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Sharma K, Angrup A, Ghosh A, Singh S, Sood A, Arora A, Sharma M, Sethi S, Rudramurthy SM, Kaur H, Ray P, Chakrabarti A. Evaluation of VITEK MS Version 3.0 MALDI-TOF for the identification of anaerobes, mycobacteria, Nocardia, and moulds. Diagn Microbiol Infect Dis 2024; 110:116477. [PMID: 39216192 DOI: 10.1016/j.diagmicrobio.2024.116477] [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: 03/12/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
PURPOSE The identification of anaerobes, Mycobacterium and Nocardia species, and moulds by MALDI-TOF-MS remains a challenge. This study aimed to evaluate the performance of MALDI-TOF in the identification of these organisms. METHODS A total of 382 strains, comprising 128 (33.5 %) anaerobes, 126(33.0 %) mycobacterial, 113(29.6 %), mycelial fungi, and 15(3.9 %) Nocardia species were evaluated by VITEK MS Version 3.0. The results were compared with the identification of the isolates by DNA sequence analysis. The DNA sequences used for analysis were the 16S rRNA for anaerobic bacteria, hsp65 gene for mycobacteria, whereas both 16S rRNA and hsp65 gene for Nocardia species, and internal transcribed spacer (ITS) and 28S rRNA gene's D1/D2 regions of fungi. RESULTS The VITEK-MS accurately identified 78.3 % (299/382) of the strains at the species, and 9.4 % (36/382) at the genus level. Misidentifications were observed in 3.9 % (15/382) isolates. Of isolates tested, 8.4 % (32/382) were not identified by the system, and 7.06 % (27/382) were not included in the IVD database. CONCLUSION An upgraded VITEK MS V3.0 database provides reasonably accurate and rapid identification of clinically relevant anaerobes, mycobacteria, Nocardia species, and moulds to the species level.
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Affiliation(s)
- Kusum Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Archana Angrup
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Anup Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India.
| | - Shreya Singh
- Dr B R Ambedkar Institute of Medical Sciences (AIMS Mohali), Chandigarh 160055, India
| | - Anshul Sood
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Amit Arora
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Megha Sharma
- Department of Medical Microbiology, All India Institute of Medical Science, Bilaspur, Himachal, Pradesh 174001, India
| | - Sunil Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Arunaloke Chakrabarti
- Doodhadhari Burfani Hospital and Research Centre, Haridwar, Uttarakhand 249411, India
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Khare R, Brown-Elliott BA. Culture, Identification, and Antimicrobial Susceptibility Testing of Pulmonary Nontuberculous Mycobacteria. Clin Chest Med 2023; 44:743-755. [PMID: 37890913 DOI: 10.1016/j.ccm.2023.06.001] [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] [Indexed: 10/29/2023]
Abstract
Nontuberculous mycobacteria (NTM) typically cause opportunistic pulmonary infections and reliable laboratory results can assist with diagnosis of disease. Microscopy can detect acid-fast bacilli from specimens though it has poor sensitivity. Solid and liquid culture are used to grow NTM, which are identified by molecular or protein-based assays. Because culture has a long turnaround time, some assays are designed to identify NTM directly from sputum specimens. When indicated, phenotypic susceptibility testing should be performed by broth microdilution as per the guidelines from the Clinical Laboratory Standards Institute. Genotypic susceptibility methods may be used to decrease the turnaround time for some antimicrobials.
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Affiliation(s)
- Reeti Khare
- Mycobacteriology Laboratory, 1400 Jackson Street, National Jewish Health, Denver, CO 80238, USA.
| | - Barbara A Brown-Elliott
- The University of TX Health Science Center at Tyler, Mycobacteria/Nocardia Laboratory, 11937 US Highway 271, Tyler, TX 75708, USA
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3
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Hamed KA, Tillotson G. A narrative review of nontuberculous mycobacterial pulmonary disease: microbiology, epidemiology, diagnosis, and management challenges. Expert Rev Respir Med 2023; 17:973-988. [PMID: 37962332 DOI: 10.1080/17476348.2023.2283135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
INTRODUCTION Nontuberculous mycobacteria (NTM) are a diverse group of mycobacterial species that are ubiquitous in the environment. They are opportunistic pathogens that can cause a range of diseases, especially in individuals with underlying structural lung disease or compromised immune systems. AREAS COVERED This paper provides an in-depth analysis of NTM infections, including microbiology, environmental sources and transmission pathways, risk factors for disease, epidemiology, clinical manifestations and diagnostic approaches, guideline-based treatment recommendations, drugs under development, and management challenges. EXPERT OPINION Future approaches to the management of NTM pulmonary disease will require therapies that are well tolerated, can be taken for a shorter time period and perhaps less frequently, have few drug-drug interactions, and are active against the various strains of pathogens. As the numbers of infections increase, such therapies will be welcomed by clinicians and patients.
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4
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Bacanelli G, Araujo FR, Verbisck NV. Improved MALDI-TOF MS Identification of Mycobacterium tuberculosis by Use of an Enhanced Cell Disruption Protocol. Microorganisms 2023; 11:1692. [PMID: 37512865 PMCID: PMC10386467 DOI: 10.3390/microorganisms11071692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Mycobacterium tuberculosis is the microorganism that causes tuberculosis, a disease affecting millions of people worldwide. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable, and cost-effective method for microorganism identification which has been used for the identification of Mycobacterium spp. isolates. However, the mycobacteria cell wall is rich in lipids, which makes it difficult to obtain proteins for MALDI-TOF MS analysis. In this study, two cell preparation protocols were compared: the MycoEx, recommended by MALDI-TOF instrument manufacturer Bruker Daltonics, and the MycoLyser protocol described herein, which used the MagNA Lyser instrument to enhance cell disruption with ethanol. Cell disruption and protein extraction steps with the two protocols were performed using the Mycobacterium tuberculosis H37Rv strain, and the MALDI-TOF MS results were compared. The MycoLyser protocol allowed for improved Biotyper identification of M. tuberculosis since the log(score) values obtained with this protocol were mostly ≥ 1.800 and significantly higher than that underwent MycoEx processing. The identification reliability was increased as well, considering the Bruker criteria. In view of these results, it is concluded that the MycoLyser protocol for mycobacterial cell disruption and protein extraction improves the MALDI-TOF MS method's efficacy for M. tuberculosis identification.
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Affiliation(s)
- Gisele Bacanelli
- Biotechnology and Biodiversity of the Central Western Region Postgraduate Program, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
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5
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Sepulcri C, Vena A, Bassetti M. Skin and soft tissue infections due to rapidly growing mycobacteria. Curr Opin Infect Dis 2023; 36:74-80. [PMID: 36718980 DOI: 10.1097/qco.0000000000000905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
PURPOSE OF REVIEW The aim of this article is to review skin and soft tissue infections due to rapidly growing mycobacteria (RGM), with a particular focus on recently published literature (2021-2022). RECENT FINDINGS RGM are increasingly reported as a cause of skin and soft tissue infections, both in the community setting and as a cause of nosocomial outbreaks. Recent advances in molecular methods have expanded the number of species of RGM and resulted in increased diagnosis. New treatment options are under evaluation particularly for Mycobacterium abscessus , the most difficult-to-treat among RGM. SUMMARY RGM are an uncommon cause of skin and soft tissue infections and a high clinical suspicion together with advanced laboratory facilities are required for diagnosis. Species identification and antimicrobial susceptibility testing are essential to drive appropriate treatment, which combines surgical debridement with prolonged antimycobacterial combination therapy.
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Affiliation(s)
- Chiara Sepulcri
- Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genova
| | - Antonio Vena
- Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genova
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Matteo Bassetti
- Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genova
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
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6
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Rodríguez‐Temporal D, Zvezdánova ME, Benedí P, Marín M, Blázquez‐Sánchez M, Ruiz‐Serrano MJ, Muñoz P, Rodríguez‐Sánchez B. Identification of Nocardia and non-tuberculous Mycobacterium species by MALDI-TOF MS using the VITEK MS coupled to IVD and RUO databases. Microb Biotechnol 2023; 16:778-783. [PMID: 36541026 PMCID: PMC10034632 DOI: 10.1111/1751-7915.14146] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/22/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022] Open
Abstract
Identification of Nocardia and Mycobacterium species by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is still a challenging task that requires both suitable protein extraction procedures and extensive databases. This study aimed to evaluate the VITEK MS Plus system coupled with updated RUO (v4.17) and IVD (v3.2) databases for the identification of Nocardia spp. and Mycobacterium spp. clinical isolates. Sample preparation was carried out using the VITEK MS Mycobacterium/Nocardia kit for protein extraction. From 90 Nocardia spp. isolates analysed, 86 (95.6%) were correctly identified at species or complex level using IVD and 78 (86.7%) using RUO. Only two strains were misidentified as other species pertaining to the same complex. Among the 106 non-tuberculous Mycobacterium clinical isolates tested from a liquid culture medium, VITEK MS identified correctly at species or complex level 96 (90.6%) isolates in the IVD mode and 89 (84.0%) isolates in the RUO mode. No misidentifications were detected. Although the IVD mode was unable to differentiate members of the M. fortuitum complex, the RUO mode correctly discriminated M. peregrinum and M. septicum. The robustness and accuracy showed by this system allow its implementation for routine identification of these microorganisms in clinical laboratories.
