resistance in 16 (59.3%) isolates, and the cfr gene was detected in 3 (11.1%) isolates. Mutations located at positions 2576 and 2534 of the 23S rRNA gene were most common. In addition, two previously undescribed variants (at positions 2083 and 2345 of the 23S rRNA gene) were also identified and may contribute to linezolid resistance.
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Costa LFR, da Silva ES, Noronha VT, Vaz-Moreira I, Nunes OC, Andrade MMD. Development of an automatic identification algorithm for antibiogram analysis. Comput Biol Med 2015; 67:104-15. [PMID: 26513468 DOI: 10.1016/j.compbiomed.2015.09.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 11/18/2022]
Abstract
Routinely, diagnostic and microbiology laboratories perform antibiogram analysis which can present some difficulties leading to misreadings and intra and inter-reader deviations. An Automatic Identification Algorithm (AIA) has been proposed as a solution to overcome some issues associated with the disc diffusion method, which is the main goal of this work. AIA allows automatic scanning of inhibition zones obtained by antibiograms. More than 60 environmental isolates were tested using susceptibility tests which were performed for 12 different antibiotics for a total of 756 readings. Plate images were acquired and classified as standard or oddity. The inhibition zones were measured using the AIA and results were compared with reference method (human reading), using weighted kappa index and statistical analysis to evaluate, respectively, inter-reader agreement and correlation between AIA-based and human-based reading. Agreements were observed in 88% cases and 89% of the tests showed no difference or a <4mm difference between AIA and human analysis, exhibiting a correlation index of 0.85 for all images, 0.90 for standards and 0.80 for oddities with no significant difference between automatic and manual method. AIA resolved some reading problems such as overlapping inhibition zones, imperfect microorganism seeding, non-homogeneity of the circumference, partial action of the antimicrobial, and formation of a second halo of inhibition. Furthermore, AIA proved to overcome some of the limitations observed in other automatic methods. Therefore, AIA may be a practical tool for automated reading of antibiograms in diagnostic and microbiology laboratories.
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Affiliation(s)
- Luan F R Costa
- LIPIS - Laboratory of Instrumentation, Image and Signal Processing, Gama Campus, University of Brasília, Brazil.
| | - Eduardo S da Silva
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Portugal.
| | - Victor T Noronha
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Portugal.
| | - Ivone Vaz-Moreira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Portugal; CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Portugal.
| | - Olga C Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Portugal.
| | - Marcelino M de Andrade
- LIPIS - Laboratory of Instrumentation, Image and Signal Processing, Gama Campus, University of Brasília, Brazil.
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In Vitro Activities of Tedizolid and Linezolid against Gram-Positive Cocci Associated with Acute Bacterial Skin and Skin Structure Infections and Pneumonia. Antimicrob Agents Chemother 2015; 59:6262-5. [PMID: 26248355 DOI: 10.1128/aac.00390-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/20/2015] [Indexed: 12/15/2022] Open
Abstract
Tedizolid is a novel, expanded-spectrum oxazolidinone with potent activity against a wide range of Gram-positive pathogens. A total of 425 isolates of Gram-positive bacteria were obtained consecutively from patients with acute bacterial skin and skin structure infections (ABSSSIs) or pneumonia. These isolates included methicillin-susceptible Staphylococcus aureus (MSSA) (n = 100), methicillin-resistant Staphylococcus aureus (MRSA) (n = 100), Streptococcus pyogenes (n = 50), Streptococcus agalactiae (n = 50), Streptococcus anginosus group (n = 75), Enterococcus faecalis (n = 50), and vancomycin-resistant enterococci (VRE) (Enterococcus faecium) (n = 50). The MICs of tedizolid and linezolid were determined by the agar dilution method. Tedizolid exhibited better in vitro activities than linezolid against MSSA (MIC90s, 0.5 versus 2 μg/ml), MRSA (MIC90s, 0.5 versus 2 μg/ml), S. pyogenes (MIC90s, 0.5 versus 2 μg/ml), S. agalactiae (MIC90s, 0.5 versus 2 μg/ml), Streptococcus anginosus group (MIC90s, 0.5 versus 2 μg/ml), E. faecalis (MIC90s, 0.5 versus 2 μg/ml), and VRE (MIC90s, 0.5 versus 2 μg/ml). The tedizolid MICs against E. faecalis (n = 3) and VRE (n = 2) intermediate to linezolid (MICs, 4 μg/ml) were 1 μg/ml and 0.5 μg/ml, respectively. The tedizolid MIC90s against S. anginosus, S. constellatus, and S. intermedius were 0.5, 1, and 0.5 μg/ml, respectively, and the rates of susceptibility based on the U.S. FDA MIC interpretive breakpoints to the isolates were 16%, 28%, and 72%, respectively. Tedizolid exhibited 2- to 4-fold better in vitro activities than linezolid against a variety of Gram-positive cocci associated with ABSSSIs and pneumonia. The lower susceptibilities of tedizolid against isolates of S. anginosus and S. constellatus than against those of S. intermedius in Taiwan were noted.
