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Ben Dhaou K, Ghariani A, Essalah L, Bouzouita I, Mahdhi S, Ben Nsir H, Frikha M, El Marzouk N, Zghal Mhiri E, Slim-Saidi NL. Evaluation of Phenotypic Tests for Carbapenemase Detection in Enterobacteriaceae in Tunisia. Microb Drug Resist 2024. [PMID: 38315778 DOI: 10.1089/mdr.2023.0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Introduction: Resistance to carbapenems in Enterobacteriaceae is a challenge for public health. Carbapenemase production is the leading mechanism. This work aims to evaluate four phenotypic methods for carbapenemase detection in comparison with a molecular method. Materials and Methods: Thirty-seven nonrepeating Enterobacteriaceae strains with decreased susceptibility to ertapenem were included. Imipenem MIC, Modified Hodge Test (MHT), Neo-Rapid Carb Kit® and KPC, MBL, and OXA-48 Confirm Kit® were performed. Isolates were tested for blaOXA-48, blaNDM, and blaVIM genes by end-point polymerase chain reaction. The results of the molecular study were used as a reference test to determine the performances of the phenotypic tests. Results: Imipenem resistance does not seem to be a good marker for carbapenemase production with a sensitivity of 54% (95% CI: 38-71). MHT showed 82% sensitivity (95% CI: 65-91). Overall, the enzymatic test showed the best performances for carbapenemase detection with 100% sensitivity (95% CI: 89-100) and the best turnaround time. The characterization of carbapenemases classes by the combined discs test demonstrated 88% overall sensitivity (95% CI: 72-95). Conclusion: The results of this study support the combination of the enzymatic and the combined disc tests for carbapenemase detection in Enterobacteria.
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Affiliation(s)
- Khouloud Ben Dhaou
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
| | - Asma Ghariani
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
| | - Leila Essalah
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
| | - Imen Bouzouita
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
- Faculty of Science, University of Tunis El Manar, Tunis, Tunisia
| | - Samia Mahdhi
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
| | - Hamida Ben Nsir
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
| | - Marwa Frikha
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
| | - Naceur El Marzouk
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
| | - Emna Zghal Mhiri
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
| | - Noura Leila Slim-Saidi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Microbiology Laboratory, Abderrahmen Mami Pneumology and Phthisiology Hospital, Ariana, Tunisia
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2
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Lovison OA, Rau RB, Lima-Morales D, Almeida EK, Crispim MN, Barreto F, Barth AL, Martins AF. High-performance method to detection of Klebsiella pneumoniae Carbapenemase in Enterobacterales by LC-MS/MS. Braz J Microbiol 2020; 51:1029-1035. [PMID: 31989451 PMCID: PMC7455676 DOI: 10.1007/s42770-019-00222-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/27/2019] [Indexed: 01/16/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CREs) have been recognized as an important threat to global health. CRE cause the majority of the difficult-to-treat infections in health-care settings and are associated with high mortality. Klebsiella pneumoniae carbapenemase (KPC)-producing CREs, in particular Klebsiella pneumoniae, are globally disseminated and responsible for a large number of outbreaks. Development of rapid methods for KPC detection can provide great clinical and epidemiological benefits to prevent KPC dissemination. The aim of this study was to standardize and validate a LC-MS/MS method to detect KPC. This method was also tested against a broad variety of species, including CRE with other carbapenemase genes and the recently reported mcr-1. For validation, 111 isolates with reduced susceptibility to carbapenems were selected (49 KPC-positive and 62 KPC-negative). The presence of four tryptic peptides related to the KPC enzyme was evaluated, and the identification of at least two of them classified the isolate as "KPC-positive." The LTLGSALAAPQR and LALEGLGVNGQ peptides were both detected in 47 of 49 isolates with the blaKPC gene. The other two peptides, GFLAAAVLAR and APIVLAVYTR, were detected in 46 and 19 isolates with the blaKPC gene, respectively. The method correctly classified 47 of 49 KPC-positive and all KPC-negative isolates yielding 96.07% of sensitivity and 100% of specificity. In conclusion, our results demonstrate that the KPC peptide markers were robustly detected by the method which presented high sensitivity and full specificity and therefore can be used as a reliable method to identify this resistance mechanism.