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Affiliation(s)
- David Rodríguez‐Temporal
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Margarita Estreya Zvezdánova
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Pablo Benedí
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)MadridSpain
| | - Mario Blázquez‐Sánchez
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - María Jesús Ruiz‐Serrano
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)MadridSpain
- Medicine Department, Faculty of MedicineUniversidad Complutense de MadridMadridSpain
| | - Belén Rodríguez‐Sánchez
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
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7
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Pastrone L, Curtoni A, Criscione G, Scaiola F, Bottino P, Guarrasi L, Iannaccone M, Timke M, Costa C, Cavallo R. Evaluation of Two Different Preparation Protocols for MALDI-TOF MS Nontuberculous Mycobacteria Identification from Liquid and Solid Media. Microorganisms 2023; 11:microorganisms11010120. [PMID: 36677412 PMCID: PMC9866535 DOI: 10.3390/microorganisms11010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) identification is essential for establishing the relevance of the isolate and for appropriate antimicrobial therapy. Traditionally, NTM identification is performed by using Line Probe Assays (LPA), a costly and time-consuming technique requiring trained personnel. MALDI-TOF MS is a promising tool for NTM identification, and its use is rapidly growing. We evaluated the newly introduced MBT Mycobacteria kit (MBT) and the MycoEx preparation protocol (Bruker Daltonics, Germany) for NTM MALDI-TOF MS identification using LPA results as a reference. Fifty NTM grown on 7H11 agar and MGIT broth were analyzed with both protocols using the Bruker Microflex® LT MALDI-TOF MS (Bruker Daltonics) instrument. MBT and MycoEx provided identification results in 97.0% and 95.0% of the cases, respectively. With both protocols, 100% of the provided results agreed with LPA with no registered mismatch. MBT achieved an elevated number of highly probable identifications (88.0% vs. 83.0%) and a higher reproducibility rate of correct results (86.6% vs. 75.8%) in comparison to MycoEx. This study provides results about MBT performance for liquid and solid media, underlining the strengths and weakness under different conditions. Our results suggest that MALDI-TOF MS could provide a great advantage for timely and cost-saving NTM identification with potential implications for patient outcome.
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Affiliation(s)
- Lisa Pastrone
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Antonio Curtoni
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Correspondence: ; Tel.: +39-011-633-7005
| | - Giulia Criscione
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Francesca Scaiola
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Paolo Bottino
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Luisa Guarrasi
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Marco Iannaccone
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Markus Timke
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
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8
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Feucherolles M, Frache G. MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology. Cells 2022; 11:cells11233900. [PMID: 36497158 PMCID: PMC9738593 DOI: 10.3390/cells11233900] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022] Open
Abstract
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.
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9
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“Omic” Approaches to Bacteria and Antibiotic Resistance Identification. Int J Mol Sci 2022; 23:ijms23179601. [PMID: 36077000 PMCID: PMC9455953 DOI: 10.3390/ijms23179601] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.
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Shu Q, Rajagopal M, Fan J, Zhan L, Kong X, He Y, Rotcheewaphan S, Lyon CJ, Sha W, Zelazny AM, Hu T. Peptidomic analysis of mycobacterial secreted proteins enables species identification. VIEW 2022. [DOI: 10.1002/viw.20210019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Qingbo Shu
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Meena Rajagopal
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Lingpeng Zhan
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Xiangxing Kong
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Yifan He
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai People's Republic of China
| | - Suwatchareeporn Rotcheewaphan
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
- Department of Microbiology, Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Wei Sha
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai People's Republic of China
| | - Adrian M. Zelazny
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
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11
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Mycobacterium chimaera Identification Using MALDI-TOF MS Technology: A Practical Approach for the Clinical Microbiology Laboratories. Microorganisms 2022; 10:microorganisms10061184. [PMID: 35744702 PMCID: PMC9228860 DOI: 10.3390/microorganisms10061184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 12/10/2022] Open
Abstract
Mycobacterium chimaera (MC) is an environmental, slowly growing, non-tuberculous mycobacterium (NTM) belonging to Mycobacterium avium complex (MAC), which recently has been linked to severe cardiovascular infections following open heart and vascular surgery. The majority of the diagnostic laboratory tests used in routine are not able to distinguish MC from M. intracellulare (MI), because of the great genetic similarity existing between these two species. The Genotype Mycobacterium NTM-DR™ represents a valid method to differentiate between these species, but it is expensive, requiring also specialized personnel. Recently, MALDI-TOF MS has been proposed to identify relevant NTM. However, a software implementation is required to distinguish between MC and MI, presenting the two microorganisms’ overlapping spectra. The present study evaluates the feasibility of applying a MALDI-TOF logarithmic-based analysis in the routine of a clinical microbiology laboratory, and proposes an easy-to-use template spreadsheet to make the results quickly interpretable. The protocol was previously validated through the identification of 87 strains of MC/MI collected from clinical and environmental samples, and it was identified using the GenoType Mycobacterium NTM-DR™ and/or WGS. The proposed protocol provides accurate identification for the isolates tested; moreover, it is less expensive and more rapid than sequencing methods and can be implemented with minimum effort.
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12
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Gleeson LE, Waterer G. Beyond antibiotics: recent developments in the diagnosis and management of nontuberculous mycobacterial infection. Breathe (Sheff) 2022; 18:210171. [PMID: 36337137 PMCID: PMC9584569 DOI: 10.1183/20734735.0171-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) pulmonary disease represents a significant clinical challenge with suboptimal therapy and increasing prevalence globally. Although clinical practice guidelines seek to standardise the approach to diagnosis and treatment of NTM disease, a lack of robust evidence limits their utility and significant variability exists in clinical practice. Here we walk through some novel approaches in diagnosis and therapy that are under development to tackle a disease where traditional strategies are failing. Prevalence of NTM disease is rising globally, yet current diagnostic and therapeutic strategies are lacking. This review describes some burgeoning diagnostic and therapeutic approaches, but it is clear that real progress will need more focused attention.https://bit.ly/3O0K2SP
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Robinne S, Saad J, Morsli M, Hamidou ZH, Tazerart F, Drancourt M, Baron SA. Rapid Identification of Mycobacterium tuberculosis Complex Using Mass Spectrometry: A Proof of Concept. Front Microbiol 2022; 13:753969. [PMID: 35432257 PMCID: PMC9008353 DOI: 10.3389/fmicb.2022.753969] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing and currently relies on DNA analysis, including whole genome sequencing (WGS), which requires a whole day. In this study, we report the unprecedented discrimination of M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative reference standard. In the first step, optimized peptide extraction applied to 36 isolates otherwise identified in five of the 11 M. tuberculosis complex variants by WGS yielded 139 MALDI-TOF spectra, which were used to identify biomarkers of interest that facilitate differentiation between variants. In a second step, 70/80 (88%) other isolates were correctly classified by an algorithm based on specific peaks. This study is the first to report a MALDI-TOF-MS method for discriminating M. tuberculosis complex mycobacteria that is easily implemented in clinical microbiology laboratories.
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Affiliation(s)
- Simon Robinne
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Jamal Saad
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Madjid Morsli
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Zelika Harouna Hamidou
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - Fatah Tazerart
- IHU Méditerranée Infection, Marseille, France
- Institut des Sciences Vétérinaires, Université de Blida 1, Blida, Algeria
| | - Michel Drancourt
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- *Correspondence: Sophie Alexandra Baron,
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14
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Akwani WC, van Vliet AH, Joel JO, Andres S, Diricks M, Maurer FP, Chambers MA, Hingley-Wilson SM. The Use of Comparative Genomic Analysis for the Development of Subspecies-Specific PCR Assays for Mycobacterium abscessus. Front Cell Infect Microbiol 2022; 12:816615. [PMID: 35419298 PMCID: PMC8995789 DOI: 10.3389/fcimb.2022.816615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/07/2022] [Indexed: 01/21/2023] Open
Abstract
Mycobacterium abscessus complex (MABC) is an important pathogen of immunocompromised patients. Accurate and rapid determination of MABC at the subspecies level is vital for optimal antibiotic therapy. Here we have used comparative genomics to design MABC subspecies-specific PCR assays. Analysis of single nucleotide polymorphisms and core genome multilocus sequence typing showed clustering of genomes into three distinct clusters representing the MABC subspecies M. abscessus, M. bolletii and M. massiliense. Pangenome analysis of 318 MABC genomes from the three subspecies allowed for the identification of 15 MABC subspecies-specific genes. In silico testing of primer sets against 1,663 publicly available MABC genomes and 66 other closely related Mycobacterium genomes showed that all assays had >97% sensitivity and >98% specificity. Subsequent experimental validation of two subspecies-specific genes each showed the PCR assays worked well in individual and multiplex format with no false-positivity with 5 other mycobacteria of clinical importance. In conclusion, we have developed a rapid, accurate, multiplex PCR-assay for discriminating MABC subspecies that could improve their detection, diagnosis and inform correct treatment choice.
