1
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Cortazzo V, Agosta M, Gaspari S, Vrenna G, Lucignano B, Onori M, Di Ruscio V, Mancinelli L, Domo D, Perno CF, Bernaschi P. First Case of VIM-1-like-Producing Pseudomonas putida Bacteremia in an Oncohematological Pediatric Patient in Italy. Antibiotics (Basel) 2023; 12:1033. [PMID: 37370352 DOI: 10.3390/antibiotics12061033] [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: 05/08/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial infections caused by multidrug-resistant (MDR) Gram-negatives are of great concern worldwide, as they are frequently associated with high mortality and morbidity rates. To date, two cases of VIM-2 metallo-β-lactamase (MBL)-producing Pseudomonas putida bacteremia have been ever reported in France and Spain between 2004 and 2010. Here, we present the first case of VIM-1-like-producing P. putida isolated in blood culture collected from an oncohematological pediatric patient admitted to Bambino Gesù Children's Hospital (IRCCS) in Rome, Italy.
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Affiliation(s)
- Venere Cortazzo
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Marilena Agosta
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Stefania Gaspari
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Gianluca Vrenna
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Barbara Lucignano
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Manuela Onori
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Valentina Di Ruscio
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Livia Mancinelli
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Danielle Domo
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
- Faculty of Medicine and Surgery, Department of Experimental Medicine, Ph.D. Course in Microbiology, Immunology, Infectious Diseases and Transplants (MIMIT), University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Paola Bernaschi
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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3
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Ferreira C, Bikkarolla SK, Frykholm K, Pohjanen S, Brito M, Lameiras C, Nunes OC, Westerlund F, Manaia CM. Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene. PLoS One 2021; 16:e0247058. [PMID: 33635888 PMCID: PMC7909683 DOI: 10.1371/journal.pone.0247058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/30/2021] [Indexed: 11/18/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.
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Affiliation(s)
- Catarina Ferreira
- CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Santosh K. Bikkarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Saga Pohjanen
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Olga C. Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail: (CMM); (FW)
| | - Célia M. Manaia
- CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
- * E-mail: (CMM); (FW)
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Laffite A, Al Salah DMM, Slaveykova VI, Otamonga JP, Poté J. Impact of anthropogenic activities on the occurrence and distribution of toxic metals, extending-spectra β-lactamases and carbapenem resistance in sub-Saharan African urban rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138129. [PMID: 32498199 DOI: 10.1016/j.scitotenv.2020.138129] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/13/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
The occurrence and dissemination of toxic metals, antibiotic resistant bacteria and their resistance genes (ARGs) in the aquatic ecosystems of sub-Saharan African countries are still understudied, despite their potential to threat human health and aquatic organisms. In this context, the co-contamination and seasonal distribution of toxic metals and ARG in river sediments receiving untreated urban sewages and hospital effluents from Kinshasa, the capital city of the Democratic Republic of the Congo were investigated. ARGs including β-lactam resistance (blaCTX-M and blaSHV), carbapenem resistance (blaVIM, blaIMP, blaKPC, blaOXA-48 and blaNDM) and total bacterial load were quantified by using quantitative polymerase chain reaction (qPCR) in total DNA extracted from sediment. The amount of toxic metals in sediments was quantified using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The results highlight high abundance of 16S rRNA and ARGs copy numbers in sediment samples. Strong pollution of rivers by toxic metals was found, with max values (mg kg-1) of 81.85(Cr), 5.09(Co), 33.84(Ni), 203.46 (Cu), 1055.92(Zn), 324.24(Pb) and 2.96(Hg). Results also highlight the high abundance of bacterial markers (8.06 × 109-2.42 × 1012 16S rRNA/g-1 DS) as well as antibiotic resistance genes (up to 4.58 × 108 ARG. g-1 DS) in the studied rivers. Significant correlations were observed between (i) metals (except Cd and Hg) and organic matter (R > 0.60, p < 0.05); and (ii) ARGs (except blaNDM) and 16S rRNA (R > 0.57, p < 0.05) suggesting a tight link between (i) metal contamination and anthropogenic pressure and (ii) microbial contamination of river and dissemination of antibiotic resistance. Results demonstrated that multi-diffuse pollution originating from human activity contribute to the spread of toxic metals and ARGs into the aquatic ecosystems.