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28
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Flamm RK, Mendes RE, Hogan PA, Ross JE, Farrell DJ, Jones RN. In vitro activity of linezolid as assessed through the 2013 LEADER surveillance program. Diagn Microbiol Infect Dis 2015; 81:283-9. [DOI: 10.1016/j.diagmicrobio.2014.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/22/2014] [Accepted: 12/24/2014] [Indexed: 11/29/2022]
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Tekin A, Dal T, Deveci Ö, Tekin R, Özcan N, Atmaca S, Dayan S. In vitro susceptibility to methicillin, vancomycin and linezolid of staphylococci isolated from bloodstream infections in eastern Turkey. Braz J Microbiol 2014; 45:829-33. [PMID: 25477914 PMCID: PMC4204965 DOI: 10.1590/s1517-83822014000300010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 12/13/2013] [Indexed: 12/02/2022] Open
Abstract
Staphylococcus species are one of the major causes of bacterial bloodstream infections. Multi-resistant staphylococci infections are major therapeutic problems. This study was aimed to detect methicillin, linezolid and vancomycin susceptibilities of Staphylococcus isolates. A total of 870 Staphylococcus strains isolated from blood cultures of hospitalized patients with BSI. Antimicrobial susceptibilities of methicillin, linezolid and vancomycin were detected according to the Clinical and Laboratory Standards Institute (CLSI). A total of 771 (88.6%) isolates were coagulase-negative staphylococci (CoNS). 700 (80.5%) isolates were methicillin-resistant (MR) and 170 (19.5%) were methicillin-susceptible (MS). All the MS isolates were also susceptible to linezolid. However 15 (1.7%) of MR strains were resistant to linezolid. The minimum inhibitory concentration range for the linezolid-resistant isolates by Etest was 6–32 μg/mL. The difference between linezolid susceptibilities for MS and MR staphylococci was not quite statistically significant (p = 0.052). There was no statistically significant difference between S. aureus and CoNS isolates for linezolid susceptibility. All of the isolates were susceptible to vancomycin. In conclusion, linezolid is currently an efficient option for the treatment of methicillin-resistant staphylococci infections.