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Affiliation(s)
- Winifred C. Akwani
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Jordan O. Joel
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Margo Diricks
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Florian P. Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark A. Chambers
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Suzanne M. Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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15
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Bajaj AO, Slechta ES, Barker AP. Rapid and Accurate Differentiation of Mycobacteroides abscessus Complex Species by Liquid Chromatography-Ultra-High-Resolution Orbitrap™ Mass Spectrometry. Front Cell Infect Microbiol 2022; 12:809348. [PMID: 35356534 PMCID: PMC8959847 DOI: 10.3389/fcimb.2022.809348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, a Liquid Chromatography-Mass Spectrometry (LC-MS) method for the identification of clinically relevant Mycobacteroides abscessus (Mabs) complex organisms is tested using a set of microbial Type strains. This methodology is based on profiling proteins derived from Mycobacteroides abscessus complex isolates. These protein profiles are then used as markers of species differentiation. To test the resolving power, speed, and accuracy of this assay four ATCC type strains and 32 recent clinical isolates of closely related Mabs species collected at ARUP laboratories (10 clinical isolate strains of M. abscessus subsp. abscessus, 10 M. abscessus subsp. massiliense, 2 M. abscessus subsp. bolletii and 10 M. chelonae) were subjected to this approach. Using multiple deconvolution algorithms, we identified hundreds of individual proteins, with subpopulations of these used as species-specific markers. This assay identified 150, 130, 140 and 110 proteoforms with isocratic elution and 230, 180, 200 and 190 proteoforms with gradient elution for M. abscessus (ATCC 19977), M. massiliense (DSM 45103), M. bolletii (DSM 45149) and M. chelonae (ATCC 35752) respectively. Taxonomic species were identified correctly down to the species level with 100% accuracy. The ability to differentiate Mycobacteroides abscessus complex at sub-species level can in-turn be helpful for patient management. Data analysis showed ~7-17 proteoforms potentially able to differentiate between subspecies. Here, we present a proof-of-principle study employing a rapid mass spectrometry-based method to identify the clinically most common species within the Mabs species complex.
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Affiliation(s)
- Amol O. Bajaj
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
- *Correspondence: Adam P. Barker, ; Amol O. Bajaj,
| | - E. Susan Slechta
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Adam P. Barker
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, United States
- *Correspondence: Adam P. Barker, ; Amol O. Bajaj,
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van den Beld MJC, Rossen JWA, Evers N, Kooistra-Smid MAMD, Reubsaet FAG. MALDI-TOF MS Using a Custom-Made Database, Biomarker Assignment, or Mathematical Classifiers Does Not Differentiate Shigella spp. and Escherichia coli. Microorganisms 2022; 10:microorganisms10020435. [PMID: 35208889 PMCID: PMC8878589 DOI: 10.3390/microorganisms10020435] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 12/22/2022] Open
Abstract
Shigella spp. and E. coli are closely related and cannot be distinguished using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) with commercially available databases. Here, three alternative approaches using MALDI-TOF MS to identify and distinguish Shigella spp., E. coli, and its pathotype EIEC were explored and evaluated using spectra of 456 Shigella spp., 42 E. coli, and 61 EIEC isolates. Identification with a custom-made database resulted in >94% Shigella identified at the genus level and >91% S. sonnei and S. flexneri at the species level, but the distinction of S. dysenteriae, S. boydii, and E. coli was poor. With biomarker assignment, 98% S. sonnei isolates were correctly identified, although specificity was low. Discriminating markers for S. dysenteriae, S. boydii, and E. coli were not assigned at all. Classification models using machine learning correctly identified Shigella in 96% of isolates, but most E. coli isolates were also assigned to Shigella. None of the proposed alternative approaches were suitable for clinical diagnostics for identifying Shigella spp., E. coli, and EIEC, reflecting their relatedness and taxonomical classification. We suggest the use of MALDI-TOF MS for the identification of the Shigella spp./E. coli complex, but other tests should be used for distinction.
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Affiliation(s)
- Maaike J. C. van den Beld
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (N.E.); (F.A.G.R.)
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (M.A.M.D.K.-S.)
- Correspondence: ; Tel.: +31-88-689-3454
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (M.A.M.D.K.-S.)
- Department of Pathology, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, UT 84132, USA
- Laboratory of Clinical Microbiology and Infectious Diseases, Isala Hospital, Dr. Van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Noah Evers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (N.E.); (F.A.G.R.)
| | - Mirjam A. M. D. Kooistra-Smid
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (M.A.M.D.K.-S.)
- Department of Medical Microbiology, Certe, Van Swietenlaan 2, 9728 NZ Groningen, The Netherlands
| | - Frans A. G. Reubsaet
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (N.E.); (F.A.G.R.)
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Multicentre study on the reproducibility of MALDI-TOF MS for nontuberculous mycobacteria identification. Sci Rep 2022; 12:1237. [PMID: 35075208 PMCID: PMC8786948 DOI: 10.1038/s41598-022-05315-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/11/2022] [Indexed: 11/08/2022] Open
Abstract
The ability of MALDI-TOF for the identification of nontuberculous mycobacteria (NTM) has improved recently thanks to updated databases and optimized protein extraction procedures. Few multicentre studies on the reproducibility of MALDI-TOF have been performed so far, none on mycobacteria. The aim of this study was to evaluate the reproducibility of MALDI-TOF for the identification of NTM in 15 laboratories in 9 European countries. A total of 98 NTM clinical isolates were grown on Löwenstein-Jensen. Biomass was collected in tubes with water and ethanol, anonymized and sent out to the 15 participating laboratories. Isolates were identified using MALDI Biotyper (Bruker Daltonics). Up to 1330 MALDI-TOF identifications were collected in the study. A score ≥ 1.6 was obtained for 100% of isolates in 5 laboratories (68.2–98.6% in the other). Species-level identification provided by MALDI-TOF was 100% correct in 8 centres and 100% correct to complex-level in 12 laboratories. In most cases, the misidentifications obtained were associated with closely related species. The variability observed for a few isolates could be due to variations in the protein extraction procedure or to MALDI-TOF system status in each centre. In conclusion, MALDI-TOF showed to be a highly reproducible method and suitable for its implementation for NTM identification.
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Mladenović KG, Grujović MŽ, Kocić-Tanackov SD, Bulut S, Iličić M, Degenek J, Semedo-Lemsaddek T. Serbian Traditional Goat Cheese: Physico-Chemical, Sensory, Hygienic and Safety Characteristics. Microorganisms 2021; 10:90. [PMID: 35056539 PMCID: PMC8778733 DOI: 10.3390/microorganisms10010090] [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: 12/10/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022] Open
Abstract
This research project aimed to investigate the physico-chemical, sensory, hygienic and safety characteristics of raw goat milk, whey, brine and traditional goat cheese during the ripening period of 28 days. Physico-chemical parameters included the determination of dry matter, fat, ash, protein, pH, water activity and NaCl content. The presence of Enterobacteriaceae and fungi was estimated on milk and cheese samples, and a sensory panel evaluated the products' features and acceptability during ripening. The results show that the cheese under study belongs to the acid full-fat cheese group. A consumer panel attributed high scores to the goat cheese, until the 21st day of ripening. After this period, the overall features altered significantly, including augmented bitterness, odor intensification and the development of molds on the surface. The presence of fungi, associated with Enterobacteriaceae, suggests that the hygiene of the production processes needs to be improved. Regarding microbial safety, the detection of putative pathogens and antibiotic resistances recommend an active surveillance of traditional foods to avoid foodborne infections and/or the dissemination of resistant microorganisms along the food chain.
