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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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Song J, Yoon S, In Y, Kim D, Lee H, Yong D, Lee K. Substantial Improvement in Nontuberculous Mycobacterial Identification Using ASTA MicroIDSys Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry with an Upgraded Database. Ann Lab Med 2022; 42:358-362. [PMID: 34907106 PMCID: PMC8677478 DOI: 10.3343/alm.2022.42.3.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/08/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
Identifying Mycobacterium using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is challenging. We evaluated the performance of MALDI-TOF MS in identifying nontuberculous mycobacteria (NTM) using the ASTA MicroIDSys system (ASTA Inc., Suwon, Korea) with the MycoDB v1.95s and upgraded MycoDB v2.0-beta databases. We tested 124 NTM isolates collected from Ogawa medium at Severance Hospital, Seoul, Korea, between January and April 2019. MicroIDSys scores were categorized into three groups: ≥140, reliable identification; 130-139, ambiguous identification; and <130, invalid identification. To validate the results, we used the reverse blot hybridization assay (Molecutech REBA MycoID, YD Diagnostics Corp., Korea). Initial analysis using MycoDB v1.95s resulted in 26.6% (33/124) reliable, 43.5% (54/124) ambiguous, and 29.8% (37/124) invalid identifications. Re-analysis using the upgraded MycoDB v2.0-beta database resulted in 94.4% (117/124) reliable, 4.0% (5/124) ambiguous, and 1.6% invalid (2/124) identifications. The percentage of reliable identifications that matched with the reference increased from 26.6% (33/124) with MycoDB v1.95s to 93.5% (116/124) with MycoDB v2.0-beta. The upgraded databases enable substantially improved NTM identification through deep learning in the inference algorithm and by considering more axes in the correlation analysis. MALDI-TOF MS using the upgraded database unambiguously identified most NTM species. Our study lays a foundation for applying MALDI-TOF MS for the simple and rapid identification of NTM isolated from solid media.
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Affiliation(s)
- Junhyup Song
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Shinyoung Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yongha In
- Department of Database Control, Nosquest Inc., Gyeonggi-do, Korea
| | - Daewon Kim
- Department of Laboratory Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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The Role of Thyroid Hormones in the Differential Diagnosis of Tuberculous and Parapneumonic Pleural Effusions. Am J Med Sci 2021; 363:495-501. [PMID: 34843677 DOI: 10.1016/j.amjms.2021.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/07/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND The differential diagnosis of tuberculous pleural effusion (TPE) and parapneumonic pleural effusion (PPE) is challenging due to similar clinical manifestations and body fluid biochemical profiles. Thyroid hormone levels change in response to lymphocyte proliferation in the peripheral blood of patients with mycobacterial infections such as tuberculosis; therefore, this study aimed to investigate the utility of assessing thyroid hormone levels to aid in the differential diagnosis of TPE and PPE. METHODS We measured free triiodothyronine (FT3), free thyroxine (FT4), and thyroid-stimulating hormone (TSH) levels in the pleural effusions of 59 newly admitted patients (32 and 27 with TPE and PPE, respectively). Hormone levels were assessed using an electrochemiluminescence technique, and the diagnostic parameters for tuberculosis were evaluated. Differences in hormone levels between patients with TPE and PPE were assessed by t-tests, and their diagnostic value for a differential diagnosis was evaluated by receiver operating characteristic curve analyses. RESULTS FT3 and FT4 levels in patients with TPE were significantly higher than those in patients with PPE (p < 0.01 and p < 0.05, respectively), whereas TSH expression did not significantly differ between the two groups (p > 0.05). FT3 and FT4 levels showed no correlation with sex or history of smoking, although FT3 levels decreased with age. The highest sensitivity was observed for the quantification of FT3 levels (84.38%). CONCLUSIONS Increased FT3 and FT4 levels could potentially be used for the differential diagnosis of TPE and PPE.