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Affiliation(s)
- Alicem Tekin
- Department of Microbiology and Clinical Microbiology Medical Faculty Dicle University Diyarbakir Turkey Department of Microbiology and Clinical Microbiology, Medical Faculty, Dicle University, Diyarbakir, Turkey
| | - Tuba Dal
- Department of Microbiology and Clinical Microbiology Medical Faculty Dicle University Diyarbakir Turkey Department of Microbiology and Clinical Microbiology, Medical Faculty, Dicle University, Diyarbakir, Turkey
| | - Özcan Deveci
- Department of Clinical Microbiology and Infectious Diseases Medical Faculty Dicle University Diyarbakir Turkey Department of Clinical Microbiology and Infectious Diseases, Medical Faculty, Dicle University, Diyarbakir, Turkey
| | - Recep Tekin
- Department of Clinical Microbiology and Infectious Diseases Medical Faculty Dicle University Diyarbakir Turkey Department of Clinical Microbiology and Infectious Diseases, Medical Faculty, Dicle University, Diyarbakir, Turkey
| | - Nida Özcan
- Department of Microbiology and Clinical Microbiology Medical Faculty Dicle University Diyarbakir Turkey Department of Microbiology and Clinical Microbiology, Medical Faculty, Dicle University, Diyarbakir, Turkey
| | - Selahattin Atmaca
- Department of Microbiology and Clinical Microbiology Medical Faculty Dicle University Diyarbakir Turkey Department of Microbiology and Clinical Microbiology, Medical Faculty, Dicle University, Diyarbakir, Turkey
| | - Saim Dayan
- Department of Clinical Microbiology and Infectious Diseases Medical Faculty Dicle University Diyarbakir Turkey Department of Clinical Microbiology and Infectious Diseases, Medical Faculty, Dicle University, Diyarbakir, Turkey
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30
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Rybak JM, Marx K, Martin CA. Early Experience with Tedizolid: Clinical Efficacy, Pharmacodynamics, and Resistance. Pharmacotherapy 2014; 34:1198-208. [DOI: 10.1002/phar.1491] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jeffrey M. Rybak
- Department of Pharmacy; University of Kentucky HealthCare; Lexington Kentucky
| | - Kayleigh Marx
- Department of Pharmacy; University of Kentucky HealthCare; Lexington Kentucky
| | - Craig A. Martin
- Department of Pharmacy; University of Kentucky HealthCare; Lexington Kentucky
- Pharmacy Practice and Science Department; University of Kentucky College of Pharmacy; Lexington Kentucky
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Abstract
Enterococcus spp. are among the common pathogens causing infective endocarditis (IE). Despite major medical advances and new potent antimicrobial agents, the mortality has not significantly improved for several decades. The usual lack of bactericidal activity of penicillin or ampicillin, the toxicity from the combination of penicillin plus aminoglycosides, and the increased reports of high-level resistance to aminoglycosides have led to the exploration of other regimens for treatment of Enterococcus faecalis IE. As an example, ampicillin plus ceftriaxone is now a well-recognized regimen for this organism. However, the emerging of new drug resistances in Enterococcus faecium dramatically reduces the therapeutic alternatives for this organism in IE which continues to be an immense challenge for clinicians even with the availability of newer antimicrobial agents. This article summarizes the current treatment options for enterococcal endocarditis and reviews of recent publications on the topic.
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Linezolid-resistant Staphylococcus aureus strain 1128105, the first known clinical isolate possessing the cfr multidrug resistance gene. Antimicrob Agents Chemother 2014; 58:6592-8. [PMID: 25155597 DOI: 10.1128/aac.03493-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Cfr methyltransferase confers resistance to six classes of drugs which target the peptidyl transferase center of the 50S ribosomal subunit, including some oxazolidinones, such as linezolid (LZD). The mobile cfr gene was identified in European veterinary isolates from the late 1990s, although the earliest report of a clinical cfr-positive strain was the 2005 Colombian methicillin-resistant Staphylococcus aureus (MRSA) isolate CM05. Here, through retrospective analysis of LZD(r) clinical strains from a U.S. surveillance program, we identified a cfr-positive MRSA isolate, 1128105, from January 2005, predating CM05 by 5 months. Molecular typing of 1128105 revealed a unique pulsed-field gel electrophoresis (PFGE) profile most similar to that of USA100, spa type t002, and multilocus sequence type 5 (ST5). In addition to cfr, LZD resistance in 1128105 is partially attributed to the presence of a single copy of the 23S rRNA gene mutation T2500A. Transformation of the ∼37-kb conjugative p1128105 cfr-bearing plasmid from 1128105 into S. aureus ATCC 29213 background strains was successful in recapitulating the Cfr antibiogram, as well as resistance to aminoglycosides and trimethoprim. A 7-kb cfr-containing region of p1128105 possessed sequence nearly identical to that found in the Chinese veterinary Proteus vulgaris isolate PV-01 and in U.S. clinical S. aureus isolate 1900, although the presence of IS431-like sequences is unique to p1128105. The cfr gene environment in this early clinical cfr-positive isolate has now been identified in Gram-positive and Gram-negative strains of clinical and veterinary origin and has been associated with multiple mobile elements, highlighting the versatility of this multidrug resistance gene and its potential for further dissemination.