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Affiliation(s)
- Katarina G. Mladenović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijica bb, 34000 Kragujevac, Serbia;
| | - Mirjana Ž. Grujović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijica bb, 34000 Kragujevac, Serbia;
| | - Sunčica D. Kocić-Tanackov
- Faculty of Technology, University in Novi Sad, Cara Lazara 1, 21000 Novi Sad, Serbia; (S.D.K.-T.); (S.B.); (M.I.); (J.D.)
| | - Sandra Bulut
- Faculty of Technology, University in Novi Sad, Cara Lazara 1, 21000 Novi Sad, Serbia; (S.D.K.-T.); (S.B.); (M.I.); (J.D.)
| | - Mirela Iličić
- Faculty of Technology, University in Novi Sad, Cara Lazara 1, 21000 Novi Sad, Serbia; (S.D.K.-T.); (S.B.); (M.I.); (J.D.)
| | - Jovana Degenek
- Faculty of Technology, University in Novi Sad, Cara Lazara 1, 21000 Novi Sad, Serbia; (S.D.K.-T.); (S.B.); (M.I.); (J.D.)
| | - Teresa Semedo-Lemsaddek
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal;
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19
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Biosafety and Proteome Profiles of Different Heat Inactivation Methods for Mycobacterium tuberculosis. Microbiol Spectr 2021; 9:e0071621. [PMID: 34937194 PMCID: PMC8694153 DOI: 10.1128/spectrum.00716-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies involving the pathogenic organism Mycobacterium tuberculosis routinely require advanced biosafety laboratory facilities, which might not be readily available in rural areas where tuberculosis burdens are high. Attempts to adapt heat inactivation techniques have led to inconsistent conclusions, and the risk of protein denaturation due to extensive heating is impractical for subsequent mass spectrometry (MS)-based protein analyses. In this study, 240 specimens with one or two loops of M. tuberculosis strain H37Rv biomass and specific inactivated solutions were proportionally assigned to six heat inactivation methods in a thermal block at 80°C and 95°C for 20, 30, and 90 min. Twenty untreated specimens served as a positive control, and bacterial growth was followed up for 12 weeks. Our results showed that 90 min of heat inactivation was necessary for samples with two loops of biomass. Further protein extraction and a matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS assay demonstrated adequate scores for bacterial identification (≥1.7), with the highest score achieved in the 80°C/90 min and 95°C/30 min treatment groups. A proteomics study also confidently identified 648 proteins with ∼93% to 96% consistent protein abundances following heating at 95°C for 20, 30, and 90 min. Heat inactivation at 95°C for 90 min yielded the most quantifiable proteins, and a functional analysis revealed proteins located in the ribosomal subunit. In summary, we proposed a heat inactivation method for the M. tuberculosis strain H37Rv and studied the preservation of protein components for subsequent bacterial identification and protein-related assays. IMPORTANCE Inactivation of Mycobacterium tuberculosis is an important step to guarantee biosafety for subsequent M. tuberculosis identification and related research, notably in areas of endemicity with minimal resources. However, certain biomolecules might be denatured or hydrolyzed because of the harsh inactivation process, and a standardized protocol is yet to be determined. We evaluated distinct heating conditions to report the inactivation efficiency and performed downstream mass spectrometry-based M. tuberculosis identification and proteomics study. The results are important and useful for both basic and clinical M. tuberculosis studies.
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20
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Castillo CR, Alishahedani ME, Gough P, Chaudhary PP, Yadav M, Matriz J, Myles IA. Assessing the effects of common topical exposures on skin bacteria associated with atopic dermatitis. SKIN HEALTH AND DISEASE 2021; 1. [PMID: 34723253 PMCID: PMC8555759 DOI: 10.1002/ski2.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Background While patients and families struggling with atopic dermatitis (AD) have documented concerns for a contributory role of skin care products in AD pathology, nearly all the skin microbiome studies to date have asked participants to avoid topical products (such as soaps or select medications) for the preceding days to weeks prior to sample collection. Thus, given the established role of the microbiome in AD, the interactions between topical exposures, dysbiosis and AD remains underrepresented in the academic literature. Objectives To address this knowledge gap, we expanded our previous evaluations to test the toxicological effects of a broader range of common chemicals, AD treatment lotions, creams and ointments using both health- and AD-associated strains of Roseomonas mucosa and Staphylococcus spp. Methods Use of in vitro culture techniques and mouse models were deployed to identify chemicals with dysbiotic or pre-biotic potential. A proof-of-concept study was subsequently performed in healthy volunteers to assess global microbiome shifts after exposure to select chemicals using dermatologic patch testing. Results Numerous chemicals possessed antibiotic properties, including many not marketed as anti-microbials. Through targeted combination of potentially beneficial chemicals, we identified combinations which promoted the growth of health-associated isolates over disease-associated strains in bacterial culture and enhanced microbe-specific outcomes in an established mouse model of AD; the most promising of which was the combination of citral and colophonium (often sold as lemon myrtle oil and pine tar). Additional studies would likely further optimize the combination of ingredients use. Similar results were seen in the proof-of-concept human studies. Conclusions Our results could offer a systematic, multiplex approach to identify which products carry dysbiotic potential and thus may guide formulation of new topicals to benefit patients with AD.
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Affiliation(s)
- C R Castillo
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - M E Alishahedani
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - P Gough
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - P P Chaudhary
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - M Yadav
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - J Matriz
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - I A Myles
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
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21
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A Case of Laryngeal Infection Secondary to Mycobacterium mageritense in an Immunocompetent Patient. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2021. [DOI: 10.1097/ipc.0000000000001054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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The key factors contributing to the risk, diagnosis and treatment of non-tuberculous mycobacterial opportunistic infections. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The incidence and prevalence of diseases caused by non-tuberculous mycobacteria (NTM) have been steadily increasing worldwide. NTM are environmental saprophytic organisms; however, a few strains are known to produce diseases in humans affecting pulmonary and extra-pulmonary sites. Although the environment is a major source of NTM infection, recent studies have shown that person-to-person dissemination could be an important transmission route for these microorganisms. Structural and functional lung defects and immunodeficiency are major risk factors for acquiring NTM infections. Diagnosis of NTM diseases is very complex owing to the necessity of distinguishing between a true pathogen and an environmental contaminant. Identification at the species level is critical due to differences in the antibiotic susceptibility patterns of various NTM strains. Such identification is mainly achieved by molecular methods; additionally, mass spectrometry (e.g., MALDI-TOF) is useful for NTM species determination. Natural resistance of NTM species to a wide spectrum of antibiotics makes prescribing treatment for NTM diseases very difficult. NTM therapy usually takes more than one year and requires multi-drug regimens, yet the outcome often remains poor. Therefore, alternatives to antibiotic therapy treatment methods is an area under active exploration. NTM infections are an active global health problem imposing the necessity for better diagnostic tools and more effective treatment methods.
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Carmona-Tello MN, Hernández-Cabrera M, Lavilla-Salgado MDC, Bolaños-Rivero M. Abscessed cellulitis with a sporotrichoid pattern that does not yield to antibiotic treatment. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2021; 39:411-412. [PMID: 34362704 DOI: 10.1016/j.eimce.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/07/2020] [Indexed: 06/13/2023]
Affiliation(s)
- María Nieves Carmona-Tello
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario Insular de Gran Canaria, Gran Canaria, Spain
| | - Michelle Hernández-Cabrera
- Unidad de Enfermedades Infecciosas y Medicina Tropical, Hospital Universitario Insular de Gran Canaria, Gran Canaria, Spain
| | | | - Margarita Bolaños-Rivero
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario Insular de Gran Canaria, Gran Canaria, Spain.
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Oka K, Morioka H, Eguchi M, Sato Y, Tetsuka N, Iguchi M, Kanematsu T, Fukano H, Hoshino Y, Kiyoi H, Yagi T. Bursitis, Bacteremia, and Disseminated Infection of Mycobacteroides (Mycobacterium) abscessus subsp. massiliense. Intern Med 2021; 60:3041-3045. [PMID: 33775997 PMCID: PMC8502645 DOI: 10.2169/internalmedicine.6189-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We herein report a 59-year-old woman with a 2-year history of chronic bursitis of the hand who took 50 mg/day prednisolone for several autoimmune diseases. Mycobacteroides abscessus subsp. massiliense was isolated from the abscess and blood culture. Combination therapy (imipenem/cilastatin, amikacin, and clarithromycin) was administered for a month. Two months later, M. massiliense was detected from a blood culture again, and disseminated lesions were found. Clarithromycin and sitafloxacin were administered following eight weeks of the same regimen. Six months after the diagnosis, M. massiliense was isolated from a blood culture, and she expired due to multiple organ failure.