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Affiliation(s)
- Amandine Laffite
- Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, CH-1211 Geneva 4, Switzerland
| | - Dhafer Mohammed M Al Salah
- Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, CH-1211 Geneva 4, Switzerland; King Abdulaziz City for Science and Technology, Joint Centers of Excellence Program, Prince Turki the 1st st, Riyadh 11442, Saudi Arabia
| | - Vera I Slaveykova
- Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, CH-1211 Geneva 4, Switzerland
| | - Jean-Paul Otamonga
- Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, B.P. 8815 Kinshasa, Democratic Republic of the Congo
| | - John Poté
- Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, CH-1211 Geneva 4, Switzerland; Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, B.P. 8815 Kinshasa, Democratic Republic of the Congo; University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190 Kinshasa XI, Democratic Republic of the Congo.
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5
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Kalra D, Singh S, Sahni A, Grover N, Kumar M, Kalra D. Utility of phenotypic methods in detection of metallo-beta-lactamases in gram-negative bacteria. JOURNAL OF MARINE MEDICAL SOCIETY 2020. [DOI: 10.4103/jmms.jmms_22_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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6
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Park JM, Kim JI, Noh JY, Kim M, Kang MJ, Pyun JC. A highly sensitive carbapenemase assay using laser desorption/ionization mass spectrometry based on a parylene-matrix chip. Enzyme Microb Technol 2017. [DOI: 10.1016/j.enzmictec.2017.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives. Infect Dis Clin North Am 2017; 30:323-345. [PMID: 27208762 DOI: 10.1016/j.idc.2016.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.
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8
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Evaluation of a modified meropenem hydrolysis assay on a large cohort of KPC and VIM carbapenemase-producing Enterobacteriaceae. PLoS One 2017; 12:e0174908. [PMID: 28384185 PMCID: PMC5383100 DOI: 10.1371/journal.pone.0174908] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/27/2017] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have spread globally and represent a serious and growing threat to public health. The introduction of rapid and sensitive methods for the detection of carbapenemase-producing bacteria is of increasing importance. The carbapenemase production can be detected using non-molecular methods (such as the modified Hodge test, the synergy test, the Carba NP test and the antibiotic hydrolysis assays) and DNA-based methods. In this study, we propose a modified version of a previously described meropenem hydrolysis assay (MHA) by MALDI-TOF MS for the phenotypic detection in 2h of carbapenemase-producing Enterobacteriaceae. The MHA was successfully applied to detect carbapenemase activity in 981 well-characterized Enterobacteriaceae strains producing KPC or VIM carbapenemases, and in 146 carbapenem fully susceptible strains. This assay, applied also to NDM and OXA-48-producing strains and to CRE with resistance mechanisms other than carbapenemase production, has proved to be able to distinguish between carbapenemase-producing and -nonproducing Enterobacteriaceae. As already stated and as observed in our hands, MHA by MALDI-TOF MS analysis is independent from the type of carbapenemases involved, it is faster and easier to perform/interpret than culture-based methods. On the other hand, it cannot detect other carbapenem resistance mechanisms, such as porin alterations and efflux mechanisms.