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Wang QY, Li RH, Shang XH. Urinary tract infection caused byEnterococcusisolates: aetiology and antimicrobial resistance patterns. J Chemother 2014; 27:117-9. [DOI: 10.1179/1973947814y.0000000192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Rincón S, Panesso D, Díaz L, Carvajal LP, Reyes J, Munita JM, Arias CA. [Resistance to "last resort" antibiotics in Gram-positive cocci: The post-vancomycin era]. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2014; 34 Suppl 1:191-208. [PMID: 24968051 PMCID: PMC4435674 DOI: 10.1590/s0120-41572014000500022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/31/2014] [Indexed: 06/03/2023]
Abstract
New therapeutic alternatives have been developed in the last years for the treatment of multidrug-resistant Gram-positive infections. Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) are considered a therapeutic challenge due to failures and lack of reliable antimicrobial options. Despite concerns related to the use of vancomycin in the treatment of severe MRSA infections in specific clinical scenarios, there is a paucity of solid clinical evidence that support the use of alternative agents (when compared to vancomycin). Linezolid, daptomycin and tigecycline are antibiotics approved in the last decade and newer cephalosporins (such as ceftaroline and ceftobiprole) and novel glycopeptides (dalvavancin, telavancin and oritavancin) have reached clinical approval or are in the late stages of clinical development. This review focuses on discussing these newer antibiotics used in the "post-vancomycin" era with emphasis on relevant chemical characteristics, spectrum of antimicrobial activity, mechanisms of action and resistance, as well as their clinical utility.
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Affiliation(s)
- Sandra Rincón
- Unidad de Genética y Resistencia Antimicrobiana (UGRA), Universidad El Bosque, Bogotá, D.C., Colombia
| | - Diana Panesso
- Unidad de Genética y Resistencia Antimicrobiana (UGRA), Universidad El Bosque, Bogotá, D.C., Colombia
- University of Texas Medical School at Houston, Houston, TX, USA
| | - Lorena Díaz
- Unidad de Genética y Resistencia Antimicrobiana (UGRA), Universidad El Bosque, Bogotá, D.C., Colombia
| | - Lina P. Carvajal
- Unidad de Genética y Resistencia Antimicrobiana (UGRA), Universidad El Bosque, Bogotá, D.C., Colombia
| | - Jinnethe Reyes
- Unidad de Genética y Resistencia Antimicrobiana (UGRA), Universidad El Bosque, Bogotá, D.C., Colombia
- University of Texas Medical School at Houston, Houston, TX, USA
| | - José M. Munita
- University of Texas Medical School at Houston, Houston, TX, USA
- Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago de Chile, Chile
| | - César A. Arias
- Unidad de Genética y Resistencia Antimicrobiana (UGRA), Universidad El Bosque, Bogotá, D.C., Colombia
- University of Texas Medical School at Houston, Houston, TX, USA
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35
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Perez F, Arias CA, Bush K, Drusano GL, Lolans K, Munoz-Price LS, Nicolau DP, Queenan AM, Rice LB, Segreti J, Shlaes DM, Weinstein RA, Bonomo RA. In Memoriam: John P. Quinn, MD. Clin Infect Dis 2014; 58:748-50. [DOI: 10.1093/cid/cit801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Arias CA, Murray BE. Emergence and management of drug-resistant enterococcal infections. Expert Rev Anti Infect Ther 2014; 6:637-55. [DOI: 10.1586/14787210.6.5.637] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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37
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Jacobs MR. Retapamulin: focus on its use in the treatment of uncomplicated superficial skin infections and impetigo. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/edm.10.45] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Abstract
Staphylococcus aureus is an important pathogen linked to serious infections both in the hospital and the community settings. The challenge to treat infections caused by S. aureus has increased because of the emergence of multidrug-resistant strains such as methicillin-resistant S. aureus (MRSA). A limited spectrum of antibiotics is available to treat MRSA infections. This chapter reviews antimicrobial agents currently in use for the treatment of MRSA infections as well as agents that are in various stages of development. This chapter also reviews the alternate approaches that are being explored for the treatment of staphylococcal infections.