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Campelo TA, Cardoso de Sousa PR, Nogueira LDL, Frota CC, Zuquim Antas PR. Revisiting the methods for detecting Mycobacterium tuberculosis: what has the new millennium brought thus far? Access Microbiol 2021; 3:000245. [PMID: 34595396 PMCID: PMC8479963 DOI: 10.1099/acmi.0.000245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/17/2021] [Indexed: 01/07/2023] Open
Abstract
Tuberculosis (TB) affects around 10 million people worldwide in 2019. Approximately 3.4 % of new TB cases are multidrug-resistant. The gold standard method for detecting Mycobacterium tuberculosis, which is the aetiological agent of TB, is still based on microbiological culture procedures, followed by species identification and drug sensitivity testing. Sputum is the most commonly obtained clinical specimen from patients with pulmonary TB. Although smear microscopy is a low-cost and widely used method, its sensitivity is 50-60 %. Thus, owing to the need to improve the performance of current microbiological tests to provide prompt treatment, different methods with varied sensitivity and specificity for TB diagnosis have been developed. Here we discuss the existing methods developed over the past 20 years, including their strengths and weaknesses. In-house and commercial methods have been shown to be promising to achieve rapid diagnosis. Combining methods for mycobacterial detection systems demonstrates a correlation of 100 %. Other assays are useful for the simultaneous detection of M. tuberculosis species and drug-related mutations. Novel approaches have also been employed to rapidly identify and quantify total mycobacteria RNA, including assessments of global gene expression measured in whole blood to identify the risk of TB. Spoligotyping, mass spectrometry and next-generation sequencing are also promising technologies; however, their cost needs to be reduced so that low- and middle-income countries can access them. Because of the large impact of M. tuberculosis infection on public health, the development of new methods in the context of well-designed and -controlled clinical trials might contribute to the improvement of TB infection control.
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Affiliation(s)
- Thales Alves Campelo
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | | | - Lucas de Lima Nogueira
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Cristiane Cunha Frota
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Paulo Renato Zuquim Antas
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Performance of lipid fingerprint-based MALDI-ToF for the diagnosis of mycobacterial infections. Clin Microbiol Infect 2021; 27:912.e1-912.e5. [PMID: 32861860 PMCID: PMC8186428 DOI: 10.1016/j.cmi.2020.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Bacterial diagnosis of mycobacteria is often challenging because of the variability of the sensitivity and specificity of the assay used, and it can be expensive to perform accurately. Although matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has become the workhorse of clinical laboratories, the current MALDI methodology (which is based on cytosolic protein profiling) for mycobacteria is still challenging due to the number of steps involved (up to seven) and potential biosafety concerns. Knowing that mycobacteria produce surface-exposed species-specific lipids, we here hypothesized that the detection of those molecules could offer a rapid, reproducible and robust method for mycobacterial identification. METHODS We evaluated the performance of an alternative methodology based on characterized species-specific lipid profiling of intact bacteria, without any sample preparation, by MALDI MS; it uses MALDI-time-of-flight (ToF) MS combined with a specific matrix (super-2,5-dihydroxybenzoic acid solubilized in an apolar solvent system) to analyse lipids of intact heat-inactivated mycobacteria. Cultured mycobacteria are heat-inactivated and loaded directly onto the MALDI target followed by addition of the matrix. Acquisition of the data is done in both positive and negative ion modes. Blinded studies were performed using 273 mycobacterial strains comprising both the Mycobacterium tuberculosis (Mtb) complex and non-tuberculous mycobacteria (NTMs) subcultured in Middlebrook 7H9 media supplemented with 10% OADC (oleic acid/dextrose/catalase) growth supplement and incubated for up to 2 weeks at 37°C. RESULTS The method we have developed is fast (<10 mins) and highly sensitive (<1000 bacteria required); 96.7% of the Mtb complex strains (204/211) were correctly assigned as MTB complex and 91.7% (22/24) NTM species were correctly assigned based only on intact bacteria species-specific lipid profiling by MALDI-ToF MS. CONCLUSIONS Intact bacterial lipid profiling provides a biosafe and unique route for rapid and accurate mycobacterial identification.