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Affiliation(s)
- Keisuke Oka
- Department of Infectious Diseases, Nagoya University Hospital, Japan
| | - Hiroshi Morioka
- Department of Infectious Diseases, Nagoya University Hospital, Japan
| | - Motoki Eguchi
- Department of Hematology, Japanese Red Cross Nagoya First Hospital, Japan
| | - Yoshitaka Sato
- Department of Infectious Diseases, Nagoya University Hospital, Japan
- Department of Virology, Nagoya University Graduate School of Medicine, Japan
| | - Nobuyuki Tetsuka
- Department of Infectious Diseases, Nagoya University Hospital, Japan
| | - Mitsutaka Iguchi
- Department of Infectious Diseases, Nagoya University Hospital, Japan
| | - Takeshi Kanematsu
- Department of Clinical Laboratory, Nagoya University Hospital, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Japan
| | - Hitoshi Kiyoi
- Department of Hematology, Nagoya University Hospital, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Hospital, Japan
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Sharma D, Rai R. Neoteric advancements in TB diagnostics and its future frame. Indian J Tuberc 2021; 68:313-320. [PMID: 34099195 DOI: 10.1016/j.ijtb.2020.10.004] [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: 04/14/2020] [Revised: 09/25/2020] [Accepted: 10/09/2020] [Indexed: 06/12/2023]
Abstract
Tuberculosis (TB) is one of the major infectious disease that causes threat to human health and leads to death in most of the cases. Mycobacterium tuberculosis is the causative agent that can affect both pulmonary and extra pulmonary regions of the body. This infection can be presented either as an active or latent form in the patients. Although this disease has been declared curable and preventable by WHO, it still holds its position as a global emergency. Over the past decade many hurdles such as low immunity, co-infections like HIV, autoimmune disorders, poverty, malnutrition and emerging trends in drug resistance patterns are hindering the eradication of this infection. However, many programmes have been launched by WHO with involvement of governments at various level to put a full stop over the disease. Under the Revised National Tuberculosis Control Programme (RNTCP) which was recently renamed as National Tuberculosis Elimination Programme (NTEP), the major focus is on eliminating tuberculosis by the year 2025. The main aim of the programme is to identify feasible quality testing, evaluate through NIKSHYA poshak yozana, restrict through BCG vaccination and assemble with public awareness to eradicate MTB. Numerous novel diagnostic techniques and molecular tools have been developed to elucidate and differentiate report of various suspected and active tuberculosis patients. However, improvements are still required to cut short the duration of the overall process ranging from screening of patients to their successful treatment.
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Affiliation(s)
- Diksha Sharma
- Department of Biotechnology, DAV College, Jalandhar, 144008, Punjab, India
| | - Rohit Rai
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara, 144411, Punjab, India.
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Use of MALDI-TOF MS (Bruker Daltonics) for identification of Mycobacterium species isolated directly from liquid medium. Enferm Infecc Microbiol Clin 2021; 39:241-243. [DOI: 10.1016/j.eimc.2020.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 02/07/2023]
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27
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Kasas S, Malovichko A, Villalba MI, Vela ME, Yantorno O, Willaert RG. Nanomotion Detection-Based Rapid Antibiotic Susceptibility Testing. Antibiotics (Basel) 2021; 10:287. [PMID: 33801939 PMCID: PMC7999052 DOI: 10.3390/antibiotics10030287] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 02/26/2021] [Accepted: 03/07/2021] [Indexed: 01/04/2023] Open
Abstract
Rapid antibiotic susceptibility testing (AST) could play a major role in fighting multidrug-resistant bacteria. Recently, it was discovered that all living organisms oscillate in the range of nanometers and that these oscillations, referred to as nanomotion, stop as soon the organism dies. This finding led to the development of rapid AST techniques based on the monitoring of these oscillations upon exposure to antibiotics. In this review, we explain the working principle of this novel technique, compare the method with current ASTs, explore its application and give some advice about its implementation. As an illustrative example, we present the application of the technique to the slowly growing and pathogenic Bordetella pertussis bacteria.
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Affiliation(s)
- Sandor Kasas
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; (A.M.); (M.I.V.)
- Unité Facultaire d’Anatomie et de Morphologie (UFAM), CUMRL, University of Lausanne, 1005 Lausanne, Switzerland
- International Joint Research Group VUB-EPFL NanoBiotechnology and NanoMedicine (NANO), Vrije Universiteit Brussel, 1050 Brussels, Belgium;
| | - Anton Malovichko
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; (A.M.); (M.I.V.)
- International Joint Research Group VUB-EPFL NanoBiotechnology and NanoMedicine (NANO), Vrije Universiteit Brussel, 1050 Brussels, Belgium;
| | - Maria Ines Villalba
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; (A.M.); (M.I.V.)
- International Joint Research Group VUB-EPFL NanoBiotechnology and NanoMedicine (NANO), Vrije Universiteit Brussel, 1050 Brussels, Belgium;
| | - María Elena Vela
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, and CONICET, Diagonal 113 y 64, 1900 La Plata, Argentina;
| | - Osvaldo Yantorno
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI-CONICET-CCT La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Argentina;
| | - Ronnie G. Willaert
- International Joint Research Group VUB-EPFL NanoBiotechnology and NanoMedicine (NANO), Vrije Universiteit Brussel, 1050 Brussels, Belgium;
- Research Group Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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Solntceva V, Kostrzewa M, Larrouy-Maumus G. Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing. Front Cell Infect Microbiol 2021; 10:621452. [PMID: 33634037 PMCID: PMC7902069 DOI: 10.3389/fcimb.2020.621452] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.
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Affiliation(s)
- Vera Solntceva
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | | | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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Carmona-Tello MN, Hernández-Cabrera M, Lavilla-Salgado MDC, Bolaños-Rivero M. Abscessed cellulitis with a sporotrichoid pattern that does not yield to antibiotic treatment. Enferm Infecc Microbiol Clin 2021; 39:S0213-005X(21)00007-0. [PMID: 33546813 DOI: 10.1016/j.eimc.2020.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022]
Affiliation(s)
- María Nieves Carmona-Tello
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario Insular de Gran Canaria, Gran Canaria, España
| | - Michele Hernández-Cabrera
- Unidad de Enfermedades Infecciosas y Medicina Tropical, Hospital Universitario Insular de Gran Canaria, Gran Canaria, España
| | | | - Margarita Bolaños-Rivero
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario Insular de Gran Canaria, Gran Canaria, España.
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Review on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid screening of microbial species: A promising bioanalytical tool. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105387] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Yoo IY, Shim HJ, Yun SA, Kang OK, Chung YN, Kim TY, Lee H, Kim J, Park YJ, Huh HJ, Lee NY. Evaluation of the ASTA MicroIDSys matrix-assisted laser desorption ionization time-of-flight mass spectrometry system for identification of mycobacteria directly from positive MGIT liquid cultures. Int J Infect Dis 2020; 102:172-177. [PMID: 33039611 DOI: 10.1016/j.ijid.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVES We evaluated the performance of the MicroIDSys Elite system, a newly developed matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry system for identification of mycobacteria directly from positive MGIT liquid cultures. METHODS Analytical specificity was evaluated with 63 reference strains grown in mycobacteria growth indicator tube media. Prospective performance evaluation was conducted with primary liquid cultures of sputum samples for identification of mycobacteria, and results were compared to multigenerational sequencing as the reference method. Liquid media subcultures were also analyzed. RESULTS The accuracy for the 63 reference strains was 98.4% (62/63). A total of 167 paired mycobacterial primary cultures and subcultures in liquid media, comprised of seven Mycobacterium tuberculosis isolates, 109 slowly growing nontuberculous mycobacterial isolates, and 51 rapidly growing nontuberculous mycobacterial isolates, was identified by the MicroIDSys Elite system. Using primary liquid cultures, the MicroIDSys Elite system correctly identified 143 (85.6%) isolates; 21 (12.6%) resulted in "no identification"; and three (1.8%) isolates were misidentified. Using liquid media subcultures with this system, 159 (95.2%) isolates were correctly identified; seven (4.2%) resulted in "no identification"; and one (0.6%) isolate was misidentified. CONCLUSION The MicroIDSys Elite system is a useful routine diagnostic tool for identification of mycobacterial species from liquid culture.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - On Kyun Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yoo Na Chung
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyeyoung Lee
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, The Catholic Kwandong University, Incheon, Republic of Korea
| | - Jayoung Kim
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, The Catholic Kwandong University, Incheon, Republic of Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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Evaluation of MALDI Biotyper Interpretation Criteria for Accurate Identification of Nontuberculous Mycobacteria. J Clin Microbiol 2020; 58:JCM.01103-20. [PMID: 32719033 DOI: 10.1128/jcm.01103-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/17/2020] [Indexed: 12/27/2022] Open
Abstract
Identification of mycobacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) requires not only a good protein extraction protocol but also an adequate cutoff score in order to provide reliable results. The aim of this study was to assess the cutoff scores proposed by the MALDI-TOF MS system for mycobacterial identification. A total of 693 clinical isolates from a liquid medium and 760 from a solid medium were analyzed, encompassing 67 different species of nontuberculous mycobacteria (NTM). MALDI-TOF MS identified 558 (80.5%) isolates from the liquid medium and 712 (93.7%) isolates from the solid medium with scores of ≥1.60. Among these, four (0.7%) misidentifications were obtained from the liquid medium and four (0.5%) from the solid medium. With regard to species diversity, MALDI-TOF MS successfully identified 64 (95.5%) different species, while PCR-reverse hybridization (GenoType Mycobacterium CM and AS assays) identified 24 (35.8%) different species. With MALDI-TOF MS scores of ≥2, all isolates were correctly identified, and with scores in the range from 1.60 to 1.99, most isolates were correctly identified, except for Mycobacterium angelicum, M. parascrofulaceum, M. peregrinum, M. porcinum, and M. gastri In conclusion, MALDI-TOF MS is a useful method for identifying a large diversity of NTM species. A score threshold of 1.60 proved useful for identifying almost all the isolates tested; only a few species required a higher score (≥2.00) to obtain a valid definitive identification.