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Affiliation(s)
- Anu Daniel
- Cubist Pharmaceuticals, Lexington, MA, USA
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39
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Diaz L, Kontoyiannis DP, Panesso D, Albert ND, Singh KV, Tran TT, Munita JM, Murray BE, Arias CA. Dissecting the mechanisms of linezolid resistance in a Drosophila melanogaster infection model of Staphylococcus aureus. J Infect Dis 2013; 208:83-91. [PMID: 23547139 DOI: 10.1093/infdis/jit138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Mini-host models are simple experimental systems to study host-pathogen interactions. We adapted a Drosophila melanogaster infection model to evaluate the in vivo effect of different mechanisms of linezolid (LNZ) resistance in Staphylococcus aureus. METHODS Fly survival was evaluated after infection with LNZ-resistant S. aureus strains NRS119 (which has mutations in 23S ribosomal RNA [rRNA]), CM-05 and 004-737X (which carry cfr), LNZ-susceptible derivatives of CM-05 and 004-737X (which lack cfr), and ATCC 29213 (an LNZ-susceptible control). Flies were then fed food mixed with LNZ (concentration, 15-500 µg/mL). Results were compared to those in mouse peritonitis, using LNZ via oral gavage at 80 and 120 mg/kg every 12 hours. RESULTS LNZ at 500 µg/mL in fly food protected against all strains, while concentrations of 15-250 µg/mL failed to protect against NRS119 (survival, 1.6%-20%). An in vivo effect of cfr was only detected at concentrations of 30 and 15 µg/mL. In the mouse peritonitis model, LNZ (at doses that mimic human pharmacokinetics) protected mice from challenge with the cfr+ 004-737X strain but was ineffective against the NRS119 strain, which carried 23S rRNA mutations. CONCLUSIONS The fly model offers promising advantages to dissect the in vivo effect of LNZ resistance in S. aureus, and findings from this model appear to be concordant with those from the mouse peritonitis model.
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Affiliation(s)
- Lorena Diaz
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
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Sierra JM, Camoez M, Tubau F, Gasch O, Pujol M, Martin R, Domínguez MA. Low prevalence of Cfr-mediated linezolid resistance among methicillin-resistant Staphylococcus aureus in a Spanish hospital: case report on linezolid resistance acquired during linezolid therapy. PLoS One 2013; 8:e59215. [PMID: 23554998 PMCID: PMC3598648 DOI: 10.1371/journal.pone.0059215] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/12/2013] [Indexed: 11/18/2022] Open
Abstract
Linezolid is an effective antimicrobial agent to treat methicillin-resistant Staphylococcus aureus (MRSA). Resistance to linezolid due to the cfr gene is described worldwide. The present study aimed to analyze the prevalence of the cfr–mediated linezolid resistance among MRSA clinical isolates in our area. A very low prevalence of cfr mediated linezolid resistance was found: only one bacteremic isolate out of 2 215 screened isolates. The only linezolid resistant isolate arose in a patient, previously colonized by MRSA, following linezolid therapy. Despite the low rate of resistance in our area, ongoing surveillance is advisable to avoid the spread of linezolid resistance.