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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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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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Hirabayashi R, Nakagawa A, Takegawa H, Tomii K. A case of pleural effusion caused by Mycobacterium fortuitum and Mycobacterium mageritense coinfection. BMC Infect Dis 2019; 19:720. [PMID: 31416441 PMCID: PMC6694650 DOI: 10.1186/s12879-019-4366-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/07/2019] [Indexed: 11/10/2022] Open
Abstract
Background Non-tuberculous mycobacteria cause chronic pulmonary infection, but pleuritis and pleural effusion are rarely associated with infection with non-tuberculous mycobacteria, especially rapid-growing mycobacteria. Case presentation A 68-year-old woman with rheumatoid arthritis who was using prednisone, azathioprine, and certolizumab pegol presented complaining of fever, dry cough, and night sweats for the past 2 weeks. Chest examination revealed bilateral opacity that was more pronounced on her right side. Bronchoalveolar lavage fluid and pleural effusion fluid were obtained, and revealed coinfection with Mycobacterium fortuitum and Mycobacterium mageritense. Imipenem/cilastatin, levofloxacin, and minocycline were prescribed for 6 months, and the patient was well and asymptomatic for the subsequent 6 months. Conclusions This is the first case report describing pleural effusion associated with coinfection with two different mycobacterial species. If the species cannot be identified, the possibility of mycobacterial coinfection should be considered.
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Affiliation(s)
- Ryosuke Hirabayashi
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, 2-1-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Atsushi Nakagawa
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, 2-1-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hiroshi Takegawa
- Department of Laboratory Medicine, Kobe City Nishi-Kobe Medical Center, 5-7-1 Kouji-dai, Nishi-ku, Kobe, Hyogo, 651-2273, Japan
| | - Keisuke Tomii
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, 2-1-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
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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: 17] [Impact Index Per Article: 2.8] [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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Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria: a systematic review and meta-analysis. Sci Rep 2018. [PMID: 29515167 PMCID: PMC5841357 DOI: 10.1038/s41598-018-22642-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium species are a significant cause of morbidity and mortality worldwide. The present study was carried out to systematically evaluate the accuracy of Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) for the identification of clinical pathogenic mycobacteria. After a rigid selection process, 19 articles involving 2,593 mycobacteria isolates were included. The pooled result agreed with the reference method identification for 85% of the isolates to genus level, with 71% (95% CI of 69% to 72%) correct to the species level. The MALDI-TOF MS correctly identified 92% of the M.tuberculosis isolates (95% CI of 0.87 to 0.96), and 68% of M. bovisisolates (95% CI of 27% to 100%) to the species level. Mycobacterium tuberculosis complex in solid media with reference strains using augmented database showing more accurate identification. The identifying accuracy rate of bioMérieuxVitek MS was slight higher than Bruker MALDI Biotyper (75% vs 72%). However, opposite results were obtained in identifications of M. fortuitum, M. kansasii, M. marinum, and M. terrae with these two systems. In summary, our results demonstrate that application of MALDI-TOF MS in clinical pathogenic mycobacteria identification is less satisfactory to date. Increasing need for improvement is important especially at species level.