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9
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Knox J, Palombo E. Performance of a MALDI-TOF MS-based imipenem hydrolysis assay incorporating zinc sulfate. Diagn Microbiol Infect Dis 2017; 87:258-260. [DOI: 10.1016/j.diagmicrobio.2016.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/21/2016] [Accepted: 11/27/2016] [Indexed: 11/25/2022]
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10
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Bialvaei AZ, Kafil HS, Asgharzadeh M, Yousef Memar M, Yousefi M. Current methods for the identification of carbapenemases. J Chemother 2017; 28:1-19. [PMID: 26256147 DOI: 10.1179/1973947815y.0000000063] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Detection of carbapenemases in clinical microbiology labs is a challenging issue. Comparison of the results of susceptibility testing with the breakpoint values of carbapenems is the first step in the screening of carbapenemase producers. To date, screening of carbapenemase-producing (CP) bacteria has been mostly performed by a selective medium. Although these media are practical for the detection of most CP isolates, the inoculated plates have to be incubated overnight. Subsequently, we need the confirmation of the carbapenemase producers present in the culture medium by additional testing [e.g. inhibition studies with liquid or solid media, modified Hodge test (MHT), or gradient strips], which can take up to another 48 hours. Despite the lack of discrimination between the three different classes of carbapenemases (KPC, MBL and OXA) and difficulties in the interpretation of the results, the MHT is usually deemed as the phenotypic reference method for the confirmation of carbapenemase production. Molecular techniques, such as real-time polymerase chain reaction (PCR) assays, in contrast to phenotypic methods that are very time consuming, are faster and allow for the quick identification of carbapenemase genes. These techniques can detect and characterize carbapenemases, including NDM- and KPC-mediated resistance, which is critical for epidemiological investigations. The aim of this review is to gather a summary of the available methods for carbapenemase detection and describe the strengths and weaknesses of each method.
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Affiliation(s)
- Abed Zahedi Bialvaei
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | - Hossein Samadi Kafil
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | | | - Mohammad Yousef Memar
- c Infectious Disease and Tropical Medicine Research Center , Tabriz University of Medical Sciences , Iran
| | - Mehdi Yousefi
- d Immunology Research Center , Tabriz University of Medical Sciences , Iran
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Knox J, Gregory C, Prendergast L, Perera C, Robson J, Waring L. Laboratory detection of intestinal carriage of carbapenemase-producing Enterobacteriaceae - A comparison of algorithms using the Carba NP test. Diagn Microbiol Infect Dis 2016; 87:17-21. [PMID: 27760718 DOI: 10.1016/j.diagmicrobio.2016.09.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 01/04/2023]
Abstract
Stool specimens spiked with a panel of 46 carbapenemase-producing Enterobacteriaceae (CPE) and 59 non-carbapenemase producers were used to compare the diagnostic accuracy of 4 testing algorithms for the detection of intestinal carriage of CPE: (1) culture on Brilliance ESBL agar followed by the Carba NP test; (2) Brilliance ESBL followed by the Carba NP test, plus chromID OXA-48 agar with no Carba NP test; (3) chromID CARBA agar followed by the Carba NP test; (4) chromID CARBA followed by the Carba NP test, plus chromID OXA-48 with no Carba NP test. All algorithms were 100% specific. When comparing algorithms (1) and (3), Brilliance ESBL agar followed by the Carba NP test was significantly more sensitive than the equivalent chromID CARBA algorithm at the lower of 2 inoculum strengths tested (84.8% versus 63.0%, respectively [P<0.02]). With the addition of chromID OXA-48 agar, the sensitivity of these algorithms was marginally increased.
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Affiliation(s)
- James Knox
- Microbiology Department, Melbourne Pathology, 103 Victoria Pde, Collingwood, Melbourne, 3066, Australia.