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Affiliation(s)
- Josep M. Sierra
- Department of Microbiology, Hospital Universitari de Bellvitge. IDIBELL, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
| | - Mariana Camoez
- Department of Microbiology, Hospital Universitari de Bellvitge. IDIBELL, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
| | - Fe Tubau
- Department of Microbiology, Hospital Universitari de Bellvitge. IDIBELL, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
| | - Oriol Gasch
- Department of Infectious Diseases, Hospital Universitari de Bellvitge. IDIBELL, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
| | - Miquel Pujol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge. IDIBELL, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
| | - Rogelio Martin
- Department of Microbiology, Hospital Universitari de Bellvitge. IDIBELL, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
| | - M. Angeles Domínguez
- Department of Microbiology, Hospital Universitari de Bellvitge. IDIBELL, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
- * E-mail:
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41
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Mechanisms of linezolid resistance among Staphylococci in a tertiary hospital. J Clin Microbiol 2012; 51:998-1001. [PMID: 23269737 DOI: 10.1128/jcm.01598-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The mechanisms of linezolid resistance among 86 staphylococcal isolates from two intensive care units were investigated. The most frequent was the G2576T mutation in the 23S rRNA (82%). The cfr gene was found in 17% of the isolates, seven S. aureus and eight S. epidermidis isolates. Four of the S. epidermidis isolates had the G2576T mutation and the cfr gene. In four S. haemolyticus isolates, the mechanism could not be identified.
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42
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Vancomycin and Linezolid Resistant Staphylococcus in Hospitalized Children. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2012. [DOI: 10.5812/pedinfect.5190] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Kadlec K, Feßler A, Hauschild T, Schwarz S. Novel and uncommon antimicrobial resistance genes in livestock-associated methicillin-resistant Staphylococcus aureus. Clin Microbiol Infect 2012; 18:745-55. [DOI: 10.1111/j.1469-0691.2012.03842.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
Treatment of enterococcal infections has long been recognized as an important clinical challenge, particularly in the setting of infective endocarditis (IE). Furthermore, the increase prevalence of isolates exhibiting multidrug resistance (MDR) to traditional anti-enterococcal antibiotics such as ampicillin, vancomycin and aminoglycosides (high-level resistance) poses immense therapeutic dilemmas in hospitals around the world. Unlike IE caused by most isolates of Enterococcus faecalis, which still retain susceptibility to ampicillin and vancomycin, the emergence and dissemination of a hospital-associated genetic clade of multidrug resistant Enterococcus faecium, markedly limits the therapeutic options. The best treatment of IE MDR enterococcal endocarditis is unknown and the paucity of antibiotics with bactericidal activity against these organisms is a cause of serious concern. Although it appears that we are winning the war against E. faecalis, the battle rages on against isolates of multidrug-resistant E. faecium.
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Affiliation(s)
- Jose M. Munita
- Laboratory for Antimicrobial Research, University of Texas Medical School at Houston, Houston, TX, USA. Clínica Alemana – Universidad del Desarrollo School of Medicine, Santiago, Chile
| | - Cesar A. Arias
- Department of Internal Medicine, Division of Infectious Diseases, Center for the Study of Emerging and Reemerging Pathogens, Houston, TX, USA. Laboratory for Antimicrobial Research, University of Texas Medical School at Houston, Houston, TX, USA. Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia. University of Texas Medical School, 6431 Fannin St, Room 2.112 MSB, Houston, TX 77030, USA
| | - Barbara E. Murray
- Department of Internal Medicine, Division of Infectious Diseases, Center for the Study of Emerging and Reemerging Pathogens, Houston, TX, USA. Laboratory of Enterococcal Research, University of Texas Medical School at Houston, Houston, TX, USA. Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, Houston, TX, USA. University of Texas Medical School, 6431 Fannin St, Room 2.112 MSB, Houston, TX 77030, USA
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Diaz L, Kiratisin P, Mendes RE, Panesso D, Singh KV, Arias CA. Transferable plasmid-mediated resistance to linezolid due to cfr in a human clinical isolate of Enterococcus faecalis. Antimicrob Agents Chemother 2012; 56:3917-22. [PMID: 22491691 PMCID: PMC3393385 DOI: 10.1128/aac.00419-12] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 04/01/2012] [Indexed: 12/26/2022] Open
Abstract
Nonmutational resistance to linezolid is due to the presence of cfr, which encodes a methyltransferase responsible for methylation of A2503 in the 23S rRNA. The cfr gene was first described in animal isolates of staphylococci, and more recently, it has been identified in Staphylococcus aureus from human clinical infections, including in an outbreak of methicillin-resistant S. aureus. In enterococci, cfr has been described in an animal isolate of Enterococcus faecalis from China. Here, we report an isolate of linezolid-resistant E. faecalis (603-50427X) recovered from a patient in Thailand who received prolonged therapy with the antibiotic for the treatment of atypical mycobacterial disease. The isolate lacked mutations in the genes coding for 23S rRNA and L3 and L4 ribosomal proteins and belonged to the multilocus sequence type (MLST) 16 (ST16), which is commonly found in enterococcal isolates from animal sources. Resistance to linezolid was associated with the presence of cfr on an ~97-kb transferable plasmid. The cfr gene environment exhibited DNA sequences similar to those of other cfr-carrying plasmids previously identified in staphylococci (nucleotide identity, 99 to 100%). The cfr-carrying plasmid was transferable by conjugation to a laboratory strain of E. faecalis (OG1RF) but not to Enterococcus faecium or S. aureus. The cfr gene was flanked by IS256-like sequences both upstream and downstream. This is the first characterization of the potential horizontal transferability of the cfr gene from a human linezolid-resistant isolate of E. faecalis.