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Manikandan M, Deenadayalan A, Vimala A, Gopal J, Chun S. Clinical MALDI mass spectrometry for tuberculosis diagnostics: Speculating the methodological blueprint and contemplating the obligation to improvise. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Rodriguez-Temporal D, Perez-Risco D, Struzka EA, Mas M, Alcaide F. Impact of updating the MALDI-TOF MS database on the identification of nontuberculous mycobacteria. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:597-602. [PMID: 28480547 DOI: 10.1002/jms.3944] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/03/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Conventional identification of mycobacteria species is slow, laborious and has low discriminatory power. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proved highly effective for identifying conventional bacteria, and it may also be useful for identifying mycobacteria. The aim of this study was to evaluate and compare MALDI-TOF MS with currently recommended molecular methods for the identification of nontuberculous mycobacteria (NTM), applying Mycobacteria Libraries v3.0 (ML3.0) and v2.0 (ML2.0). A total of 240 clinical isolates of 41 NTM species grown on solid media were analysed: 132 isolates of slow-growing mycobacteria and 108 of rapid-growing mycobacteria. MALDI-TOF MS, using ML3.0, identified 192 (80%) NTM isolates with a score ≥1.7, encompassing 35 (85.4%) different species, that is, 17 (7.1%; p = 0.0863) isolates and 15 (36.6%; p = 0.0339) species more than currently recommended molecular techniques (polymerase chain reaction reverse hybridization). All these isolates were correctly identified according to molecular identification methods. The application of ML3.0 also identified 15 (6.2%) NTM isolates more than ML2.0 (p < 0.01). The scores obtained with MALDI-TOF MS using ML3.0 (mean score: 1.960) were higher in 147 (61.2%) isolates than when using ML2.0 (mean score: 1.797; p < 0.01). Three of the species analysed were not included in either database, so they were not recognized by this system. In conclusion, MALDI-TOF MS identified more isolates and species than the recommended polymerase chain reaction reverse hybridization assays. Although the new ML3.0 is not the definitive database, it yielded better results than ML2.0. This shows that the updating of the MALDI-TOF MS database plays an essential role in mycobacterial identification. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- D Rodriguez-Temporal
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, Universitat de Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - D Perez-Risco
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, Universitat de Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - E A Struzka
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - M Mas
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - F Alcaide
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, Universitat de Barcelona, Hospitalet de Llobregat, Barcelona, Spain
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Wang HY, Uh Y, Kim S, Shim TS, Lee H. Evaluation of the Quantamatrix Multiplexed Assay Platform system for simultaneous detection of Mycobacterium tuberculosis and the rifampicin resistance gene using cultured mycobacteria. Int J Infect Dis 2017. [PMID: 28627431 DOI: 10.1016/j.ijid.2017.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The differentiation of Mycobacterium tuberculosis complex (MTBC) from non-tuberculous mycobacteria (NTM) is of primary importance for infection control and the selection of anti-tuberculosis drugs. Up to date data on rifampicin (RIF)-resistant tuberculosis (TB) is essential for the early management of multidrug-resistant TB. The aim of this study was to evaluate the usefulness of a newly developed multiplexed, bead-based bioassay (Quantamatrix Multiplexed Assay Platform, QMAP) for the rapid differentiation of 23 Mycobacterium species including MTBC and RIF-resistant strains. METHODS A total of 314 clinical Mycobacterium isolates cultured from respiratory specimens were used in this study. RESULTS The sensitivity and specificity of the QMAP system for Mycobacterium species were 100% (95% CI 99.15-100%, p<0.0001) and 97.8% (95% CI 91.86-99.87%, p<0.0001), respectively. The results of conventional drug susceptibility testing and the QMAP Dual-ID assay were completely concordant for all clinical isolates (100%, 95% CI 98.56-100%). Out of 223 M. tuberculosis (MTB) isolates, 196 were pan-susceptible and 27 were resistant to RIF according to QMAP results. All of the mutations in the RIF resistance-determining region detected by the QMAP system were confirmed by rpoB sequence analysis and a REBA MTB-Rifa reverse blot hybridization assay. The majority of the mutations (n=26, 96.3%), including those missing wild-type probe signals, were located in three codons (529-534, 524-529, and 514-520), and 17 (65.4%) of these mutations were detected by three mutation probes (531TTG, 526TAC, and 516GTC). CONCLUSIONS The entire QMAP system assay takes about 3h to complete, while results from the culture-based conventional method can take up to 48-72h. Although improvements to the QMAP system are needed for direct respiratory specimens, it may be useful for rapid screening, not only to identify and accurately discriminate MTBC from NTM, but also to identify RIF-resistant MTB strains in positive culture samples.
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Affiliation(s)
- Hye-Young Wang
- Optipharm, Inc., Wonju Eco Environmental Technology Center, Wonju, Gangwon, 26493, Republic of Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju, Gangwon, 26426, Republic of Korea.
| | - Seoyong Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, Republic of Korea
| | - Tae-Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05535, Republic of Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, Republic of Korea.