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Affiliation(s)
- Otávio A Lovison
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas (PPGCF), Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Renata B Rau
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas (PPGCF), Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório Nacional Agropecuário no Rio Grande do Sul (LANAGRO/RS), Porto Alegre, Brazil
| | - Daiana Lima-Morales
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Evellyn K Almeida
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Faculdade de Farmácia - Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marina N Crispim
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fabiano Barreto
- Laboratório Nacional Agropecuário no Rio Grande do Sul (LANAGRO/RS), Porto Alegre, Brazil
| | - Afonso L Barth
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas (PPGCF), Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Faculdade de Farmácia - Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Andreza F Martins
- Programa de Pós-Graduação em Ciências Farmacêuticas (PPGCF), Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
- Laboratório de Microbiologia Aplicada, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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Horvath TD, Haidacher SJ, Oezguen N, Hoch KM, Auchtung JM, Haag AM. Ruggedness testing of liquid chromatography-tandem mass spectrometry system components using microbiome-relevant methods and matrices. J Microbiol Methods 2020; 177:106020. [PMID: 32795635 DOI: 10.1016/j.mimet.2020.106020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/24/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Recently, an opportunity to perform a broad ruggedness assessment of our liquid chromatography-tandem mass spectrometry (LC-MS/MS) system presented itself during the analytical planning phase of a large-scale human fecal microbiome study. The specific aim of this project was to study the microbial-mediated metabolism of a targeted set of bile acids/salts by mixed bacterial communities cultured from the feces of 12 healthy volunteers when grown in a custom growth medium and following exposure to different clinically-relevant antibiotics. The magnitude of this study offered a rare opportunity to significantly stress procedures and LC-MS/MS system components comprised in our bile acid/salt targeted metabolomics method. With this second specific aim in mind, we modified the sample analysis plan to include a series of figure-of-merit (FoM)-based tests that are commonly used in regulated bioanalytical labs to assess LC and MS system ruggedness for a specific assay - these FoM-based testing parameters were monitored continuously over the course of sample analysis and the results are presented in this report. In total, the assessment included 1206 sequential injections (180 calibration standards, 136 blank-internal standard samples, and 890 diluted medium samples) that took place over 8-days. Completion of the 8-days of non-stop sample analysis revealed no critical hardware or software failures, and the analysis of the FoM-based tests indicated no observable degradation of system performance over the number of samples and time tested. The FoM-based test metrics presented may be used as a template to assess the ruggedness of any LC-MS/MS-based targeted metabolomics workflow.
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Affiliation(s)
- Thomas D Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, 1102 Bates Ave, Houston, TX 77030, United States
| | - Sigmund J Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, 1102 Bates Ave, Houston, TX 77030, United States
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, 1102 Bates Ave, Houston, TX 77030, United States
| | - Kathleen M Hoch
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, 1102 Bates Ave, Houston, TX 77030, United States
| | - Jennifer M Auchtung
- Food Science and Technology Department, the University of Nebraska-Lincoln, 1901 N 21(st) Street, Lincoln, NE 68588, United States
| | - Anthony M Haag
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, 1102 Bates Ave, Houston, TX 77030, United States.
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Welker M, van Belkum A. One System for All: Is Mass Spectrometry a Future Alternative for Conventional Antibiotic Susceptibility Testing? Front Microbiol 2019; 10:2711. [PMID: 31849870 PMCID: PMC6901965 DOI: 10.3389/fmicb.2019.02711] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
The two main pillars of clinical microbiological diagnostics are the identification of potentially pathogenic microorganisms from patient samples and the testing for antibiotic susceptibility (AST) to allow efficient treatment with active antimicrobial agents. While routine microbial species identification is increasingly performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routine AST still largely relies on conventional and molecular techniques such as broth microdilution or disk and gradient diffusion tests, PCR and automated variants thereof. However, shortly after the introduction of MALDI-TOF MS based routine identification, first attempts to perform AST on the same instruments were reported. Today, a number of different approaches to perform AST with MALDI-TOF MS and other MS techniques have been proposed, some restricted to particular microbial taxa and resistance mechanisms while others being more generic. Further, while some of the methods are in a stage of proof of principles, others are already commercialized. In this review we discuss the different principal approaches of mass spectrometry based AST and evaluate the advantages and disadvantages compared to conventional and molecular techniques. At present, the possibility that MS will soon become a routine tool for AST seems unlikely – still, the same was true for routine microbial identification a mere 15 years ago.