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Imai M, Kimura Y, Tanno D, Saito K, Honda M, Takano Y, Ohashi K, Toyokawa M, Ohana N, Yamadera Y, Shimura H. Validation of MALDI-TOF MS devices in reanalysis of unidentified pathogenic bacteria detected in blood cultures. Fukushima J Med Sci 2020; 66:103-112. [PMID: 32713872 PMCID: PMC7470759 DOI: 10.5387/fms.2020-09] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In hospital microbial laboratories, morphological and biochemical analyses are performed to identify pathogenic microbes;however, these procedures lack rapidity and accuracy. Recently, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has been clinically utilized, and is expected to enable rapid and accurate microbial identification. We aimed to validate two MALDI-TOF MS devices available in Japan: the VITEK-MS (BioMérieux) and the Microflex LT (Bruker Daltonics). Clinically isolated bacteria, 100 samples in all, detected in blood cultures but incompletely identified by conventional procedures, were reanalyzed using the two devices. The VITEK-MS and Microflex LT, respectively, identified 49% (49/100) and 80% (80/100) of the tested bacteria at the species level, as well as 96% (96/100) and 95% (95/100) at the genus level. Among those reidentified strains, 26% (26/100) at the species level and 88% (88/100) at the genus level were concordant with each other, though three strains were unmatched. Moreover, four bacterial strains were unable to be identified using the VITEK-MS, versus five using the Microflex LT. MALDI-TOF MS devices can provide more rapid and accurate bacterial identification than ever before;however, the characteristics of each system were slightly different;therefore, it is necessary to understand the difference in performance of MALDI-TOF MS models.
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Affiliation(s)
- Minako Imai
- Department of Clinical Laboratory Medicine, Fukushima Medical University Hospital
| | - Yukio Kimura
- Department of Laboratory Medicine, Fukushima Medical University
| | - Daiki Tanno
- Department of Clinical Laboratory Medicine, Fukushima Medical University Hospital.,Department of Laboratory Medicine, Fukushima Medical University
| | - Kyoichi Saito
- Department of Laboratory Medicine, Fukushima Medical University
| | - Mutsuko Honda
- Department of Clinical Laboratory Medicine, Fukushima Medical University Hospital
| | - Yukiko Takano
- Department of Clinical Laboratory Medicine, Fukushima Medical University Hospital
| | - Kazutaka Ohashi
- Department of Clinical Laboratory Medicine, Fukushima Medical University Hospital
| | - Masahiro Toyokawa
- Department of Clinical Laboratory Medicine, Fukushima Medical University Hospital.,Department of Laboratory Medicine, Fukushima Medical University.,Preparing Section for New Faculty of Medical Science, Fukushima Medical University
| | - Noboru Ohana
- Department of Laboratory Medicine, Fukushima Medical University
| | - Yukio Yamadera
- Department of Clinical Laboratory Medicine, Fukushima Medical University Hospital
| | - Hiroki Shimura
- Department of Laboratory Medicine, Fukushima Medical University
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Ghielmetti G, Hilbe M, Friedel U, Menegatti C, Bacciarini L, Stephan R, Bloemberg G. Mycobacterial infections in wild boars (Sus scrofa) from Southern Switzerland: Diagnostic improvements, epidemiological situation and zoonotic potential. Transbound Emerg Dis 2020; 68:573-586. [PMID: 32640107 PMCID: PMC8247353 DOI: 10.1111/tbed.13717] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
The occurrence of mycobacterial infections in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. In addition to the well-known pathogenic members of the Mycobacterium tuberculosis - complex (MTBC), over 180 non-tuberculous mycobacteria (NTM) species have been described. Although the large majority of the NTM is assumed to be non-pathogenic to most individuals, an increasing trend in NTM infections has been observed over the last decades. The reasons of such augmentation are probably more than one: improved laboratory diagnostics, an increasing number of immunocompromised patients and individuals with lung damage are some of the possible aspects. Mandibular lymph nodes of 176 hunted wild boars from the pre-Alpine region of Canton Ticino, Switzerland, were collected. Following gross inspection, each lymph node was subjected to culture and to an IS6110 based real-time PCR specific for MTBC members. Histology was performed of a selection of lymph nodes (n = 14) presenting gross visible lesions. Moreover, accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) species identification was compared with sequence analysis of a combination of housekeeping genes. Mycobacteria of the MTBC were detected in 2.8% of the wild boars (n = 5; CI95% 1.2-6.5) and were all confirmed to be Mycobacterium microti by molecular methods. In addition, based on the examined lymph nodes, NTM were detected in 57.4% (n = 101; CI95% 50.0-64.5) of the wild boars originating from the study area. The 111 isolates belonged to 24 known species and three potentially undescribed Mycobacterium species. M. avium subsp. hominissuis thereby predominated (22.5%) and was found in lymph nodes with and without macroscopic changes. Overall, the present findings show that, with the exception of undescribed Mycobacterium species where identification was not possible (3.6%; 4/111), MALDI-TOF MS had a high concordance rate (90.1%; 100/111 isolates) to the sequence-based reference method.
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Affiliation(s)
- Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Monika Hilbe
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Ute Friedel
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Guido Bloemberg
- Institute for Food Safety and Hygiene, National Reference Center for Enteropathogenic Bacteria and Listeria, University of Zurich, Zurich, Switzerland
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Identification and drug susceptibility testing for nontuberculous mycobacteria. J Formos Med Assoc 2020; 119 Suppl 1:S32-S41. [DOI: 10.1016/j.jfma.2020.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/23/2020] [Accepted: 05/04/2020] [Indexed: 11/17/2022] Open
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Kalbian I, Park JW, Goswami K, Lee YK, Parvizi J, Koo KH. Culture-negative periprosthetic joint infection: prevalence, aetiology, evaluation, recommendations, and treatment. INTERNATIONAL ORTHOPAEDICS 2020; 44:1255-1261. [DOI: 10.1007/s00264-020-04627-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/12/2020] [Indexed: 02/08/2023]
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O’Connor JA, O’Reilly B, Corcoran GD, O’Mahony J, Lucey B. A comparison of the HAIN Genotype CM reverse hybridisation assay with the Bruker MicroFlex LT MALDI-TOF mass spectrometer for identification of clinically relevant mycobacterial species. Br J Biomed Sci 2020; 77:152-155. [DOI: 10.1080/09674845.2020.1732639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- JA O’Connor
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - B O’Reilly
- Laboratory Medicine, Diagnostic Directorate, Cork University Hospital, Cork, Ireland
| | - GD Corcoran
- Laboratory Medicine, Diagnostic Directorate, Cork University Hospital, Cork, Ireland
| | - J O’Mahony
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - B Lucey
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
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Li Y, Shan M, Zhu Z, Mao X, Yan M, Chen Y, Zhu Q, Li H, Gu B. Application of MALDI-TOF MS to rapid identification of anaerobic bacteria. BMC Infect Dis 2019; 19:941. [PMID: 31699042 PMCID: PMC6836477 DOI: 10.1186/s12879-019-4584-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been rapidly developed and widely used as an analytical technique in clinical laboratories with high accuracy in microorganism identification. OBJECTIVE To validate the efficacy of MALDI-TOF MS in identification of clinical pathogenic anaerobes. METHODS Twenty-eight studies covering 6685 strains of anaerobic bacteria were included in this meta-analysis. Fixed-effects models based on the P-value and the I-squared were used for meta-analysis to consider the possibility of heterogeneity between studies. Statistical analyses were performed by using STATA 12.0. RESULTS The identification accuracy of MALDI-TOF MS was 84% for species (I2 = 98.0%, P < 0.1), and 92% for genus (I2 = 96.6%, P < 0.1). Thereinto, the identification accuracy of Bacteroides was the highest at 96% with a 95% CI of 95-97%, followed by Lactobacillus spp., Parabacteroides spp., Clostridium spp., Propionibacterium spp., Prevotella spp., Veillonella spp. and Peptostreptococcus spp., and their correct identification rates were all above 90%, while the accuracy of rare anaerobic bacteria was relatively low. Meanwhile, the overall capabilities of two MALDI-TOF MS systems were different. The identification accuracy rate was 90% for VITEK MS vs. 86% for MALDI biotyper system. CONCLUSIONS Our research showed that MALDI-TOF-MS was satisfactory in genus identification of clinical pathogenic anaerobic bacteria. However, this method still suffers from different drawbacks in precise identification of rare anaerobe and species levels of common anaerobic bacteria.