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Comparison of Saramis 4.12 and IVD 3.0 Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria from Solid and Liquid Culture Media. J Clin Microbiol 2017; 55:2045-2054. [PMID: 28424252 DOI: 10.1128/jcm.00006-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/04/2017] [Indexed: 01/25/2023] Open
Abstract
During the last decade, many investigators have studied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for identification of mycobacteria. Diverse and contradictory results indicated that optimal level for routine testing has not been reached yet. This work aimed to assess Vitek MS through two distinct versions, Saramis v4.12 RUO and the IVD v3.0, under conditions close to routine laboratory practice. Overall, 111 mycobacterial isolates were subjected to protein extraction and same spectra were matched against both databases. The IVD v3.0 database proved to be superior to Saramis v4.12 and its identification rates remarkably increased, from 67% to 94% for isolates grown on Middlebrook 7H10 solid medium and from 62% to 91% for isolates grown on mycobacterial growth indicator tube (MGIT) liquid medium. With this new version, IVD v3.0, MALDI-TOF MS might be integrated into routine clinical diagnostics, although molecular techniques remain mandatory in some cases.
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Neuschlova M, Vladarova M, Kompanikova J, Sadlonova V, Novakova E. Identification of Mycobacterium Species by MALDI-TOF Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 28623484 DOI: 10.1007/5584_2017_26] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Matrix-assisted laser desorption ionization - time-of-flight (MALDI-TOF) mass spectrometry enables to identify microorganisms by comparison of the protein content with reference spectra in the database. The aim of this study was to evaluate the efficacy of phenotypic identification of mycobacteria by MALDI-TOF mass spectrometry in laboratory practice. Seventy five isolates of mycobacteria were identified by molecular and phenotypic method, and the results were compared by MALDI-TOF. For MALDI-TOF, material was processed according to the Bruker Daltonics protocol and Mycobacterial Library database version 2.0, with 313 reference mycobacteria spectra. All except one of the 72 isolates agreed with regard to the species and genus by both methods. Forty three isolates were identified as the M. tuberculosis complex by MALDI-TOF. Thirty one isolates of nontuberculous mycobacteria were consistently identified by both methods to the species level. We conclude that MALDI-TOF mass spectrometry is an accurate method of bacterial identification. Simplicity, speed, and economic availability of the method makes it suitable for mycobacteria identification in a routine laboratory.
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Affiliation(s)
- M Neuschlova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4B, 036 01, Martin, Slovakia
| | - M Vladarova
- Clinical Biochemistry, Joint Stock Company, Department of Clinical Microbiology, University of Zilina, 47A V. Spanyola Street, 010 01, Zilina, Slovakia
| | - J Kompanikova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4B, 036 01, Martin, Slovakia
| | - V Sadlonova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4B, 036 01, Martin, Slovakia
| | - E Novakova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4B, 036 01, Martin, Slovakia.
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16
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Chien JY, Yu CJ, Hsueh PR. Identification of nontuberculous mycobacteria in MGIT by matrix-assisted laser desorption/ionization mass spectrometry. Future Microbiol 2016; 11:1025-33. [DOI: 10.2217/fmb.16.20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: The performance of Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying species of nontuberculous mycobacteria (NTM) in flagged Mycobacteria Growth Indicator Tubes (MGIT)s is unclear. Materials & methods: A total of 92 sequential MGIT-positive nontuberculous mycobacteria isolates, including Mycobacterium intracellulare, M. abscessus complex, M. avium complex and M. avium, were used to compare the performance of the MALDI-TOF MS for species-level identification with that of the BluePoint MycoID plus kit and final identification. Results: A total of 44 (47.8%) and 80 (87.0%) isolates were correctly identified to the species level by the MALDI-TOF MS and BluePoint MycoID plus kit, respectively. Conclusion: The procedure of MALDI-TOF MS in MGITs inoculated with clinical specimens is needed to be further optimized.