| | - Claire Gregory
- Microbiology Department, Melbourne Pathology, 103 Victoria Pde, Collingwood, Melbourne, 3066, Australia
| | - Louise Prendergast
- Microbiology Department, Melbourne Pathology, 103 Victoria Pde, Collingwood, Melbourne, 3066, Australia
| | - Chandrika Perera
- Microbiology Department, Melbourne Pathology, 103 Victoria Pde, Collingwood, Melbourne, 3066, Australia
| | - Jennifer Robson
- Microbiology Department, Sullivan Nicolaides Pathology, PO, Box 344, Indooroopilly, Brisbane, 4068, Australia
| | - Lynette Waring
- Microbiology Department, Melbourne Pathology, 103 Victoria Pde, Collingwood, Melbourne, 3066, Australia
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12
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Overview of Molecular Diagnostics in Multiple-Drug-Resistant Organism Prevention: Focus on Multiple-Drug-Resistant Gram-Negative Bacterial Organisms. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Knox J, Gregory C, Prendergast L, Waring L. Performance of a modified version of the Carba NP test and the CarbAcineto NP test. Pathology 2016; 48:98-100. [DOI: 10.1016/j.pathol.2015.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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14
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Mirande C, Canard I, Buffet Croix Blanche S, Charrier JP, van Belkum A, Welker M, Chatellier S. Rapid detection of carbapenemase activity: benefits and weaknesses of MALDI-TOF MS. Eur J Clin Microbiol Infect Dis 2015; 34:2225-34. [DOI: 10.1007/s10096-015-2473-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/16/2015] [Indexed: 11/28/2022]
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15
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Phenotypic detection of carbapenemase-producing Enterobacteriaceae by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry and the Carba NP test. J Clin Microbiol 2014; 52:4075-7. [PMID: 25187633 DOI: 10.1128/jcm.02121-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared the diagnostic accuracy of the Carba NP test with that of a straightforward matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) method for detecting carbapenemase-producing Enterobacteriaceae (CPE). Using PCR as the reference method, both tests demonstrated a sensitivity of 87% and a specificity of 100%. MALDI-TOF MS offers a potential alternative for the rapid detection of CPE in the clinical laboratory setting.
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Hrabák J, Chudáčková E, Papagiannitsis CC. Detection of carbapenemases in Enterobacteriaceae: a challenge for diagnostic microbiological laboratories. Clin Microbiol Infect 2014; 20:839-53. [PMID: 24813781 DOI: 10.1111/1469-0691.12678] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Carbapenemase-producing bacteria have now spread all over the world. Infections caused by those bacteria are difficult to treat. Therefore, there is an urgent need for accurate and fast detection of carbapenemases in diagnostic laboratories. In this review, we summarize screening methods for suspected isolates, direct assays for confirmation of carbapenemase activity (e.g. the Carba NP test and matrix-assisted laser desorption ionization time-of-flight mass spectrometry carbapenem hydrolysis assay), inhibitor-based methods for carbapenemase classification, and molecular-genetic techniques for precise identification of carbapenemase genes. We also propose a workflow for carbapenemase identification in diagnostic laboratories.
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Affiliation(s)
- J Hrabák
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic
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17
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Lupo A, Papp-Wallace KM, Sendi P, Bonomo RA, Endimiani A. Non-phenotypic tests to detect and characterize antibiotic resistance mechanisms in Enterobacteriaceae. Diagn Microbiol Infect Dis 2013; 77:179-94. [PMID: 24091103 DOI: 10.1016/j.diagmicrobio.2013.06.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 06/12/2013] [Indexed: 02/07/2023]
Abstract
In the past 2 decades, we have observed a rapid increase of infections due to multidrug-resistant Enterobacteriaceae. Regrettably, these isolates possess genes encoding for extended-spectrum β-lactamases (e.g., blaCTX-M, blaTEM, blaSHV) or plasmid-mediated AmpCs (e.g., blaCMY) that confer resistance to last-generation cephalosporins. Furthermore, other resistance traits against quinolones (e.g., mutations in gyrA and parC, qnr elements) and aminoglycosides (e.g., aminoglycosides modifying enzymes and 16S rRNA methylases) are also frequently co-associated. Even more concerning is the rapid increase of Enterobacteriaceae carrying genes conferring resistance to carbapenems (e.g., blaKPC, blaNDM). Therefore, the spread of these pathogens puts in peril our antibiotic options. Unfortunately, standard microbiological procedures require several days to isolate the responsible pathogen and to provide correct antimicrobial susceptibility test results. This delay impacts the rapid implementation of adequate antimicrobial treatment and infection control countermeasures. Thus, there is emerging interest in the early and more sensitive detection of resistance mechanisms. Modern non-phenotypic tests are promising in this respect, and hence, can influence both clinical outcome and healthcare costs. In this review, we present a summary of the most advanced methods (e.g., next-generation DNA sequencing, multiplex PCRs, real-time PCRs, microarrays, MALDI-TOF MS, and PCR/ESI MS) presently available for the rapid detection of antibiotic resistance genes in Enterobacteriaceae. Taking into account speed, manageability, accuracy, versatility, and costs, the possible settings of application (research, clinic, and epidemiology) of these methods and their superiority against standard phenotypic methods are discussed.