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Affiliation(s)
- Ying Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Mingzhu Shan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, 214200, China
| | - Mingju Yan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qiuju Zhu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hongchun Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Bing Gu
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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Brown-Elliott BA, Fritsche TR, Olson BJ, Vasireddy S, Vasireddy R, Iakhiaeva E, Alame D, Wallace RJ, Branda JA. Comparison of Two Commercial Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of Nontuberculous Mycobacteria. Am J Clin Pathol 2019; 152:527-536. [PMID: 31314059 PMCID: PMC6733354 DOI: 10.1093/ajcp/aqz073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES This multicenter study's aim was to assess the performance of two commercially available matrix-assisted laser desorption/ionization time of flight mass spectrometry systems in identifying a challenge collection of clinically relevant nontuberculous mycobacteria (NTM). METHODS NTM clinical isolates (n = 244) belonging to 23 species/subspecies were identified by gene sequencing and analyzed using Bruker Biotyper with Mycobacterial Library v5.0.0 and bioMérieux VITEK MS with v3.0 database. RESULTS Using the Bruker or bioMérieux systems, 92% and 95% of NTM strains, respectively, were identified at least to the complex/group level; 62% and 57%, respectively, were identified to the highest taxonomic level. Differentiation between members of Mycobacterium abscessus, M fortuitum, M mucogenicum, M avium, and M terrae complexes/groups was problematic for both systems, as was identification of M chelonae for the Bruker system. CONCLUSIONS Both systems identified most NTM isolates to the group/complex level, and many to the highest taxonomic level. Performance was comparable.
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Affiliation(s)
| | - Thomas R Fritsche
- Marshfield Clinic Health System, Marshfield, WI
- University of Wisconsin, La Crosse
| | | | | | | | | | - Diana Alame
- Thomas Jefferson University, Philadelphia, PA
| | | | - John A Branda
- Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, MA
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Bacanelli G, Olarte LC, Silva MR, Rodrigues RA, Carneiro PAM, Kaneene JB, Pasquatti TN, Takatani H, Zumárraga MJ, Etges RN, Araújo FR, Verbisck NV. Matrix Assisted Laser Desorption Ionization-Time-of-Flight mass spectrometry identification of Mycobacterium bovis in Bovinae. J Vet Med Sci 2019; 81:1400-1408. [PMID: 31462609 PMCID: PMC6863732 DOI: 10.1292/jvms.19-0214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this study, Matrix Assisted Laser Desorption Ionization-Time-of-Flight (MALDI-TOF) mass spectrometry was used to identify Mycobacterium bovis from cattle and buffalo tissue isolates from the North and South regions of Brazil, grown in solid medium and previously identified by Polymerase Chain Reaction (PCR) based on Region of Difference 4 (RD4), sequencing and spoligotyping. For this purpose, the protein extraction protocol and the mass spectra reference database were optimized for the identification of 80 clinical isolates of mycobacteria. As a result of this optimization, it was possible to identify and differentiate M. bovis from other members of the Mycobacterium tuberculosis complex with 100% specificity, 90.91% sensitivity and 91.25% reliability. MALDI-TOF MS methodology described herein provides successful identification of M. bovis within bovine/bubaline clinical samples, demonstrating its usefulness for bovine tuberculosis diagnosis in the future.
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Affiliation(s)
- Gisele Bacanelli
- Biotechnology and Biodiversity of the Central Western Region Postgraduate Program, Federal University of Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil
| | - Larissa C Olarte
- Biochemistry and Molecular Biology Multicentric Postgraduate Program, Federal University of Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil
| | - Márcio R Silva
- Embrapa Dairy Cattle, Juiz de Fora, MG, 36038-330, Brazil
| | - Rudielle A Rodrigues
- Veterinary Sciences Postgraduate Program, Faculty of Veterinary Medicine, Federal University of Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil
| | - Paulo A M Carneiro
- Center for Comparative Epidemiology, Michigan State University, East Lansing, MI, 48824, U.S.A
| | - John B Kaneene
- Center for Comparative Epidemiology, Michigan State University, East Lansing, MI, 48824, U.S.A
| | | | - Haruo Takatani
- Agricultural Defense Agency of Amazonas, Manaus, AM, 69028-407, Brazil
| | - Martin J Zumárraga
- Institute of Biotechnology, CICVyA/INTA, Buenos Aires, B1686IGC, Argentina
| | - Rodrigo N Etges
- Secretary of Agriculture, Livestock and Irrigation, Porto Alegre, RS, 90150-004, Brazil
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Rotcheewaphan S, Lemon JK, Desai UU, Henderson CM, Zelazny AM. Rapid one-step protein extraction method for the identification of mycobacteria using MALDI-TOF MS. Diagn Microbiol Infect Dis 2019; 94:355-360. [PMID: 31053254 DOI: 10.1016/j.diagmicrobio.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/06/2019] [Accepted: 03/10/2019] [Indexed: 11/19/2022]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry is a quick and accurate method for mycobacterial identification from protein extracts. Our new one-step extraction method successfully reduced routine multistep extraction procedure time from over 60 min to under 10 min and used only 1 μL loopful of mycobacteria while providing clinically acceptable identification scores (≥1.8). Overall, 86.8% and 4.4% of mycobacteria isolates (n = 68) were identified to the species/complex and genus levels, respectively, by one-step loop extraction method, comparable to the routine extraction method. Viability studies confirmed killing of mycobacterial isolates after 5 min in the extraction solution replacing lengthy heat killing step. Retrospective 7-month data analysis showed 100% of rapidly and slowly growing mycobacterial isolates were identified to the species/complex level by rapid extraction methods. Our rapid extraction methods substantially reduced processing time and microbial biomass required for testing without sacrificing quality and accuracy of mycobacterial identification.
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Affiliation(s)
- Suwatchareeporn Rotcheewaphan
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA; Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jamie K Lemon
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Uma U Desai
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Christina M Henderson
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA.
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Neumann AC, Bauer D, Hoelscher M, Haisch C, Wieser A. Identifying Dormant Growth State of Mycobacteria by Orthogonal Analytical Approaches on a Single Cell and Ensemble Basis. Anal Chem 2018; 91:881-887. [DOI: 10.1021/acs.analchem.8b03646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- A.-C. Neumann
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
| | - D. Bauer
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Munich, Germany
| | - M. Hoelscher
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
| | - C. Haisch
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Munich, Germany
| | - A. Wieser
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
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43
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Performance of RGM Medium for Isolation of Nontuberculous Mycobacteria from Respiratory Specimens from Non-Cystic Fibrosis Patients. J Clin Microbiol 2018; 57:JCM.01519-18. [PMID: 30487305 DOI: 10.1128/jcm.01519-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/20/2018] [Indexed: 11/20/2022] Open
Abstract
A new selective medium for rapidly growing mycobacteria (RGM medium) was evaluated on respiratory specimens from non-cystic fibrosis patients and compared to the mycobacterial growth indicator tube (MGIT) system and Middlebrook 7H11 agar for the isolation of all nontuberculous mycobacteria (NTM). A total of 203 mucolyzed respiratory specimens collected from 163 patients were inoculated on RGM medium and incubated at both 30°C (RGM30) and 35°C (RGM35) over a 28-day period. N-Acetyl-l-cysteine-sodium hydroxide (NALC-NaOH)-decontaminated specimens were inoculated into MGIT and Middlebrook 7H11 agar and incubated at 35°C for 42 days. NTM were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) or gene sequencing. A total of 133 NTM isolates were recovered overall from 101 (49.8%) specimens collected from 85 (52.1%) patients by a combination of all culture methods. The sensitivity of RGM30 for the recovery of NTM was significantly higher than that of either the MGIT system (76.7% versus 59.4%; P = 0.01) or Middlebrook 7H11 agar (76.7% versus 47.4%; P = 0.0001) alone, but it was not significantly different from that of an acid-fast bacillus culture (AFC) which includes both MGIT and Middlebrook 7H11 agar (76.7% versus 63.9%; P = 0.0647). RGM35 had significantly lower sensitivity than the MGIT system (49.6% versus 59.4%; P = 0.0367) and AFC (49.6% versus 63.9%; P = 0.0023). RGM medium was highly effective at inhibiting the growth of nonmycobacterial organisms in the respiratory specimens, with breakthrough contamination rates of 5.4% and 4.4% for RGM30 and RGM35, respectively.