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Affiliation(s)
- Lorena Diaz
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, Texas
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Diana Panesso
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, Texas
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Kavindra V. Singh
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, Texas
| | - Cesar A. Arias
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, Texas
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
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Ikeda-Dantsuji Y, Nakae T, Ariyoshi K, Mizuno H, Moriyama H, Nagura O, Suwabe A, Fukuchi K, Honda J, Kaku M, Kohno S, Mikamo H, Niki Y, Takesue Y, Tomono K, Yanagihara K, Hanaki H. Limited detectability of linezolid-resistant Staphylococcus aureus by the Etest method and its improvement using enriched media. J Med Microbiol 2012; 61:998-1002. [DOI: 10.1099/jmm.0.043695-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Taiji Nakae
- Laboratory for Antimicrobial Agents, Kitasato University, Tokyo, Japan
| | - Koichi Ariyoshi
- Department of Laboratory Medicine, Yamaguchi University Hospital, Yamaguchi, Japan
| | - Hidekazu Mizuno
- Department of Laboratory Medicine, Yamaguchi University Hospital, Yamaguchi, Japan
| | - Hidehiko Moriyama
- Department of Laboratory Medicine, Shimane University Hospital, Shimane, Japan
| | - Osanori Nagura
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Akira Suwabe
- Department of Laboratory Medicine, Iwate Medical University School of Medicine, Morioka, Iwate, Japan
| | - Kunihiko Fukuchi
- Department of Laboratory Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Junichi Honda
- Department of Infection Control, St Mary’s Hospital, Fukuoka, Japan
| | - Mitsuo Kaku
- Central Clinical Laboratory, Department of Infection Control and Laboratory Diagnostics, Internal Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Shigeru Kohno
- The Second Department of Internal Medicine, Nagasaki University School of Medicine, Japan
| | - Hiroshige Mikamo
- Department of Infection Control and Prevention, Aichi Medical University, Aichi, Japan
| | - Yoshihito Niki
- Department of Clinical Infectious Diseases, Showa University School of Medicine, Tokyo, Japan
| | - Yoshio Takesue
- Department of Infection Control and Prevention, Hyogo College of Medicine, Hyogo, Japan
| | - Kazunori Tomono
- Department of Clinical Infectious Disease, Osaka University School of Medicine, Osaka, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Hideaki Hanaki
- Laboratory for Antimicrobial Agents, Kitasato University, Tokyo, Japan
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Brown-Elliott BA, Nash KA, Wallace RJ. Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. Clin Microbiol Rev 2012; 25:545-82. [PMID: 22763637 PMCID: PMC3416486 DOI: 10.1128/cmr.05030-11] [Citation(s) in RCA: 335] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Within the past 10 years, treatment and diagnostic guidelines for nontuberculous mycobacteria have been recommended by the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA). Moreover, the Clinical and Laboratory Standards Institute (CLSI) has published and recently (in 2011) updated recommendations including suggested antimicrobial and susceptibility breakpoints. The CLSI has also recommended the broth microdilution method as the gold standard for laboratories performing antimicrobial susceptibility testing of nontuberculous mycobacteria. This article reviews the laboratory, diagnostic, and treatment guidelines together with established and probable drug resistance mechanisms of the nontuberculous mycobacteria.