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Affiliation(s)
- Martin Welker
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
| | - Alex van Belkum
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
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5
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Systematic Comparison of Four Methods for Detection of Carbapenemase-Producing Enterobacterales Directly from Blood Cultures. J Clin Microbiol 2019; 57:JCM.00709-19. [PMID: 31413083 PMCID: PMC6813004 DOI: 10.1128/jcm.00709-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/07/2019] [Indexed: 01/30/2023] Open
Abstract
Early identification of infections caused by carbapenemase-producing Enterobacterales (CPE) can help to optimize patient treatment and improve outcome. In this study, protocols for rapid detection of carbapenemase production directly from positive blood cultures were developed applying a concentration and hemolysis step before a test for carbapenemase production was performed. Early identification of infections caused by carbapenemase-producing Enterobacterales (CPE) can help to optimize patient treatment and improve outcome. In this study, protocols for rapid detection of carbapenemase production directly from positive blood cultures were developed applying a concentration and hemolysis step before a test for carbapenemase production was performed. Four different methods (three modified colorimetric assays [β-Carba, bcCarba NP, and NeoRapid Carb] and a variation of the carbapenem inactivation method [CIM] test with blood cultures [bcCIM]) were assessed on blood cultures spiked with 185 different molecularly characterized Enterobacterales isolates. The challenge collection included 81 carbapenemase-negative isolates and 104 CPEs (OXA-48 [n = 25], NDM [n = 20], KPC [n = 18], VIM [n = 25], GIM [n = 5], OXA-48-like [n = 9], and OXA-48-like plus NDM [n = 2]). The sensitivity/specificity was 99.0%/95.1% for bcCarba NP, 99.0%/91.4% for NeoRapid Carb, 100%/95.1% for β-Carba and 100%/100% for bcCIM. Weakly hydrolyzing carbapenemases (e.g., OXA-48-like) were also well detected by the assays. The time to result was 20 to 45 min for β-Carba, 2 to 3 h for bcCarba NP, 2.5 to 2 h for NeoRapid Carb, and 18 to 24 h for bcCIM. In conclusion, all assays demonstrated good detection of CPE. The protocols can be easily implemented in any clinical microbiology laboratory and could help to optimize therapy early in bloodstream infections by CPE.
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6
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Wang H, Drake SK, Youn JH, Rosenberg AZ, Chen Y, Gucek M, Suffredini AF, Dekker JP. Peptide Markers for Rapid Detection of KPC Carbapenemase by LC-MS/MS. Sci Rep 2017; 7:2531. [PMID: 28566732 PMCID: PMC5451396 DOI: 10.1038/s41598-017-02749-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/19/2017] [Indexed: 12/18/2022] Open
Abstract
Carbapenemase producing organisms (CPOs) represent an urgent public health threat, and the need for new rapid methods to detect these organisms has been widely recognized. CPOs carrying the Klebsiella pneumoniae carbapenemase (blaKPC) gene have caused outbreaks globally with substantial attributable mortality. Here we describe the validation of a rapid MS method for the direct detection of unique tryptic peptides of the KPC protein in clinical bacterial isolates with an isolate-to-result time of less than 90 minutes. Using a genoproteomic discovery approach that combines theoretical peptidome analysis and liquid chromatography-tandem MS (LC-MS/MS), we selected three high abundance peptide markers of the KPC protein that can be robustly detected following rapid tryptic digestion. Protein BLAST analysis confirmed that the chosen peptide markers were unique to KPC. A blinded validation set containing 20 KPC-positive and 80 KPC-negative clinical isolates, performed in triplicate (300 runs) demonstrated 100% sensitivity and 100% specificity (60/60 positive identifications, 240/240 negative identifications) using defined rules for positive calls. The most robust tryptic peptide marker in the validation was LTLGSALAAPQR. The peptide discovery and detection methods validated here are general and should be broadly applicable to allow the direct and rapid detection of other resistance determinants.
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Affiliation(s)
- Honghui Wang
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Steven K Drake
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jung-Ho Youn
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Avi Z Rosenberg
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yong Chen
- Proteomics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marjan Gucek
- Proteomics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anthony F Suffredini
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - John P Dekker
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA.
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