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Affiliation(s)
- Agnese Lupo
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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18
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Multiple broad-spectrum Beta-lactamase targets for comprehensive surveillance. J Clin Microbiol 2013; 51:3423-5. [PMID: 23926166 DOI: 10.1128/jcm.01488-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time PCR testing for blaKPC, blaNDM, blaVIM, blaIMP, and blaCTX-M was performed on rectal swabs obtained from residents of two long-term acute-care facilities. While blaKPC was detected in 69/102 swabs (67.6%), testing for four other targets increased the positivity rate for a broad-spectrum β-lactamase to 73.5% (McNemar's P = 0.03).
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Voulgari E, Poulou A, Koumaki V, Tsakris A. Carbapenemase-producing Enterobacteriaceae: now that the storm is finally here, how will timely detection help us fight back? Future Microbiol 2013; 8:27-39. [PMID: 23252491 DOI: 10.2217/fmb.12.130] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Acquired carbapenemases of the Ambler Classes A, B and D have gradually disseminated over the past decade among isolates of the Enterobacteriaceae family. Located on highly mobile genetic elements, these enzymes have established their presence in successful bacterial clones, signaling the prelude to a novel endemic era in the hospital setting. In such a context, prompt detection of carbapenemase-producing microorganisms seems warranted, not only for the selection of an appropriate antibiotic regimen, but also for organizing and implementing effective surveillance and infection control measures. However, issues regarding detection, confirmatory testing and characterization persist. Determination of carbapenemase production via susceptibility pattern interpretation may not always be feasible, confirmatory testing remains debatable and precise characterization is a challenge for the clinical laboratory. We aim to review the current situation from a laboratory point of view, highlighting the tools that have been proposed in an effort to help outline reliable screening and detection procedures, with inhibitor-based phenotypic testing as the cornerstone of these strategies, and discuss the necessity for implementing identification of possible producers in the everyday workflow.
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Affiliation(s)
- Evangelia Voulgari
- Department of Microbiology, Medical School, University of Athens, Athens, Greece
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Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions. Clin Microbiol Rev 2013; 25:682-707. [PMID: 23034326 DOI: 10.1128/cmr.05035-11] [Citation(s) in RCA: 834] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
SUMMARY The spread of Enterobacteriaceae, primarily Klebsiella pneumoniae, producing KPC, VIM, IMP, and NDM carbapenemases, is causing an unprecedented public health crisis. Carbapenemase-producing enterobacteria (CPE) infect mainly hospitalized patients but also have been spreading in long-term care facilities. Given their multidrug resistance, therapeutic options are limited and, as discussed here, should be reevaluated and optimized. Based on susceptibility data, colistin and tigecycline are commonly used to treat CPE infections. Nevertheless, a review of the literature revealed high failure rates in cases of monotherapy with these drugs, whilst monotherapy with either a carbapenem or an aminoglycoside appeared to be more effective. Combination therapies not including carbapenems were comparable to aminoglycoside and carbapenem monotherapies. Higher success rates have been achieved with carbapenem-containing combinations. Pharmacodynamic simulations and experimental infections indicate that modification of the current patterns of carbapenem use against CPE warrants further attention. Epidemiological data, though fragmentary in many countries, indicate CPE foci and transmission routes, to some extent, whilst also underlining the lack of international collaborative systems that could react promptly and effectively. Fortunately, there are sound studies showing successful containment of CPE by bundles of measures, among which the most important are active surveillance cultures, separation of carriers, and assignment of dedicated nursing staff.