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Flamm RK, Farrell DJ, Mendes RE, Ross JE, Sader HS, Jones RN. LEADER surveillance program results for 2010: an activity and spectrum analysis of linezolid using 6801 clinical isolates from the United States (61 medical centers). Diagn Microbiol Infect Dis 2012; 74:54-61. [PMID: 22704791 DOI: 10.1016/j.diagmicrobio.2012.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/11/2012] [Indexed: 11/16/2022]
Abstract
The LEADER program monitors the in vitro activity of linezolid and comparator agents across the United States using reference broth microdilution and supportive molecular susceptibility-based investigations. This report summarizes the data from the 2010 program, the seventh consecutive year. A total of 61 medical centers from the USA including 7 medical centers specializing in children's healthcare provided a total of 6801 Gram-positive pathogens. The medical centers represented all 9 US Bureau of Census geographic regions. The organisms tested by reference broth microdilution were 3105 Staphylococcus aureus, 944 coagulase-negative staphylococci (CoNS), 934 Enterococci, 803 Streptococcus pneumoniae, 604 β-haemolytic streptococci, and 411 viridans group and other streptococci. The MIC(90) value for each of the above 6 targeted groups of organisms was 1 μg/mL. The "all organism" linezolid-resistant and nonsusceptible rate was 0.38%, which has been constant at 0.34% (2009) to 0.45% (2006) for the last 4 years. For Staphylococcus aureus, only 0.06% of the isolates were linezolid-resistant (MIC, ≥8 μg/mL); however, 2 additional methicillin-resistant Staphylococcus aureus had a cfr and a MIC of only 4 μg/mL. Resistance to linezolid was detected in 7 enterococci (0.75%) and 14 CoNS isolates (1.48%). This also represents a stable rate of resistance noted since the 2006 LEADER program report. Of note, for the first time in the 7 years of the Leader Program a linezolid-resistant Streptococcus pneumoniae was encountered. Overall, the results of the LEADER program demonstrate that linezolid maintains excellent in vitro activity against target Gram-positive pathogens across the USA. The LEADER program continues to provide valuable reference and molecular-level monitoring of linezolid activity.
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49
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Morosini MI, Cercenado E, Ardanuy C, Torres C. Detección fenotípica de mecanismos de resistencia en microorganismos grampositivos. Enferm Infecc Microbiol Clin 2012; 30:325-32. [DOI: 10.1016/j.eimc.2011.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 09/08/2011] [Indexed: 10/14/2022]
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50
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A loop-mediated isothermal amplification method for rapid detection of the multidrug-resistance gene cfr. Gene 2012; 504:140-3. [PMID: 22579470 DOI: 10.1016/j.gene.2012.04.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/29/2012] [Accepted: 04/18/2012] [Indexed: 11/24/2022]
Abstract
We developed and evaluated the specificity and sensitivity of a loop-mediated isothermal amplification (LAMP) method for rapid detection of the multidrug-resistance gene cfr. A pair of outer primers and a pair of inner primers and one loop primer were specially designed for recognizing seven distinct sequences on the target cfr gene. The amplification reaction was performed within only 35 min under isothermal conditions at 63 °C in a regular water bath with visual measurement. The LAMP assay showed higher sensitivity than the conventional PCR, with a detection limit of 1 pg per tube of chicken Staphylococcus sciuri genomic DNA. The detection rate of cfr gene for 50 Staphylococcus clinical strains by LAMP assays was 16% and appeared 100% consistence with the result by PCR method. The LAMP method reported here demonstrated a potential and valuable means for detection of the multidrug-resistance gene cfr: easy, rapid, visual, specific, accurate and sensitive, especially useful for on-the-spot investigation.
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