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Cost-effective implementation of a custom MALDI-TOF library for the identification of South Australian Nocardia isolates. Pathology 2018; 50:753-757. [PMID: 30482608 DOI: 10.1016/j.pathol.2018.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/14/2018] [Accepted: 08/19/2018] [Indexed: 01/14/2023]
Abstract
Mass spectrometry plays a significant role in the routine identification of micro-organisms and provides the ability to incorporate newly found pathogens into the database in a cost-effective fashion. This work aims to highlight the role of mass spectrometry through improved identification of Nocardia species in a diagnostic clinical microbiology laboratory. Prior to this study we constructed a custom in-house matrix-assisted laser desorption ionisation-time of flight (MALDI-TOF) library for Nocardia isolates consisting of isolates identified to the species level. Subsequently over a period of 5 years, we isolated a further 153 Nocardia clinical isolates, of which 91.5% (140/153) were identified correctly with the custom MALDI-TOF library and 8.5% (13/153) needed further molecular sequencing for final identification. We estimate our cost savings to be approximately 9,800 AUD overall with this implementation over the study period. Continued expansion and maintenance of this custom library will eventually result in little or no 16S ribosomal DNA sequencing needed for specific identification of Nocardia isolates.
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Golichenari B, Velonia K, Nosrati R, Nezami A, Farokhi-Fard A, Abnous K, Behravan J, Tsatsakis AM. Label-free nano-biosensing on the road to tuberculosis detection. Biosens Bioelectron 2018; 113:124-135. [DOI: 10.1016/j.bios.2018.04.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/14/2018] [Accepted: 04/28/2018] [Indexed: 12/16/2022]
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Evaluation of the Vitek MS v3.0 Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Mycobacterium and Nocardia Species. J Clin Microbiol 2018; 56:JCM.00237-18. [PMID: 29643203 DOI: 10.1128/jcm.00237-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/08/2018] [Indexed: 11/20/2022] Open
Abstract
This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of Mycobacterium and Nocardia species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the M. tuberculosis, M. abscessus, and M. avium complexes and within the M. fortuitum and M. mucogenicum groups could be differentiated. Among the 312 Nocardia isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex level. Species within the N. nova and N. transvalensis complexes could not always be differentiated. Eleven percent of the isolates (103/963) underwent repeat testing in order to get a final result. Identification of a representative set of Mycobacterium and Nocardia species was highly reproducible, with 297 of 300 (99%) replicates correctly identified using multiple kit lots, instruments, analysts, and sites. These findings demonstrate that the system is robust and has utility for the routine identification of mycobacteria and Nocardia in clinical practice.
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Lainhart W, Yarbrough ML, Jean S, Burnham CAD. New Bugs and New Drugs: Updates in Clinical Microbiology. J Appl Lab Med 2018; 2:925-940. [PMID: 33636835 DOI: 10.1373/jalm.2017.023101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/05/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND The landscape of clinical microbiology laboratories is changing. As new technologies are introduced, we are better able to detect and identify pathogens and to recognize and characterize emerging antimicrobial resistance mechanisms. CONTENT In this review, a selected cross-section of current hot topics in clinical microbiology is discussed. These topics include (a) diagnostics for urinary tract and sexually transmitted infections; (b) phenotypic and genotypic methods of detecting carbapenem resistance and discussion of newly approved anti-infective agents for these multi-drug resistant organisms; and (c) the significance, epidemiology, and identification of the emerging pathogens Mycobacterium chimaera and Candida auris. SUMMARY Communication between clinical microbiologists and their clinical colleagues is imperative to convey the significance of emerging pathogens and resistance determinants, as well as the performance characteristics of new diagnostic methods. Additionally, as antimicrobial resistance is surging, it is important to comprehensively evaluate the resistance profiles of clinical isolates to facilitate antimicrobial stewardship and inform infection prevention measures. Although antimicrobial resistance is a global public health crisis, it is encouraging that new anti-infective agents are in the pipeline and being approved for use in patients.
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Affiliation(s)
- William Lainhart
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Melanie L Yarbrough
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Sophonie Jean
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
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Murugaiyan J, Lewin A, Kamal E, Bakuła Z, van Ingen J, Ulmann V, Unzaga Barañano MJ, Humięcka J, Safianowska A, Roesler UH, Jagielski T. MALDI Spectra Database for Rapid Discrimination and Subtyping of Mycobacterium kansasii. Front Microbiol 2018; 9:587. [PMID: 29670585 PMCID: PMC5893902 DOI: 10.3389/fmicb.2018.00587] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/14/2018] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium kansasii is an emerging non-tuberculous mycobacterial (NTM) pathogen capable of causing severe lung disease. Of the seven currently recognized M. kansasii genotypes (I-VII), genotypes I and II are most prevalent and have been associated with human disease, whereas the other five (III-VII) genotypes are predominantly of environmental origin and are believed to be non-pathogenic. Subtyping of M. kansasii serves as a valuable tool to guide clinicians in pursuing diagnosis and to initiate the proper timely treatment. Most of the previous rapid diagnostic tests for mycobacteria employing the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology focused on species-level identification. The purpose of this study was to establish MALDI-TOF MS reference spectra database for discrimination of M. kansasii at the genotype level. A panel of 32 strains, representatives of M. kansasii genotypes I-VI were selected, whole cell proteins extracted and measured with MALDI-TOF MS. A unique main spectra (MSP) library was created using MALDI Biotyper Compass Explorer software. The spectra reproducibility was assessed by computing composite correlation index and MSPs cross-matching. One hundred clinical M. kansasii isolates used for testing of the database resulted in 90% identification at genus-level, 7% identification at species-level and 2% identification was below the threshold of log score value 1.7, of which all were correct at genotype level. One strain could not be identified. On the other hand, 37% of strains were identified at species level, 40% at genus level and 23% was not identified with the manufacturer's database. The MALDI-TOF MS was proven a rapid and robust tool to detect and differentiate between M. kansasii genotypes. It is concluded that MALDI-TOF MS has a potential to be incorporated into the routine diagnostic workflow of M. kansasii and possibly other NTM species.
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Affiliation(s)
- Jayaseelan Murugaiyan
- Centre for Infectious Medicine, Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Astrid Lewin
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Elisabeth Kamal
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Zofia Bakuła
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Vit Ulmann
- Institute of Public Health, Ostrava, Czechia
| | | | - Joanna Humięcka
- Hospital for Infectious Diseases in Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Aleksandra Safianowska
- Department of Internal Medicine, Pulmonology, and Allergology, Medical University of Warsaw, Warsaw, Poland
| | - Uwe H Roesler
- Centre for Infectious Medicine, Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Tomasz Jagielski
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
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Evaluation of Two Protein Extraction Protocols Based on Freezing and Mechanical Disruption for Identifying Nontuberculous Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry from Liquid and Solid Cultures. J Clin Microbiol 2018; 56:JCM.01548-17. [PMID: 29367300 DOI: 10.1128/jcm.01548-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/19/2018] [Indexed: 01/30/2023] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has proved to be a useful diagnostic method for identifying conventional bacteria. In the case of mycobacteria, a good protein extraction protocol is essential in order to obtain reliable identification results. To date, no such protocol has been definitively established. The aim of this study was to compare the manufacturer's recommended protein extraction protocol (protocol A) with two novel protocols (protocols B and C), which apply different freezing temperatures and mechanical disruption times using an automatic tissue homogenizer. A total of 302 clinical isolates, comprising 41 nontuberculous mycobacteria (NTM) species, were grown in parallel on solid and liquid media and analyzed: 174 isolates were slow-growing mycobacteria (SGM) and 128 isolates were rapid-growing mycobacteria (RGM). Overall, MALDI-TOF MS identified a higher number of NTM isolates from solid than from liquid media, especially with protocol C (83.4 and 68.2%, respectively; P < 0.05). From solid media, this protein extraction method identified 57.9 and 3.9% more isolates than protocols A (P < 0.001) and B (P < 0.05), respectively. In the case of liquid media, protocol C identified 49.7 and 6.3% more isolates than protocols A and B, respectively (P < 0.001). With regard to the growth rate, MALDI-TOF MS identified more RGM isolates than SGM isolates in all of the protocols studied. In conclusion, the application of freezing and automatic tissue homogenizer improved protein extraction of NTM and boosted identification rates. Consequently, MALDI-TOF MS, which is a cheap and simple method, could be a helpful tool for identifying NTM species in clinical laboratories.
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50
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Shetye S. MALDI-TOF MS for rapid identification of Mycobacterium species in liquid culture media. ACTA ACUST UNITED AC 2018. [DOI: 10.15406/jbmoa.2018.06.00185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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