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Ruskova L, Raclavsky V. The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2012; 155:239-52. [PMID: 22286809 DOI: 10.5507/bp.2011.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology. METHODS AND RESULTS Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization. CONCLUSIONS We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.
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Affiliation(s)
- Lenka Ruskova
- Department of Microbiology, Palacky University Olomouc, Czech Republic
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Using matrix-assisted laser desorption ionization-time of flight mass spectrometry to detect carbapenem resistance within 1 to 2.5 hours. J Clin Microbiol 2011; 49:3321-4. [PMID: 21795515 DOI: 10.1128/jcm.00287-11] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In recent years, the percentage of carbapenem-resistant bacteria has increased at an alarming pace and become a major threat for patient survival. Carbapenemase-induced carbapenem resistance can be confirmed through the detection of carbapenem degradation using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). This method works for strains carrying NDM-1, VIM-1, VIM-2, KPC-2, and different IMP enzymes.
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Real-time PCR for detection of NDM-1 carbapenemase genes from spiked stool samples. Antimicrob Agents Chemother 2011; 55:4038-43. [PMID: 21690281 DOI: 10.1128/aac.01734-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An in-house quantitative real-time PCR (qPCR) assay using TaqMan chemistry has been developed to detect NDM-1 carbapenemase genes from bacterial isolates and directly from stool samples. The qPCR amplification of bla(NDM-1) DNA was linear over 10 log dilutions (r(2) = 0.99), and the amplification efficiency was 1.03. The qPCR detection limit was reproducibly 1 CFU, or 10 plasmid molecules, and there was no cross-reaction with DNA extracted from several multidrug-resistant bacteria harboring other β-lactam resistance genes. Feces spiked with decreasing amounts of enterobacterial isolates producing NDM-1 were spread on ChromID ESBL and on CHROMagar KPC media and were subjected to the qPCR. The limits of carbapenem-resistant bacterial detection from stools was reproducibly 1 × 10(1) to 3 × 10(1) CFU/100 mg feces with ChromID ESBL medium. The CHROMagar KPC culture medium had higher limits of detection (1 × 10(1) to 4 × 10(3) CFU/ml), especially with bacterial isolates having low carbapenem MICs. The limits of detection with the qPCR assay were reproducibly below 1 × 10(1) CFU/100 mg of feces by qPCR assay. Samples spiked with NDM-1-negative bacteria were negative by qPCR. The sensitivity and specificity of the bla(NDM-1) qPCR assay on spiked samples were 100% in both cases. Using an automated DNA extraction system (QIAcube system), the qPCR assay was reproducible. The use of qPCR is likely to shorten the time for bla(NDM-1) detection from 48 h to 4 h and will be a valuable tool for outbreak follow-up in order to rapidly isolate colonized patients and assign them to cohorts.
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Evaluation of a DNA microarray (Check-MDR CT102) for rapid detection of TEM, SHV, and CTX-M extended-spectrum β-lactamases and of KPC, OXA-48, VIM, IMP, and NDM-1 carbapenemases. J Clin Microbiol 2011; 49:1608-13. [PMID: 21325547 DOI: 10.1128/jcm.02607-10] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Check-MDR CT102 microarray, aimed at identifying bacteria producing extended-spectrum β-lactamase (ESBL) (SHV, TEM, and CTX-M) and carbapenemase (KPC, OXA-48, VIM, IMP, and NDM-1), was evaluated on a total of 144 Gram-negative strains expressing various β-lactamases. The sensitivity and specificity were 100% for most tested genes, suggesting that this assay allows accurate identification of common ESBL and carbapenemase producers from bacterial cultures.
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Bahar MA, Jamali S, Samadikuchaksaraei A. Imipenem-resistant Pseudomonas aeruginosa strains carry metallo-β-lactamase gene blaVIM in a level I Iranian burn hospital. Burns 2010; 36:826-30. [DOI: 10.1016/j.burns.2009.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/08/2009] [Accepted: 10/11/2009] [Indexed: 10/20/2022]
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