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Affiliation(s)
- Jung-Yien Chien
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Departments of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chong-Jen Yu
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Departments of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Departments of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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Mareković I, Bošnjak Z, Jakopović M, Boras Z, Janković M, Popović-Grle S. Evaluation of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry in Identification of Nontuberculous Mycobacteria. Chemotherapy 2016; 61:167-70. [DOI: 10.1159/000442517] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/16/2015] [Indexed: 11/19/2022]
Abstract
Background/Aims: Species-level identification of nontuberculous mycobacteria (NTM) is important in making decisions about the necessity and choice of antimicrobial treatment. The reason is predictable clinical significance and the susceptibility profile of specific NTM species. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is recognized as a diagnostic tool for routine identification of bacteria and yeasts in the clinical laboratory based on protein fingerprint analysis. The aim of the study was to evaluate MALDI-TOF MS in the identification of NTM. Methods: A total of 25 NTM isolates from liquid cultures were identified with both polymerase chain reaction (PCR)-based hybridization assay and MALDI-TOF MS at the University Hospital Center Zagreb. Results: PCR-based hybridization assay identified 96% (24/25) and MALDI-TOF MS 80% (20/25) of tested NTM isolates. Five isolates with no reliable MALDI-TOF MS identification belonged to the Mycobacterium avium-intracellulare complex. Seventy percent (14/20) of NTM isolates successfully identified with MALDI-TOF MS had a score higher than 2.0, indicating reliable species identification. Conclusion: MALDI-TOF MS is a promising tool for the identification of NTM. With a further improvement of the protein extraction protocol, especially regarding the M. avium-intracellulare complex, MALDI-TOF MS could be an additional standard method for identification of NTM.
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Kehrmann J, Schoerding AK, Murali R, Wessel S, Koehling HL, Mosel F, Buer J. Performance of Vitek MS in identifying nontuberculous mycobacteria from MGIT liquid medium and Lowenstein–Jensen solid medium. Diagn Microbiol Infect Dis 2016; 84:43-47. [DOI: 10.1016/j.diagmicrobio.2015.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/30/2015] [Accepted: 10/04/2015] [Indexed: 10/22/2022]
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Kodana M, Tarumoto N, Kawamura T, Saito T, Ohno H, Maesaki S, Ikebuchi K. Utility of the MALDI-TOF MS method to identify nontuberculous mycobacteria. J Infect Chemother 2015; 22:32-5. [PMID: 26603481 DOI: 10.1016/j.jiac.2015.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/10/2015] [Accepted: 09/23/2015] [Indexed: 11/15/2022]
Abstract
In comparison to the conventional real-time polymerase chain reaction method (PCR method) or the DNA-DNA hybridization method (DDH method), the utility of NTM identification by the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method has seldom been reported. In this study, 75 clinical NTM isolates from our hospital between April 2013 and July 2014 were identified and analyzed using PCR, DDH, and MALDI-TOF MS methods, and the results for the MALDI-TOF MS method were compared with the others. Identification at the species level was in agreement for 71 (94.5%) of the 75 isolates. For further details, identification was possible for 23 (95.8%) of 24 Mycobacterium avium, 11 (100%) of 11 Mycobacterium intracellulare, and 1 (50%) of 2 isolates mixed with M. avium and M. intracellulare. Mycobacterium ksansasii, Mycobacterium abscessus, Mycobacterium fortuitum, Mycobacterium gordonae, and Mycobacterium chelonae identified by DDH method were same result by MALDI-TOF MS. Additionally, Mycobacterium mucogenicum, which could not be identified by the DDH method, was identified by the MALDI-TOF MS method. However, two isolates identified as Mycobacterium terrae by DDH method could not be identified by the MALDI-TOF MS method and were determined to be Mycobacterium arupense by 16S ribosomal RNA (rRNA) sequence analysis. The present findings show that, for rare bacterial species, identification is sometimes not possible, but, in most cases, the results of identification by the MALDI-TOF MS method have a high concordance rate with the results of the PCR and DDH methods.
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Affiliation(s)
- Masahiro Kodana
- Clinical Laboratory Medicine, Saitama Medical University Hospital, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Japan.
| | - Tohru Kawamura
- Clinical Laboratory Medicine, Saitama Medical University Hospital, Japan
| | - Taeko Saito
- Clinical Laboratory Medicine, Saitama Medical University Hospital, Japan
| | - Hideaki Ohno
- Department of Infectious Disease and Infection Control, Saitama Medical Center, Saitama Medical University, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Japan
| | - Kenji Ikebuchi
- Clinical Laboratory Medicine, Saitama Medical University Hospital, Japan
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